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2022
Normant Vincent, Kuhn Lauriane, Munier Mathilde, Hammann Philippe, Mislin Gaëtan L. A., Schalk Isabelle J.
How the Presence of Hemin Affects the Expression of the Different Iron Uptake Pathways in Pseudomonas aeruginosa Cells Article de journal
Dans: ACS infectious diseases, vol. 8, no. 1, p. 183–196, 2022, ISSN: 2373-8227.
Résumé | Liens | BibTeX | Étiquettes: Hemin, hemin (heme) uptake, Iron, iron homeostasis, iron uptake, outer membrane transporters, PPSE, proteomics, Pseudomonas aeruginosa, siderophore, Siderophores
@article{normant_how_2022,
title = {How the Presence of Hemin Affects the Expression of the Different Iron Uptake Pathways in Pseudomonas aeruginosa Cells},
author = {Vincent Normant and Lauriane Kuhn and Mathilde Munier and Philippe Hammann and Gaëtan L. A. Mislin and Isabelle J. Schalk},
doi = {10.1021/acsinfecdis.1c00525},
issn = {2373-8227},
year = {2022},
date = {2022-01-01},
journal = {ACS infectious diseases},
volume = {8},
number = {1},
pages = {183--196},
abstract = {Iron is an essential nutriment for almost all organisms, but this metal is poorly bioavailable. During infection, bacteria access iron from the host by importing either iron or heme. Pseudomonas aeruginosa, a gram-negative pathogen, secretes two siderophores, pyoverdine (PVD) and pyochelin (PCH), to access iron and is also able to use many siderophores produced by other microorganisms (called xenosiderophores). To access heme, P. aeruginosa uses three distinct uptake pathways, named Has, Phu, and Hxu. We previously showed that P. aeruginosa expresses the Has and Phu heme uptake systems and the PVD- and PCH-dependent iron uptake pathways in iron-restricted growth conditions, using proteomic and RT-qPCR approaches. Here, using the same approaches, we show that physiological concentrations of hemin in the bacterial growth medium result in the repression of the expression of the proteins of the PVD- and PCH-dependent iron uptake pathways, leading to less production of these two siderophores. This indicates that the pathogen adapts its phenotype to use hemin as an iron source rather than produce PVD and PCH to access iron. Moreover, the presence of both hemin and a xenosiderophore resulted in (i) the strong induction of the expression of the proteins of the added xenosiderophore uptake pathway, (ii) repression of the PVD- and PCH-dependent iron uptake pathways, and (iii) no effect on the expression levels of the Has, Phu, or Hxu systems, indicating that bacteria use both xenosiderophores and heme to access iron.},
keywords = {Hemin, hemin (heme) uptake, Iron, iron homeostasis, iron uptake, outer membrane transporters, PPSE, proteomics, Pseudomonas aeruginosa, siderophore, Siderophores},
pubstate = {published},
tppubtype = {article}
}
Iron is an essential nutriment for almost all organisms, but this metal is poorly bioavailable. During infection, bacteria access iron from the host by importing either iron or heme. Pseudomonas aeruginosa, a gram-negative pathogen, secretes two siderophores, pyoverdine (PVD) and pyochelin (PCH), to access iron and is also able to use many siderophores produced by other microorganisms (called xenosiderophores). To access heme, P. aeruginosa uses three distinct uptake pathways, named Has, Phu, and Hxu. We previously showed that P. aeruginosa expresses the Has and Phu heme uptake systems and the PVD- and PCH-dependent iron uptake pathways in iron-restricted growth conditions, using proteomic and RT-qPCR approaches. Here, using the same approaches, we show that physiological concentrations of hemin in the bacterial growth medium result in the repression of the expression of the proteins of the PVD- and PCH-dependent iron uptake pathways, leading to less production of these two siderophores. This indicates that the pathogen adapts its phenotype to use hemin as an iron source rather than produce PVD and PCH to access iron. Moreover, the presence of both hemin and a xenosiderophore resulted in (i) the strong induction of the expression of the proteins of the added xenosiderophore uptake pathway, (ii) repression of the PVD- and PCH-dependent iron uptake pathways, and (iii) no effect on the expression levels of the Has, Phu, or Hxu systems, indicating that bacteria use both xenosiderophores and heme to access iron.
Hémono Mickaële, Haller Alexandre, Chicher Johana, Duchêne Anne-Marie, Ngondo Richard Patryk
The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins Article de journal
Dans: BMC Biol, vol. 20, no. 1, p. 13, 2022, ISSN: 1741-7007.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{pmid35012549b,
title = {The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins},
author = {Mickaële Hémono and Alexandre Haller and Johana Chicher and Anne-Marie Duchêne and Richard Patryk Ngondo},
doi = {10.1186/s12915-021-01213-y},
issn = {1741-7007},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {BMC Biol},
volume = {20},
number = {1},
pages = {13},
abstract = {BACKGROUND: Mitochondria require thousands of proteins to fulfill their essential function in energy production and other fundamental biological processes. These proteins are mostly encoded by the nuclear genome, translated in the cytoplasm before being imported into the organelle. RNA binding proteins (RBPs) are central players in the regulation of this process by affecting mRNA translation, stability, or localization. CLUH is an RBP recognizing specifically mRNAs coding for mitochondrial proteins, but its precise molecular function and interacting partners remain undiscovered in mammals.
RESULTS: Here we reveal for the first time CLUH interactome in mammalian cells. Using both co-IP and BioID proximity-labeling approaches, we identify novel molecular partners interacting stably or transiently with CLUH in HCT116 cells and mouse embryonic stem cells. We reveal stable RNA-independent interactions of CLUH with itself and with SPAG5 in cytosolic granular structures. More importantly, we uncover an unexpected proximity of CLUH to mitochondrial proteins and their cognate mRNAs in the cytosol. We show that this interaction occurs during the process of active translation and is dependent on CLUH TPR domain.
CONCLUSIONS: Overall, through the analysis of CLUH interactome, our study sheds a new light on CLUH molecular function by revealing new partners and by highlighting its link to the translation and subcellular localization of some mRNAs coding for mitochondrial proteins.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Mitochondria require thousands of proteins to fulfill their essential function in energy production and other fundamental biological processes. These proteins are mostly encoded by the nuclear genome, translated in the cytoplasm before being imported into the organelle. RNA binding proteins (RBPs) are central players in the regulation of this process by affecting mRNA translation, stability, or localization. CLUH is an RBP recognizing specifically mRNAs coding for mitochondrial proteins, but its precise molecular function and interacting partners remain undiscovered in mammals.
RESULTS: Here we reveal for the first time CLUH interactome in mammalian cells. Using both co-IP and BioID proximity-labeling approaches, we identify novel molecular partners interacting stably or transiently with CLUH in HCT116 cells and mouse embryonic stem cells. We reveal stable RNA-independent interactions of CLUH with itself and with SPAG5 in cytosolic granular structures. More importantly, we uncover an unexpected proximity of CLUH to mitochondrial proteins and their cognate mRNAs in the cytosol. We show that this interaction occurs during the process of active translation and is dependent on CLUH TPR domain.
CONCLUSIONS: Overall, through the analysis of CLUH interactome, our study sheds a new light on CLUH molecular function by revealing new partners and by highlighting its link to the translation and subcellular localization of some mRNAs coding for mitochondrial proteins.
RESULTS: Here we reveal for the first time CLUH interactome in mammalian cells. Using both co-IP and BioID proximity-labeling approaches, we identify novel molecular partners interacting stably or transiently with CLUH in HCT116 cells and mouse embryonic stem cells. We reveal stable RNA-independent interactions of CLUH with itself and with SPAG5 in cytosolic granular structures. More importantly, we uncover an unexpected proximity of CLUH to mitochondrial proteins and their cognate mRNAs in the cytosol. We show that this interaction occurs during the process of active translation and is dependent on CLUH TPR domain.
CONCLUSIONS: Overall, through the analysis of CLUH interactome, our study sheds a new light on CLUH molecular function by revealing new partners and by highlighting its link to the translation and subcellular localization of some mRNAs coding for mitochondrial proteins.
Ponce J. R. Jaramillo, Kapps D., Paulus C., Chicher J., Frugier M.
Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein Article de journal
Dans: J Biol Chem, p. 101987, 2022, ISBN: 35487244, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Labex, PPSE, Unité ARN
@article{nokey,
title = {Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein},
author = {J. R. Jaramillo Ponce and D. Kapps and C. Paulus and J. Chicher and M. Frugier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35487244},
doi = {0.1016/j.jbc.2022.101987},
isbn = {35487244},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {J Biol Chem},
pages = {101987},
abstract = {Aminoacyl-tRNA synthetases (aaRSs) attach amino acids to their cognate transfer RNAs. In eukaryotes, a subset of cytosolic aaRSs is organized into a multi-synthetase complex (MSC), along with specialized scaffolding proteins referred to as aaRS-interacting multifunctional proteins (AIMPs). In Plasmodium, the causative agent of malaria, the tRNA import protein (tRip), is a membrane protein that has been shown to participate in tRNA trafficking; here, we show that tRip also functions as an AIMP. We identified three aaRSs, namely the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases, which were specifically co-immunoprecipitated with tRip in P. berghei blood stage parasites. All four proteins contain an N-terminal GST-like domain that was demonstrated to be involved in MSC assembly. In contrast to previous studies, further dissection of GST-like interactions identified two exclusive heterotrimeric complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS). Gel filtration and light scattering suggest a 2:2:2 stoichiometry for both complexes but with distinct biophysical properties, and mutational analysis further revealed that the GST-like domains of QRS and MRS use different strategies to bind ERS. Taken together our results demonstrate that neither the singular homodimerization of tRip, nor its localization in the parasite plasma membrane prevents the formation of MSCs in Plasmodium. Besides, the extracellular localization of the tRNA-binding module of tRip is compensated by the presence of additional tRNA-binding modules fused to MRS and QRS, providing each MSC with two spatially distinct functions: aminoacylation of intraparasitic tRNAs and binding of extracellular tRNAs. This unique host-pathogen interaction is discussed.},
note = {1083-351X (Electronic)
0021-9258 (Linking)
Journal Article},
keywords = {FRUGIER, Labex, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Aminoacyl-tRNA synthetases (aaRSs) attach amino acids to their cognate transfer RNAs. In eukaryotes, a subset of cytosolic aaRSs is organized into a multi-synthetase complex (MSC), along with specialized scaffolding proteins referred to as aaRS-interacting multifunctional proteins (AIMPs). In Plasmodium, the causative agent of malaria, the tRNA import protein (tRip), is a membrane protein that has been shown to participate in tRNA trafficking; here, we show that tRip also functions as an AIMP. We identified three aaRSs, namely the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases, which were specifically co-immunoprecipitated with tRip in P. berghei blood stage parasites. All four proteins contain an N-terminal GST-like domain that was demonstrated to be involved in MSC assembly. In contrast to previous studies, further dissection of GST-like interactions identified two exclusive heterotrimeric complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS). Gel filtration and light scattering suggest a 2:2:2 stoichiometry for both complexes but with distinct biophysical properties, and mutational analysis further revealed that the GST-like domains of QRS and MRS use different strategies to bind ERS. Taken together our results demonstrate that neither the singular homodimerization of tRip, nor its localization in the parasite plasma membrane prevents the formation of MSCs in Plasmodium. Besides, the extracellular localization of the tRNA-binding module of tRip is compensated by the presence of additional tRNA-binding modules fused to MRS and QRS, providing each MSC with two spatially distinct functions: aminoacylation of intraparasitic tRNAs and binding of extracellular tRNAs. This unique host-pathogen interaction is discussed.
2021
Waltz Florent, Salinas-Giegé Thalia, Englmeier Robert, Meichel Herrade, Soufari Heddy, Kuhn Lauriane, Pfeffer Stefan, Förster Friedrich, Engel Benjamin D., Giegé Philippe, Drouard Laurence, Hashem Yaser
How to build a ribosome from RNA fragments in Chlamydomonas mitochondria Article de journal
Dans: Nature Communications, vol. 12, no. 1, p. 7176, 2021, ISSN: 2041-1723.
Résumé | Liens | BibTeX | Étiquettes: Chlamydomonas reinhardtii, Cryoelectron Microscopy, mitochondria, Mitochondrial Proteins, Mitochondrial Ribosomes, PPSE, Ribosomal Proteins, ribosomes, RNA
@article{waltz_how_2021,
title = {How to build a ribosome from RNA fragments in Chlamydomonas mitochondria},
author = {Florent Waltz and Thalia Salinas-Giegé and Robert Englmeier and Herrade Meichel and Heddy Soufari and Lauriane Kuhn and Stefan Pfeffer and Friedrich Förster and Benjamin D. Engel and Philippe Giegé and Laurence Drouard and Yaser Hashem},
doi = {10.1038/s41467-021-27200-z},
issn = {2041-1723},
year = {2021},
date = {2021-12-01},
journal = {Nature Communications},
volume = {12},
number = {1},
pages = {7176},
abstract = {Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.},
keywords = {Chlamydomonas reinhardtii, Cryoelectron Microscopy, mitochondria, Mitochondrial Proteins, Mitochondrial Ribosomes, PPSE, Ribosomal Proteins, ribosomes, RNA},
pubstate = {published},
tppubtype = {article}
}
Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.
Schiaffini Marlene, Chicois Clara, Pouclet Aude, Chartier Tiphaine, Ubrig Elodie, Gobert Anthony, Zuber Hélène, Mutterer Jérôme, Chicher Johana, Kuhn Lauriane, Hammann Philippe, Gagliardi Dominique, Garcia Damien
A NYN domain protein directly interacts with DECAPPING1 and is required for phyllotactic pattern Article de journal
Dans: Plant Physiology, p. kiab529, 2021, ISSN: 1532-2548.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{schiaffini_nyn_2021,
title = {A NYN domain protein directly interacts with DECAPPING1 and is required for phyllotactic pattern},
author = {Marlene Schiaffini and Clara Chicois and Aude Pouclet and Tiphaine Chartier and Elodie Ubrig and Anthony Gobert and Hélène Zuber and Jérôme Mutterer and Johana Chicher and Lauriane Kuhn and Philippe Hammann and Dominique Gagliardi and Damien Garcia},
doi = {10.1093/plphys/kiab529},
issn = {1532-2548},
year = {2021},
date = {2021-11-01},
urldate = {2021-11-01},
journal = {Plant Physiology},
pages = {kiab529},
abstract = {In eukaryotes, general mRNA decay requires the decapping complex. The activity of this complex depends on its catalytic subunit, DECAPPING2 (DCP2), and its interaction with decapping enhancers, including its main partner DECAPPING1 (DCP1). Here, we report that in Arabidopsis thaliana, DCP1 also interacts with a NYN domain endoribonuclease, hence named DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1). Interestingly, we found DNE1 predominantly associated with DCP1, but not with DCP2, and reciprocally, suggesting the existence of two distinct protein complexes. We also showed that the catalytic residues of DNE1 are required to repress the expression of mRNAs in planta upon transient expression. The overexpression of DNE1 in transgenic lines led to growth defects and a similar gene deregulation signature than inactivation of the decapping complex. Finally, the combination of dne1 and dcp2 mutations revealed a functional redundancy between DNE1 and DCP2 in controlling phyllotactic pattern formation. Our work identifies DNE1, a hitherto unknown DCP1 protein partner highly conserved in the plant kingdom and identifies its importance for developmental robustness.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
In eukaryotes, general mRNA decay requires the decapping complex. The activity of this complex depends on its catalytic subunit, DECAPPING2 (DCP2), and its interaction with decapping enhancers, including its main partner DECAPPING1 (DCP1). Here, we report that in Arabidopsis thaliana, DCP1 also interacts with a NYN domain endoribonuclease, hence named DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1). Interestingly, we found DNE1 predominantly associated with DCP1, but not with DCP2, and reciprocally, suggesting the existence of two distinct protein complexes. We also showed that the catalytic residues of DNE1 are required to repress the expression of mRNAs in planta upon transient expression. The overexpression of DNE1 in transgenic lines led to growth defects and a similar gene deregulation signature than inactivation of the decapping complex. Finally, the combination of dne1 and dcp2 mutations revealed a functional redundancy between DNE1 and DCP2 in controlling phyllotactic pattern formation. Our work identifies DNE1, a hitherto unknown DCP1 protein partner highly conserved in the plant kingdom and identifies its importance for developmental robustness.
Incarbone Marco, Clavel Marion, Monsion Baptiste, Kuhn Lauriane, Scheer Hélène, Vantard Émilie, Poignavent Vianney, Dunoyer Patrice, Genschik Pascal, Ritzenthaler Christophe
Dans: The Plant Cell, vol. 33, no. 11, p. 3402–3420, 2021, ISSN: 1532-298X.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{incarbone_immunocapture_2021,
title = {Immunocapture of dsRNA-bound proteins provides insight into Tobacco rattle virus replication complexes and reveals Arabidopsis DRB2 to be a wide-spectrum antiviral effector},
author = {Marco Incarbone and Marion Clavel and Baptiste Monsion and Lauriane Kuhn and Hélène Scheer and Émilie Vantard and Vianney Poignavent and Patrice Dunoyer and Pascal Genschik and Christophe Ritzenthaler},
doi = {10.1093/plcell/koab214},
issn = {1532-298X},
year = {2021},
date = {2021-11-01},
journal = {The Plant Cell},
volume = {33},
number = {11},
pages = {3402--3420},
abstract = {Plant RNA viruses form organized membrane-bound replication complexes to replicate their genomes. This process requires virus- and host-encoded proteins and leads to the production of double-stranded RNA (dsRNA) replication intermediates. Here, we describe the use of Arabidopsis thaliana expressing GFP-tagged dsRNA-binding protein (B2:GFP) to pull down dsRNA and associated proteins in planta upon infection with Tobacco rattle virus (TRV). Mass spectrometry analysis of the dsRNA-B2:GFP-bound proteins from infected plants revealed the presence of viral proteins and numerous host proteins. Among a selection of nine host candidate proteins, eight showed relocalization upon infection, and seven of these colocalized with B2-labeled TRV replication complexes. Infection of A. thaliana T-DNA mutant lines for eight such factors revealed that genetic knockout of dsRNA-BINDING PROTEIN 2 (DRB2) leads to increased TRV accumulation and DRB2 overexpression caused a decrease in the accumulation of four different plant RNA viruses, indicating that DRB2 has a potent and wide-ranging antiviral activity. We propose B2:GFP-mediated pull down of dsRNA to be a versatile method to explore virus replication complex proteomes and to discover key host virus replication factors. Given the universality of dsRNA, development of this tool holds great potential to investigate RNA viruses in other host organisms.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Plant RNA viruses form organized membrane-bound replication complexes to replicate their genomes. This process requires virus- and host-encoded proteins and leads to the production of double-stranded RNA (dsRNA) replication intermediates. Here, we describe the use of Arabidopsis thaliana expressing GFP-tagged dsRNA-binding protein (B2:GFP) to pull down dsRNA and associated proteins in planta upon infection with Tobacco rattle virus (TRV). Mass spectrometry analysis of the dsRNA-B2:GFP-bound proteins from infected plants revealed the presence of viral proteins and numerous host proteins. Among a selection of nine host candidate proteins, eight showed relocalization upon infection, and seven of these colocalized with B2-labeled TRV replication complexes. Infection of A. thaliana T-DNA mutant lines for eight such factors revealed that genetic knockout of dsRNA-BINDING PROTEIN 2 (DRB2) leads to increased TRV accumulation and DRB2 overexpression caused a decrease in the accumulation of four different plant RNA viruses, indicating that DRB2 has a potent and wide-ranging antiviral activity. We propose B2:GFP-mediated pull down of dsRNA to be a versatile method to explore virus replication complex proteomes and to discover key host virus replication factors. Given the universality of dsRNA, development of this tool holds great potential to investigate RNA viruses in other host organisms.
Roche Béatrice, Garcia-Rivera Mariel A., Normant Vincent, Kuhn Lauriane, Hammann Philippe, Brönstrup Mark, Mislin Gaëtan L. A., Schalk Isabelle J.
A role for PchHI as the ABC transporter in iron acquisition by the siderophore pyochelin in Pseudomonas aeruginosa Article de journal
Dans: Environmental Microbiology, 2021, ISSN: 1462-2920.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{roche_role_2021,
title = {A role for PchHI as the ABC transporter in iron acquisition by the siderophore pyochelin in Pseudomonas aeruginosa},
author = {Béatrice Roche and Mariel A. Garcia-Rivera and Vincent Normant and Lauriane Kuhn and Philippe Hammann and Mark Brönstrup and Gaëtan L. A. Mislin and Isabelle J. Schalk},
doi = {10.1111/1462-2920.15811},
issn = {1462-2920},
year = {2021},
date = {2021-10-01},
journal = {Environmental Microbiology},
abstract = {Iron is an essential nutrient for bacterial growth but poorly bioavailable. Bacteria scavenge ferric iron by synthesizing and secreting siderophores, small compounds with a high affinity for iron. Pyochelin (PCH) is one of the two siderophores produced by the opportunistic pathogen Pseudomonas aeruginosa. After capturing a ferric iron molecule, PCH-Fe is imported back into bacteria first by the outer membrane transporter FptA and then by the inner membrane permease FptX. Here, using molecular biology, 55 Fe uptake assays, and LC-MS/MS quantification, we first find a role for PchHI as the heterodimeric ABC transporter involved in the siderophore-free iron uptake into the bacterial cytoplasm. We also provide the first evidence that PCH is able to reach the bacterial periplasm and cytoplasm when both FptA and FptX are expressed. Finally, we detected an interaction between PchH and FptX, linking the ABC transporter PchHI with the inner permease FptX in the PCH-Fe uptake pathway. These results pave the way for a better understanding of the PCH siderophore pathway, giving future directions to tackle P. aeruginosa infections.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Iron is an essential nutrient for bacterial growth but poorly bioavailable. Bacteria scavenge ferric iron by synthesizing and secreting siderophores, small compounds with a high affinity for iron. Pyochelin (PCH) is one of the two siderophores produced by the opportunistic pathogen Pseudomonas aeruginosa. After capturing a ferric iron molecule, PCH-Fe is imported back into bacteria first by the outer membrane transporter FptA and then by the inner membrane permease FptX. Here, using molecular biology, 55 Fe uptake assays, and LC-MS/MS quantification, we first find a role for PchHI as the heterodimeric ABC transporter involved in the siderophore-free iron uptake into the bacterial cytoplasm. We also provide the first evidence that PCH is able to reach the bacterial periplasm and cytoplasm when both FptA and FptX are expressed. Finally, we detected an interaction between PchH and FptX, linking the ABC transporter PchHI with the inner permease FptX in the PCH-Fe uptake pathway. These results pave the way for a better understanding of the PCH siderophore pathway, giving future directions to tackle P. aeruginosa infections.
Arquier Nathalie, Bjordal Marianne, Hammann Philippe, Kuhn Lauriane, Léopold Pierre
Brain adiponectin signaling controls peripheral insulin response in Drosophila Article de journal
Dans: Nature Communications, vol. 12, no. 1, p. 5633, 2021, ISSN: 2041-1723.
Résumé | Liens | BibTeX | Étiquettes: Adiponectin, Animals, Brain, Cell Line, Drosophila melanogaster, Drosophila Proteins, Energy Metabolism, Genetically Modified, Hemolymph, Homeostasis, Insulin, Juvenile Hormones, Larva, Neurons, PPSE, Receptors, Signal Transduction
@article{arquier_brain_2021,
title = {Brain adiponectin signaling controls peripheral insulin response in Drosophila},
author = {Nathalie Arquier and Marianne Bjordal and Philippe Hammann and Lauriane Kuhn and Pierre Léopold},
doi = {10.1038/s41467-021-25940-6},
issn = {2041-1723},
year = {2021},
date = {2021-09-01},
journal = {Nature Communications},
volume = {12},
number = {1},
pages = {5633},
abstract = {The brain plays a key role in energy homeostasis, detecting nutrients, metabolites and circulating hormones from peripheral organs and integrating this information to control food intake and energy expenditure. Here, we show that a group of neurons in the Drosophila larval brain expresses the adiponectin receptor (AdipoR) and controls systemic growth and metabolism through insulin signaling. We identify glucose-regulated protein 78 (Grp78) as a circulating antagonist of AdipoR function produced by fat cells in response to dietary sugar. We further show that central AdipoR signaling inhibits peripheral Juvenile Hormone (JH) response, promoting insulin signaling. In conclusion, we identify a neuroendocrine axis whereby AdipoR-positive neurons control systemic insulin response.},
keywords = {Adiponectin, Animals, Brain, Cell Line, Drosophila melanogaster, Drosophila Proteins, Energy Metabolism, Genetically Modified, Hemolymph, Homeostasis, Insulin, Juvenile Hormones, Larva, Neurons, PPSE, Receptors, Signal Transduction},
pubstate = {published},
tppubtype = {article}
}
The brain plays a key role in energy homeostasis, detecting nutrients, metabolites and circulating hormones from peripheral organs and integrating this information to control food intake and energy expenditure. Here, we show that a group of neurons in the Drosophila larval brain expresses the adiponectin receptor (AdipoR) and controls systemic growth and metabolism through insulin signaling. We identify glucose-regulated protein 78 (Grp78) as a circulating antagonist of AdipoR function produced by fat cells in response to dietary sugar. We further show that central AdipoR signaling inhibits peripheral Juvenile Hormone (JH) response, promoting insulin signaling. In conclusion, we identify a neuroendocrine axis whereby AdipoR-positive neurons control systemic insulin response.
Khong Minh-Thuong, Berl Valérie, Kuhn Lauriane, Hammann Philippe, Lepoittevin Jean-Pierre
Chemical Modifications Induced by Phthalic Anhydride, a Respiratory Sensitizer, in Reconstructed Human Epidermis: A Combined HRMAS NMR and LC-MS/MS Proteomic Approach Article de journal
Dans: Chemical Research in Toxicology, vol. 34, no. 9, p. 2087–2099, 2021, ISSN: 1520-5010.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{khong_chemical_2021,
title = {Chemical Modifications Induced by Phthalic Anhydride, a Respiratory Sensitizer, in Reconstructed Human Epidermis: A Combined HRMAS NMR and LC-MS/MS Proteomic Approach},
author = {Minh-Thuong Khong and Valérie Berl and Lauriane Kuhn and Philippe Hammann and Jean-Pierre Lepoittevin},
doi = {10.1021/acs.chemrestox.1c00172},
issn = {1520-5010},
year = {2021},
date = {2021-09-01},
journal = {Chemical Research in Toxicology},
volume = {34},
number = {9},
pages = {2087--2099},
abstract = {Chemical skin and respiratory allergies are becoming a major health problem. To date our knowledge on the process of protein haptenation is still limited and mainly derived from studies performed in solution using model nucleophiles. In order to better understand chemical interactions between chemical allergens and the skin, we have investigated the reactivity of phthalic anhydride 1 (PA), a chemical respiratory sensitizer, toward reconstructed human epidermis (RHE). This study was performed using a new approach combining HRMAS NMR to investigate the in situ chemical reactivity and LC-MS/MS to identify modified epidermal proteins. In RHE, the reaction of PA appeared to be quite fast and the major product formed was phthalic acid. Two amide type adducts on lysine residues were observed and after 8h of incubation, we also observed the formation of an imide type cyclized adducts with lysine. In parallel, RHE samples topically exposed to phthalic anhydride (13C)-1 were analyzed using the shotgun proteomics method. Thus, 948 different proteins were extracted and identified, 135 of which being modified by PA, i.e., 14.2% of the extracted proteome. A total of 211 amino acids were modified by PA and validated by fragmentation spectra. We thus identified 154 modified lysines, 22 modified histidines, 30 modified tyrosines, and 5 modified arginines. The rate of modified residues, as a proportion of the total number of modifiable nucleophilic residues in RHE, was rather low (1%). At the protein level, modified proteins were mainly type I and type II keratins and other proteins which are abundant in the epidermis such as protein S100A, Caspase 14, annexin A2, serpin B3, fatty-acid binding protein 5, histone H2, H3, H4, etc. However, the most modified protein, mainly on histidine residues, was filaggrin, a protein that is of low abundance (0.0266 mol %) and rich in histidine.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Chemical skin and respiratory allergies are becoming a major health problem. To date our knowledge on the process of protein haptenation is still limited and mainly derived from studies performed in solution using model nucleophiles. In order to better understand chemical interactions between chemical allergens and the skin, we have investigated the reactivity of phthalic anhydride 1 (PA), a chemical respiratory sensitizer, toward reconstructed human epidermis (RHE). This study was performed using a new approach combining HRMAS NMR to investigate the in situ chemical reactivity and LC-MS/MS to identify modified epidermal proteins. In RHE, the reaction of PA appeared to be quite fast and the major product formed was phthalic acid. Two amide type adducts on lysine residues were observed and after 8h of incubation, we also observed the formation of an imide type cyclized adducts with lysine. In parallel, RHE samples topically exposed to phthalic anhydride (13C)-1 were analyzed using the shotgun proteomics method. Thus, 948 different proteins were extracted and identified, 135 of which being modified by PA, i.e., 14.2% of the extracted proteome. A total of 211 amino acids were modified by PA and validated by fragmentation spectra. We thus identified 154 modified lysines, 22 modified histidines, 30 modified tyrosines, and 5 modified arginines. The rate of modified residues, as a proportion of the total number of modifiable nucleophilic residues in RHE, was rather low (1%). At the protein level, modified proteins were mainly type I and type II keratins and other proteins which are abundant in the epidermis such as protein S100A, Caspase 14, annexin A2, serpin B3, fatty-acid binding protein 5, histone H2, H3, H4, etc. However, the most modified protein, mainly on histidine residues, was filaggrin, a protein that is of low abundance (0.0266 mol %) and rich in histidine.
Nettersheim Jo-Ann, Janel-Bintz Régine, Kuhn Lauriane, Cordonnier Agnès M.
DNA polymerase η is a substrate for calpain: a possible mechanism for pol η retention in UV-induced replication foci Article de journal
Dans: Journal of Cell Science, vol. 134, no. 13, p. jcs258637, 2021, ISSN: 1477-9137.
Résumé | Liens | BibTeX | Étiquettes: calpain, Calpain protease, CAPNS1, DNA Damage, DNA damage response, DNA polymerase η, DNA Repair, DNA Replication, DNA-Directed DNA Polymerase, PPSE, Replication foci, Translesion DNA synthesis
@article{nettersheim_dna_2021,
title = {DNA polymerase η is a substrate for calpain: a possible mechanism for pol η retention in UV-induced replication foci},
author = {Jo-Ann Nettersheim and Régine Janel-Bintz and Lauriane Kuhn and Agnès M. Cordonnier},
doi = {10.1242/jcs.258637},
issn = {1477-9137},
year = {2021},
date = {2021-07-01},
journal = {Journal of Cell Science},
volume = {134},
number = {13},
pages = {jcs258637},
abstract = {DNA polymerase η (pol η) is specifically required for translesion DNA synthesis across UV-induced DNA lesions. Recruitment of this error-prone DNA polymerase is tightly regulated during replication to avoid mutagenesis and perturbation of fork progression. Here, we report that pol η interacts with the calpain small subunit-1 (CAPNS1) in a yeast two-hybrid screening. This interaction is functional, as demonstrated by the ability of endogenous calpain to mediate calcium-dependent cleavage of pol η in cell-free extracts and in living cells treated with a calcium ionophore. The proteolysis of pol η was found to occur at position 465, leading to a catalytically active truncated protein containing the PCNA-interacting motif PIP1. Unexpectedly, cell treatment with the specific calpain inhibitor calpeptin resulted in a decreased extent of pol η foci after UV irradiation, indicating that calpain positively regulates pol η accumulation in replication foci.},
keywords = {calpain, Calpain protease, CAPNS1, DNA Damage, DNA damage response, DNA polymerase η, DNA Repair, DNA Replication, DNA-Directed DNA Polymerase, PPSE, Replication foci, Translesion DNA synthesis},
pubstate = {published},
tppubtype = {article}
}
DNA polymerase η (pol η) is specifically required for translesion DNA synthesis across UV-induced DNA lesions. Recruitment of this error-prone DNA polymerase is tightly regulated during replication to avoid mutagenesis and perturbation of fork progression. Here, we report that pol η interacts with the calpain small subunit-1 (CAPNS1) in a yeast two-hybrid screening. This interaction is functional, as demonstrated by the ability of endogenous calpain to mediate calcium-dependent cleavage of pol η in cell-free extracts and in living cells treated with a calcium ionophore. The proteolysis of pol η was found to occur at position 465, leading to a catalytically active truncated protein containing the PCNA-interacting motif PIP1. Unexpectedly, cell treatment with the specific calpain inhibitor calpeptin resulted in a decreased extent of pol η foci after UV irradiation, indicating that calpain positively regulates pol η accumulation in replication foci.
Mancera-Martínez Eder, Dong Yihan, Makarian Joelle, Srour Ola, Thiébeauld Odon, Jamsheer Muhammed, Chicher Johana, Hammann Philippe, Schepetilnikov Mikhail, Ryabova Lyubov A.
Phosphorylation of a reinitiation supporting protein, RISP, determines its function in translation reinitiation Article de journal
Dans: Nucleic Acids Research, vol. 49, no. 12, p. 6908–6924, 2021, ISSN: 1362-4962.
Résumé | Liens | BibTeX | Étiquettes: Arabidopsis, Arabidopsis Proteins, Caulimovirus, Eukaryotic, Eukaryotic Initiation Factor-2B, Eukaryotic Initiation Factor-3, Large, Peptide Chain Initiation, Phosphorylation, PPSE, Ribosomal Protein S6, Ribosome Subunits, translational
@article{mancera-martinez_phosphorylation_2021,
title = {Phosphorylation of a reinitiation supporting protein, RISP, determines its function in translation reinitiation},
author = {Eder Mancera-Martínez and Yihan Dong and Joelle Makarian and Ola Srour and Odon Thiébeauld and Muhammed Jamsheer and Johana Chicher and Philippe Hammann and Mikhail Schepetilnikov and Lyubov A. Ryabova},
doi = {10.1093/nar/gkab501},
issn = {1362-4962},
year = {2021},
date = {2021-07-01},
journal = {Nucleic Acids Research},
volume = {49},
number = {12},
pages = {6908--6924},
abstract = {Reinitiation supporting protein, RISP, interacts with 60S (60S ribosomal subunit) and eIF3 (eukaryotic initiation factor 3) in plants. TOR (target-of-rapamycin) mediates RISP phosphorylation at residue Ser267, favoring its binding to eL24 (60S ribosomal protein L24). In a viral context, RISP, when phosphorylated, binds the CaMV transactivator/ viroplasmin, TAV, to assist in an exceptional mechanism of reinitiation after long ORF translation. Moreover, we show here that RISP interacts with eIF2 via eIF2β and TOR downstream target 40S ribosomal protein eS6. A RISP phosphorylation knockout, RISP-S267A, binds preferentially eIF2β, and both form a ternary complex with eIF3a in vitro. Accordingly, transient overexpression in plant protoplasts of RISP-S267A, but not a RISP phosphorylation mimic, RISP-S267D, favors translation initiation. In contrast, RISP-S267D preferentially binds eS6, and, when bound to the C-terminus of eS6, can capture 60S in a highly specific manner in vitro, suggesting that it mediates 60S loading during reinitiation. Indeed, eS6-deficient plants are highly resistant to CaMV due to their reduced reinitiation capacity. Strikingly, an eS6 phosphomimic, when stably expressed in eS6-deficient plants, can fully restore the reinitiation deficiency of these plants in cellular and viral contexts. These results suggest that RISP function in translation (re)initiation is regulated by phosphorylation at Ser267.},
keywords = {Arabidopsis, Arabidopsis Proteins, Caulimovirus, Eukaryotic, Eukaryotic Initiation Factor-2B, Eukaryotic Initiation Factor-3, Large, Peptide Chain Initiation, Phosphorylation, PPSE, Ribosomal Protein S6, Ribosome Subunits, translational},
pubstate = {published},
tppubtype = {article}
}
Reinitiation supporting protein, RISP, interacts with 60S (60S ribosomal subunit) and eIF3 (eukaryotic initiation factor 3) in plants. TOR (target-of-rapamycin) mediates RISP phosphorylation at residue Ser267, favoring its binding to eL24 (60S ribosomal protein L24). In a viral context, RISP, when phosphorylated, binds the CaMV transactivator/ viroplasmin, TAV, to assist in an exceptional mechanism of reinitiation after long ORF translation. Moreover, we show here that RISP interacts with eIF2 via eIF2β and TOR downstream target 40S ribosomal protein eS6. A RISP phosphorylation knockout, RISP-S267A, binds preferentially eIF2β, and both form a ternary complex with eIF3a in vitro. Accordingly, transient overexpression in plant protoplasts of RISP-S267A, but not a RISP phosphorylation mimic, RISP-S267D, favors translation initiation. In contrast, RISP-S267D preferentially binds eS6, and, when bound to the C-terminus of eS6, can capture 60S in a highly specific manner in vitro, suggesting that it mediates 60S loading during reinitiation. Indeed, eS6-deficient plants are highly resistant to CaMV due to their reduced reinitiation capacity. Strikingly, an eS6 phosphomimic, when stably expressed in eS6-deficient plants, can fully restore the reinitiation deficiency of these plants in cellular and viral contexts. These results suggest that RISP function in translation (re)initiation is regulated by phosphorylation at Ser267.
Dahlet Thomas, Truss Matthias, Frede Ute, Adhami Hala Al, Bardet Anaïs F., Dumas Michael, Vallet Judith, Chicher Johana, Hammann Philippe, Kottnik Sarah, Hansen Peter, Luz Uschi, Alvarez Gonzalo, Auclair Ghislain, Hecht Jochen, Robinson Peter N., Hagemeier Christian, Weber Michael
E2F6 initiates stable epigenetic silencing of germline genes during embryonic development Article de journal
Dans: Nature Communications, vol. 12, no. 1, p. 3582, 2021, ISSN: 2041-1723.
Résumé | Liens | BibTeX | Étiquettes: Animals, Binding Sites, Cell Differentiation, CpG Islands, CRISPR-Cas Systems, DNA Methylation, E2F6 Transcription Factor, Embryonic Development, Epigenesis, Gene Silencing, Genetic, Germ Cells, Knockout, Mice, Mouse Embryonic Stem Cells, Polycomb Repressive Complex 1, PPSE, RNA, Small Interfering
@article{dahlet_e2f6_2021,
title = {E2F6 initiates stable epigenetic silencing of germline genes during embryonic development},
author = {Thomas Dahlet and Matthias Truss and Ute Frede and Hala Al Adhami and Anaïs F. Bardet and Michael Dumas and Judith Vallet and Johana Chicher and Philippe Hammann and Sarah Kottnik and Peter Hansen and Uschi Luz and Gonzalo Alvarez and Ghislain Auclair and Jochen Hecht and Peter N. Robinson and Christian Hagemeier and Michael Weber},
doi = {10.1038/s41467-021-23596-w},
issn = {2041-1723},
year = {2021},
date = {2021-06-01},
journal = {Nature Communications},
volume = {12},
number = {1},
pages = {3582},
abstract = {In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development.},
keywords = {Animals, Binding Sites, Cell Differentiation, CpG Islands, CRISPR-Cas Systems, DNA Methylation, E2F6 Transcription Factor, Embryonic Development, Epigenesis, Gene Silencing, Genetic, Germ Cells, Knockout, Mice, Mouse Embryonic Stem Cells, Polycomb Repressive Complex 1, PPSE, RNA, Small Interfering},
pubstate = {published},
tppubtype = {article}
}
In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development.
Gasser Véronique, Kuhn Lauriane, Hubert Thibaut, Aussel Laurent, Hammann Philippe, Schalk Isabelle J.
The Esterase PfeE, the Achilles' Heel in the Battle for Iron between Pseudomonas aeruginosa and Escherichia coli Article de journal
Dans: International Journal of Molecular Sciences, vol. 22, no. 6, p. 2814, 2021, ISSN: 1422-0067.
Résumé | Liens | BibTeX | Étiquettes: Carrier Proteins, co-cultures, enterobactin, Escherichia coli, Escherichia coli Proteins, Esterases, Iron, iron homeostasis, iron uptake, outer membrane transporters, PPSE, Pseudomonas aeruginosa, siderophore, TonB
@article{gasser_esterase_2021,
title = {The Esterase PfeE, the Achilles' Heel in the Battle for Iron between Pseudomonas aeruginosa and Escherichia coli},
author = {Véronique Gasser and Lauriane Kuhn and Thibaut Hubert and Laurent Aussel and Philippe Hammann and Isabelle J. Schalk},
doi = {10.3390/ijms22062814},
issn = {1422-0067},
year = {2021},
date = {2021-03-01},
urldate = {2021-03-01},
journal = {International Journal of Molecular Sciences},
volume = {22},
number = {6},
pages = {2814},
abstract = {Bacteria access iron, a key nutrient, by producing siderophores or using siderophores produced by other microorganisms. The pathogen Pseudomonas aeruginosa produces two siderophores but is also able to pirate enterobactin (ENT), the siderophore produced by Escherichia coli. ENT-Fe complexes are imported across the outer membrane of P. aeruginosa by the two outer membrane transporters PfeA and PirA. Iron is released from ENT in the P. aeruginosa periplasm by hydrolysis of ENT by the esterase PfeE. We show here that pfeE gene deletion renders P. aeruginosa unable to grow in the presence of ENT because it is unable to access iron via this siderophore. Two-species co-cultures under iron-restricted conditions show that P. aeruginosa strongly represses the growth of E. coli as long it is able to produce its own siderophores. Both strains are present in similar proportions in the culture as long as the siderophore-deficient P. aeruginosa strain is able to use ENT produced by E. coli to access iron. If pfeE is deleted, E. coli has the upper hand in the culture and P. aeruginosa growth is repressed. Overall, these data show that PfeE is the Achilles' heel of P. aeruginosa in communities with bacteria producing ENT.},
keywords = {Carrier Proteins, co-cultures, enterobactin, Escherichia coli, Escherichia coli Proteins, Esterases, Iron, iron homeostasis, iron uptake, outer membrane transporters, PPSE, Pseudomonas aeruginosa, siderophore, TonB},
pubstate = {published},
tppubtype = {article}
}
Bacteria access iron, a key nutrient, by producing siderophores or using siderophores produced by other microorganisms. The pathogen Pseudomonas aeruginosa produces two siderophores but is also able to pirate enterobactin (ENT), the siderophore produced by Escherichia coli. ENT-Fe complexes are imported across the outer membrane of P. aeruginosa by the two outer membrane transporters PfeA and PirA. Iron is released from ENT in the P. aeruginosa periplasm by hydrolysis of ENT by the esterase PfeE. We show here that pfeE gene deletion renders P. aeruginosa unable to grow in the presence of ENT because it is unable to access iron via this siderophore. Two-species co-cultures under iron-restricted conditions show that P. aeruginosa strongly represses the growth of E. coli as long it is able to produce its own siderophores. Both strains are present in similar proportions in the culture as long as the siderophore-deficient P. aeruginosa strain is able to use ENT produced by E. coli to access iron. If pfeE is deleted, E. coli has the upper hand in the culture and P. aeruginosa growth is repressed. Overall, these data show that PfeE is the Achilles' heel of P. aeruginosa in communities with bacteria producing ENT.
Enkler Ludovic, Rinaldi Bruno, Craene Johan Owen, Hammann Philippe, Nureki Osamu, Senger Bruno, Friant Sylvie, Becker Hubert D.
Cex1 is a component of the COPI intracellular trafficking machinery Article de journal
Dans: Biology Open, vol. 10, no. 3, p. bio058528, 2021, ISSN: 2046-6390.
Résumé | Liens | BibTeX | Étiquettes: Arc1, Cex1, COPI coat, PPSE, SCYL1, trafficking
@article{enkler_cex1_2021,
title = {Cex1 is a component of the COPI intracellular trafficking machinery},
author = {Ludovic Enkler and Bruno Rinaldi and Johan Owen Craene and Philippe Hammann and Osamu Nureki and Bruno Senger and Sylvie Friant and Hubert D. Becker},
doi = {10.1242/bio.058528},
issn = {2046-6390},
year = {2021},
date = {2021-03-01},
journal = {Biology Open},
volume = {10},
number = {3},
pages = {bio058528},
abstract = {COPI (coatomer complex I) coated vesicles are involved in Golgi-to-ER and intra-Golgi trafficking pathways, and mediate retrieval of ER resident proteins. Functions and components of the COPI-mediated trafficking pathways, beyond the canonical set of Sec/Arf proteins, are constantly increasing in number and complexity. In mammalian cells, GORAB, SCYL1 and SCYL3 proteins regulate Golgi morphology and protein glycosylation in concert with the COPI machinery. Here, we show that Cex1, homologous to the mammalian SCYL proteins, is a component of the yeast COPI machinery, by interacting with Sec27, Sec28 and Sec33 (Ret1/Cop1) proteins of the COPI coat. Cex1 was initially reported to mediate channeling of aminoacylated tRNA outside of the nucleus. Our data show that Cex1 localizes at membrane compartments, on structures positive for the Sec33 α-COP subunit. Moreover, the Wbp1 protein required for N-glycosylation and interacting via its di-lysine motif with the Sec27 β'-COP subunit is mis-targeted in cex1Δ deletion mutant cells. Our data point to the possibility of developing Cex1 yeast-based models to study neurodegenerative disorders linked to pathogenic mutations of its human homologue SCYL1.},
keywords = {Arc1, Cex1, COPI coat, PPSE, SCYL1, trafficking},
pubstate = {published},
tppubtype = {article}
}
COPI (coatomer complex I) coated vesicles are involved in Golgi-to-ER and intra-Golgi trafficking pathways, and mediate retrieval of ER resident proteins. Functions and components of the COPI-mediated trafficking pathways, beyond the canonical set of Sec/Arf proteins, are constantly increasing in number and complexity. In mammalian cells, GORAB, SCYL1 and SCYL3 proteins regulate Golgi morphology and protein glycosylation in concert with the COPI machinery. Here, we show that Cex1, homologous to the mammalian SCYL proteins, is a component of the yeast COPI machinery, by interacting with Sec27, Sec28 and Sec33 (Ret1/Cop1) proteins of the COPI coat. Cex1 was initially reported to mediate channeling of aminoacylated tRNA outside of the nucleus. Our data show that Cex1 localizes at membrane compartments, on structures positive for the Sec33 α-COP subunit. Moreover, the Wbp1 protein required for N-glycosylation and interacting via its di-lysine motif with the Sec27 β'-COP subunit is mis-targeted in cex1Δ deletion mutant cells. Our data point to the possibility of developing Cex1 yeast-based models to study neurodegenerative disorders linked to pathogenic mutations of its human homologue SCYL1.
Scheer Hélène, Almeida Caroline, Ferrier Emilie, Simonnot Quentin, Poirier Laure, Pflieger David, Sement François M., Koechler Sandrine, Piermaria Christina, Krawczyk Paweł, Mroczek Seweryn, Chicher Johana, Kuhn Lauriane, Dziembowski Andrzej, Hammann Philippe, Zuber Hélène, Gagliardi Dominique
The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis Article de journal
Dans: Nature Communications, vol. 12, no. 1, p. 1298, 2021, ISSN: 2041-1723.
Résumé | Liens | BibTeX | Étiquettes: Arabidopsis, Arabidopsis Proteins, Co-Repressor Proteins, DEAD-box RNA Helicases, Gene Expression Regulation, Humans, messenger, Plant, PPSE, Proto-Oncogene Proteins, Ribonucleoproteins, RNA, RNA Nucleotidyltransferases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Small Interfering, Tobacco, transcriptome, Uridine
@article{scheer_tutase_2021,
title = {The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis},
author = {Hélène Scheer and Caroline Almeida and Emilie Ferrier and Quentin Simonnot and Laure Poirier and David Pflieger and François M. Sement and Sandrine Koechler and Christina Piermaria and Paweł Krawczyk and Seweryn Mroczek and Johana Chicher and Lauriane Kuhn and Andrzej Dziembowski and Philippe Hammann and Hélène Zuber and Dominique Gagliardi},
doi = {10.1038/s41467-021-21382-2},
issn = {2041-1723},
year = {2021},
date = {2021-02-01},
journal = {Nature Communications},
volume = {12},
number = {1},
pages = {1298},
abstract = {Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3' terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.},
keywords = {Arabidopsis, Arabidopsis Proteins, Co-Repressor Proteins, DEAD-box RNA Helicases, Gene Expression Regulation, Humans, messenger, Plant, PPSE, Proto-Oncogene Proteins, Ribonucleoproteins, RNA, RNA Nucleotidyltransferases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Small Interfering, Tobacco, transcriptome, Uridine},
pubstate = {published},
tppubtype = {article}
}
Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3' terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.
Montavon T C, Baldaccini M, Lefevre M, Girardi E, Chane-Woon-Ming B, Messmer M, Hammann P, Chicher J, Pfeffer S
Human DICER helicase domain recruits PKR and modulates its antiviral activity Article de journal
Dans: PLoS Pathog, vol. 17, no. 5, p. e1009549, 2021, ISBN: 33984068, (1553-7374 (Electronic) 1553-7366 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, PPSE, Unité ARN
@article{Montavon2021,
title = {Human DICER helicase domain recruits PKR and modulates its antiviral activity},
author = {T C Montavon and M Baldaccini and M Lefevre and E Girardi and B Chane-Woon-Ming and M Messmer and P Hammann and J Chicher and S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33984068},
doi = {0.1371/journal.ppat.1009549},
isbn = {33984068},
year = {2021},
date = {2021-01-01},
journal = {PLoS Pathog},
volume = {17},
number = {5},
pages = {e1009549},
abstract = {The antiviral innate immune response mainly involves type I interferon (IFN) in mammalian cells. The contribution of the RNA silencing machinery remains to be established, but several recent studies indicate that the ribonuclease DICER can generate viral siRNAs in specific conditions. It has also been proposed that type I IFN and RNA silencing could be mutually exclusive antiviral responses. In order to decipher the implication of DICER during infection of human cells with alphaviruses such as the Sindbis virus and Semliki forest virus, we determined its interactome by proteomics analysis. We show that DICER specifically interacts with several double-stranded RNA binding proteins and RNA helicases during viral infection. In particular, proteins such as DHX9, ADAR-1 and the protein kinase RNA-activated (PKR) are enriched with DICER in virus-infected cells. We demonstrate that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to this protein in an RNAi-independent, PKR-dependent, manner.},
note = {1553-7374 (Electronic)
1553-7366 (Linking)
Journal Article},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The antiviral innate immune response mainly involves type I interferon (IFN) in mammalian cells. The contribution of the RNA silencing machinery remains to be established, but several recent studies indicate that the ribonuclease DICER can generate viral siRNAs in specific conditions. It has also been proposed that type I IFN and RNA silencing could be mutually exclusive antiviral responses. In order to decipher the implication of DICER during infection of human cells with alphaviruses such as the Sindbis virus and Semliki forest virus, we determined its interactome by proteomics analysis. We show that DICER specifically interacts with several double-stranded RNA binding proteins and RNA helicases during viral infection. In particular, proteins such as DHX9, ADAR-1 and the protein kinase RNA-activated (PKR) are enriched with DICER in virus-infected cells. We demonstrate that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to this protein in an RNAi-independent, PKR-dependent, manner.
Méteignier Louis-Valentin, Ghandour Rabea, Zimmerman Aude, Kuhn Lauriane, Meurer Jörg, Zoschke Reimo, Hammani Kamel
Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo Article de journal
Dans: Nucleic Acids Research, vol. 49, no. 2, p. 1114–1132, 2021, ISSN: 1362-4962.
Résumé | Liens | BibTeX | Étiquettes: 16S, 23S, Arabidopsis, Arabidopsis Proteins, Chloroplast Proteins, Chloroplasts, Gene Expression Regulation, Organelle Biogenesis, Peptide Termination Factors, Plant, Polyribosomes, PPSE, Protein Biosynthesis, Recombinant Proteins, Ribonucleoproteins, Ribosomal, ribosomes, RNA, Substrate Specificity
@article{meteignier_arabidopsis_2021,
title = {Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo},
author = {Louis-Valentin Méteignier and Rabea Ghandour and Aude Zimmerman and Lauriane Kuhn and Jörg Meurer and Reimo Zoschke and Kamel Hammani},
doi = {10.1093/nar/gkaa1244},
issn = {1362-4962},
year = {2021},
date = {2021-01-01},
journal = {Nucleic Acids Research},
volume = {49},
number = {2},
pages = {1114--1132},
abstract = {The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.},
keywords = {16S, 23S, Arabidopsis, Arabidopsis Proteins, Chloroplast Proteins, Chloroplasts, Gene Expression Regulation, Organelle Biogenesis, Peptide Termination Factors, Plant, Polyribosomes, PPSE, Protein Biosynthesis, Recombinant Proteins, Ribonucleoproteins, Ribosomal, ribosomes, RNA, Substrate Specificity},
pubstate = {published},
tppubtype = {article}
}
The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.
2020
Tidu A, Janvier A, Schaeffer L, Sosnowski P, Kuhn L, Hammann P, Westhof E, Eriani G, Martin F
The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation Article de journal
Dans: RNA, vol. 27, no. 3, p. 253-264, 2020.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, PPSE, Unité ARN
@article{A.2020,
title = {The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation},
author = {A Tidu and A Janvier and L Schaeffer and P Sosnowski and L Kuhn and P Hammann and E Westhof and G Eriani and F Martin
},
url = {https://rnajournal.cshlp.org/content/early/2020/12/02/rna.078121.120},
doi = {10.1261/rna.078121.120 },
year = {2020},
date = {2020-12-02},
journal = {RNA},
volume = {27},
number = {3},
pages = {253-264},
abstract = {SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5'UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus. },
keywords = {ERIANI, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5'UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus.
Perraud Quentin, Kuhn Lauriane, Fritsch Sarah, Graulier Gwenaëlle, Gasser Véronique, Normant Vincent, Hammann Philippe, Schalk Isabelle J.
Opportunistic use of catecholamine neurotransmitters as siderophores to access iron by Pseudomonas aeruginosa Article de journal
Dans: Environmental Microbiology, 2020, ISSN: 1462-2920.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{perraud_opportunistic_2020,
title = {Opportunistic use of catecholamine neurotransmitters as siderophores to access iron by Pseudomonas aeruginosa},
author = {Quentin Perraud and Lauriane Kuhn and Sarah Fritsch and Gwenaëlle Graulier and Véronique Gasser and Vincent Normant and Philippe Hammann and Isabelle J. Schalk},
doi = {10.1111/1462-2920.15372},
issn = {1462-2920},
year = {2020},
date = {2020-12-01},
journal = {Environmental Microbiology},
abstract = {Iron is an essential nutrient for bacterial growth and the cause of a fierce battle between the pathogen and host during infection. Bacteria have developed several strategies to access iron from the host, the most common being the production of siderophores, small iron-chelating molecules secreted into the bacterial environment. The opportunist pathogen Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a wide panoply of xenosiderophores, siderophores produced by other microorganisms. Here, we demonstrate that catecholamine neurotransmitters (dopamine, l-DOPA, epinephrine and norepinephrine) are able to chelate iron and efficiently bring iron into P. aeruginosa cells via TonB-dependent transporters (TBDTs). Bacterial growth assays under strong iron-restricted conditions and with numerous mutants showed that the TBDTs involved are PiuA and PirA. PiuA exhibited more pronounced specificity for dopamine uptake than for norepinephrine, epinephrine and l-DOPA, whereas PirA specificity appeared to be higher for l-DOPA and norepinephrine. Proteomic and qRT-PCR approaches showed pirA transcription and expression to be induced in the presence of all four catecholamines. Finally, the oxidative properties of catecholamines enable them to reduce iron, and we observed ferrous iron uptake via the FeoABC system in the presence of l-DOPA.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Iron is an essential nutrient for bacterial growth and the cause of a fierce battle between the pathogen and host during infection. Bacteria have developed several strategies to access iron from the host, the most common being the production of siderophores, small iron-chelating molecules secreted into the bacterial environment. The opportunist pathogen Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a wide panoply of xenosiderophores, siderophores produced by other microorganisms. Here, we demonstrate that catecholamine neurotransmitters (dopamine, l-DOPA, epinephrine and norepinephrine) are able to chelate iron and efficiently bring iron into P. aeruginosa cells via TonB-dependent transporters (TBDTs). Bacterial growth assays under strong iron-restricted conditions and with numerous mutants showed that the TBDTs involved are PiuA and PirA. PiuA exhibited more pronounced specificity for dopamine uptake than for norepinephrine, epinephrine and l-DOPA, whereas PirA specificity appeared to be higher for l-DOPA and norepinephrine. Proteomic and qRT-PCR approaches showed pirA transcription and expression to be induced in the presence of all four catecholamines. Finally, the oxidative properties of catecholamines enable them to reduce iron, and we observed ferrous iron uptake via the FeoABC system in the presence of l-DOPA.
Soufari Heddy, Waltz Florent, Parrot Camila, Durrieu-Gaillard Stéphanie, Bochler Anthony, Kuhn Lauriane, Sissler Marie, Hashem Yaser
Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis. Article de journal
Dans: Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 47, p. 29851–29861, 2020, ISSN: 1091-6490 0027-8424.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{soufari_structure_2020,
title = {Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.},
author = {Heddy Soufari and Florent Waltz and Camila Parrot and Stéphanie Durrieu-Gaillard and Anthony Bochler and Lauriane Kuhn and Marie Sissler and Yaser Hashem},
doi = {10.1073/pnas.2011301117},
issn = {1091-6490 0027-8424},
year = {2020},
date = {2020-11-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {47},
pages = {29851--29861},
abstract = {Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.
Soufari Heddy, Parrot Camila, Kuhn Lauriane, Waltz Florent, Hashem Yaser
Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM. Article de journal
Dans: Nature communications, vol. 11, no. 1, p. 5195, 2020, ISSN: 2041-1723 2041-1723.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{soufari_specific_2020,
title = {Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM.},
author = {Heddy Soufari and Camila Parrot and Lauriane Kuhn and Florent Waltz and Yaser Hashem},
doi = {10.1038/s41467-020-18814-w},
issn = {2041-1723 2041-1723},
year = {2020},
date = {2020-10-01},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5195},
abstract = {Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole P(D) module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the P(P) to the P(D) module.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole P(D) module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the P(P) to the P(D) module.
Incarbone Marco, Scheer Hélene, Hily Jean-Michel, Kuhn Lauriane, Erhardt Mathieu, Dunoyer Patrice, Altenbach Denise, Ritzenthaler Christophe
Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana. Article de journal
Dans: Viruses, vol. 12, no. 10, 2020, ISSN: 1999-4915 1999-4915.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{incarbone_characterization_2020,
title = {Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana.},
author = {Marco Incarbone and Hélene Scheer and Jean-Michel Hily and Lauriane Kuhn and Mathieu Erhardt and Patrice Dunoyer and Denise Altenbach and Christophe Ritzenthaler},
doi = {10.3390/v12101121},
issn = {1999-4915 1999-4915},
year = {2020},
date = {2020-10-01},
journal = {Viruses},
volume = {12},
number = {10},
abstract = {Tomato bushy stunt virus (TBSV), the type member of the genus Tombusvirus in the family Tombusviridae is one of the best studied plant viruses. The TBSV natural and experimental host range covers a wide spectrum of plants including agricultural crops, ornamentals, vegetables and Nicotiana benthamiana. However, Arabidopsis thaliana, the well-established model organism in plant biology, genetics and plant-microbe interactions is absent from the list of known TBSV host plant species. Most of our recent knowledge of the virus life cycle has emanated from studies in Saccharomyces cerevisiae, a surrogate host for TBSV that lacks crucial plant antiviral mechanisms such as RNA interference (RNAi). Here, we identified and characterized a TBSV isolate able to infect Arabidopsis with high efficiency. We demonstrated by confocal and 3D electron microscopy that in Arabidopsis TBSV-BS3Ng replicates in association with clustered peroxisomes in which numerous spherules are induced. A dsRNA-centered immunoprecipitation analysis allowed the identification of TBSV-associated host components including DRB2 and DRB4, which perfectly localized to replication sites, and NFD2 that accumulated in larger viral factories in which peroxisomes cluster. By challenging knock-out mutants for key RNAi factors, we showed that TBSV-BS3Ng undergoes a non-canonical RNAi defensive reaction. In fact, unlike other RNA viruses described, no 22nt TBSV-derived small RNA are detected in the absence of DCL4, indicating that this virus is DCL2-insensitive. The new Arabidopsis-TBSV-BS3Ng pathosystem should provide a valuable new model for dissecting plant-virus interactions in complement to Saccharomyces cerevisiae.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Tomato bushy stunt virus (TBSV), the type member of the genus Tombusvirus in the family Tombusviridae is one of the best studied plant viruses. The TBSV natural and experimental host range covers a wide spectrum of plants including agricultural crops, ornamentals, vegetables and Nicotiana benthamiana. However, Arabidopsis thaliana, the well-established model organism in plant biology, genetics and plant-microbe interactions is absent from the list of known TBSV host plant species. Most of our recent knowledge of the virus life cycle has emanated from studies in Saccharomyces cerevisiae, a surrogate host for TBSV that lacks crucial plant antiviral mechanisms such as RNA interference (RNAi). Here, we identified and characterized a TBSV isolate able to infect Arabidopsis with high efficiency. We demonstrated by confocal and 3D electron microscopy that in Arabidopsis TBSV-BS3Ng replicates in association with clustered peroxisomes in which numerous spherules are induced. A dsRNA-centered immunoprecipitation analysis allowed the identification of TBSV-associated host components including DRB2 and DRB4, which perfectly localized to replication sites, and NFD2 that accumulated in larger viral factories in which peroxisomes cluster. By challenging knock-out mutants for key RNAi factors, we showed that TBSV-BS3Ng undergoes a non-canonical RNAi defensive reaction. In fact, unlike other RNA viruses described, no 22nt TBSV-derived small RNA are detected in the absence of DCL4, indicating that this virus is DCL2-insensitive. The new Arabidopsis-TBSV-BS3Ng pathosystem should provide a valuable new model for dissecting plant-virus interactions in complement to Saccharomyces cerevisiae.
Normant Vincent, Josts Inokentijs, Kuhn Lauriane, Perraud Quentin, Fritsch Sarah, Hammann Philippe, Mislin Gaëtan L A, Tidow Henning, Schalk Isabelle J
Nocardamine-Dependent Iron Uptake in Pseudomonas aeruginosa: Exclusive Involvement of the FoxA Outer Membrane Transporter. Article de journal
Dans: ACS chemical biology, vol. 15, no. 10, p. 2741–2751, 2020, ISSN: 1554-8937 1554-8929.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{normant_nocardamine-dependent_2020,
title = {Nocardamine-Dependent Iron Uptake in Pseudomonas aeruginosa: Exclusive Involvement of the FoxA Outer Membrane Transporter.},
author = {Vincent Normant and Inokentijs Josts and Lauriane Kuhn and Quentin Perraud and Sarah Fritsch and Philippe Hammann and Gaëtan L A Mislin and Henning Tidow and Isabelle J Schalk},
doi = {10.1021/acschembio.0c00535},
issn = {1554-8937 1554-8929},
year = {2020},
date = {2020-10-01},
journal = {ACS chemical biology},
volume = {15},
number = {10},
pages = {2741--2751},
abstract = {Iron is a key nutrient for almost all living organisms. Paradoxically, it is poorly soluble and consequently poorly bioavailable. Bacteria have thus developed multiple strategies to access this metal. One of the most common consists of the use of siderophores, small compounds that chelate ferric iron with very high affinity. Many bacteria are able to produce their own siderophores or use those produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a large panel of exosiderophores. We investigated the ability of P. aeruginosa to use nocardamine (NOCA) and ferrioxamine B (DFOB) as exosiderophores under iron-limited planktonic growth conditions. Proteomic and RT-qPCR approaches showed induction of the transcription and expression of the outer membrane transporter FoxA in the presence of NOCA or DFOB in the bacterial environment. Expression of the proteins of the heme- or pyoverdine- and pyochelin-dependent iron uptake pathways was not affected by the presence of these two tris-hydroxamate siderophores. (55)Fe uptake assays using foxA mutants showed ferri-NOCA to be exclusively transported by FoxA, whereas ferri-DFOB was transported by FoxA and at least one other unidentified transporter. The crystal structure of FoxA complexed with NOCA-Fe revealed very similar siderophore binding sites between NOCA-Fe and DFOB-Fe. We discuss iron uptake by hydroxamate exosiderophores in P. aeruginosa cells in light of these results.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Iron is a key nutrient for almost all living organisms. Paradoxically, it is poorly soluble and consequently poorly bioavailable. Bacteria have thus developed multiple strategies to access this metal. One of the most common consists of the use of siderophores, small compounds that chelate ferric iron with very high affinity. Many bacteria are able to produce their own siderophores or use those produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa produces two siderophores, pyoverdine and pyochelin, and is also able to use a large panel of exosiderophores. We investigated the ability of P. aeruginosa to use nocardamine (NOCA) and ferrioxamine B (DFOB) as exosiderophores under iron-limited planktonic growth conditions. Proteomic and RT-qPCR approaches showed induction of the transcription and expression of the outer membrane transporter FoxA in the presence of NOCA or DFOB in the bacterial environment. Expression of the proteins of the heme- or pyoverdine- and pyochelin-dependent iron uptake pathways was not affected by the presence of these two tris-hydroxamate siderophores. (55)Fe uptake assays using foxA mutants showed ferri-NOCA to be exclusively transported by FoxA, whereas ferri-DFOB was transported by FoxA and at least one other unidentified transporter. The crystal structure of FoxA complexed with NOCA-Fe revealed very similar siderophore binding sites between NOCA-Fe and DFOB-Fe. We discuss iron uptake by hydroxamate exosiderophores in P. aeruginosa cells in light of these results.
Kröll-Hermi Ariane, Ebstein Frédéric, Stoetzel Corinne, Geoffroy Véronique, Schaefer Elise, Scheidecker Sophie, Bär Séverine, Takamiya Masanari, Kawakami Koichi, Zieba Barbara A, Studer Fouzia, Pelletier Valerie, Eyermann Carine, Speeg-Schatz Claude, Laugel Vincent, Lipsker Dan, Sandron Florian, McGinn Steven, Boland Anne, Deleuze Jean-François, Kuhn Lauriane, Chicher Johana, Hammann Philippe, Friant Sylvie, Etard Christelle, Krüger Elke, Muller Jean, Strähle Uwe, Dollfus Hélène
Proteasome subunit PSMC3 variants cause neurosensory syndrome combining deafness and cataract due to proteotoxic stress. Article de journal
Dans: EMBO molecular medicine, vol. 12, no. 7, p. e11861, 2020, ISSN: 1757-4684 1757-4676 1757-4676.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{kroll-hermi_proteasome_2020,
title = {Proteasome subunit PSMC3 variants cause neurosensory syndrome combining deafness and cataract due to proteotoxic stress.},
author = {Ariane Kröll-Hermi and Frédéric Ebstein and Corinne Stoetzel and Véronique Geoffroy and Elise Schaefer and Sophie Scheidecker and Séverine Bär and Masanari Takamiya and Koichi Kawakami and Barbara A Zieba and Fouzia Studer and Valerie Pelletier and Carine Eyermann and Claude Speeg-Schatz and Vincent Laugel and Dan Lipsker and Florian Sandron and Steven McGinn and Anne Boland and Jean-François Deleuze and Lauriane Kuhn and Johana Chicher and Philippe Hammann and Sylvie Friant and Christelle Etard and Elke Krüger and Jean Muller and Uwe Strähle and Hélène Dollfus},
doi = {10.15252/emmm.201911861},
issn = {1757-4684 1757-4676 1757-4676},
year = {2020},
date = {2020-07-01},
journal = {EMBO molecular medicine},
volume = {12},
number = {7},
pages = {e11861},
abstract = {The ubiquitin-proteasome system degrades ubiquitin-modified proteins to maintain protein homeostasis and to control signalling. Whole-genome sequencing of patients with severe deafness and early-onset cataracts as part of a neurological, sensorial and cutaneous novel syndrome identified a unique deep intronic homozygous variant in the PSMC3 gene, encoding the proteasome ATPase subunit Rpt5, which lead to the transcription of a cryptic exon. The proteasome content and activity in patient's fibroblasts was however unaffected. Nevertheless, patient's cells exhibited impaired protein homeostasis characterized by accumulation of ubiquitinated proteins suggesting severe proteotoxic stress. Indeed, the TCF11/Nrf1 transcriptional pathway allowing proteasome recovery after proteasome inhibition is permanently activated in the patient's fibroblasts. Upon chemical proteasome inhibition, this pathway was however impaired in patient's cells, which were unable to compensate for proteotoxic stress although a higher proteasome content and activity. Zebrafish modelling for knockout in PSMC3 remarkably reproduced the human phenotype with inner ear development anomalies as well as cataracts, suggesting that Rpt5 plays a major role in inner ear, lens and central nervous system development.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The ubiquitin-proteasome system degrades ubiquitin-modified proteins to maintain protein homeostasis and to control signalling. Whole-genome sequencing of patients with severe deafness and early-onset cataracts as part of a neurological, sensorial and cutaneous novel syndrome identified a unique deep intronic homozygous variant in the PSMC3 gene, encoding the proteasome ATPase subunit Rpt5, which lead to the transcription of a cryptic exon. The proteasome content and activity in patient's fibroblasts was however unaffected. Nevertheless, patient's cells exhibited impaired protein homeostasis characterized by accumulation of ubiquitinated proteins suggesting severe proteotoxic stress. Indeed, the TCF11/Nrf1 transcriptional pathway allowing proteasome recovery after proteasome inhibition is permanently activated in the patient's fibroblasts. Upon chemical proteasome inhibition, this pathway was however impaired in patient's cells, which were unable to compensate for proteotoxic stress although a higher proteasome content and activity. Zebrafish modelling for knockout in PSMC3 remarkably reproduced the human phenotype with inner ear development anomalies as well as cataracts, suggesting that Rpt5 plays a major role in inner ear, lens and central nervous system development.
Perraud Quentin, Cantero Paola, Roche Béatrice, Gasser Véronique, Normant Vincent P, Kuhn Lauriane, Hammann Philippe, Mislin Gaëtan L A, Ehret-Sabatier Laurence, Schalk Isabelle J
Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms. Article de journal
Dans: Molecular & cellular proteomics : MCP, vol. 19, no. 4, p. 589–607, 2020, ISSN: 1535-9484 1535-9476 1535-9476.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{perraud_phenotypic_2020,
title = {Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms.},
author = {Quentin Perraud and Paola Cantero and Béatrice Roche and Véronique Gasser and Vincent P Normant and Lauriane Kuhn and Philippe Hammann and Gaëtan L A Mislin and Laurence Ehret-Sabatier and Isabelle J Schalk},
doi = {10.1074/mcp.RA119.001829},
issn = {1535-9484 1535-9476 1535-9476},
year = {2020},
date = {2020-04-01},
journal = {Molecular & cellular proteomics : MCP},
volume = {19},
number = {4},
pages = {589--607},
abstract = {Bacteria secrete siderophores to access iron, a key nutrient poorly bioavailable and the source of strong competition between microorganisms in most biotopes. Many bacteria also use siderophores produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa, an opportunistic pathogen, produces two siderophores, pyoverdine and pyochelin, and is also able to use a panel of exosiderophores. We first investigated expression of the various iron-uptake pathways of P. aeruginosa in three different growth media using proteomic and RT-qPCR approaches and observed three different phenotypic patterns, indicating complex phenotypic plasticity in the expression of the various iron-uptake pathways. We then investigated the phenotypic plasticity of iron-uptake pathway expression in the presence of various exosiderophores (present individually or as a mixture) under planktonic growth conditions, as well as in an epithelial cell infection assay. In all growth conditions tested, catechol-type exosiderophores were clearly more efficient in inducing the expression of their corresponding transporters than the others, showing that bacteria opt for the use of catechol siderophores to access iron when they are present in the environment. In parallel, expression of the proteins of the pyochelin pathway was significantly repressed under most conditions tested, as well as that of proteins of the pyoverdine pathway, but to a lesser extent. There was no effect on the expression of the heme and ferrous uptake pathways. Overall, these data provide precise insights on how P. aeruginosa adjusts the expression of its various iron-uptake pathways (phenotypic plasticity and switching) to match varying levels of iron and competition.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Bacteria secrete siderophores to access iron, a key nutrient poorly bioavailable and the source of strong competition between microorganisms in most biotopes. Many bacteria also use siderophores produced by other microorganisms (exosiderophores) in a piracy strategy. Pseudomonas aeruginosa, an opportunistic pathogen, produces two siderophores, pyoverdine and pyochelin, and is also able to use a panel of exosiderophores. We first investigated expression of the various iron-uptake pathways of P. aeruginosa in three different growth media using proteomic and RT-qPCR approaches and observed three different phenotypic patterns, indicating complex phenotypic plasticity in the expression of the various iron-uptake pathways. We then investigated the phenotypic plasticity of iron-uptake pathway expression in the presence of various exosiderophores (present individually or as a mixture) under planktonic growth conditions, as well as in an epithelial cell infection assay. In all growth conditions tested, catechol-type exosiderophores were clearly more efficient in inducing the expression of their corresponding transporters than the others, showing that bacteria opt for the use of catechol siderophores to access iron when they are present in the environment. In parallel, expression of the proteins of the pyochelin pathway was significantly repressed under most conditions tested, as well as that of proteins of the pyoverdine pathway, but to a lesser extent. There was no effect on the expression of the heme and ferrous uptake pathways. Overall, these data provide precise insights on how P. aeruginosa adjusts the expression of its various iron-uptake pathways (phenotypic plasticity and switching) to match varying levels of iron and competition.
Janel-Bintz Régine, Kuhn Lauriane, Frit Philippe, Chicher Johana, Wagner Jérôme, Haracska Lajos, Hammann Philippe, Cordonnier Agnès M
Proteomic Analysis of DNA Synthesis on a Structured DNA Template in Human Cellular Extracts: Interplay Between NHEJ and Replication-Associated Proteins. Article de journal
Dans: Proteomics, vol. 20, no. 3-4, p. e1900184, 2020, ISSN: 1615-9861 1615-9853.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{janel-bintz_proteomic_2020,
title = {Proteomic Analysis of DNA Synthesis on a Structured DNA Template in Human Cellular Extracts: Interplay Between NHEJ and Replication-Associated Proteins.},
author = {Régine Janel-Bintz and Lauriane Kuhn and Philippe Frit and Johana Chicher and Jérôme Wagner and Lajos Haracska and Philippe Hammann and Agnès M Cordonnier},
doi = {10.1002/pmic.201900184},
issn = {1615-9861 1615-9853},
year = {2020},
date = {2020-02-01},
journal = {Proteomics},
volume = {20},
number = {3-4},
pages = {e1900184},
abstract = {It is established that short inverted repeats trigger base substitution mutagenesis in human cells. However, how the replication machinery deals with structured DNA is unknown. It has been previously reported that in human cell-free extracts, DNA primer extension using a structured single-stranded template is transiently blocked at DNA hairpins. Here, the proteomic analysis of proteins bound to the DNA template is reported and evidence that the DNA-PK complex (DNA-PKcs and the Ku heterodimer) recognizes, and is activated by, structured single-stranded DNA is provided. Hijacking the DNA-PK complex by double-stranded oligonucleotides results in a large removal of the pausing sites and an elevated DNA extension efficiency. Conversely, DNA-PKcs inhibition results in its stabilization on the template, along with other proteins acting downstream in the Non-Homologous End-Joining (NHEJ) pathway, especially the XRCC4-DNA ligase 4 complex and the cofactor PAXX. Retention of NHEJ factors to the DNA in the absence of DNA-PKcs activity correlates with additional halts of primer extension, suggesting that these proteins hinder the progression of the DNA synthesis at these sites. Overall these results raise the possibility that, upon binding to hairpins formed onto ssDNA during fork progression, the DNA-PK complex interferes with replication fork dynamics in vivo.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
It is established that short inverted repeats trigger base substitution mutagenesis in human cells. However, how the replication machinery deals with structured DNA is unknown. It has been previously reported that in human cell-free extracts, DNA primer extension using a structured single-stranded template is transiently blocked at DNA hairpins. Here, the proteomic analysis of proteins bound to the DNA template is reported and evidence that the DNA-PK complex (DNA-PKcs and the Ku heterodimer) recognizes, and is activated by, structured single-stranded DNA is provided. Hijacking the DNA-PK complex by double-stranded oligonucleotides results in a large removal of the pausing sites and an elevated DNA extension efficiency. Conversely, DNA-PKcs inhibition results in its stabilization on the template, along with other proteins acting downstream in the Non-Homologous End-Joining (NHEJ) pathway, especially the XRCC4-DNA ligase 4 complex and the cofactor PAXX. Retention of NHEJ factors to the DNA in the absence of DNA-PKcs activity correlates with additional halts of primer extension, suggesting that these proteins hinder the progression of the DNA synthesis at these sites. Overall these results raise the possibility that, upon binding to hairpins formed onto ssDNA during fork progression, the DNA-PK complex interferes with replication fork dynamics in vivo.
Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y
Structural Insights Into the Mammalian Late-Stage Initiation Complexes Article de journal
Dans: Cell Rep, vol. 31, no. 1, p. 107497, 2020, ISBN: 32268096.
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, PPSE, Unité ARN
@article{,
title = {Structural Insights Into the Mammalian Late-Stage Initiation Complexes},
author = {A Simonetti and E Guca and A Bochler and L Kuhn and Y Hashem},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32268096?dopt=Abstract},
doi = {10.1016/j.celrep.2020.03.061},
isbn = {32268096},
year = {2020},
date = {2020-01-01},
journal = {Cell Rep},
volume = {31},
number = {1},
pages = {107497},
abstract = {In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.},
keywords = {ENNIFAR, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
Rol-Moreno J, Kuhn L, Marzi S, Simonetti A
Grad-cryo-EM: Tool to Isolate Translation Initiation Complexes From Rabbit Reticulocyte Lysate Suitable for Structural Studies Chapitre d'ouvrage
Dans: Arluison, V; Wien, F (Ed.): RNA Spectroscopy: Methods and Protocols, vol. 2113, p. 329-339, Springer Protocols, Humana Press, New York, NY, 2020, ISBN: 32006323.
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, PPSE, ROMBY, Unité ARN
@inbook{,
title = {Grad-cryo-EM: Tool to Isolate Translation Initiation Complexes From Rabbit Reticulocyte Lysate Suitable for Structural Studies},
author = {J Rol-Moreno and L Kuhn and S Marzi and A Simonetti},
editor = {V Arluison and F Wien},
url = {https://pubmed.ncbi.nlm.nih.gov/32006323},
doi = {10.1007/978-1-0716-0278-2_21},
isbn = {32006323},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
booktitle = {RNA Spectroscopy: Methods and Protocols},
volume = {2113},
pages = {329-339},
publisher = {Springer Protocols, Humana Press},
address = {New York, NY},
series = {Methods in Molecular Biology},
abstract = {Since its development, single-particle cryogenic electron microscopy (cryo-EM) has played a central role in the study at medium resolution of both bacterial and eukaryotic ribosomal complexes. With the advent of the direct electron detectors and new processing software which allow obtaining structures at atomic resolution, formerly obtained only by X-ray crystallography, cryo-EM has become the method of choice for the structural analysis of the translation machinery. In most of the cases, the ribosomal complexes at different stages of the translation process are assembled in vitro from purified components, which limit the analysis to previously well-characterized complexes with known factors composition. The initiation phase of the protein synthesis is a very dynamic process during which several proteins interact with the translation apparatus leading to the formation of a chronological series of initiation complexes (ICs). Here we describe a method to isolate ICs assembled on natural in vitro transcribed mRNA directly from rabbit reticulocyte lysate (RRL) by sucrose density gradient centrifugation. The Grad-cryo-EM approach allows investigating structures and composition of intermediate ribosomal complexes prepared in near-native condition by cryo-EM and mass spectrometry analyses. This is a powerful approach, which could be used to study translation initiation of any mRNAs, including IRES containing ones, and which could be adapted to different cell extracts.},
keywords = {ENNIFAR, PPSE, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Since its development, single-particle cryogenic electron microscopy (cryo-EM) has played a central role in the study at medium resolution of both bacterial and eukaryotic ribosomal complexes. With the advent of the direct electron detectors and new processing software which allow obtaining structures at atomic resolution, formerly obtained only by X-ray crystallography, cryo-EM has become the method of choice for the structural analysis of the translation machinery. In most of the cases, the ribosomal complexes at different stages of the translation process are assembled in vitro from purified components, which limit the analysis to previously well-characterized complexes with known factors composition. The initiation phase of the protein synthesis is a very dynamic process during which several proteins interact with the translation apparatus leading to the formation of a chronological series of initiation complexes (ICs). Here we describe a method to isolate ICs assembled on natural in vitro transcribed mRNA directly from rabbit reticulocyte lysate (RRL) by sucrose density gradient centrifugation. The Grad-cryo-EM approach allows investigating structures and composition of intermediate ribosomal complexes prepared in near-native condition by cryo-EM and mass spectrometry analyses. This is a powerful approach, which could be used to study translation initiation of any mRNAs, including IRES containing ones, and which could be adapted to different cell extracts.
Chernorudskiy A, Varone E, Colombo S F, Fumagalli S, Cagnotto A, Cattaneo A, Briens M, Baltzinger M, Kuhn L, Bachi A, Berardi A, Salmona M, Musco G, Borgese N, Lescure A, Zito E
Selenoprotein N is an endoplasmic reticulum calcium sensor that links luminal calcium levels to a redox activity Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 117, no. 35, p. 21288-21298, 2020, ISBN: 32817544.
Résumé | Liens | BibTeX | Étiquettes: LESCURE, PPSE, Unité ARN
@article{,
title = {Selenoprotein N is an endoplasmic reticulum calcium sensor that links luminal calcium levels to a redox activity},
author = {A Chernorudskiy and E Varone and S F Colombo and S Fumagalli and A Cagnotto and A Cattaneo and M Briens and M Baltzinger and L Kuhn and A Bachi and A Berardi and M Salmona and G Musco and N Borgese and A Lescure and E Zito},
url = {https://pubmed.ncbi.nlm.nih.gov/32817544/},
doi = {10.1073/pnas.2003847117},
isbn = {32817544},
year = {2020},
date = {2020-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {117},
number = {35},
pages = {21288-21298},
abstract = {The endoplasmic reticulum (ER) is the reservoir for calcium in cells. Luminal calcium levels are determined by calcium-sensing proteins that trigger calcium dynamics in response to calcium fluctuations. Here we report that Selenoprotein N (SEPN1) is a type II transmembrane protein that senses ER calcium fluctuations by binding this ion through a luminal EF-hand domain. In vitro and in vivo experiments show that via this domain, SEPN1 responds to diminished luminal calcium levels, dynamically changing its oligomeric state and enhancing its redox-dependent interaction with cellular partners, including the ER calcium pump sarcoplasmic/endoplasmic reticulum calcium ATPase (SERCA). Importantly, single amino acid substitutions in the EF-hand domain of SEPN1 identified as clinical variations are shown to impair its calcium-binding and calcium-dependent structural changes, suggesting a key role of the EF-hand domain in SEPN1 function. In conclusion, SEPN1 is a ER calcium sensor that responds to luminal calcium depletion, changing its oligomeric state and acting as a reductase to refill ER calcium stores.},
keywords = {LESCURE, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The endoplasmic reticulum (ER) is the reservoir for calcium in cells. Luminal calcium levels are determined by calcium-sensing proteins that trigger calcium dynamics in response to calcium fluctuations. Here we report that Selenoprotein N (SEPN1) is a type II transmembrane protein that senses ER calcium fluctuations by binding this ion through a luminal EF-hand domain. In vitro and in vivo experiments show that via this domain, SEPN1 responds to diminished luminal calcium levels, dynamically changing its oligomeric state and enhancing its redox-dependent interaction with cellular partners, including the ER calcium pump sarcoplasmic/endoplasmic reticulum calcium ATPase (SERCA). Importantly, single amino acid substitutions in the EF-hand domain of SEPN1 identified as clinical variations are shown to impair its calcium-binding and calcium-dependent structural changes, suggesting a key role of the EF-hand domain in SEPN1 function. In conclusion, SEPN1 is a ER calcium sensor that responds to luminal calcium depletion, changing its oligomeric state and acting as a reductase to refill ER calcium stores.
Pernod K, Schaeffer L, Chicher J, Hok E, Rick C, Geslain R, Eriani G, Westhof E, Ryckelynck M, Martin F
The Nature of the Purine at Position 34 in tRNAs of 4-codon Boxes Is Correlated With Nucleotides at Positions 32 and 38 to Maintain Decoding Fidelity Article de journal
Dans: Nucleic Acids Res, vol. 48, no. 11, p. 6170-6183, 2020, ISBN: 32266934.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, PPSE, RYCKELYNCK, Unité ARN, WESTHOF
@article{,
title = {The Nature of the Purine at Position 34 in tRNAs of 4-codon Boxes Is Correlated With Nucleotides at Positions 32 and 38 to Maintain Decoding Fidelity},
author = {K Pernod and L Schaeffer and J Chicher and E Hok and C Rick and R Geslain and G Eriani and E Westhof and M Ryckelynck and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32266934?dopt=Abstract},
doi = {10.1093/nar/gkaa221},
isbn = {32266934},
year = {2020},
date = {2020-01-01},
journal = {Nucleic Acids Res},
volume = {48},
number = {11},
pages = {6170-6183},
abstract = {Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.},
keywords = {ERIANI, PPSE, RYCKELYNCK, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
Summer Sabrina, Smirnova Anna, Gabriele Alessandro, Toth Ursula, Fasemore Akinyemi Mandela, Förstner Konrad U, Kuhn Lauriane, Chicher Johana, Hammann Philippe, Mitulović Goran, Entelis Nina, Tarassov Ivan, Rossmanith Walter, Smirnov Alexandre
YBEY is an essential biogenesis factor for mitochondrial ribosomes. Article de journal
Dans: Nucleic acids research, vol. 48, no. 17, p. 9762–9786, 2020, ISSN: 1362-4962 0305-1048 0305-1048.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{summer_ybey_2020,
title = {YBEY is an essential biogenesis factor for mitochondrial ribosomes.},
author = {Sabrina Summer and Anna Smirnova and Alessandro Gabriele and Ursula Toth and Akinyemi Mandela Fasemore and Konrad U Förstner and Lauriane Kuhn and Johana Chicher and Philippe Hammann and Goran Mitulović and Nina Entelis and Ivan Tarassov and Walter Rossmanith and Alexandre Smirnov},
doi = {10.1093/nar/gkaa148},
issn = {1362-4962 0305-1048 0305-1048},
year = {2020},
date = {2020-01-01},
journal = {Nucleic acids research},
volume = {48},
number = {17},
pages = {9762--9786},
abstract = {Ribosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3'-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts). Here we show that the deletion of human YBEY results in a severe respiratory deficiency and morphologically abnormal mitochondria as an apparent consequence of impaired mitochondrial translation. Reduced stability of 12S rRNA and the deficiency of several proteins of the small ribosomal subunit in YBEY knockout cells pointed towards a defect in mitochondrial ribosome biogenesis. The specific interaction of mitoribosomal protein uS11m with YBEY suggests that the latter helps to properly incorporate uS11m into the nascent small subunit in its late assembly stage. This scenario shows similarities with final stages of cytosolic ribosome biogenesis, and may represent a late checkpoint before the mitoribosome engages in translation.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Ribosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3'-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts). Here we show that the deletion of human YBEY results in a severe respiratory deficiency and morphologically abnormal mitochondria as an apparent consequence of impaired mitochondrial translation. Reduced stability of 12S rRNA and the deficiency of several proteins of the small ribosomal subunit in YBEY knockout cells pointed towards a defect in mitochondrial ribosome biogenesis. The specific interaction of mitoribosomal protein uS11m with YBEY suggests that the latter helps to properly incorporate uS11m into the nascent small subunit in its late assembly stage. This scenario shows similarities with final stages of cytosolic ribosome biogenesis, and may represent a late checkpoint before the mitoribosome engages in translation.
Bajczyk Mateusz, Lange Heike, Bielewicz Dawid, Szewc Lukasz, Bhat Susheel S, Dolata Jakub, Kuhn Lauriane, Szweykowska-Kulinska Zofia, Gagliardi Dominique, Jarmolowski Artur
SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis. Article de journal
Dans: Nucleic acids research, vol. 48, no. 12, p. 6839–6854, 2020, ISSN: 1362-4962 0305-1048 0305-1048.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{bajczyk_serrate_2020,
title = {SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis.},
author = {Mateusz Bajczyk and Heike Lange and Dawid Bielewicz and Lukasz Szewc and Susheel S Bhat and Jakub Dolata and Lauriane Kuhn and Zofia Szweykowska-Kulinska and Dominique Gagliardi and Artur Jarmolowski},
doi = {10.1093/nar/gkaa373},
issn = {1362-4962 0305-1048 0305-1048},
year = {2020},
date = {2020-01-01},
journal = {Nucleic acids research},
volume = {48},
number = {12},
pages = {6839--6854},
abstract = {SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.
Méteignier Louis-Valentin, Ghandour Rabea, Meierhoff Karin, Zimmerman Aude, Chicher Johana, Baumberger Nicolas, Alioua Abdelmalek, Meurer Jörg, Zoschke Reimo, Hammani Kamel
The Arabidopsis mTERF-repeat MDA1 protein plays a dual function in transcription and stabilization of specific chloroplast transcripts within the psbE and ndhH operons. Article de journal
Dans: The New phytologist, vol. 227, no. 5, p. 1376–1391, 2020, ISSN: 1469-8137 0028-646X 0028-646X.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{meteignier_arabidopsis_2020,
title = {The Arabidopsis mTERF-repeat MDA1 protein plays a dual function in transcription and stabilization of specific chloroplast transcripts within the psbE and ndhH operons.},
author = {Louis-Valentin Méteignier and Rabea Ghandour and Karin Meierhoff and Aude Zimmerman and Johana Chicher and Nicolas Baumberger and Abdelmalek Alioua and Jörg Meurer and Reimo Zoschke and Kamel Hammani},
doi = {10.1111/nph.16625},
issn = {1469-8137 0028-646X 0028-646X},
year = {2020},
date = {2020-01-01},
journal = {The New phytologist},
volume = {227},
number = {5},
pages = {1376--1391},
abstract = {The mTERF gene family encodes for nucleic acid binding proteins that are predicted to regulate organellar gene expression in eukaryotes. Despite the implication of this gene family in plant development and response to abiotic stresses, a precise molecular function was assigned to only a handful number of its c. 30 members in plants. Using a reverse genetics approach in Arabidopsis thaliana and combining molecular and biochemical techniques, we revealed new functions for the chloroplast mTERF protein, MDA1. We demonstrated that MDA1 associates in vivo with components of the plastid-encoded RNA polymerase and transcriptional active chromosome complexes. MDA1 protein binds in vivo and in vitro with specificity to 27-bp DNA sequences near the 5'-end of psbE and ndhA chloroplast genes to stimulate their transcription, and additionally promotes the stabilization of the 5'-ends of processed psbE and ndhA messenger (m)RNAs. Finally, we provided evidence that MDA1 function in gene transcription likely coordinates RNA folding and the action of chloroplast RNA-binding proteins on mRNA stabilization. Our results provide examples for the unexpected implication of DNA binding proteins and gene transcription in the regulation of mRNA stability in chloroplasts, blurring the boundaries between DNA and RNA metabolism in this organelle.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The mTERF gene family encodes for nucleic acid binding proteins that are predicted to regulate organellar gene expression in eukaryotes. Despite the implication of this gene family in plant development and response to abiotic stresses, a precise molecular function was assigned to only a handful number of its c. 30 members in plants. Using a reverse genetics approach in Arabidopsis thaliana and combining molecular and biochemical techniques, we revealed new functions for the chloroplast mTERF protein, MDA1. We demonstrated that MDA1 associates in vivo with components of the plastid-encoded RNA polymerase and transcriptional active chromosome complexes. MDA1 protein binds in vivo and in vitro with specificity to 27-bp DNA sequences near the 5'-end of psbE and ndhA chloroplast genes to stimulate their transcription, and additionally promotes the stabilization of the 5'-ends of processed psbE and ndhA messenger (m)RNAs. Finally, we provided evidence that MDA1 function in gene transcription likely coordinates RNA folding and the action of chloroplast RNA-binding proteins on mRNA stabilization. Our results provide examples for the unexpected implication of DNA binding proteins and gene transcription in the regulation of mRNA stability in chloroplasts, blurring the boundaries between DNA and RNA metabolism in this organelle.
Chico Jose Manuel, Lechner Esther, Fernandez-Barbero Gemma, Canibano Esther, García-Casado Gloria, Franco-Zorrilla Jose Manuel, Hammann Philippe, Zamarreño Angel M, García-Mina Jose M, Rubio Vicente, Genschik Pascal, Solano Roberto
CUL3(BPM) E3 ubiquitin ligases regulate MYC2, MYC3, and MYC4 stability and JA responses. Article de journal
Dans: Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 11, p. 6205–6215, 2020, ISSN: 1091-6490 0027-8424 0027-8424.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{chico_cul3bpm_2020,
title = {CUL3(BPM) E3 ubiquitin ligases regulate MYC2, MYC3, and MYC4 stability and JA responses.},
author = {Jose Manuel Chico and Esther Lechner and Gemma Fernandez-Barbero and Esther Canibano and Gloria García-Casado and Jose Manuel Franco-Zorrilla and Philippe Hammann and Angel M Zamarreño and Jose M García-Mina and Vicente Rubio and Pascal Genschik and Roberto Solano},
doi = {10.1073/pnas.1912199117},
issn = {1091-6490 0027-8424 0027-8424},
year = {2020},
date = {2020-01-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {11},
pages = {6205--6215},
abstract = {The jasmonate (JA)-pathway regulators MYC2, MYC3, and MYC4 are central nodes in plant signaling networks integrating environmental and developmental signals to fine-tune JA defenses and plant growth. Continuous activation of MYC activity is potentially lethal. Hence, MYCs need to be tightly regulated in order to optimize plant fitness. Among the increasing number of mechanisms regulating MYC activity, protein stability is arising as a major player. However, how the levels of MYC proteins are modulated is still poorly understood. Here, we report that MYC2, MYC3, and MYC4 are targets of BPM (BTB/POZ-MATH) proteins, which act as substrate adaptors of CUL3-based E3 ubiquitin ligases. Reduction of function of CUL3(BPM) in amiR-bpm lines, bpm235 triple mutants, and cul3ab double mutants enhances MYC2 and MYC3 stability and accumulation and potentiates plant responses to JA such as root-growth inhibition and MYC-regulated gene expression. Moreover, MYC3 polyubiquitination levels are reduced in amiR-bpm lines. BPM3 protein is stabilized by JA, suggesting a negative feedback regulatory mechanism to control MYC activity, avoiding harmful runaway responses. Our results uncover a layer for JA-pathway regulation by CUL3(BPM)-mediated degradation of MYC transcription factors.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The jasmonate (JA)-pathway regulators MYC2, MYC3, and MYC4 are central nodes in plant signaling networks integrating environmental and developmental signals to fine-tune JA defenses and plant growth. Continuous activation of MYC activity is potentially lethal. Hence, MYCs need to be tightly regulated in order to optimize plant fitness. Among the increasing number of mechanisms regulating MYC activity, protein stability is arising as a major player. However, how the levels of MYC proteins are modulated is still poorly understood. Here, we report that MYC2, MYC3, and MYC4 are targets of BPM (BTB/POZ-MATH) proteins, which act as substrate adaptors of CUL3-based E3 ubiquitin ligases. Reduction of function of CUL3(BPM) in amiR-bpm lines, bpm235 triple mutants, and cul3ab double mutants enhances MYC2 and MYC3 stability and accumulation and potentiates plant responses to JA such as root-growth inhibition and MYC-regulated gene expression. Moreover, MYC3 polyubiquitination levels are reduced in amiR-bpm lines. BPM3 protein is stabilized by JA, suggesting a negative feedback regulatory mechanism to control MYC activity, avoiding harmful runaway responses. Our results uncover a layer for JA-pathway regulation by CUL3(BPM)-mediated degradation of MYC transcription factors.
Bochler A, Querido J B, Prilepskaja T, Soufari H, Simonetti A, Cistia M L Del, Kuhn L, Ribeiro A R, Valášek L S, Hashem Y
Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts Article de journal
Dans: Cell Rep, vol. 33, no. 12, p. 108534, 2020, ISBN: 33357443.
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, ES6(S) ES7(S) ES9(S) Trypanosoma cruzi cryo-EM eIF1 eIF2 eIF3 eIF5-CTD k-DDX60 the 43S pre-initiation complex translation initiation, HASCHEM, PPSE, Unité ARN
@article{,
title = {Structural Differences in Translation Initiation between Pathogenic Trypanosomatids and Their Mammalian Hosts},
author = {A Bochler and J B Querido and T Prilepskaja and H Soufari and A Simonetti and M L Del Cistia and L Kuhn and A R Ribeiro and L S Valášek and Y Hashem},
url = {https://pubmed.ncbi.nlm.nih.gov/33357443/},
doi = {10.1016/j.celrep.2020.108534},
isbn = {33357443},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Cell Rep},
volume = {33},
number = {12},
pages = {108534},
abstract = {Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires binding of initiator Met-tRNAiMet and several eukaryotic initiation factors (eIFs) to the small ribosomal subunit (40S). Compared to their mammalian hosts, trypanosomatids present significant structural differences in their 40S, suggesting substantial variability in translation initiation. Here, we determine the structure of the 43S PIC from Trypanosoma cruzi, the parasite causing Chagas disease. Our structure shows numerous specific features, such as the variant eIF3 structure and its unique interactions with the large rRNA expansion segments (ESs) 9S, 7S, and 6S, and the association of a kinetoplastid-specific DDX60-like helicase. It also reveals the 40S-binding site of the eIF5 C-terminal domain and structures of key terminal tails of several conserved eIFs underlying their activities within the PIC. Our results are corroborated by glutathione S-transferase (GST) pull-down assays in both human and T. cruzi and mass spectrometry data.},
keywords = {ENNIFAR, ES6(S) ES7(S) ES9(S) Trypanosoma cruzi cryo-EM eIF1 eIF2 eIF3 eIF5-CTD k-DDX60 the 43S pre-initiation complex translation initiation, HASCHEM, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires binding of initiator Met-tRNAiMet and several eukaryotic initiation factors (eIFs) to the small ribosomal subunit (40S). Compared to their mammalian hosts, trypanosomatids present significant structural differences in their 40S, suggesting substantial variability in translation initiation. Here, we determine the structure of the 43S PIC from Trypanosoma cruzi, the parasite causing Chagas disease. Our structure shows numerous specific features, such as the variant eIF3 structure and its unique interactions with the large rRNA expansion segments (ESs) 9S, 7S, and 6S, and the association of a kinetoplastid-specific DDX60-like helicase. It also reveals the 40S-binding site of the eIF5 C-terminal domain and structures of key terminal tails of several conserved eIFs underlying their activities within the PIC. Our results are corroborated by glutathione S-transferase (GST) pull-down assays in both human and T. cruzi and mass spectrometry data.
2019
Bouchoucha Ayoub, Waltz Florent, Bonnard Géraldine, Arrivé Mathilde, Hammann Philippe, Kuhn Lauriane, Schelcher Cédric, Zuber Hélène, Gobert Anthony, Giegé Philippe
Determination of protein-only RNase P interactome in Arabidopsis mitochondria and chloroplasts identifies a complex between PRORP1 and another NYN domain nuclease. Article de journal
Dans: The Plant journal : for cell and molecular biology, vol. 100, no. 3, p. 549–561, 2019, ISSN: 1365-313X 0960-7412.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{bouchoucha_determination_2019,
title = {Determination of protein-only RNase P interactome in Arabidopsis mitochondria and chloroplasts identifies a complex between PRORP1 and another NYN domain nuclease.},
author = {Ayoub Bouchoucha and Florent Waltz and Géraldine Bonnard and Mathilde Arrivé and Philippe Hammann and Lauriane Kuhn and Cédric Schelcher and Hélène Zuber and Anthony Gobert and Philippe Giegé},
doi = {10.1111/tpj.14458},
issn = {1365-313X 0960-7412},
year = {2019},
date = {2019-11-01},
journal = {The Plant journal : for cell and molecular biology},
volume = {100},
number = {3},
pages = {549--561},
abstract = {The essential type of endonuclease that removes 5' leader sequences from transfer RNA precursors is called RNase P. While ribonucleoprotein RNase P enzymes containing a ribozyme are found in all domains of life, another type of RNase P called 'PRORP', for 'PROtein-only RNase P', is composed of protein that occurs only in a wide variety of eukaryotes, in organelles and in the nucleus. Here, to find how PRORP functions integrate with other cell processes, we explored the protein interaction network of PRORP1 in Arabidopsis mitochondria and chloroplasts. Although PRORP proteins function as single subunit enzymes in vitro, we found that PRORP1 occurs in protein complexes and is present in high-molecular-weight fractions that contain mitochondrial ribosomes. The analysis of immunoprecipitated protein complexes identified proteins involved in organellar gene expression processes. In particular, direct interaction was established between PRORP1 and MNU2 a mitochondrial nuclease. A specific domain of MNU2 and a conserved signature of PRORP1 were found to be directly accountable for this protein interaction. Altogether, results revealed the existence of an RNA maturation complex in Arabidopsis mitochondria and suggested that PRORP proteins cooperated with other gene expression factors for RNA maturation in vivo.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The essential type of endonuclease that removes 5' leader sequences from transfer RNA precursors is called RNase P. While ribonucleoprotein RNase P enzymes containing a ribozyme are found in all domains of life, another type of RNase P called 'PRORP', for 'PROtein-only RNase P', is composed of protein that occurs only in a wide variety of eukaryotes, in organelles and in the nucleus. Here, to find how PRORP functions integrate with other cell processes, we explored the protein interaction network of PRORP1 in Arabidopsis mitochondria and chloroplasts. Although PRORP proteins function as single subunit enzymes in vitro, we found that PRORP1 occurs in protein complexes and is present in high-molecular-weight fractions that contain mitochondrial ribosomes. The analysis of immunoprecipitated protein complexes identified proteins involved in organellar gene expression processes. In particular, direct interaction was established between PRORP1 and MNU2 a mitochondrial nuclease. A specific domain of MNU2 and a conserved signature of PRORP1 were found to be directly accountable for this protein interaction. Altogether, results revealed the existence of an RNA maturation complex in Arabidopsis mitochondria and suggested that PRORP proteins cooperated with other gene expression factors for RNA maturation in vivo.
Lange Heike, Ndecky Simon Y A, Gomez-Diaz Carlos, Pflieger David, Butel Nicolas, Zumsteg Julie, Kuhn Lauriane, Piermaria Christina, Chicher Johana, Christie Michael, Karaaslan Ezgi S, Lang Patricia L M, Weigel Detlef, Vaucheret Hervé, Hammann Philippe, Gagliardi Dominique
RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Article de journal
Dans: Nature communications, vol. 10, no. 1, p. 3871, 2019, ISSN: 2041-1723 2041-1723.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{lange_rst1_2019,
title = {RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis.},
author = {Heike Lange and Simon Y A Ndecky and Carlos Gomez-Diaz and David Pflieger and Nicolas Butel and Julie Zumsteg and Lauriane Kuhn and Christina Piermaria and Johana Chicher and Michael Christie and Ezgi S Karaaslan and Patricia L M Lang and Detlef Weigel and Hervé Vaucheret and Philippe Hammann and Dominique Gagliardi},
doi = {10.1038/s41467-019-11807-4},
issn = {2041-1723 2041-1723},
year = {2019},
date = {2019-08-01},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3871},
abstract = {The RNA exosome is a key 3'-5' exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The RNA exosome is a key 3'-5' exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans.
Lalaouna D, Baude J, Wu Z, Tomasini A, Chicher J, Marzi S, Vandenesch F, Romby P, Caldelari I, Moreau K
RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation Article de journal
Dans: Nucleic Acids Res, vol. 47, no. 18, p. 9871-9887, 2019, ISBN: 31504767.
Résumé | Liens | BibTeX | Étiquettes: PPSE, ROMBY, Unité ARN
@article{Lalaouna2019,
title = {RsaC sRNA modulates the oxidative stress response of \textit{Staphylococcus aureus} during manganese starvation},
author = {D Lalaouna and J Baude and Z Wu and A Tomasini and J Chicher and S Marzi and F Vandenesch and P Romby and I Caldelari and K Moreau},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31504767?dopt=Abstract},
doi = {10.1093/nar/gkz728},
isbn = {31504767},
year = {2019},
date = {2019-01-01},
journal = {Nucleic Acids Res},
volume = {47},
number = {18},
pages = {9871-9887},
abstract = {The human opportunistic pathogen Staphylococcus aureus produces numerous small regulatory RNAs (sRNAs) for which functions are still poorly understood. Here, we focused on an atypical and large sRNA called RsaC. Its length varies between different isolates due to the presence of repeated sequences at the 5′ end while its 3′ part is structurally independent and highly conserved. Using MS2-affinity purification coupled with RNA sequencing (MAPS) and quantitative differential proteomics, sodA mRNA was identified as a primary target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. Remarkably, rsaC gene is co-transcribed with the major manganese ABC transporter MntABC and, consequently, RsaC is mainly produced in response to Mn starvation. This 3′UTR-derived sRNA is released from mntABC-RsaC precursor after cleavage by RNase III. The mature and stable form of RsaC inhibits the synthesis of the Mn-containing enzyme SodA synthesis and favors the oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. In addition, other putative targets of RsaC are involved in oxidative stress (ROS and NOS) and metal homeostasis (Fe and Zn). Consequently, RsaC may balance two interconnected defensive responses, i.e. oxidative stress and metal-dependent nutritional immunity.},
keywords = {PPSE, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
The human opportunistic pathogen Staphylococcus aureus produces numerous small regulatory RNAs (sRNAs) for which functions are still poorly understood. Here, we focused on an atypical and large sRNA called RsaC. Its length varies between different isolates due to the presence of repeated sequences at the 5′ end while its 3′ part is structurally independent and highly conserved. Using MS2-affinity purification coupled with RNA sequencing (MAPS) and quantitative differential proteomics, sodA mRNA was identified as a primary target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. Remarkably, rsaC gene is co-transcribed with the major manganese ABC transporter MntABC and, consequently, RsaC is mainly produced in response to Mn starvation. This 3′UTR-derived sRNA is released from mntABC-RsaC precursor after cleavage by RNase III. The mature and stable form of RsaC inhibits the synthesis of the Mn-containing enzyme SodA synthesis and favors the oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. In addition, other putative targets of RsaC are involved in oxidative stress (ROS and NOS) and metal homeostasis (Fe and Zn). Consequently, RsaC may balance two interconnected defensive responses, i.e. oxidative stress and metal-dependent nutritional immunity.
Arbogast Florent, Arnold Johan, Hammann Philippe, Kuhn Lauriane, Chicher Johana, Murera Diane, Weishaar Justine, Muller Sylviane, Fauny Jean-Daniel, Gros Frédéric
ATG5 is required for B cell polarization and presentation of particulate antigens. Article de journal
Dans: Autophagy, vol. 15, no. 2, p. 280–294, 2019, ISSN: 1554-8635 1554-8627 1554-8627.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{arbogast_atg5_2019,
title = {ATG5 is required for B cell polarization and presentation of particulate antigens.},
author = {Florent Arbogast and Johan Arnold and Philippe Hammann and Lauriane Kuhn and Johana Chicher and Diane Murera and Justine Weishaar and Sylviane Muller and Jean-Daniel Fauny and Frédéric Gros},
doi = {10.1080/15548627.2018.1516327},
issn = {1554-8635 1554-8627 1554-8627},
year = {2019},
date = {2019-01-01},
journal = {Autophagy},
volume = {15},
number = {2},
pages = {280--294},
abstract = {The involvement of macroautophagy/autophagy proteins in B-cell receptor (BCR) trafficking, although suspected, is not well understood. We show that ATG5 (autophagy related 5) contributes to BCR polarization after stimulation and internalization into LAMP1 (lysosomal-associated membrane protein 1)(+) and major histocompatibility complex class II (MHC-II)(+) compartments. BCR polarization is crucial in the context of immobilized antigen processing. Moreover, antigen presentation to cognate T cells is decreased in the absence of ATG5 when the model antigen OVAL/ovalbumin is provided in an immobilized form in contrast to the normal presentation of soluble OVAL. We further show that ATG5 is required for centrosome polarization and actin nucleation in the immune synapse area. This event is accompanied by an increased interaction between ATG16L1 (autophagy related 16-like 1 [S. cerevisiae]) and the microtubule-organizing center-associated protein PCM1 (pericentriolar material 1). In the human B cell line BJAB, PCM1 is required for BCR polarization after stimulation. We thus propose that the ATG12 (autophagy related 12)-ATG5-ATG16L1 complex under BCR stimulation allows its interaction with PCM1 and consequently facilitates centrosome relocalization to the immune synapse, optimizing the presentation of particulate antigens. Abbreviations: ACTB: actin beta; ACTR2/3: ARP2/3 actin-related protein 2/3; APC: antigen-presenting cells; ATG: autophagy-related; BCR: B cell receptor; BECN1/Beclin 1: beclin 1, autophagy related; CDC42: cell division cycle 42; Cr2: complement receptor 2; CSFE: carboxyfluorescein succinimidyl ester; DAPI: 4',6-diamidino-2-phenylindole dihydrochloride; EEA1: early endosome antigen 1; ELISA: enzyme-linked immunosorbent assay; FITC: fluorescein isothyocyanate; GC: germinal center; GJA1/CX3: gap junction protein, alpha 1; Ig: immunoglobulin; LAMP1: lysosomal-associated membrane protein 1; LAP: LC3-associated phagocytosis; LM: littermate; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/ERK: mitogen activated protein kinase; MHC-II: major histocompatibility complex class II; MIIC: MHC class II compartment; OVAL: ovalbumin; PBS: phosphate-buffered saline; PCM1: pericentriolar material 1; PtdIns3K: phosphatidylinositol 3-kinase; PTPRC/CD45RB/B220; Protein tyrosine phosphatase, receptor type, C; SYK: spleen tyrosine kinase; TBS: Tris-buffered saline; TCR: T cell receptor; ULK1: unc-51 like kinase 1.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The involvement of macroautophagy/autophagy proteins in B-cell receptor (BCR) trafficking, although suspected, is not well understood. We show that ATG5 (autophagy related 5) contributes to BCR polarization after stimulation and internalization into LAMP1 (lysosomal-associated membrane protein 1)(+) and major histocompatibility complex class II (MHC-II)(+) compartments. BCR polarization is crucial in the context of immobilized antigen processing. Moreover, antigen presentation to cognate T cells is decreased in the absence of ATG5 when the model antigen OVAL/ovalbumin is provided in an immobilized form in contrast to the normal presentation of soluble OVAL. We further show that ATG5 is required for centrosome polarization and actin nucleation in the immune synapse area. This event is accompanied by an increased interaction between ATG16L1 (autophagy related 16-like 1 [S. cerevisiae]) and the microtubule-organizing center-associated protein PCM1 (pericentriolar material 1). In the human B cell line BJAB, PCM1 is required for BCR polarization after stimulation. We thus propose that the ATG12 (autophagy related 12)-ATG5-ATG16L1 complex under BCR stimulation allows its interaction with PCM1 and consequently facilitates centrosome relocalization to the immune synapse, optimizing the presentation of particulate antigens. Abbreviations: ACTB: actin beta; ACTR2/3: ARP2/3 actin-related protein 2/3; APC: antigen-presenting cells; ATG: autophagy-related; BCR: B cell receptor; BECN1/Beclin 1: beclin 1, autophagy related; CDC42: cell division cycle 42; Cr2: complement receptor 2; CSFE: carboxyfluorescein succinimidyl ester; DAPI: 4',6-diamidino-2-phenylindole dihydrochloride; EEA1: early endosome antigen 1; ELISA: enzyme-linked immunosorbent assay; FITC: fluorescein isothyocyanate; GC: germinal center; GJA1/CX3: gap junction protein, alpha 1; Ig: immunoglobulin; LAMP1: lysosomal-associated membrane protein 1; LAP: LC3-associated phagocytosis; LM: littermate; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/ERK: mitogen activated protein kinase; MHC-II: major histocompatibility complex class II; MIIC: MHC class II compartment; OVAL: ovalbumin; PBS: phosphate-buffered saline; PCM1: pericentriolar material 1; PtdIns3K: phosphatidylinositol 3-kinase; PTPRC/CD45RB/B220; Protein tyrosine phosphatase, receptor type, C; SYK: spleen tyrosine kinase; TBS: Tris-buffered saline; TCR: T cell receptor; ULK1: unc-51 like kinase 1.
Waltz Florent, Nguyen Tan-Trung, Arrivé Mathilde, Bochler Anthony, Chicher Johana, Hammann Philippe, Kuhn Lauriane, Quadrado Martine, Mireau Hakim, Hashem Yaser, Giegé Philippe
Small is big in Arabidopsis mitochondrial ribosome. Article de journal
Dans: Nature plants, vol. 5, no. 1, p. 106–117, 2019, ISSN: 2055-0278 2055-0278.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{waltz_small_2019,
title = {Small is big in Arabidopsis mitochondrial ribosome.},
author = {Florent Waltz and Tan-Trung Nguyen and Mathilde Arrivé and Anthony Bochler and Johana Chicher and Philippe Hammann and Lauriane Kuhn and Martine Quadrado and Hakim Mireau and Yaser Hashem and Philippe Giegé},
doi = {10.1038/s41477-018-0339-y},
issn = {2055-0278 2055-0278},
year = {2019},
date = {2019-01-01},
journal = {Nature plants},
volume = {5},
number = {1},
pages = {106--117},
abstract = {Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in mitochondrial translation remains unclear. Here we present the biochemical characterization of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identified 19 plant-specific mitoribosome proteins, of which ten are PPR proteins. The knockout mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes, including lethality and severe growth delay. The molecular analysis of rppr1 mutants using ribosome profiling, as well as the analysis of mitochondrial protein levels, demonstrate rPPR1 to be a generic translation factor that is a novel function for PPR proteins. Finally, single-particle cryo-electron microscopy (cryo-EM) reveals the unique structural architecture of Arabidopsis mitoribosomes, characterized by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, in terms of both structure and protein content.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in mitochondrial translation remains unclear. Here we present the biochemical characterization of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identified 19 plant-specific mitoribosome proteins, of which ten are PPR proteins. The knockout mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes, including lethality and severe growth delay. The molecular analysis of rppr1 mutants using ribosome profiling, as well as the analysis of mitochondrial protein levels, demonstrate rPPR1 to be a generic translation factor that is a novel function for PPR proteins. Finally, single-particle cryo-electron microscopy (cryo-EM) reveals the unique structural architecture of Arabidopsis mitoribosomes, characterized by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, in terms of both structure and protein content.
Trinquier Aude, Ulmer Jonathan E, Gilet Laetitia, Figaro Sabine, Hammann Philippe, Kuhn Lauriane, Braun Frédérique, Condon Ciarán
tRNA Maturation Defects Lead to Inhibition of rRNA Processing via Synthesis of pppGpp. Article de journal
Dans: Molecular cell, vol. 74, no. 6, p. 1227–1238.e3, 2019, ISSN: 1097-4164 1097-2765.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{trinquier_trna_2019,
title = {tRNA Maturation Defects Lead to Inhibition of rRNA Processing via Synthesis of pppGpp.},
author = {Aude Trinquier and Jonathan E Ulmer and Laetitia Gilet and Sabine Figaro and Philippe Hammann and Lauriane Kuhn and Frédérique Braun and Ciarán Condon},
doi = {10.1016/j.molcel.2019.03.030},
issn = {1097-4164 1097-2765},
year = {2019},
date = {2019-01-01},
journal = {Molecular cell},
volume = {74},
number = {6},
pages = {1227--1238.e3},
abstract = {rRNAs and tRNAs universally require processing from longer primary transcripts to become functional for translation. Here, we describe an unsuspected link between tRNA maturation and the 3' processing of 16S rRNA, a key step in preparing the small ribosomal subunit for interaction with the Shine-Dalgarno sequence in prokaryotic translation initiation. We show that an accumulation of either 5' or 3' immature tRNAs triggers RelA-dependent production of the stringent response alarmone (p)ppGpp in the Gram-positive model organism Bacillus subtilis. The accumulation of (p)ppGpp and accompanying decrease in GTP levels specifically inhibit 16S rRNA 3' maturation. We suggest that cells can exploit this mechanism to sense potential slowdowns in tRNA maturation and adjust rRNA processing accordingly to maintain the appropriate functional balance between these two major components of the translation apparatus.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
rRNAs and tRNAs universally require processing from longer primary transcripts to become functional for translation. Here, we describe an unsuspected link between tRNA maturation and the 3' processing of 16S rRNA, a key step in preparing the small ribosomal subunit for interaction with the Shine-Dalgarno sequence in prokaryotic translation initiation. We show that an accumulation of either 5' or 3' immature tRNAs triggers RelA-dependent production of the stringent response alarmone (p)ppGpp in the Gram-positive model organism Bacillus subtilis. The accumulation of (p)ppGpp and accompanying decrease in GTP levels specifically inhibit 16S rRNA 3' maturation. We suggest that cells can exploit this mechanism to sense potential slowdowns in tRNA maturation and adjust rRNA processing accordingly to maintain the appropriate functional balance between these two major components of the translation apparatus.
2018
Olmo Roenick P, Ferreira Alvaro G A, Izidoro-Toledo Tatiane C, Aguiar Eric R G R, de Faria Isaque J S, de Souza Kátia P R, Osório Kátia P, Kuhn Lauriane, Hammann Philippe, de Andrade Elisa G, Todjro Yaovi Mathias, Rocha Marcele N, Leite Thiago H J F, Amadou Siad C G, Armache Juliana N, Paro Simona, de Oliveira Caroline D, Carvalho Fabiano D, Moreira Luciano A, Marois Eric, Imler Jean-Luc, Marques João T
Control of dengue virus in the midgut of Aedes aegypti by ectopic expression of the dsRNA-binding protein Loqs2. Article de journal
Dans: Nature microbiology, vol. 3, no. 12, p. 1385–1393, 2018, ISSN: 2058-5276 2058-5276.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{olmo_control_2018,
title = {Control of dengue virus in the midgut of Aedes aegypti by ectopic expression of the dsRNA-binding protein Loqs2.},
author = {Roenick P Olmo and Alvaro G A Ferreira and Tatiane C Izidoro-Toledo and Eric R G R Aguiar and Isaque J S de Faria and Kátia P R de Souza and Kátia P Osório and Lauriane Kuhn and Philippe Hammann and Elisa G de Andrade and Yaovi Mathias Todjro and Marcele N Rocha and Thiago H J F Leite and Siad C G Amadou and Juliana N Armache and Simona Paro and Caroline D de Oliveira and Fabiano D Carvalho and Luciano A Moreira and Eric Marois and Jean-Luc Imler and João T Marques},
doi = {10.1038/s41564-018-0268-6},
issn = {2058-5276 2058-5276},
year = {2018},
date = {2018-12-01},
journal = {Nature microbiology},
volume = {3},
number = {12},
pages = {1385--1393},
abstract = {Dengue virus (DENV) is an arbovirus transmitted to humans by Aedes mosquitoes(1). In the insect vector, the small interfering RNA (siRNA) pathway is an important antiviral mechanism against DENV(2-5). However, it remains unclear when and where the siRNA pathway acts during the virus cycle. Here, we show that the siRNA pathway fails to efficiently silence DENV in the midgut of Aedes aegypti although it is essential to restrict systemic replication. Accumulation of DENV-derived siRNAs in the midgut reveals that impaired silencing results from a defect downstream of small RNA biogenesis. Notably, silencing triggered by endogenous and exogenous dsRNAs remained effective in the midgut where known components of the siRNA pathway, including the double-stranded RNA (dsRNA)-binding proteins Loquacious and r2d2, had normal expression levels. We identified an Aedes-specific paralogue of loquacious and r2d2, hereafter named loqs2, which is not expressed in the midgut. Loqs2 interacts with Loquacious and r2d2 and is required to control systemic replication of DENV and also Zika virus. Furthermore, ectopic expression of Loqs2 in the midgut of transgenic mosquitoes is sufficient to restrict DENV replication and dissemination. Together, our data reveal a mechanism of tissue-specific regulation of the mosquito siRNA pathway controlled by Loqs2.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
Dengue virus (DENV) is an arbovirus transmitted to humans by Aedes mosquitoes(1). In the insect vector, the small interfering RNA (siRNA) pathway is an important antiviral mechanism against DENV(2-5). However, it remains unclear when and where the siRNA pathway acts during the virus cycle. Here, we show that the siRNA pathway fails to efficiently silence DENV in the midgut of Aedes aegypti although it is essential to restrict systemic replication. Accumulation of DENV-derived siRNAs in the midgut reveals that impaired silencing results from a defect downstream of small RNA biogenesis. Notably, silencing triggered by endogenous and exogenous dsRNAs remained effective in the midgut where known components of the siRNA pathway, including the double-stranded RNA (dsRNA)-binding proteins Loquacious and r2d2, had normal expression levels. We identified an Aedes-specific paralogue of loquacious and r2d2, hereafter named loqs2, which is not expressed in the midgut. Loqs2 interacts with Loquacious and r2d2 and is required to control systemic replication of DENV and also Zika virus. Furthermore, ectopic expression of Loqs2 in the midgut of transgenic mosquitoes is sufficient to restrict DENV replication and dissemination. Together, our data reveal a mechanism of tissue-specific regulation of the mosquito siRNA pathway controlled by Loqs2.
Chicois Clara, Scheer Hélène, Garcia Shahïnez, Zuber Hélène, Mutterer Jérôme, Chicher Johana, Hammann Philippe, Gagliardi Dominique, Garcia Damien
The UPF1 interactome reveals interaction networks between RNA degradation and translation repression factors in Arabidopsis. Article de journal
Dans: The Plant journal : for cell and molecular biology, vol. 96, no. 1, p. 119–132, 2018, ISSN: 1365-313X 0960-7412, (Place: England).
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{chicois_upf1_2018,
title = {The UPF1 interactome reveals interaction networks between RNA degradation and translation repression factors in Arabidopsis.},
author = {Clara Chicois and Hélène Scheer and Shahïnez Garcia and Hélène Zuber and Jérôme Mutterer and Johana Chicher and Philippe Hammann and Dominique Gagliardi and Damien Garcia},
doi = {10.1111/tpj.14022},
issn = {1365-313X 0960-7412},
year = {2018},
date = {2018-10-01},
journal = {The Plant journal : for cell and molecular biology},
volume = {96},
number = {1},
pages = {119--132},
abstract = {The RNA helicase UP-FRAMESHIFT (UPF1) is a key factor of nonsense-mediated decay (NMD), a mRNA decay pathway involved in RNA quality control and in the fine-tuning of gene expression. UPF1 recruits UPF2 and UPF3 to constitute the NMD core complex, which is conserved across eukaryotes. No other components of UPF1-containing ribonucleoproteins (RNPs) are known in plants, despite its key role in regulating gene expression. Here, we report the identification of a large set of proteins that co-purify with the Arabidopsis UPF1, either in an RNA-dependent or RNA-independent manner. We found that like UPF1, several of its co-purifying proteins have a dual localization in the cytosol and in P-bodies, which are dynamic structures formed by the condensation of translationally repressed mRNPs. Interestingly, more than half of the proteins of the UPF1 interactome also co-purify with DCP5, a conserved translation repressor also involved in P-body formation. We identified a terminal nucleotidyltransferase, ribonucleases and several RNA helicases among the most significantly enriched proteins co-purifying with both UPF1 and DCP5. Among these, RNA helicases are the homologs of DDX6/Dhh1, known as translation repressors in humans and yeast, respectively. Overall, this study reports a large set of proteins associated with the Arabidopsis UPF1 and DCP5, two components of P-bodies, and reveals an extensive interaction network between RNA degradation and translation repression factors. Using this resource, we identified five hitherto unknown components of P-bodies in plants, pointing out the value of this dataset for the identification of proteins potentially involved in translation repression and/or RNA degradation.},
note = {Place: England},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The RNA helicase UP-FRAMESHIFT (UPF1) is a key factor of nonsense-mediated decay (NMD), a mRNA decay pathway involved in RNA quality control and in the fine-tuning of gene expression. UPF1 recruits UPF2 and UPF3 to constitute the NMD core complex, which is conserved across eukaryotes. No other components of UPF1-containing ribonucleoproteins (RNPs) are known in plants, despite its key role in regulating gene expression. Here, we report the identification of a large set of proteins that co-purify with the Arabidopsis UPF1, either in an RNA-dependent or RNA-independent manner. We found that like UPF1, several of its co-purifying proteins have a dual localization in the cytosol and in P-bodies, which are dynamic structures formed by the condensation of translationally repressed mRNPs. Interestingly, more than half of the proteins of the UPF1 interactome also co-purify with DCP5, a conserved translation repressor also involved in P-body formation. We identified a terminal nucleotidyltransferase, ribonucleases and several RNA helicases among the most significantly enriched proteins co-purifying with both UPF1 and DCP5. Among these, RNA helicases are the homologs of DDX6/Dhh1, known as translation repressors in humans and yeast, respectively. Overall, this study reports a large set of proteins associated with the Arabidopsis UPF1 and DCP5, two components of P-bodies, and reveals an extensive interaction network between RNA degradation and translation repression factors. Using this resource, we identified five hitherto unknown components of P-bodies in plants, pointing out the value of this dataset for the identification of proteins potentially involved in translation repression and/or RNA degradation.
Goto Akira, Okado Kiyoshi, Martins Nelson, Cai Hua, Barbier Vincent, Lamiable Olivier, Troxler Laurent, Santiago Estelle, Kuhn Lauriane, Paik Donggi, Silverman Neal, Holleufer Andreas, Hartmann Rune, Liu Jiyong, Peng Tao, Hoffmann Jules A, Meignin Carine, Daeffler Laurent, Imler Jean-Luc
The Kinase IKKβ Regulates a STING- and NF-κB-Dependent Antiviral Response Pathway in Drosophila Article de journal
Dans: Immunity, no. 49, p. 225-234, 2018.
Résumé | Liens | BibTeX | Étiquettes: hoffmann, imler, M3i, meignin, PPSE
@article{Goto2018,
title = {The Kinase IKKβ Regulates a STING- and NF-κB-Dependent Antiviral Response Pathway in Drosophila},
author = {Akira Goto and Kiyoshi Okado and Nelson Martins and Hua Cai and Vincent Barbier and Olivier Lamiable and Laurent Troxler and Estelle Santiago and Lauriane Kuhn and Donggi Paik and Neal Silverman and Andreas Holleufer and Rune Hartmann and Jiyong Liu and Tao Peng and Jules A Hoffmann and Carine Meignin and Laurent Daeffler and Jean-Luc Imler},
editor = {Elsevier Inc.},
url = {https://doi.org/10.1016/j.immuni.2018.07.013},
doi = {j.immuni.2018.07.013},
year = {2018},
date = {2018-08-21},
journal = {Immunity},
number = {49},
pages = {225-234},
abstract = {Antiviral immunity in Drosophila involves RNA interference and poorly characterized inducible responses. Here, we showed that two components of the IMD pathway, the kinase dIKKβ and the transcription factor Relish, were required to control infection by two picorna-like viruses. We identified a set of genes induced by viral infection and regulated by dIKKβ and Relish, which included an ortholog of STING. We showed that dSTING participated in the control of infection by picorna-like viruses, acting upstream of dIKKβ to regulate expression of Nazo, an antiviral factor. Our data reveal an antiviral function for STING in an animal model devoid of interferons and suggest an evolutionarily ancient role for this molecule in antiviral immunity.},
keywords = {hoffmann, imler, M3i, meignin, PPSE},
pubstate = {published},
tppubtype = {article}
}
Antiviral immunity in Drosophila involves RNA interference and poorly characterized inducible responses. Here, we showed that two components of the IMD pathway, the kinase dIKKβ and the transcription factor Relish, were required to control infection by two picorna-like viruses. We identified a set of genes induced by viral infection and regulated by dIKKβ and Relish, which included an ortholog of STING. We showed that dSTING participated in the control of infection by picorna-like viruses, acting upstream of dIKKβ to regulate expression of Nazo, an antiviral factor. Our data reveal an antiviral function for STING in an animal model devoid of interferons and suggest an evolutionarily ancient role for this molecule in antiviral immunity.
Wang Fengjuan, Bonam Srinivasa Reddy, Schall Nicolas, Kuhn Lauriane, Hammann Philippe, Chaloin Olivier, Madinier Jean-Baptiste, Briand Jean-Paul, Page Nicolas, Muller Sylviane
Blocking nuclear export of HSPA8 after heat shock stress severely alters cell survival. Article de journal
Dans: Scientific reports, vol. 8, no. 1, p. 16820, 2018, ISSN: 2045-2322 2045-2322.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{wang_blocking_2018,
title = {Blocking nuclear export of HSPA8 after heat shock stress severely alters cell survival.},
author = {Fengjuan Wang and Srinivasa Reddy Bonam and Nicolas Schall and Lauriane Kuhn and Philippe Hammann and Olivier Chaloin and Jean-Baptiste Madinier and Jean-Paul Briand and Nicolas Page and Sylviane Muller},
doi = {10.1038/s41598-018-34887-6},
issn = {2045-2322 2045-2322},
year = {2018},
date = {2018-01-01},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16820},
abstract = {The nuclear translocation of endogenous heat shock cognate protein HSPA8 is a requisite for cell survival during oxidative and heat shock stress. Upon these events, cytoplasmic HSPA8 is thought to concentrate within the nucleus and nucleolus. When the situation returns to normal, HSPA8 is released from its nuclear/nucleolar anchors and redistributes into the cytoplasm. By using different stress conditions and a 21-mer phosphopeptide tool called P140, which binds HSPA8 and hampers its chaperone properties, we deciphered the cellular and molecular effects arising during this vital cytoplasmic-nuclear-cytoplasmic shuttling process. Using the non-metastatic fibroblastoid cell line MRL/N-1 derived from a MRL/MpTn-gld/gld lupus-prone mouse, we discovered that P140 treatment neutralized the egress of HSPA8 from nucleus to cytoplasm in the cell recovery phase. This lack of relocation of HSPA8 into the cytoplasm of heat-shocked MRL/N-1 cells altered the ability of these cells to survive when a second mild oxidative stress mimicking inflammatory conditions was applied. Crosslinking experiments followed by proteomics studies showed that P140 binds regions close to nuclear import and export signal sequences encompassed within the HSPA8 structure. These data are consistent with HSPA8 having a crucial cell protective role against reactive oxygen species (ROS) production by mitochondria during inflammatory conditions.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
The nuclear translocation of endogenous heat shock cognate protein HSPA8 is a requisite for cell survival during oxidative and heat shock stress. Upon these events, cytoplasmic HSPA8 is thought to concentrate within the nucleus and nucleolus. When the situation returns to normal, HSPA8 is released from its nuclear/nucleolar anchors and redistributes into the cytoplasm. By using different stress conditions and a 21-mer phosphopeptide tool called P140, which binds HSPA8 and hampers its chaperone properties, we deciphered the cellular and molecular effects arising during this vital cytoplasmic-nuclear-cytoplasmic shuttling process. Using the non-metastatic fibroblastoid cell line MRL/N-1 derived from a MRL/MpTn-gld/gld lupus-prone mouse, we discovered that P140 treatment neutralized the egress of HSPA8 from nucleus to cytoplasm in the cell recovery phase. This lack of relocation of HSPA8 into the cytoplasm of heat-shocked MRL/N-1 cells altered the ability of these cells to survive when a second mild oxidative stress mimicking inflammatory conditions was applied. Crosslinking experiments followed by proteomics studies showed that P140 binds regions close to nuclear import and export signal sequences encompassed within the HSPA8 structure. These data are consistent with HSPA8 having a crucial cell protective role against reactive oxygen species (ROS) production by mitochondria during inflammatory conditions.
Poirier Isabelle, Pallud Marie, Kuhn Lauriane, Hammann Philippe, Demortière Arnaud, Jamali Arash, Chicher Johana, Caplat Christelle, Gallon Régis Kevin, Bertrand Martine
Toxicological effects of CdSe nanocrystals on the marine diatom Phaeodactylum tricornutum: The first mass spectrometry-based proteomic approach. Article de journal
Dans: Ecotoxicology and environmental safety, vol. 152, p. 78–90, 2018, ISSN: 1090-2414 0147-6513.
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{poirier_toxicological_2018,
title = {Toxicological effects of CdSe nanocrystals on the marine diatom Phaeodactylum tricornutum: The first mass spectrometry-based proteomic approach.},
author = {Isabelle Poirier and Marie Pallud and Lauriane Kuhn and Philippe Hammann and Arnaud Demortière and Arash Jamali and Johana Chicher and Christelle Caplat and Régis Kevin Gallon and Martine Bertrand},
doi = {10.1016/j.ecoenv.2018.01.043},
issn = {1090-2414 0147-6513},
year = {2018},
date = {2018-01-01},
journal = {Ecotoxicology and environmental safety},
volume = {152},
pages = {78--90},
abstract = {In the marine environment, benthic diatoms from estuarine and coastal sediments are among the first targets of nanoparticle pollution whose potential toxicity on marine organisms is still largely unknown. It is therefore relevant to improve our knowledge of interactions between these new pollutants and microalgae, the key players in the control of marine resources. In this study, the response of P. tricornutum to CdSe nanocrystals (CdSe NPs) of 5 nm (NP5) and 12 nm (NP12) in diameter was evaluated through microscopic, physiological, biochemical and proteomic approaches. NP5 and NP12 affected cell growth but oxygen production was only slightly decreased by NP5 after 1-d incubation time. In our experimental conditions, a high CdSe NP dissolution was observed during the first day of culture, leading to Cd bioaccumulation and oxidative stress, particularly with NP12. However, after a 7-day incubation time, proteomic analysis highlighted that P. tricornutum responded to CdSe NP toxicity by regulating numerous proteins involved in protection against oxidative stress, cellular redox homeostasis, Ca(2+) regulation and signalling, S-nitrosylation and S-glutathionylation processes and cell damage repair. These proteome changes allowed algae cells to regulate their intracellular ROS level in contaminated cultures. P. tricornutum was also capable to control its intracellular Cd concentration at a sufficiently low level to preserve its growth. To our knowledge, this is the first work allowing the identification of proteins differentially expressed by P. tricornutum subjected to NPs and thus the understanding of some molecular pathways involved in its cellular response to nanoparticles. SIGNIFICANCE: The microalgae play a key role in the control of marine resources. Moreover, they produce 50% of the atmospheric oxygen. CdSe NPs are extensively used in the industry of renewable energies and it is regrettably expected that these pollutants will sometime soon appear in the marine environment through surface runoff, urban effluents and rivers. Since estuarine and coastal sediments concentrate pollutants, benthic microalgae which live in superficial sediments will be among the first targets of nanoparticle pollution. Thus, it is relevant to improve our knowledge of interactions between diatoms and nanoparticles. Proteomics is a powerful tool for understanding the molecular mechanisms triggered by nanoparticle exposure, and our study is the first one to use this tool to identify proteins differentially expressed by P. tricornutum subjected to CdSe nanocrystals. This work is fundamental to improve our knowledge about the defence mechanisms developed by algae cells to counteract damage caused by CdSe NPs.},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
In the marine environment, benthic diatoms from estuarine and coastal sediments are among the first targets of nanoparticle pollution whose potential toxicity on marine organisms is still largely unknown. It is therefore relevant to improve our knowledge of interactions between these new pollutants and microalgae, the key players in the control of marine resources. In this study, the response of P. tricornutum to CdSe nanocrystals (CdSe NPs) of 5 nm (NP5) and 12 nm (NP12) in diameter was evaluated through microscopic, physiological, biochemical and proteomic approaches. NP5 and NP12 affected cell growth but oxygen production was only slightly decreased by NP5 after 1-d incubation time. In our experimental conditions, a high CdSe NP dissolution was observed during the first day of culture, leading to Cd bioaccumulation and oxidative stress, particularly with NP12. However, after a 7-day incubation time, proteomic analysis highlighted that P. tricornutum responded to CdSe NP toxicity by regulating numerous proteins involved in protection against oxidative stress, cellular redox homeostasis, Ca(2+) regulation and signalling, S-nitrosylation and S-glutathionylation processes and cell damage repair. These proteome changes allowed algae cells to regulate their intracellular ROS level in contaminated cultures. P. tricornutum was also capable to control its intracellular Cd concentration at a sufficiently low level to preserve its growth. To our knowledge, this is the first work allowing the identification of proteins differentially expressed by P. tricornutum subjected to NPs and thus the understanding of some molecular pathways involved in its cellular response to nanoparticles. SIGNIFICANCE: The microalgae play a key role in the control of marine resources. Moreover, they produce 50% of the atmospheric oxygen. CdSe NPs are extensively used in the industry of renewable energies and it is regrettably expected that these pollutants will sometime soon appear in the marine environment through surface runoff, urban effluents and rivers. Since estuarine and coastal sediments concentrate pollutants, benthic microalgae which live in superficial sediments will be among the first targets of nanoparticle pollution. Thus, it is relevant to improve our knowledge of interactions between diatoms and nanoparticles. Proteomics is a powerful tool for understanding the molecular mechanisms triggered by nanoparticle exposure, and our study is the first one to use this tool to identify proteins differentially expressed by P. tricornutum subjected to CdSe nanocrystals. This work is fundamental to improve our knowledge about the defence mechanisms developed by algae cells to counteract damage caused by CdSe NPs.
Montavon Thomas, Kwon Yerim, Zimmermann Aude, Hammann Philippe, Vincent Timothée, Cognat Valérie, Bergdoll Marc, Michel Fabrice, Dunoyer Patrice
Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates. Article de journal
Dans: The Plant journal : for cell and molecular biology, vol. 95, no. 2, p. 204–218, 2018, ISSN: 1365-313X 0960-7412, (Place: England).
Résumé | Liens | BibTeX | Étiquettes: PPSE
@article{montavon_characterization_2018,
title = {Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates.},
author = {Thomas Montavon and Yerim Kwon and Aude Zimmermann and Philippe Hammann and Timothée Vincent and Valérie Cognat and Marc Bergdoll and Fabrice Michel and Patrice Dunoyer},
doi = {10.1111/tpj.13941},
issn = {1365-313X 0960-7412},
year = {2018},
date = {2018-01-01},
journal = {The Plant journal : for cell and molecular biology},
volume = {95},
number = {2},
pages = {204--218},
abstract = {In the model plant Arabidopsis thaliana, four Dicer-like proteins (DCL1-4) mediate the production of various classes of small RNAs (sRNAs). Among these four proteins, DCL4 is by far the most versatile RNaseIII-like enzyme, and previously identified dcl4 missense alleles were shown to uncouple the production of the various classes of DCL4-dependent sRNAs. Yet little is known about the molecular mechanism behind this uncoupling. Here, by studying the subcellular localization, interactome and binding to the sRNA precursors of three distinct dcl4 missense alleles, we simultaneously highlight the absolute requirement of a specific residue in the helicase domain for the efficient production of all DCL4-dependent sRNAs, and identify, within the PAZ domain, an important determinant of DCL4 versatility that is mandatory for the efficient processing of intramolecular fold-back double-stranded RNA (dsRNA) precursors, but that is dispensable for the production of small interfering RNAs (siRNAs) from RDR-dependent dsRNA susbtrates. This study not only provides insights into the DCL4 mode of action, but also delineates interesting tools to further study the complexity of RNA silencing pathways in plants, and possibly other organisms.},
note = {Place: England},
keywords = {PPSE},
pubstate = {published},
tppubtype = {article}
}
In the model plant Arabidopsis thaliana, four Dicer-like proteins (DCL1-4) mediate the production of various classes of small RNAs (sRNAs). Among these four proteins, DCL4 is by far the most versatile RNaseIII-like enzyme, and previously identified dcl4 missense alleles were shown to uncouple the production of the various classes of DCL4-dependent sRNAs. Yet little is known about the molecular mechanism behind this uncoupling. Here, by studying the subcellular localization, interactome and binding to the sRNA precursors of three distinct dcl4 missense alleles, we simultaneously highlight the absolute requirement of a specific residue in the helicase domain for the efficient production of all DCL4-dependent sRNAs, and identify, within the PAZ domain, an important determinant of DCL4 versatility that is mandatory for the efficient processing of intramolecular fold-back double-stranded RNA (dsRNA) precursors, but that is dispensable for the production of small interfering RNAs (siRNAs) from RDR-dependent dsRNA susbtrates. This study not only provides insights into the DCL4 mode of action, but also delineates interesting tools to further study the complexity of RNA silencing pathways in plants, and possibly other organisms.
2017
Kuhn Lauriane, Majzoub Karim, Einhorn Evelyne, Chicher Johana, Pompon Julien, Imler Jean-Luc, Hammann Philippe, Meignin Carine
Definition of a RACK1 Interaction Network in Drosophila melanogaster Using SWATH-MS Article de journal
Dans: G3 (Bethesda), 2017, ISSN: 2160-1836.
Résumé | Liens | BibTeX | Étiquettes: imler, M3i, meignin, PPSE
@article{kuhn_definition_2017,
title = {Definition of a RACK1 Interaction Network in Drosophila melanogaster Using SWATH-MS},
author = {Lauriane Kuhn and Karim Majzoub and Evelyne Einhorn and Johana Chicher and Julien Pompon and Jean-Luc Imler and Philippe Hammann and Carine Meignin},
doi = {10.1534/g3.117.042564},
issn = {2160-1836},
year = {2017},
date = {2017-12-31},
journal = {G3 (Bethesda)},
abstract = {Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins. These data represent the first SWATH spectral library available for Drosophila and will be a useful resource for the community. A total of 52 interacting proteins were identified, including several molecules involved in translation such as structural components of the ribosome, factors regulating translation initiation or elongation and RNA binding proteins. Among these 52 proteins, 15 were identified as partners by the SWATH strategy only. Interestingly, these 15 proteins are significantly enriched for the functions translation and nucleic acid binding. This enrichment reflects the engagement of RACK1 at the ribosome and highlights the added value of SWATH analysis. A functional screen did not reveal any protein sharing the interesting properties of RACK1, which is required for IRES-dependent translation and not essential for cell viability. Intriguingly however, 10 of the RACK1 partners identified restrict replication of Cricket paralysis virus, an IRES-containing virus.},
keywords = {imler, M3i, meignin, PPSE},
pubstate = {published},
tppubtype = {article}
}
Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins. These data represent the first SWATH spectral library available for Drosophila and will be a useful resource for the community. A total of 52 interacting proteins were identified, including several molecules involved in translation such as structural components of the ribosome, factors regulating translation initiation or elongation and RNA binding proteins. Among these 52 proteins, 15 were identified as partners by the SWATH strategy only. Interestingly, these 15 proteins are significantly enriched for the functions translation and nucleic acid binding. This enrichment reflects the engagement of RACK1 at the ribosome and highlights the added value of SWATH analysis. A functional screen did not reveal any protein sharing the interesting properties of RACK1, which is required for IRES-dependent translation and not essential for cell viability. Intriguingly however, 10 of the RACK1 partners identified restrict replication of Cricket paralysis virus, an IRES-containing virus.
Gross L, Vicens Q, Einhorn E, Noireterre A, Schaeffer L, Kuhn L, Imler JL, Eriani G, Meignin C, Martin F
The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure Article de journal
Dans: Nucleic Acids Res, vol. 45, no. 15, p. 8993-9004, 2017, ISBN: 28911115.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, PPSE, Unité ARN
@article{,
title = {The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure},
author = {L Gross and Q Vicens and E Einhorn and A Noireterre and L Schaeffer and L Kuhn and JL Imler and G Eriani and C Meignin and F Martin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/28911115?dopt=Abstract},
doi = {10.1093/nar/gkx622},
isbn = {28911115},
year = {2017},
date = {2017-01-01},
journal = {Nucleic Acids Res},
volume = {45},
number = {15},
pages = {8993-9004},
abstract = {Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.},
keywords = {ERIANI, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.
Carapito C, Kuhn L, Karim L, Rompais M, Rabilloud T, Schwenzer H, Sissler M
Two proteomic methodologies for defining N-termini of mature human mitochondrial aminoacyl-tRNA synthetases. Article de journal
Dans: Methods, vol. 113, p. 111-119, 2017, ISBN: 27793688.
Résumé | Liens | BibTeX | Étiquettes: PPSE, SISSLER, Unité ARN
@article{,
title = {Two proteomic methodologies for defining N-termini of mature human mitochondrial aminoacyl-tRNA synthetases.},
author = {C Carapito and L Kuhn and L Karim and M Rompais and T Rabilloud and H Schwenzer and M Sissler},
url = {https://www.ncbi.nlm.nih.gov/pubmed/27793688?dopt=Abstract},
doi = {10.1016/j.ymeth.2016.10.012},
isbn = {27793688},
year = {2017},
date = {2017-01-01},
journal = {Methods},
volume = {113},
pages = {111-119},
abstract = {Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are encoded in the nucleus, synthesized in the cytosol and targeted for importation into mitochondria by a N-terminal mitochondrial targeting sequence. This targeting sequence is presumably cleaved upon entry into the mitochondria, following a process still not fully deciphered in human, despite essential roles for the mitochondrial biogenesis. Maturation processes are indeed essential both for the release of a functional enzyme and to route correctly the protein within mitochondria. The absence of consensus sequences for cleavage sites and the discovery of possible multiple proteolytic steps render predictions of N-termini difficult. Further, the knowledge of the cleavages is key for the design of protein constructions compatible with efficient production in bacterial strains. Finally, full comprehension becomes essential because a growing number of mutations are found in genes coding for mt-aaRS. In the present study, we take advantage of proteomic methodological developments and identified, in mitochondria, three N-termini for the human mitochondrial aspartyl-tRNA synthetase. This first description of the co-existence of different forms opens new perspectives in the biological understanding of this enzyme. Those methods are extended to the whole set of human mt-aaRSs and methodological advice are provided for further investigations.},
keywords = {PPSE, SISSLER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are encoded in the nucleus, synthesized in the cytosol and targeted for importation into mitochondria by a N-terminal mitochondrial targeting sequence. This targeting sequence is presumably cleaved upon entry into the mitochondria, following a process still not fully deciphered in human, despite essential roles for the mitochondrial biogenesis. Maturation processes are indeed essential both for the release of a functional enzyme and to route correctly the protein within mitochondria. The absence of consensus sequences for cleavage sites and the discovery of possible multiple proteolytic steps render predictions of N-termini difficult. Further, the knowledge of the cleavages is key for the design of protein constructions compatible with efficient production in bacterial strains. Finally, full comprehension becomes essential because a growing number of mutations are found in genes coding for mt-aaRS. In the present study, we take advantage of proteomic methodological developments and identified, in mitochondria, three N-termini for the human mitochondrial aspartyl-tRNA synthetase. This first description of the co-existence of different forms opens new perspectives in the biological understanding of this enzyme. Those methods are extended to the whole set of human mt-aaRSs and methodological advice are provided for further investigations.