Imagerie

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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 Laurianne 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},

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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}