Imagerie PI2

@article{pmid36598775,

title = {Nucleos'ID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides},

author = {Clarisse Gosset-Erard and Mévie Didierjean and Jérome Pansanel and Antony Lechner and Philippe Wolff and Lauriane Kuhn and Frédéric Aubriet and Emmanuelle Leize-Wagner and Patrick Chaimbault and Yannis-Nicolas François},

doi = {10.1021/acs.analchem.2c04722},

issn = {1520-6882},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Anal Chem},

volume = {95},

issue = {2},

pages = {1608-1617},

abstract = {As RNA post-transcriptional modifications are of growing interest, several methods were developed for their characterization. One of them established for their identification, at the nucleosidic level, is the hyphenation of separation methods, such as liquid chromatography or capillary electrophoresis, to tandem mass spectrometry. However, to our knowledge, no software is yet available for the untargeted identification of RNA post-transcriptional modifications from MS/MS data-dependent acquisitions. Thus, very long and tedious manual data interpretations are required. To meet the need of easier and faster data interpretation, a new user-friendly search engine, called Nucleos'ID, was developed for CE-MS/MS and LC-MS/MS users. Performances of this new software were evaluated on CE-MS/MS data from nucleoside analyses of already well-described  transfer RNA and  total tRNA extract. All samples showed great true positive, true negative, and false discovery rates considering the database size containing all modified and unmodified nucleosides referenced in the literature. The true positive and true negative rates obtained were above 0.94, while the false discovery rates were between 0.09 and 0.17. To increase the level of sample complexity, untargeted identification of several RNA modifications from  70S ribosome was achieved by the Nucleos'ID search following CE-MS/MS analysis.},

keywords = {ARN-MS, PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36308692,

title = {Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts},

author = {Lauriane Kuhn and Timothée Vincent and Philippe Hammann and Hélène Zuber},

doi = {10.1007/978-1-0716-1967-4_11},

issn = {1940-6029},

year  = {2023},

date = {2023-01-01},

journal = {Methods Mol Biol},

volume = {2426},

pages = {243--265},

abstract = {Immunoprecipitation mass spectrometry (IP-MS) is a popular method for the identification of protein-protein interactions. This approach is particularly powerful when information is collected without a priori knowledge and has been successively used as a first key step for the elucidation of many complex protein networks. IP-MS consists in the affinity purification of a protein of interest and of its interacting proteins followed by protein identification and quantification by mass spectrometry analysis. We developed an R package, named IPinquiry, dedicated to IP-MS analysis and based on the spectral count quantification method. The main purpose of this package is to provide a simple R pipeline with a limited number of processing steps to facilitate data exploration for biologists. This package allows to perform differential analysis of protein accumulation between two groups of IP experiments, to retrieve protein annotations, to export results, and to create different types of graphics. Here we describe the step-by-step procedure for an interactome analysis using IPinquiry from data loading to result export and plot production.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36617674,

title = {Proteomics-based determination of double stranded RNA interactome reveals known and new factors involved in Sindbis virus infection},

author = {Erika Girardi and Melanie Messmer and Paula Lopez and Aurelie Fender and Johana Chicher and Beatrice Chane-Woon-Ming and Philippe Hammann and Sebastien Pfeffer},

doi = {10.1261/rna.079270.122},

issn = {1469-9001},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {RNA},

volume = {29},

issue = {3},

pages = {361-375},

abstract = {Viruses are obligate intracellular parasites, which depend on the host cellular machineries to replicate their genome and complete their infectious cycle. Long double stranded (ds)RNA is a common viral by-product originating during RNA virus replication and is universally sensed as a danger signal to trigger the antiviral response. As a result, viruses hide dsRNA intermediates into viral replication factories and have evolved strategies to hijack cellular proteins for their benefit. The characterization of the host factors associated with viral dsRNA and involved in viral replication remains a major challenge to develop new antiviral drugs against RNA viruses. Here, we performed anti-dsRNA immunoprecipitation followed by mass spectrometry analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (Splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.},

keywords = {PFEFFER, PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36422372,

title = {A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source},

author = {Pauline Chaignaud and Christelle Gruffaz and Adrien Borreca and Stéphanie Fouteau and Lauriane Kuhn and Jérémy Masbou and Zoé Rouy and Philippe Hammann and Gwenaël Imfeld and David Roche and Stéphane Vuilleumier},

doi = {10.3390/microorganisms10112302},

issn = {2076-2607},

year  = {2022},

date = {2022-11-01},

journal = {Microorganisms},

volume = {10},

number = {11},

abstract = {Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects on aquatic life and potentially also on humans. We report on the isolation and characterisation of strain MD1, an aerobic methylotrophic bacterium growing with metformin as its sole carbon, nitrogen and energy source. Strain MD1 degrades metformin into dimethylamine used for growth, and guanylurea as a side-product. Sequence analysis of its fully assembled genome showed its affiliation to . Differential proteomics and transcriptomics, as well as mini-transposon mutagenesis of the strain, point to genes and proteins essential for growth with metformin and potentially associated with hydrolytic C-N cleavage of metformin or with cellular transport of metformin and guanylurea. The obtained results suggest the recent evolution of the growth-supporting capacity of strain MD1 to degrade metformin. Our results identify candidate proteins of the enzymatic system for metformin transformation in strain MD1 and will inform future research on the fate of metformin and its degradation products in the environment and in humans.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36050837,

title = {FRIENDLY (FMT) is an RNA binding protein associated with cytosolic ribosomes at the mitochondrial surface},

author = {Mickaele Hemono and Thalia Salinas-Giegé and Jeanne Roignant and Audrey Vingadassalon and Philippe Hammann and Elodie Ubrig and Patryk Ngondo and Anne-Marie Duchêne},

doi = {10.1111/tpj.15962},

issn = {1365-313X},

year  = {2022},

date = {2022-10-01},

urldate = {2022-10-01},

journal = {Plant J},

volume = {112},

number = {2},

pages = {309--321},

abstract = {The spatial organization of protein synthesis in the eukaryotic cell is essential for maintaining the integrity of the proteome and the functioning of the cell. Translation on free polysomes or on ribosomes associated with the endoplasmic reticulum has been studied for a long time. More recent data have revealed selective translation of mRNAs in other compartments, in particular at the surface of mitochondria. Although these processes have been described in many organisms, particularky in plants, the mRNA targeting and localized translation mechanisms remain poorly understood. Here, the Arabidopsis thaliana Friendly (FMT) protein is shown to be a cytosolic RNA binding protein that associates with cytosolic ribosomes at the surface of mitochondria. FMT knockout delays seedling development and causes mitochondrial clustering. The mutation also disrupts the mitochondrial proteome, as well as the localization of nuclear transcripts encoding mitochondrial proteins at the surface of mitochondria. These data indicate that FMT participates in the localization of mRNAs and their translation at the surface of mitochondria.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35500104,

title = {Uptake Mechanisms and Regulatory Responses to MECAM- and DOTAM-Based Artificial Siderophores and Their Antibiotic Conjugates in },

author = {Sarah Fritsch and Véronique Gasser and Carsten Peukert and Lukas Pinkert and Lauriane Kuhn and Quentin Perraud and Vincent Normant and Mark Brönstrup and Isabelle J Schalk},

doi = {10.1021/acsinfecdis.2c00049},

issn = {2373-8227},

year  = {2022},

date = {2022-06-01},

journal = {ACS Infect Dis},

volume = {8},

number = {6},

pages = {1134--1146},

abstract = {The development of new antibiotics against Gram-negative bacteria has to deal with the low permeability of the outer membrane. This obstacle can be overcome by utilizing siderophore-dependent iron uptake pathways as entrance routes for antibiotic uptake. Iron-chelating siderophores are actively imported by bacteria, and their conjugation to antibiotics allows smuggling the latter into bacterial cells. Synthetic siderophore mimetics based on MECAM (1,3,5-,',″-tris-(2,3-dihydroxybenzoyl)-triaminomethylbenzene) and DOTAM (1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane) cores, both chelating iron via catechol groups, have been recently applied as versatile carriers of functional cargo. In the present study, we show that MECAM and the MECAM-ampicillin conjugate  transport iron into  cells via the catechol-type outer membrane transporters PfeA and PirA and DOTAM solely via PirA. Differential proteomics and quantitative real-time polymerase chain reaction (qRT-PCR) showed that MECAM import induced the expression of , whereas  led to an increase in the expression of  and , a gene conferring ampicillin resistance. The presence of DOTAM did not induce the expression of  but upregulated the expression of two zinc transporters ( and ), pointing out that bacteria become zinc starved in the presence of this compound. Iron uptake experiments with radioactive Fe demonstrated that import of this nutrient by MECAM and DOTAM was as efficient as with the natural siderophore enterobactin. The study provides a functional validation for DOTAM- and MECAM-based artificial siderophore mimetics as vehicles for the delivery of cargo into Gram-negative bacteria.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35417704,

title = {The Arabidopsis F-box protein FBW2 targets AGO1 for degradation to prevent spurious loading of illegitimate small RNA},

author = {Thibaut Hacquard and Marion Clavel and Patricia Baldrich and Esther Lechner and Imma Pérez-Salamó and Mikhail Schepetilnikov and Benoît Derrien and Marieke Dubois and Philippe Hammann and Lauriane Kuhn and Danaé Brun and Nathalie Bouteiller and Nicolas Baumberger and Hervé Vaucheret and Blake C Meyers and Pascal Genschik},

doi = {10.1016/j.celrep.2022.110671},

issn = {2211-1247},

year  = {2022},

date = {2022-04-01},

journal = {Cell Rep},

volume = {39},

number = {2},

pages = {110671},

abstract = {RNA silencing is a conserved mechanism in eukaryotes involved in development and defense against viruses. In plants, ARGONAUTE1 (AGO1) protein plays a central role in both microRNA- and small interfering RNA-directed silencing, and its expression is regulated at multiple levels. Here, we report that the F-box protein FBW2 assembles an SCF complex that selectively targets for proteolysis AGO1 when it is unloaded and mutated. Although FBW2 loss of function does not lead to strong growth or developmental defects, it significantly increases RNA-silencing activity. Interestingly, under conditions in which small-RNA accumulation is affected, the failure to degrade AGO1 in fbw2 mutants becomes more deleterious for the plant. Accordingly, the non-degradable AGO1 protein assembles high-molecular-weight complexes and binds illegitimate small RNA, leading to off-target cleavage. Therefore, control of AGO1 homeostasis by FBW2 plays an important role in quality control of RNA silencing.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34791434,

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  = {2022},

date = {2022-02-01},

urldate = {2022-02-01},

journal = {Plant Physiol},

volume = {188},

number = {2},

pages = {1174--1188},

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{pmid34664350,

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  = {2022},

date = {2022-02-01},

journal = {Environ Microbiol},

volume = {24},

number = {2},

pages = {866--877},

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,  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{pmid33350053,

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  = {2022},

date = {2022-02-01},

journal = {Environ Microbiol},

volume = {24},

number = {2},

pages = {878--893},

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{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}

}

@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}

}

@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},

volume = {298},

issue = {6},

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}

}

@article{pmid34878758,

title = {How the Presence of Hemin Affects the Expression of the Different Iron Uptake Pathways in  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 Infect Dis},

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. , 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,  uses three distinct uptake pathways, named Has, Phu, and Hxu. We previously showed that  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 = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}