I2CT

@article{lange_rst1_2019,

title = {RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis.},

author = {Heike Lange and Simon Y A Ndecky and Carlos Gomez-Diaz and David Pflieger and Nicolas Butel and Julie Zumsteg and Lauriane Kuhn and Christina Piermaria and Johana Chicher and Michael Christie and Ezgi S Karaaslan and Patricia L M Lang and Detlef Weigel and Hervé Vaucheret and Philippe Hammann and Dominique Gagliardi},

doi = {10.1038/s41467-019-11807-4},

issn = {2041-1723 2041-1723},

year  = {2019},

date = {2019-08-01},

journal = {Nature communications},

volume = {10},

number = {1},

pages = {3871},

abstract = {The RNA exosome is a key 3'-5' exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{Lalaouna2019,

title = {RsaC sRNA modulates the oxidative stress response of \textit{Staphylococcus aureus} during manganese starvation},

author = {D Lalaouna and J Baude and Z Wu and A Tomasini and J Chicher and S Marzi and F Vandenesch and P Romby and I Caldelari and K Moreau},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31504767?dopt=Abstract},

doi = {10.1093/nar/gkz728},

isbn = {31504767},

year  = {2019},

date = {2019-01-01},

journal = {Nucleic Acids Res},

volume = {47},

number = {18},

pages = {9871-9887},

abstract = {The human opportunistic pathogen Staphylococcus aureus produces numerous small regulatory RNAs (sRNAs) for which functions are still poorly understood. Here, we focused on an atypical and large sRNA called RsaC. Its length varies between different isolates due to the presence of repeated sequences at the 5′ end while its 3′ part is structurally independent and highly conserved. Using MS2-affinity purification coupled with RNA sequencing (MAPS) and quantitative differential proteomics, sodA mRNA was identified as a primary target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. Remarkably, rsaC gene is co-transcribed with the major manganese ABC transporter MntABC and, consequently, RsaC is mainly produced in response to Mn starvation. This 3′UTR-derived sRNA is released from mntABC-RsaC precursor after cleavage by RNase III. The mature and stable form of RsaC inhibits the synthesis of the Mn-containing enzyme SodA synthesis and favors the oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. In addition, other putative targets of RsaC are involved in oxidative stress (ROS and NOS) and metal homeostasis (Fe and Zn). Consequently, RsaC may balance two interconnected defensive responses, i.e. oxidative stress and metal-dependent nutritional immunity.},

keywords = {PPSE, ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{arbogast_atg5_2019,

title = {ATG5 is required for B cell polarization and presentation of particulate antigens.},

author = {Florent Arbogast and Johan Arnold and Philippe Hammann and Lauriane Kuhn and Johana Chicher and Diane Murera and Justine Weishaar and Sylviane Muller and Jean-Daniel Fauny and Frédéric Gros},

doi = {10.1080/15548627.2018.1516327},

issn = {1554-8635 1554-8627 1554-8627},

year  = {2019},

date = {2019-01-01},

journal = {Autophagy},

volume = {15},

number = {2},

pages = {280--294},

abstract = {The involvement of macroautophagy/autophagy proteins in B-cell receptor (BCR) trafficking, although suspected, is not well understood. We show that ATG5 (autophagy related 5) contributes to BCR polarization after stimulation and internalization into LAMP1 (lysosomal-associated membrane protein 1)(+) and major histocompatibility complex class II (MHC-II)(+) compartments. BCR polarization is crucial in the context of immobilized antigen processing. Moreover, antigen presentation to cognate T cells is decreased in the absence of ATG5 when the model antigen OVAL/ovalbumin is provided in an immobilized form in contrast to the normal presentation of soluble OVAL. We further show that ATG5 is required for centrosome polarization and actin nucleation in the immune synapse area. This event is accompanied by an increased interaction between ATG16L1 (autophagy related 16-like 1 [S. cerevisiae]) and the microtubule-organizing center-associated protein PCM1 (pericentriolar material 1). In the human B cell line BJAB, PCM1 is required for BCR polarization after stimulation. We thus propose that the ATG12 (autophagy related 12)-ATG5-ATG16L1 complex under BCR stimulation allows its interaction with PCM1 and consequently facilitates centrosome relocalization to the immune synapse, optimizing the presentation of particulate antigens. Abbreviations: ACTB: actin beta; ACTR2/3: ARP2/3 actin-related protein 2/3; APC: antigen-presenting cells; ATG: autophagy-related; BCR: B cell receptor; BECN1/Beclin 1: beclin 1, autophagy related; CDC42: cell division cycle 42; Cr2: complement receptor 2; CSFE: carboxyfluorescein succinimidyl ester; DAPI: 4',6-diamidino-2-phenylindole dihydrochloride; EEA1: early endosome antigen 1; ELISA: enzyme-linked immunosorbent assay; FITC: fluorescein isothyocyanate; GC: germinal center; GJA1/CX3: gap junction protein, alpha 1; Ig: immunoglobulin; LAMP1: lysosomal-associated membrane protein 1; LAP: LC3-associated phagocytosis; LM: littermate; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/ERK: mitogen activated protein kinase; MHC-II: major histocompatibility complex class II; MIIC: MHC class II compartment; OVAL: ovalbumin; PBS: phosphate-buffered saline; PCM1: pericentriolar material 1; PtdIns3K: phosphatidylinositol 3-kinase; PTPRC/CD45RB/B220; Protein tyrosine phosphatase, receptor type, C; SYK: spleen tyrosine kinase; TBS: Tris-buffered saline; TCR: T cell receptor; ULK1: unc-51 like kinase 1.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{waltz_small_2019,

title = {Small is big in Arabidopsis mitochondrial ribosome.},

author = {Florent Waltz and Tan-Trung Nguyen and Mathilde Arrivé and Anthony Bochler and Johana Chicher and Philippe Hammann and Lauriane Kuhn and Martine Quadrado and Hakim Mireau and Yaser Hashem and Philippe Giegé},

doi = {10.1038/s41477-018-0339-y},

issn = {2055-0278 2055-0278},

year  = {2019},

date = {2019-01-01},

journal = {Nature plants},

volume = {5},

number = {1},

pages = {106--117},

abstract = {Mitochondria are responsible for energy production through aerobic respiration, and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in mitochondrial translation remains unclear. Here we present the biochemical characterization of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identified 19 plant-specific mitoribosome proteins, of which ten are PPR proteins. The knockout mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes, including lethality and severe growth delay. The molecular analysis of rppr1 mutants using ribosome profiling, as well as the analysis of mitochondrial protein levels, demonstrate rPPR1 to be a generic translation factor that is a novel function for PPR proteins. Finally, single-particle cryo-electron microscopy (cryo-EM) reveals the unique structural architecture of Arabidopsis mitoribosomes, characterized by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, in terms of both structure and protein content.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{trinquier_trna_2019,

title = {tRNA Maturation Defects Lead to Inhibition of rRNA Processing via Synthesis of pppGpp.},

author = {Aude Trinquier and Jonathan E Ulmer and Laetitia Gilet and Sabine Figaro and Philippe Hammann and Lauriane Kuhn and Frédérique Braun and Ciarán Condon},

doi = {10.1016/j.molcel.2019.03.030},

issn = {1097-4164 1097-2765},

year  = {2019},

date = {2019-01-01},

journal = {Molecular cell},

volume = {74},

number = {6},

pages = {1227--1238.e3},

abstract = {rRNAs and tRNAs universally require processing from longer primary transcripts to become functional for translation. Here, we describe an unsuspected link between tRNA maturation and the 3' processing of 16S rRNA, a key step in preparing the small ribosomal subunit for interaction with the Shine-Dalgarno sequence in prokaryotic translation initiation. We show that an accumulation of either 5' or 3' immature tRNAs triggers RelA-dependent production of the stringent response alarmone (p)ppGpp in the Gram-positive model organism Bacillus subtilis. The accumulation of (p)ppGpp and accompanying decrease in GTP levels specifically inhibit 16S rRNA 3' maturation. We suggest that cells can exploit this mechanism to sense potential slowdowns in tRNA maturation and adjust rRNA processing accordingly to maintain the appropriate functional balance between these two major components of the translation apparatus.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{olmo_control_2018,

title = {Control of dengue virus in the midgut of Aedes aegypti by ectopic expression of the dsRNA-binding protein Loqs2.},

author = {Roenick P Olmo and Alvaro G A Ferreira and Tatiane C Izidoro-Toledo and Eric R G R Aguiar and Isaque J S de Faria and Kátia P R de Souza and Kátia P Osório and Lauriane Kuhn and Philippe Hammann and Elisa G de Andrade and Yaovi Mathias Todjro and Marcele N Rocha and Thiago H J F Leite and Siad C G Amadou and Juliana N Armache and Simona Paro and Caroline D de Oliveira and Fabiano D Carvalho and Luciano A Moreira and Eric Marois and Jean-Luc Imler and João T Marques},

doi = {10.1038/s41564-018-0268-6},

issn = {2058-5276 2058-5276},

year  = {2018},

date = {2018-12-01},

journal = {Nature microbiology},

volume = {3},

number = {12},

pages = {1385--1393},

abstract = {Dengue virus (DENV) is an arbovirus transmitted to humans by Aedes mosquitoes(1). In the insect vector, the small interfering RNA (siRNA) pathway is an important antiviral mechanism against DENV(2-5). However, it remains unclear when and where the siRNA pathway acts during the virus cycle. Here, we show that the siRNA pathway fails to efficiently silence DENV in the midgut of Aedes aegypti although it is essential to restrict systemic replication. Accumulation of DENV-derived siRNAs in the midgut reveals that impaired silencing results from a defect downstream of small RNA biogenesis. Notably, silencing triggered by endogenous and exogenous dsRNAs remained effective in the midgut where known components of the siRNA pathway, including the double-stranded RNA (dsRNA)-binding proteins Loquacious and r2d2, had normal expression levels. We identified an Aedes-specific paralogue of loquacious and r2d2, hereafter named loqs2, which is not expressed in the midgut. Loqs2 interacts with Loquacious and r2d2 and is required to control systemic replication of DENV and also Zika virus. Furthermore, ectopic expression of Loqs2 in the midgut of transgenic mosquitoes is sufficient to restrict DENV replication and dissemination. Together, our data reveal a mechanism of tissue-specific regulation of the mosquito siRNA pathway controlled by Loqs2.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{chicois_upf1_2018,

title = {The UPF1 interactome reveals interaction networks between RNA degradation and translation repression factors in Arabidopsis.},

author = {Clara Chicois and Hélène Scheer and Shahïnez Garcia and Hélène Zuber and Jérôme Mutterer and Johana Chicher and Philippe Hammann and Dominique Gagliardi and Damien Garcia},

doi = {10.1111/tpj.14022},

issn = {1365-313X 0960-7412},

year  = {2018},

date = {2018-10-01},

journal = {The Plant journal : for cell and molecular biology},

volume = {96},

number = {1},

pages = {119--132},

abstract = {The RNA helicase UP-FRAMESHIFT (UPF1) is a key factor of nonsense-mediated decay (NMD), a mRNA decay pathway involved in RNA quality control and in the fine-tuning of gene expression. UPF1 recruits UPF2 and UPF3 to constitute the NMD core complex, which is conserved across eukaryotes. No other components of UPF1-containing ribonucleoproteins (RNPs) are known in plants, despite its key role in regulating gene expression. Here, we report the identification of a large set of proteins that co-purify with the Arabidopsis UPF1, either in an RNA-dependent or RNA-independent manner. We found that like UPF1, several of its co-purifying proteins have a dual localization in the cytosol and in P-bodies, which are dynamic structures formed by the condensation of translationally repressed mRNPs. Interestingly, more than half of the proteins of the UPF1 interactome also co-purify with DCP5, a conserved translation repressor also involved in P-body formation. We identified a terminal nucleotidyltransferase, ribonucleases and several RNA helicases among the most significantly enriched proteins co-purifying with both UPF1 and DCP5. Among these, RNA helicases are the homologs of DDX6/Dhh1, known as translation repressors in humans and yeast, respectively. Overall, this study reports a large set of proteins associated with the Arabidopsis UPF1 and DCP5, two components of P-bodies, and reveals an extensive interaction network between RNA degradation and translation repression factors. Using this resource, we identified five hitherto unknown components of P-bodies in plants, pointing out the value of this dataset for the identification of proteins potentially involved in translation repression and/or RNA degradation.},

note = {Place: England},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{Goto2018,

title = {The Kinase IKKβ Regulates a STING- and NF-κB-Dependent Antiviral Response Pathway in Drosophila},

author = {Akira Goto and Kiyoshi Okado and Nelson Martins and Hua Cai and Vincent Barbier and Olivier Lamiable and Laurent Troxler and Estelle Santiago and Lauriane Kuhn and Donggi Paik and Neal Silverman and Andreas Holleufer and Rune Hartmann and Jiyong Liu and Tao Peng and Jules A Hoffmann and Carine Meignin and Laurent Daeffler and Jean-Luc Imler},

editor = {Elsevier Inc.},

url = {https://doi.org/10.1016/j.immuni.2018.07.013},

doi = {j.immuni.2018.07.013},

year  = {2018},

date = {2018-08-21},

journal = {Immunity},

number = {49},

pages = {225-234},

abstract = {Antiviral immunity in Drosophila involves RNA interference and poorly characterized inducible responses. Here, we showed that two components of the IMD pathway, the kinase dIKKβ and the transcription factor Relish, were required to control infection by two picorna-like viruses. We identified a set of genes induced by viral infection and regulated by dIKKβ and Relish, which included an ortholog of STING. We showed that dSTING participated in the control of infection by picorna-like viruses, acting upstream of dIKKβ to regulate expression of Nazo, an antiviral factor. Our data reveal an antiviral function for STING in an animal model devoid of interferons and suggest an evolutionarily ancient role for this molecule in antiviral immunity.},

keywords = {hoffmann, imler, M3i, meignin, PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{wang_blocking_2018,

title = {Blocking nuclear export of HSPA8 after heat shock stress severely alters cell survival.},

author = {Fengjuan Wang and Srinivasa Reddy Bonam and Nicolas Schall and Lauriane Kuhn and Philippe Hammann and Olivier Chaloin and Jean-Baptiste Madinier and Jean-Paul Briand and Nicolas Page and Sylviane Muller},

doi = {10.1038/s41598-018-34887-6},

issn = {2045-2322 2045-2322},

year  = {2018},

date = {2018-01-01},

journal = {Scientific reports},

volume = {8},

number = {1},

pages = {16820},

abstract = {The nuclear translocation of endogenous heat shock cognate protein HSPA8 is a requisite for cell survival during oxidative and heat shock stress. Upon these events, cytoplasmic HSPA8 is thought to concentrate within the nucleus and nucleolus. When the situation returns to normal, HSPA8 is released from its nuclear/nucleolar anchors and redistributes into the cytoplasm. By using different stress conditions and a 21-mer phosphopeptide tool called P140, which binds HSPA8 and hampers its chaperone properties, we deciphered the cellular and molecular effects arising during this vital cytoplasmic-nuclear-cytoplasmic shuttling process. Using the non-metastatic fibroblastoid cell line MRL/N-1 derived from a MRL/MpTn-gld/gld lupus-prone mouse, we discovered that P140 treatment neutralized the egress of HSPA8 from nucleus to cytoplasm in the cell recovery phase. This lack of relocation of HSPA8 into the cytoplasm of heat-shocked MRL/N-1 cells altered the ability of these cells to survive when a second mild oxidative stress mimicking inflammatory conditions was applied. Crosslinking experiments followed by proteomics studies showed that P140 binds regions close to nuclear import and export signal sequences encompassed within the HSPA8 structure. These data are consistent with HSPA8 having a crucial cell protective role against reactive oxygen species (ROS) production by mitochondria during inflammatory conditions.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{poirier_toxicological_2018,

title = {Toxicological effects of CdSe nanocrystals on the marine diatom Phaeodactylum tricornutum: The first mass spectrometry-based proteomic approach.},

author = {Isabelle Poirier and Marie Pallud and Lauriane Kuhn and Philippe Hammann and Arnaud Demortière and Arash Jamali and Johana Chicher and Christelle Caplat and Régis Kevin Gallon and Martine Bertrand},

doi = {10.1016/j.ecoenv.2018.01.043},

issn = {1090-2414 0147-6513},

year  = {2018},

date = {2018-01-01},

journal = {Ecotoxicology and environmental safety},

volume = {152},

pages = {78--90},

abstract = {In the marine environment, benthic diatoms from estuarine and coastal sediments are among the first targets of nanoparticle pollution whose potential toxicity on marine organisms is still largely unknown. It is therefore relevant to improve our knowledge of interactions between these new pollutants and microalgae, the key players in the control of marine resources. In this study, the response of P. tricornutum to CdSe nanocrystals (CdSe NPs) of 5 nm (NP5) and 12 nm (NP12) in diameter was evaluated through microscopic, physiological, biochemical and proteomic approaches. NP5 and NP12 affected cell growth but oxygen production was only slightly decreased by NP5 after 1-d incubation time. In our experimental conditions, a high CdSe NP dissolution was observed during the first day of culture, leading to Cd bioaccumulation and oxidative stress, particularly with NP12. However, after a 7-day incubation time, proteomic analysis highlighted that P. tricornutum responded to CdSe NP toxicity by regulating numerous proteins involved in protection against oxidative stress, cellular redox homeostasis, Ca(2+) regulation and signalling, S-nitrosylation and S-glutathionylation processes and cell damage repair. These proteome changes allowed algae cells to regulate their intracellular ROS level in contaminated cultures. P. tricornutum was also capable to control its intracellular Cd concentration at a sufficiently low level to preserve its growth. To our knowledge, this is the first work allowing the identification of proteins differentially expressed by P. tricornutum subjected to NPs and thus the understanding of some molecular pathways involved in its cellular response to nanoparticles. SIGNIFICANCE: The microalgae play a key role in the control of marine resources. Moreover, they produce 50% of the atmospheric oxygen. CdSe NPs are extensively used in the industry of renewable energies and it is regrettably expected that these pollutants will sometime soon appear in the marine environment through surface runoff, urban effluents and rivers. Since estuarine and coastal sediments concentrate pollutants, benthic microalgae which live in superficial sediments will be among the first targets of nanoparticle pollution. Thus, it is relevant to improve our knowledge of interactions between diatoms and nanoparticles. Proteomics is a powerful tool for understanding the molecular mechanisms triggered by nanoparticle exposure, and our study is the first one to use this tool to identify proteins differentially expressed by P. tricornutum subjected to CdSe nanocrystals. This work is fundamental to improve our knowledge about the defence mechanisms developed by algae cells to counteract damage caused by CdSe NPs.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{montavon_characterization_2018,

title = {Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates.},

author = {Thomas Montavon and Yerim Kwon and Aude Zimmermann and Philippe Hammann and Timothée Vincent and Valérie Cognat and Marc Bergdoll and Fabrice Michel and Patrice Dunoyer},

doi = {10.1111/tpj.13941},

issn = {1365-313X 0960-7412},

year  = {2018},

date = {2018-01-01},

journal = {The Plant journal : for cell and molecular biology},

volume = {95},

number = {2},

pages = {204--218},

abstract = {In the model plant Arabidopsis thaliana, four Dicer-like proteins (DCL1-4) mediate the production of various classes of small RNAs (sRNAs). Among these four proteins, DCL4 is by far the most versatile RNaseIII-like enzyme, and previously identified dcl4 missense alleles were shown to uncouple the production of the various classes of DCL4-dependent sRNAs. Yet little is known about the molecular mechanism behind this uncoupling. Here, by studying the subcellular localization, interactome and binding to the sRNA precursors of three distinct dcl4 missense alleles, we simultaneously highlight the absolute requirement of a specific residue in the helicase domain for the efficient production of all DCL4-dependent sRNAs, and identify, within the PAZ domain, an important determinant of DCL4 versatility that is mandatory for the efficient processing of intramolecular fold-back double-stranded RNA (dsRNA) precursors, but that is dispensable for the production of small interfering RNAs (siRNAs) from RDR-dependent dsRNA susbtrates. This study not only provides insights into the DCL4 mode of action, but also delineates interesting tools to further study the complexity of RNA silencing pathways in plants, and possibly other organisms.},

note = {Place: England},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{kuhn_definition_2017,

title = {Definition of a RACK1 Interaction Network in Drosophila melanogaster Using SWATH-MS},

author = {Lauriane Kuhn and Karim Majzoub and Evelyne Einhorn and Johana Chicher and Julien Pompon and Jean-Luc Imler and Philippe Hammann and Carine Meignin},

doi = {10.1534/g3.117.042564},

issn = {2160-1836},

year  = {2017},

date = {2017-12-31},

journal = {G3 (Bethesda)},

abstract = {Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins. These data represent the first SWATH spectral library available for Drosophila and will be a useful resource for the community. A total of 52 interacting proteins were identified, including several molecules involved in translation such as structural components of the ribosome, factors regulating translation initiation or elongation and RNA binding proteins. Among these 52 proteins, 15 were identified as partners by the SWATH strategy only. Interestingly, these 15 proteins are significantly enriched for the functions translation and nucleic acid binding. This enrichment reflects the engagement of RACK1 at the ribosome and highlights the added value of SWATH analysis. A functional screen did not reveal any protein sharing the interesting properties of RACK1, which is required for IRES-dependent translation and not essential for cell viability. Intriguingly however, 10 of the RACK1 partners identified restrict replication of Cricket paralysis virus, an IRES-containing virus.},

keywords = {imler, M3i, meignin, PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure},

author = {L Gross and Q Vicens and E Einhorn and A Noireterre and L Schaeffer and L Kuhn and JL Imler and G Eriani and C Meignin and F Martin},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28911115?dopt=Abstract},

doi = {10.1093/nar/gkx622},

isbn = {28911115},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Nucleic Acids Res},

volume = {45},

number = {15},

pages = {8993-9004},

abstract = {Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.},

keywords = {ERIANI, meignin, PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Two proteomic methodologies for defining N-termini of mature human mitochondrial aminoacyl-tRNA synthetases.},

author = {C Carapito and L Kuhn and L Karim and M Rompais and T Rabilloud and H Schwenzer and M Sissler},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27793688?dopt=Abstract},

doi = {10.1016/j.ymeth.2016.10.012},

isbn = {27793688},

year  = {2017},

date = {2017-01-01},

journal = {Methods},

volume = {113},

pages = {111-119},

abstract = {Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are encoded in the nucleus, synthesized in the cytosol and targeted for importation into mitochondria by a N-terminal mitochondrial targeting sequence. This targeting sequence is presumably cleaved upon entry into the mitochondria, following a process still not fully deciphered in human, despite essential roles for the mitochondrial biogenesis. Maturation processes are indeed essential both for the release of a functional enzyme and to route correctly the protein within mitochondria. The absence of consensus sequences for cleavage sites and the discovery of possible multiple proteolytic steps render predictions of N-termini difficult. Further, the knowledge of the cleavages is key for the design of protein constructions compatible with efficient production in bacterial strains. Finally, full comprehension becomes essential because a growing number of mutations are found in genes coding for mt-aaRS. In the present study, we take advantage of proteomic methodological developments and identified, in mitochondria, three N-termini for the human mitochondrial aspartyl-tRNA synthetase. This first description of the co-existence of different forms opens new perspectives in the biological understanding of this enzyme. Those methods are extended to the whole set of human mt-aaRSs and methodological advice are provided for further investigations.},

keywords = {PPSE, SISSLER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The RNA targetome of Staphylococcus aureus non-coding RNA RsaA: impact on cell surface properties and defense mechanisms.},

author = {A Tomasini and K Moreau and J Chicher and T Geissmann and F Vandenesch and P Romby and S Marzi and I Caldelari},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28379505},

doi = {10.1093/nar/gkx219},

isbn = {28379505},

year  = {2017},

date = {2017-01-01},

journal = {Nucleic Acids Res},

volume = {45},

number = {11},

pages = {6746-6760},

abstract = {The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non-coding RNAs (sRNAs). Many of the sRNAs regulate gene expression through base-pairings with mRNAs. However, characterization of the direct sRNA targets in Gram-positive bacteria remained a difficult challenge. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaA sRNA of S. aureus, known to repress the synthesis of the transcriptional regulator MgrA. Several mRNAs were enriched with RsaA expanding its regulatory network. Besides mgrA, several of these mRNAs encode a family of SsaA-like enzymes involved in peptidoglycan metabolism and the secreted anti-inflammatory FLIPr protein. Using a combination of in vivo and in vitro approaches, these mRNAs were validated as direct RsaA targets. Quantitative differential proteomics of wild-type and mutant strains corroborated the MAPS results. Additionally, it revealed that RsaA indirectly activated the synthesis of surface proteins supporting previous data that RsaA stimulated biofilm formation and favoured chronic infections. All together, this study shows that MAPS could also be easily applied in Gram-positive bacteria for identification of sRNA targetome.},

keywords = {PPSE, ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Structure of the 70S ribosome from human pathogen Staphylococcus aureus.},

author = {I Khusainov and Q Vicens and A Bochler and F Grosse and A Myasnikov and J F Ménétret and J Chicher and S Marzi and P Romby and G Yusupova and M Yusupov and Y Hashem},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28123039?dopt=Abstract},

doi = {10.1093/nar/gkw1126},

isbn = {28123039},

year  = {2017},

date = {2017-01-01},

journal = {Nucleic Acids Res},

volume = {45},

number = {2},

pages = {1026},

abstract = {Erratum for Structure of the 70S ribosome from human pathogen Staphylococcus aureus.},

keywords = {PPSE, ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein},

author = {J Brito Querido and E Mancera-Martinez and Q Vicens and A Bochler and J Chicher and A Simonetti and Y Hashem},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29107485?dopt=Abstract},

doi = {10.1016/j.str.2017.09.014},

isbn = {29107485},

year  = {2017},

date = {2017-01-01},

journal = {Structure},

volume = {25},

number = {12},

pages = {1785-1794},

abstract = {Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti-kinetoplastid therapeutic molecules that can replace the scarce and highly cytotoxic current drugs. The kinetoplastid ribosome represents a potential therapeutic target due to its relative structural divergence when compared with its human counterpart. However, several kinetoplastid-specific ribosomal features remain uncharacterized. Here, we present the near-atomic cryoelectron microscopy structure of a novel bona fide kinetoplastid-specific ribosomal (r-) protein (KSRP) bound to the ribosome. KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. KSRP also interacts with the r-protein eS6 at a region that is only conserved in kinetoplastids. The kinetoplastid-specific ribosomal environment of KSRP provides a promising target for the design of safer anti-kinetoplastidian drugs.},

keywords = {PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{kuhn_definition_2017b,

title = {Definition of a RACK1 Interaction Network in Drosophila melanogaster Using SWATH-MS},

author = {Lauriane Kuhn and Karim Majzoub and Evelyne Einhorn and Johana Chicher and Julien Pompon and Jean-Luc Imler and Philippe Hammann and Carine Meignin},

doi = {10.1534/g3.117.042564},

issn = {2160-1836},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {G3 (Bethesda)},

abstract = {Receptor for Activated C kinase 1 (RACK1) is a scaffold protein that has been found in association with several signaling complexes, and with the 40S subunit of the ribosome. Using the model organism Drosophila melanogaster, we recently showed that RACK1 is required at the ribosome for IRES-mediated translation of viruses. Here, we report a proteomic characterization of the interactome of RACK1 in Drosophila S2 cells. We carried out Label-Free quantitation using both Data-Dependent and Data-Independent Acquisition and observed a significant advantage for the Sequential Window Acquisition of all THeoretical fragment-ion spectra (SWATH) method both in terms of identification of interactants and quantification of low abundance proteins. These data represent the first SWATH spectral library available for Drosophila and will be a useful resource for the community. A total of 52 interacting proteins were identified, including several molecules involved in translation such as structural components of the ribosome, factors regulating translation initiation or elongation and RNA binding proteins. Among these 52 proteins, 15 were identified as partners by the SWATH strategy only. Interestingly, these 15 proteins are significantly enriched for the functions translation and nucleic acid binding. This enrichment reflects the engagement of RACK1 at the ribosome and highlights the added value of SWATH analysis. A functional screen did not reveal any protein sharing the interesting properties of RACK1, which is required for IRES-dependent translation and not essential for cell viability. Intriguingly however, 10 of the RACK1 partners identified restrict replication of Cricket paralysis virus, an IRES-containing virus.},

keywords = {meignin, PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{gross_ires5utr_2017,

title = {The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure},

author = {Lauriane Gross and Quentin Vicens and Evelyne Einhorn and Audrey Noireterre and Laure Schaeffer and Lauriane Kuhn and Jean-Luc Imler and Gilbert Eriani and Carine Meignin and Franck Martin},

doi = {10.1093/nar/gkx622},

issn = {1362-4962},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Nucleic Acids Research},

volume = {45},

number = {15},

pages = {8993--9004},

abstract = {Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.},

keywords = {meignin, PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{carapito_two_2017,

title = {Two proteomic methodologies for defining N-termini of mature human mitochondrial aminoacyl-tRNA synthetases.},

author = {Christine Carapito and Lauriane Kuhn and Loukmane Karim and Magali Rompais and Thierry Rabilloud and Hagen Schwenzer and Marie Sissler},

doi = {10.1016/j.ymeth.2016.10.012},

issn = {1095-9130 1046-2023},

year  = {2017},

date = {2017-01-01},

journal = {Methods (San Diego, Calif.)},

volume = {113},

pages = {111--119},

abstract = {Human mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are encoded in the nucleus, synthesized in the cytosol and targeted for importation into mitochondria by a N-terminal mitochondrial targeting sequence. This targeting sequence is presumably cleaved upon entry into the mitochondria, following a process still not fully deciphered in human, despite essential roles for the mitochondrial biogenesis. Maturation processes are indeed essential both for the release of a functional enzyme and to route correctly the protein within mitochondria. The absence of consensus sequences for cleavage sites and the discovery of possible multiple proteolytic steps render predictions of N-termini difficult. Further, the knowledge of the cleavages is key for the design of protein constructions compatible with efficient production in bacterial strains. Finally, full comprehension becomes essential because a growing number of mutations are found in genes coding for mt-aaRS. In the present study, we take advantage of proteomic methodological developments and identified, in mitochondria, three N-termini for the human mitochondrial aspartyl-tRNA synthetase. This first description of the co-existence of different forms opens new perspectives in the biological understanding of this enzyme. Those methods are extended to the whole set of human mt-aaRSs and methodological advice are provided for further investigations.},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}

@article{debard_nonconventional_2017,

title = {Nonconventional localizations of cytosolic aminoacyl-tRNA synthetases in yeast and human cells.},

author = {Sylvain Debard and Gaétan Bader and Johan-Owen De Craene and Ludovic Enkler and Séverine Bär and Daphné Laporte and Philippe Hammann and Evelyne Myslinski and Bruno Senger and Sylvie Friant and Hubert Dominique Becker},

doi = {10.1016/j.ymeth.2016.09.017},

issn = {1095-9130 1046-2023},

year  = {2017},

date = {2017-01-01},

journal = {Methods (San Diego, Calif.)},

volume = {113},

pages = {91--104},

abstract = {By definition, cytosolic aminoacyl-tRNA synthetases (aaRSs) should be restricted to the cytosol of eukaryotic cells where they supply translating ribosomes with their aminoacyl-tRNA substrates. However, it has been shown that other translationally-active compartments like mitochondria and plastids can simultaneously contain the cytosolic aaRS and its corresponding organellar ortholog suggesting that both forms do not share the same organellar function. In addition, a fair number of cytosolic aaRSs have also been found in the nucleus of cells from several species. Hence, these supposedly cytosolic-restricted enzymes have instead the potential to be multi-localized. As expected, in all examples that were studied so far, when the cytosolic aaRS is imported inside an organelle that already contains its bona fide corresponding organellar-restricted aaRSs, the cytosolic form was proven to exert a nonconventional and essential function. Some of these essential functions include regulating homeostasis and protecting against various stresses. It thus becomes critical to assess meticulously the subcellular localization of each of these cytosolic aaRSs to unravel their additional roles. With this objective in mind, we provide here a review on what is currently known about cytosolic aaRSs multi-compartmentalization and we describe all commonly used protocols and procedures for identifying the compartments in which cytosolic aaRSs relocalize in yeast and human cells.},

note = {Place: United States},

keywords = {PPSE},

pubstate = {published},

tppubtype = {article}

}