Yoann Augagneur - Academia.edu (original) (raw)

Papers by Yoann Augagneur

mSystems

Predicting the outcome of bacterial colonization and infections, based on extensive genomic and t... more Predicting the outcome of bacterial colonization and infections, based on extensive genomic and transcriptomic data from a given pathogen, would be of substantial help for clinicians in treating and curing patients. In this report, genome-wide association studies and random forest algorithms have defined gene combinations that differentiate human from animal strains, colonization from diseases, and nonsevere from severe diseases, while it revealed the importance of IGRs and CDS, but not small RNAs (sRNAs), in anticipating an outcome.

International Journal of Molecular Sciences

Staphylococcus aureus is a widespread livestock and human pathogen that colonizes diverse microen... more Staphylococcus aureus is a widespread livestock and human pathogen that colonizes diverse microenvironments within its host. Its adaptation to the environmental conditions encountered within humans relies on coordinated gene expression. This requires a sophisticated regulatory network, among which regulatory RNAs (usually called sRNAs) have emerged as key players over the last 30 years. In S. aureus, sRNAs regulate target genes at the post-transcriptional level through base–pair interactions. The functional characterization of a subset revealed that they participate in all biological processes, including virulence, metabolic adaptation, and antibiotic resistance. In this review, we report 30 years of S. aureus sRNA studies, from their discovery to the in-depth characterizations of some of them. We also discuss their actual in vivo contribution, which is still lagging behind, and their place within the complex regulatory network. These shall be key aspects to consider in order to cle...

Nucleic Acids Research, 2018

Bacterial type I toxin-antitoxin (TA) systems are widespread, and consist of a stable toxic pepti... more Bacterial type I toxin-antitoxin (TA) systems are widespread, and consist of a stable toxic peptide whose expression is monitored by a labile RNA antitoxin. We characterized Staphylococcus aureus SprA2/SprA2 AS module, which shares nucleotide similarities with the SprA1/SprA1 AS TA system. We demonstrated that SprA2/SprA2 AS encodes a functional type I TA system, with the cis-encoded SprA2 AS antitoxin acting in trans to prevent ribosomal loading onto SprA2 RNA. We proved that both TA systems are distinct, with no cross-regulation between the antitoxins in vitro or in vivo. SprA2 expresses PepA2, a toxic peptide which internally triggers bacterial death. Conversely, although PepA2 does not affect bacteria when it is present in the extracellular medium, it is highly toxic to other host cells such as polymorphonuclear neutrophils and erythrocytes. Finally, we showed that SprA2 AS expression is lowered during osmotic shock and stringent response, which indicates that the system responds to specific triggers. Therefore, the SprA2/SprA2 AS module is not redundant with SprA1/SprA1 AS , and its PepA2 peptide exhibits an original dual mode of action against bacteria and host cells. This suggests an altruistic behavior for S. aureus in which clones producing PepA2 in vivo shall die as they induce cytotoxicity, thereby promoting the success of the community.

We report the draft genome sequence of a Staphylococcus aureusNCTC8325 derivative, strain HG003. ... more We report the draft genome sequence of a Staphylococcus aureusNCTC8325 derivative, strain HG003. HG003 contains func-tional global regulators rsbU and tcaR and is therefore considered as a reference for studies of regulation and virulence. The ge-nome is composed of 2,797,898 bp and will be essential for subsequent RNAseq analysis.

10.1074/jbc.M111.268946 Access the most updated version of this article at doi: . JBC Affinity Si... more 10.1074/jbc.M111.268946 Access the most updated version of this article at doi: . JBC Affinity Sites Find articles, minireviews, Reflections and Classics on similar topics on the Alerts: When a correction for this article is posted • When this article is cited • to choose from all of JBC's e-mail alerts Click here http://www.jbc.org/content/286/33/28940.full.html#ref-list-1 This article cites 34 references, 16 of which can be accessed free at

L’objectif de la these est d’etudier les effets du metabolisme du L-malate et du citrate chez Oen... more L’objectif de la these est d’etudier les effets du metabolisme du L-malate et du citrate chez Oenococcus oeni et Lactococcus lactis. L’etude menee chez O. Oeni a mis en evidence une inhibition de la croissance en presence de citrate a pH bas, laquelle serait liee principalement a la production d’acide acetique. Dans une deuxieme partie du travail, la construction d’une souche de L. Lactis deficiente pour l’oxaloacetate decarboxylase a mis en evidence un ralentissement de la croissance en presence de citrate avec un effet plus important a pH bas. De plus, ce ralentissement ne serait pas liee en une alteration du maintien du pH intracellulaire mais plus vraisemblablement en une accumulation transitoire de l’oxaloacetate. L’etude plus approfondie de la toxicite de l’acetate et de l’effet de la mutation dans le gene codant l’oxaloacetate decarboxylase permettra une meilleure connaissance et comprehension du metabolisme des acides organiques chez les bacteries lactiques.

Frontiers in Microbiology, 2021

Bacterial gene expression is under the control of a large set of molecules acting at multiple lev... more Bacterial gene expression is under the control of a large set of molecules acting at multiple levels. In addition to the transcription factors (TFs) already known to be involved in global regulation of gene expression, small regulatory RNAs (sRNAs) are emerging as major players in gene regulatory networks, where they allow environmental adaptation and fitness. Developments in high-throughput screening have enabled their detection in the entire bacterial kingdom. These sRNAs influence a plethora of biological processes, including but not limited to outer membrane synthesis, metabolism, TF regulation, transcription termination, virulence, and antibiotic resistance and persistence. Almost always noncoding, they regulate target genes at the post-transcriptional level, usually through base-pair interactions with mRNAs, alone or with the help of dedicated chaperones. There is growing evidence that sRNA-mediated mechanisms of actions are far more diverse than initially thought, and that th...

Scientific Reports, 2017

Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and ... more Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and outbreaks. Regulatory RNAs (sRNAs) are major players in adaptive responses, including antibiotic resistance. They were extensively studied in gram-negative bacteria, but less information is available for gram-positive pathogens. No sRNAs are described in E. faecium. We sought to identify a set of sRNAs expressed in vancomycin-resistant E. faecium Aus0004 strain to assess their roles in daptomycin response and resistance. Genomic and transcriptomic analyses revealed a set of 61 sRNA candidates, including 10 that were further tested and validated by Northern and qPCR. RNA-seq was performed with and without subinhibitory concentrations (SICs) of daptomycin, an antibiotic used to treat enterococcal infections. After daptomycin SIC exposure, the expression of 260 coding and srna genes was altered, with 80 upregulated and 180 downregulated, including 51% involved in carbohydrate and transport metabolisms. Daptomycin SIC exposure significantly affected the expression of seven sRNAs, including one experimentally confirmed, sRNA_0160. We studied sRNA expression in isogenic mutants with increasing levels of daptomycin resistance and observed that expression of several sRNAs, including sRNA_0160, was modified in the stepwise mutants. This first genome-wide sRNA identification in E. faecium suggests that some sRNAs are linked to antibiotic stress response and resistance. Enterococci are commensals of the gastrointestinal microbiota of many animal species 1. Within the genus, Enterococcus faecalis and Enterococcus faecium have emerged as major opportunistic pathogens 2. They have become resistant to numerous antibiotics 3 , with the spread of vancomycin-resistant enterococci (VRE), especially in E. faecium 4. The latter is part of the ESKAPE (E. faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) group of major multidrug-resistant (MDR) nosocomial pathogens 5. E. faecium antimicrobial resistance is worrisome because of the dissemination of hospital-adapted clones belonging to the clonal complex 17 (CC17) 6. Epidemic CC17 strains are part of a human hospital-adapted lineage (clade A1) that emerged from the animal-associated lineage (clade A2) after the introduction of antibiotics, and which differs genetically from the human community-associated lineage (clade B) 7. Thanks to its huge genomic plasticity and metabolic versatility, E. faecium is a highly adapted commensal bacterial species that can turn into an opportunistic pathogen 8. Despite their paramount importance, the mechanisms involved in this physiological transition have not been adequately investigated 9 .

Scientific reports, Jan 4, 2017

The human pathogen Staphylococcus aureus expresses a set of transcriptional factors and small RNA... more The human pathogen Staphylococcus aureus expresses a set of transcriptional factors and small RNAs (sRNAs) to adapt to environmental variations. Recent harmonization of staphylococcal sRNA data allowed us to search for novel sRNAs using DETR'PROK, a computational pipeline for identifying sRNA in prokaryotes. We performed RNA-Seq on Newman strain and identified a set of 48 sRNA candidates. To avoid bioinformatic artefacts, we applied a series of cut-offs and tested experimentally each selected intergenic region. This narrowed the field to 24 expressed sRNAs, of which 21 were new and designated with Srn identifiers. Further examination of these loci revealed that one exhibited an unusual condensed sRNA cluster of about 650 nucleotides. We determined the transcriptional start sites within this region and demonstrated the presence of three contiguous sRNA genes (srn_9342, srn_9344 and srn_9345) expressed from the positive strand, and two others (srn_9343 and srn_9346) transcribed fr...

Http Www Theses Fr, 2007

Journal of Applied Microbiology, 2007

Aims: Citrate metabolism generates metabolic energy through the generation of a membrane potentia... more Aims: Citrate metabolism generates metabolic energy through the generation of a membrane potential and a pH gradient. The purpose of this work was to study the influence of oxaloacetate decarboxylase in citrate metabolism and intracellular pH maintenance in relation to acidic conditions. Methods and Results: A Lactococcus lactis oxaloacetate decarboxylase mutant [ILCitM (pFL3)] was constructed by double homologous recombination. During culture with citrate, and whatever the initial pH, the growth rate of the mutant was lower. In addition, the production of diacetyl and acetoin was altered in the mutant strain. However, our results indicated no relationship with a change in the maintenance of intracellular pH. Experiments performed on resting cells clearly showed that oxaloacetate accumulated temporarily in the supernatant of the mutant. This accumulation could be involved in the perturbations observed during citrate metabolism, as the addition of oxaloacetate in M17 medium inhibited the growth of L. lactis. Conclusions: The mutation of oxaloacetate decarboxylase perturbed citrate metabolism and reduced the benefits of its utilization during growth under acidic conditions. Significance and impact of the study: This study allows a better understanding of citrate metabolism and the role of oxaloacetate decarboxylase in the tolerance of lactic acid bacteria to acidic conditions.

Archives of Microbiology, 2007

In this study we analyzed under various pH conditions including low pH, the effects of L-malic ac... more In this study we analyzed under various pH conditions including low pH, the effects of L-malic acid and citric acid, combined or not, on the growth, the proton motive force components and the transcription level of selected genes of the heterolactic bacterium Oenococcus oeni. It is shown here that L-malate enhanced the growth yield at pH equal or below 4.5 while the presence of citrate in media led to a complete and unexpected inhibition of the growth at pH 3.2. Nevertheless, whatever the growth conditions, both L-malate and citrate participated in the enhancement of the transmembrane pH gradient, whereas the membrane potential decreased with the pH. These results suggested that it was not citrate that was directly responsible for the inhibition observed in cultures done at low pH, but probably its end products. This was confirmed since, in media containing L-malate, the addition of acetate substantially impaired the growth rate of the bacterium and slightly the membrane potential and pH gradient. Finally, study of the expression of genes involved in the metabolism of organic acids showed that at pH 4.5 and 3.2 the presence of L-malate led to an increased amount of mRNA of mleP encoding a malate transporter.

Molecular Microbiology, 2019

In Staphylococcus aureus, the transcription factor CodY modulates the expression of hundreds of g... more In Staphylococcus aureus, the transcription factor CodY modulates the expression of hundreds of genes, including most virulence factors, in response to the availability of key nutrients like GTP and branched-chain amino acids. Despite numerous studies examining how CodY controls gene expression directly or indirectly, virtually nothing is known about the extent to which CodY exerts its effect through small regulatory RNAs (sRNAs). Herein, we report the first set of sRNAs under the control of CodY. We reveal that staphylococcal sRNA RsaD is overexpressed >20-fold in a CodY-deficient strain in three S. aureus clinical isolates and in S. epidermidis. We validated CodY-dependent regulation of rsaD and demonstrate that CodY directly represses rsaD expression by binding the promoter. Using a combination of molecular techniques, we show that RsaD post-transcriptionally regulates alsS (acetolactate synthase) mRNA and enzyme levels. We further show that RsaD redirects carbon overflow metabolism, contributing to stationary phase cell death during exposure to weak acid stress. Taken together, our data delineate a role for CodY in controlling sRNA expression in a major human pathogen and indicate that RsaD may integrate nutrient depletion and other signals to mount a response to physiological stress experienced by S. aureus in diverse environments.

Genome Announcements, 2014

We report the draft genome sequence of a Staphylococcus aureus NCTC8325 derivative, strain HG003.... more We report the draft genome sequence of a Staphylococcus aureus NCTC8325 derivative, strain HG003. HG003 contains functional global regulators rsbU and tcaR and is therefore considered as a reference for studies of regulation and virulence. The genome is composed of 2,797,898 bp and will be essential for subsequent RNAseq analysis.

RNA, 2015

An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed an... more An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;Staphylococcal Regulatory RNA Database&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; (SRD, http://srd.genouest.org/) compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes novel and simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the sRNA&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s genetic location in S. aureus strain N315 which served as a reference. From a set of 894 sequences and after an in-depth cleaning, SRD provides a list of 575 srn exempt of redundant sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validity and significance. RNA-seq analysis performed on strains N315, NCTC8325, and Newman allowed us to provide further details, upgrade the initial annotation, and identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159 sRNAs sequences were used to predict the number and location of srns in 18 S. aureus strains and 10 other Staphylococci. A comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. In addition, sRNA structure predictions obtained with MFold are accessible. A BLAST server and the intaRNA program, which is dedicated to target prediction, were implemented. SRD is the first sRNA database centered on a genus; it is a user-friendly and scalable device with the possibility to submit new sequences that should spread in the literature.

Scientific Reports, 2015

Phosphoethanolamine methyltransferases (PMTs) catalyze the three-step methylation of phosphoethan... more Phosphoethanolamine methyltransferases (PMTs) catalyze the three-step methylation of phosphoethanolamine to form phosphocholine, a critical step in the synthesis of phosphatidylcholine in a select number of eukaryotes including human malaria parasites, nematodes and plants. Genetic studies in the malaria parasite Plasmodium falciparum have shown that the methyltransferase PfPMT plays a critical function in parasite development and differentiation. The presence of PMT orthologs in other malaria parasites that infect humans and their absence in mammals make them ideal targets for the development of selective antimalarials with broad specificity against different Plasmodium species. Here we describe the X-ray structures and biochemical properties of PMT orthologs from Plasmodium vivax and Plasmodium knowlesi and show that both enzymes are inhibited by amodiaquine and NSC158011, two drugs with potent antimalarial activity. Metabolic studies in a yeast mutant that relies on PkPMT or PvPMT for survival demonstrated that these compounds inhibit phosphatidylcholine biosynthesis from ethanolamine. Our structural and functional data provide insights into the mechanism of catalysis and inhibition of PMT enzymes and set the stage for a better design of more specific and selective antimalarial drugs. OPEN SUBJECT AREAS: X-RAY CRYSTALLOGRAPHY BIOCHEMISTRY PARASITE DEVELOPMENT

Genome announcements, 2015

We report here the draft genome sequence of Staphylococcus aureus subsp. aureus strain UAMS-1. UA... more We report here the draft genome sequence of Staphylococcus aureus subsp. aureus strain UAMS-1. UAMS-1 is a virulent oxacillin-susceptible clinical isolate. Its genome is composed of 2,763,963 bp and will be useful for further gene expression analysis using RNA sequencing (RNA-seq) technology.

Proceedings of the National Academy of Sciences, 2012

Unique peptide-morpholino oligomer (PMO) conjugates have been designed to bind and promote the cl... more Unique peptide-morpholino oligomer (PMO) conjugates have been designed to bind and promote the cleavage of specificm R N Aa s a tool to inhibit gene function and parasite growth. The new conjugates were validated using the P. falciparum gyrase mRNA as a target (PfGyrA). Assays in vitro demonstrated a selective degradation of the PfGyrA mRNA directed by the external guide sequences, which are morpholino oligomers in the conjugates. Fluorescence microscopy revealed that labeled conjugates are delivered into Plasmodium-infected erythrocytes during all intraerythrocytic stages of parasite development. Consistent with the expression of PfGyrA in all stages of parasite development, proliferation assays showed that these conjugates have potent antimalarial activity, blocking early development, maturation, and replication of the parasite. The conjugates were equally effective against drug sensitive and resistant P. falciparum strains. The potency, selectivity, and predicted safety of PMO conjugates make this approach attractive for the development of a unique class of target-specific antimalarials and for largescale functional analysis of the malarial genome.

Proceedings of the National Academy of Sciences, 2013

Efficient transmission of Plasmodium species between humans and Anopheles mosquitoes is a major c... more Efficient transmission of Plasmodium species between humans and Anopheles mosquitoes is a major contributor to the global burden of malaria. Gametocytogenesis, the process by which parasites switch from asexual replication within human erythrocytes to produce male and female gametocytes, is a critical step in malaria transmission and Plasmodium genetic diversity. Nothing is known about the pathways that regulate gametocytogenesis and only few of the current drugs that inhibit asexual replication are also capable of inhibiting gametocyte development and blocking malaria transmission. Here we provide genetic and pharmacological evidence indicating that the pathway for synthesis of phosphatidylcholine in Plasmodium falciparum membranes from host serine is essential for parasite gametocytogenesis and malaria transmission. Parasites lacking the phosphoethanolamine N-methyltransferase enzyme, which catalyzes the limiting step in this pathway, are severely altered in gametocyte development, are incapable of producing mature-stage gametocytes, and are not transmitted to mosquitoes. Chemical screening identified 11 inhibitors of phosphoethanolamine N-methyltransferase that block parasite intraerythrocytic asexual replication and gametocyte differentiation in the low micromolar range. Kinetic studies in vitro as well as functional complementation assays and lipid metabolic analyses in vivo on the most promising inhibitor NSC-158011 further demonstrated the specificity of inhibition. These studies set the stage for further optimization of NSC-158011 for development of a class of dual activity antimalarials to block both intraerythrocytic asexual replication and gametocytogenesis.