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1. Antigen specific activation of cytotoxic CD8+ T cells by Staphylococcus aureus infected dendritic cells

Author

Adèle Friot, Sophia Djebali, Séverine Valsesia, Peggy Parroche, Maxence Dubois, Jessica Baude, François Vandenesch, Jacqueline Marvel, and Yann Leverrier

Subjects
Staphylococcus aureus, antigen-specific activation, cytotoxic CD8+ T cells, DC2.4, dendritic cells, cytotoxicity, Microbiology, QR1-502
Abstract

Staphylococcus aureus (S. aureus) is a pathogen associated with a wide variety of diseases, from minor to life-threatening infections. Antibiotic-resistant strains have emerged, leading to increasing concern about the control of S. aureus infections. The development of vaccines may be one way to overcome these resistant strains. However, S. aureus ability to internalize into cells – and thus to form a reservoir escaping humoral immunity – is a challenge for vaccine development. A role of T cells in the elimination of persistent S. aureus has been established in mice but it remains to be established if CD8+ T cells could display a cytotoxic activity against S. aureus infected cells. We examined in vitro the ability of CD8+ T cells to recognize and kill dendritic cells infected with S. aureus. We first evidenced that both primary mouse dendritic cells and DC2.4 cell line can be infected with S. aureus. We then generated a strain of S. aureus expressing a model CD8 epitope and transgenic F5 CD8+ T cells recognizing this model epitope were used as reporter T cells. In response to S. aureus-infected dendritic cells, F5 CD8+ T cells produced IFN-γ in an antigen-specific manner and displayed an increased ability to kill infected cells. Altogether, these results demonstrate that cells infected by S. aureus display bacteria-derived epitopes at their surface that are recognized by CD8+ T cells. This paves the way for the development of CD8+ T cell-based therapies against S. aureus.

Published
2023
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2. Confocal spectral microscopy, a non-destructive approach to follow contamination and biofilm formation of mCherry Staphylococcus aureus on solid surfaces

Author

Muhammad Tanveer Munir, Nattar Maneewan, Julien Pichon, Mohammed Gharbia, Ismael Oumarou-Mahamane, Jessica Baude, Chantal Thorin, Didier Lepelletier, Patrice Le Pape, Matthieu Eveillard, Mark Irle, Hélène Pailhoriès, Florence Aviat, Christophe Belloncle, Michel Federighi, and Laurence Dubreil

Subjects
Medicine, Science
Abstract

Abstract Methods to test the safety of wood material for hygienically sensitive places are indirect, destructive and limited to incomplete microbial recovery via swabbing, brushing and elution-based techniques. Therefore, we chose mCherry Staphylococcus aureus as a model bacterium for solid and porous surface contamination. Confocal spectral laser microscope (CSLM) was employed to characterize and use the autofluorescence of Sessile oak (Quercus petraea), Douglas fir (Pseudotsuga menziesii) and poplar (Populus euramericana alba L.) wood discs cut into transversal (RT) and tangential (LT) planes. The red fluorescent area occupied by bacteria was differentiated from that of wood, which represented the bacterial quantification, survival and bio-distribution on surfaces from one hour to one week after inoculation. More bacteria were present near the surface on LT face wood as compared to RT and they persisted throughout the study period. Furthermore, this innovative methodology identified that S. aureus formed a dense biofilm on melamine but not on oak wood in similar inoculation and growth conditions. Conclusively, the endogenous fluorescence of materials and the model bacterium permitted direct quantification of surface contamination by using CSLM and it is a promising tool for hygienic safety evaluation.

Published
2021
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3. Correction: The TIR Homologue Lies near Resistance Genes in Staphylococcus aureus, Coupling Modulation of Virulence and Antimicrobial Susceptibility.

Author

Sabine Patot, Paul R C Imbert, Jessica Baude, Patricia Martins Simões, Jean-Baptiste Campergue, Arthur Louche, Reindert Nijland, Michèle Bès, Anne Tristan, Frédéric Laurent, Adrien Fischer, Jacques Schrenzel, François Vandenesch, Suzana P Salcedo, Patrice François, and Gérard Lina

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

[This corrects the article DOI: 10.1371/journal.ppat.1006092.].

Published
2017
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4. The TIR Homologue Lies near Resistance Genes in Staphylococcus aureus, Coupling Modulation of Virulence and Antimicrobial Susceptibility.

Author

Sabine Patot, Paul Imbert, Jessica Baude, Patricia Martins Simões, Jean-Baptiste Campergue, Arthur Louche, Reindert Nijland, Michèle Bès, Anne Tristan, Frédéric Laurent, Adrien Fischer, Jacques Schrenzel, François Vandenesch, Suzana Salcedo, Patrice François, and Gérard Lina

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

Toll/interleukin-1 receptor (TIR) domains in Toll-like receptors are essential for initiating and propagating the eukaryotic innate immune signaling cascade. Here, we investigate TirS, a Staphylococcus aureus TIR mimic that is part of a novel bacterial invasion mechanism. Its ectopic expression in eukaryotic cells inhibited TLR signaling, downregulating the NF-kB pathway through inhibition of TLR2, TLR4, TLR5, and TLR9. Skin lesions induced by the S. aureus knockout tirS mutant increased in a mouse model compared with wild-type and restored strains even though the tirS-mutant and wild-type strains did not differ in bacterial load. TirS also was associated with lower neutrophil and macrophage activity, confirming a central role in virulence attenuation through local inflammatory responses. TirS invariably localizes within the staphylococcal chromosomal cassettes (SCC) containing the fusC gene for fusidic acid resistance but not always carrying the mecA gene. Of note, sub-inhibitory concentration of fusidic acid increased tirS expression. Epidemiological studies identified no link between this effector and clinical presentation but showed a selective advantage with a SCCmec element with SCC fusC/tirS. Thus, two key traits determining the success and spread of bacterial infections are linked.

Published
2017
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5. What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii

Author

Maïwenn Pineau, B. Shiny Martis, Raphaël Forquet, Jessica Baude, Camille Villard, Lucie Grand, Florence Popowycz, Laurent Soulère, Florence Hommais, William Nasser, Sylvie Reverchon, and Sam Meyer

Subjects
Genetics, DNA, Bacterial, biology, Chemistry, DNA, Superhelical, Topoisomerase, Circular bacterial chromosome, Promoter, biology.organism_classification, DNA gyrase, Dickeya dadantii, Anti-Bacterial Agents, chemistry.chemical_compound, DNA Topoisomerases, Type I, Enterobacteriaceae, DNA Gyrase, biology.protein, DNA supercoil, Gene, DNA
Abstract

DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by gyrase inhibition were categorised as “supercoiling-sensitive”. Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine. We showed that the drug is active against topoisomerase I from this species, and analysed the first transcriptomic response of a Gram-negative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in terms of expression level, spatial and orientational organisation along the chromosome. Altogether, these results highlight that the supercoiling-sensitivity is a complex feature, which depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after gyrase or topoisomerase I inhibition.

Published
2022

6. NorK, a novel norfloxacin efflux pump in Staphylococcus aureus

Author

S. Bastien, François Vandenesch, Laura Camus, Karen Moreau, Paul Briaud, and Jessica Baude

Subjects
Chemistry, Staphylococcus aureus, medicine, Gene family, Efflux, medicine.disease_cause, Gene, Norfloxacin, Microbiology, medicine.drug
Abstract

A novel efflux pump similar to Nor efflux pumps and designated as NorK was identified in Staphylococcus aureus. It contributes to norfloxacin resistance and presents a high level of expression in different strains. Its expression is not regulated by MgrA, unlike other genes of the nor gene family, suggesting that NorK could be important in the absence of expression of other nor genes.

Published
2019
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7. Necrotizing Soft Tissue Infections Staphylococcus aureus - but not Streptococcus pyogenes-isolates display high rate of internalization and cytotoxicity toward human myoblasts

Author

Thomas Henry, Pascal Leblanc, Michèle Bes, Yves Gillet, Andreas Itzek, Binh An Diep, Sylvère Bastien, François Vandenesch, Anne Tristan, Anna Norrby-Teglund, Jessica Baude, Stephanie Duguez, and Karen Moreau

Subjects
Pyomyositis, Streptococcus, media_common.quotation_subject, Biology, medicine.disease_cause, medicine.disease, Group A, Microbiology, Staphylococcus aureus, Streptococcus pyogenes, medicine, Coagulase, Internalization, Tropism, media_common
Abstract

Necrotizing Soft Tissue Infections (NSTIs), often reaching the deep fascia and muscle, are mainly caused by group A Streptococcus (GAS) and to a lesser extent by Staphylococcus aureus (SA). Conversely SA is a leading etiologic agent of pyomyositis suggesting that SA could have a specific tropism for the muscle. To assess the pathogenicity of these two bacterial species for muscles cells in comparison to keratinocytes, adhesion and invasion of NSTI-GAS and NSTI-SA were assessed on these cells. Bloodstream infections (BSI) SA isolates and non-invasive coagulase negative Staphylococci (CNS) isolates were used as controls.SA isolates from NSTI and from BSI exhibited stronger internalization into human keratinocytes and myoblasts than CNS or NSTI-GAS. While the median level of SA internalization culminated at 2% in human keratinocytes, it reached over 30% in human myoblasts due to a higher percentage of infected myoblasts (>11%) as compared to keratinocytes (psmα and RNAIII transcripts in NSTI group as compared to hematogenous group. However, the two groups were not discriminated at the genomic level. The cellular basis of high internalization rate in myoblasts was attributed to higher expression of α5β1 integrin in myoblasts as compared to keratinocytes. Major contribution of FnbpAB-integrin α5β1 pathway to internalization was confirmed by isogenic mutants.Our findings suggest the contribution of NSTI-SA severity by its unique propensity to invade and kill myoblasts, a property not shared by NSTI-GAS.ImportanceNecrotizing Soft Tissue Infection (NSTI) is a severe infection caused mainly by group A Streptococcus (GAS) and occasionally by S. aureus (SA); the latter being more often associated with pyomyositis. NSTIs frequently involve the deep fascia and may provoke muscle necrosis. The goal of this study was to determine the tropism and pathogenicity of these two bacterial species for muscle cells. The results revealed a high tropism of SA for myoblasts and myotubes followed by cytotoxicity as opposed to GAS that did not invade these cells. This study uncover a novel mechanism of SA contribution to NSTI with a direct muscle involvement, while in GAS NSTI this is likely indirect, for instance, secondary to vascular occlusion.

Published
2019
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9. Impact of Currently Marketed Tampons and Menstrual Cups on Staphylococcus aureus Growth and Toxic Shock Syndrome Toxin 1 Production In Vitro

Author

Louis Nonfoux, Jean Thioulouse, Jessica Baude, Daniel Muller, Cédric Badiou, Myriam Chiaruzzi, Anne Tristan, Claire Prigent-Combaret, Gerard Lina, Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Physiology, medicine.disease_cause, Applied Microbiology and Biotechnology, law.invention, Enterotoxins, 0302 clinical medicine, law, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, [STAT.AP]Statistics [stat]/Applications [stat.AP], Superantigens, Ecology, Public and Environmental Health Microbiology, Staphylococcal Infections, Shock, Septic, Staphylococcus aureus, Shock (circulatory), Vagina, Toxic shock syndrome toxin-1, Female, medicine.symptom, [STAT.ME]Statistics [stat]/Methodology [stat.ME], [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], Biotechnology, Tampon, 030106 microbiology, Bacterial Toxins, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, medicine, Humans, Cotton Fiber, Menstrual Hygiene Products, business.industry, Toxin, Toxic shock syndrome, medicine.disease, equipment and supplies, In vitro, Culture Media, Oxygen, Menstrual cup, Biofilms, business, Food Science, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Fifteen currently marketed intravaginal protection products (11 types of tampon and 4 types of menstrual cup) were tested by the modified tampon sac method to determine their effect on Staphylococcus aureus growth and toxic shock syndrome toxin 1 (TSST-1) production. Most tampons reduced S. aureus growth and TSST-1 production, with differences based on brand and composition, and the level of S. aureus growth was higher in destructured than in unaltered tampons. We observed higher levels of S. aureus growth and toxin production in menstrual cups than in tampons, potentially due to the additional air introduced into the bag by cups, with differences based on cup composition and size. IMPORTANCE Menstrual toxic shock syndrome is a rare but severe disease. It occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock syndrome toxin 1 using intravaginal protection, such as tampons or menstrual cups. Intravaginal protection induces TSS by the collection of catamenial products, which act as a growth medium for S. aureus . Previous studies evaluated the impact of tampon composition on S. aureus producing toxic shock syndrome toxin 1, but they are not recent and did not include menstrual cups. This study demonstrates that highly reproducible results for S. aureus growth and TSST-1 production can be obtained by using a simple protocol that reproduces the physiological conditions of tampon and cup usage as closely as possible, providing recommendations for tampon or cup use to both manufacturers and consumers. Notably, our results do not show that menstrual cups are safer than tampons and suggest that they require similar precautions.

Published
2018

10. The TIR Homologue Lies near Resistance Genes in Staphylococcus aureus, Coupling Modulation of Virulence and Antimicrobial Susceptibility

Author

Jacques Schrenzel, Adrien Nicolas Fischer, Reindert Nijland, Arthur Louche, Anne Tristan, Sabine Patot, Patrice Francois, François Vandenesch, Jessica Baude, Suzana P. Salcedo, Gerard Lina, Paul R. C. Imbert, Michèle Bes, Jean-Baptiste Campergue, Patricia Martins Simoes, Frédéric Laurent, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, University Medical Center [Utrecht], Wageningen University and Research [Wageningen] (WUR), Hôpitaux Universitaires de Genève (HUG), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Staphylococcus, Pathology and Laboratory Medicine, Biochemistry, Toll-Like Receptors/genetics, Mice, Bacterial Proteins/genetics/immunology, Biology (General), Immune Response, ddc:616, Membrane Glycoproteins, Effector, Toll-Like Receptors, 3. Good health, Bacterial Pathogens, Staphylococcus aureus, Medical Microbiology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, QH301-705.5, Virulence Factors, Knockout, 030106 microbiology, Immunology, Virulence, Microbiology, digestive system, 03 medical and health sciences, Signs and Symptoms, Bacterial Proteins, Genetics, Humans, Penicillin-Binding Proteins, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, Staphylococcal Skin Infections/drug therapy/microbiology, Signal Transduction/immunology, Bacteria, Animal, Macrophages, Neutrophils/immunology, Organisms, Biology and Life Sciences, Proteins, Receptors, Interleukin-1/genetics/immunology, Receptors, Interleukin-1, Correction, biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Laboratorium voor Phytopathologie, Mice, Inbred C57BL, TLR2, 030104 developmental biology, Virulence Factors/genetics/immunology, Laboratory of Phytopathology, Lesions, Parasitology, Immunologic diseases. Allergy, EPS, Fusidic Acid, Cloning, 0301 basic medicine, Penicillin-Binding Proteins/genetics, Neutrophils, Macrophages/immunology, medicine.disease_cause, Inbred C57BL, Immune Receptors, Receptors, Medicine and Health Sciences, Mice, Knockout, Immune System Proteins, Animal Models, Membrane Glycoproteins/genetics/immunology, Infectious Diseases, Experimental Organism Systems, Fusidic Acid/pharmacology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Methicillin-resistant Staphylococcus aureus, Staphylococcal Skin Infections, Signal transduction, Pathogens, Research Article, Signal Transduction, Skin Infections, Mouse Models, Dermatology, Biology, Research and Analysis Methods, Cell Line, Model Organisms, Diagnostic Medicine, Virology, parasitic diseases, medicine, Life Science, Animals, Myeloid Differentiation Factor 88/deficiency/genetics, Inflammation, Innate immune system, SCCmec, Staphylococcus aureus/genetics/immunology/pathogenicity, Cell Biology, RC581-607, Disease Models, Animal, HEK293 Cells, Disease Models, Myeloid Differentiation Factor 88, Ectopic expression, Interleukin-1
Abstract

Toll/interleukin-1 receptor (TIR) domains in Toll-like receptors are essential for initiating and propagating the eukaryotic innate immune signaling cascade. Here, we investigate TirS, a Staphylococcus aureus TIR mimic that is part of a novel bacterial invasion mechanism. Its ectopic expression in eukaryotic cells inhibited TLR signaling, downregulating the NF-kB pathway through inhibition of TLR2, TLR4, TLR5, and TLR9. Skin lesions induced by the S. aureus knockout tirS mutant increased in a mouse model compared with wild-type and restored strains even though the tirS-mutant and wild-type strains did not differ in bacterial load. TirS also was associated with lower neutrophil and macrophage activity, confirming a central role in virulence attenuation through local inflammatory responses. TirS invariably localizes within the staphylococcal chromosomal cassettes (SCC) containing the fusC gene for fusidic acid resistance but not always carrying the mecA gene. Of note, sub-inhibitory concentration of fusidic acid increased tirS expression. Epidemiological studies identified no link between this effector and clinical presentation but showed a selective advantage with a SCCmec element with SCC fusC/tirS. Thus, two key traits determining the success and spread of bacterial infections are linked., Author Summary Pathogenic microbes have evolved elaborate strategies to manipulate host defenses to establish and spread in the host population. One such mechanism involves disruption of the immune signaling cascade orchestrated by the Toll-like receptors (TLRs), which sense microbial attack. TLR signaling elicits a proinflammatory response that controls immune cell recruitment to infected tissues. Here, we show that Staphylococcus aureus, an opportunistic human pathogen, expresses a host defense–like protein, TirS, that actively perturbs the initial TLR activation stage. Results with isolated human cells and mouse models show that TirS is a broad innate immune inhibitor of TLR-dependent signaling and modulates bacterial virulence, attenuating local inflammation. Moreover, the tirS gene lies near antimicrobial resistance genes for an antibiotic that enhances TirS production, shifting the balance to favor the pathogen and promote disease. Understanding mechanisms by which S. aureus modulates the immune response may lead to novel approaches for preventing and treating infection.

Published
2017

11. Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum

Author

Florence Hommais, Ludovic Vial, Camille Villard, Jessica Baude, Xavier Nesme, Céline Lavire, Tony Campillo, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), EcoGenome project of the French Agence Nationale de la Recherche ANR-BLAN 08-0090, French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)

Subjects
0301 basic medicine, Siderophore, Coumaric Acids, Operon, Iron, Siderophores, Genetics and Molecular Biology, Applied Microbiology and Biotechnology, Ferulic acid, 03 medical and health sciences, chemistry.chemical_compound, Gene expression, Gene, Biotransformation, Regulation of gene expression, chemistry.chemical_classification, Ecology, biology, Chemistry, Gene Expression Profiling, Bacterial, Agrobacterium tumefaciens, Gene Expression Regulation, Bacterial, Hydroxycinnamic acid, biology.organism_classification, Microarray Analysis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Culture Media, 030104 developmental biology, Biochemistry, Gene Expression Regulation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Metabolic Networks and Pathways, Food Science, Biotechnology
Abstract

The rhizosphere-inhabiting species Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (HCAs), especially ferulic acid and p -coumaric acid, via the novel A. fabrum HCA degradation pathway. Gene expression profiles of A. fabrum strain C58 were investigated in the presence of HCAs, using a C58 whole-genome oligoarray. Both ferulic acid and p -coumaric acid caused variations in the expression of more than 10% of the C58 genes. Genes of the A. fabrum HCA degradation pathway, together with the genes involved in iron acquisition, were among the most highly induced in the presence of HCAs. Two operons coding for the biosynthesis of a particular siderophore, as well as genes of the A. fabrum HCA degradation pathway, have been described as being specific to the species. We demonstrate here their coordinated expression, emphasizing the interdependence between the iron concentration in the growth medium and the rate at which ferulic acid is degraded by cells. The coordinated expression of these functions may be advantageous in HCA-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. The present results confirm that there is cooperation between the A. fabrum -specific genes, defining a particular ecological niche. IMPORTANCE We previously identified seven genomic regions in Agrobacterium fabrum that were specifically present in all of the members of this species only. Here we demonstrated that two of these regions, encoding the hydroxycinnamic acid degradation pathway and the iron acquisition pathway, were regulated in a coordinated manner. The coexpression of these functions may be advantageous in hydroxycinnamic acid-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. These data support the view that bacterial genomic species emerged from a bacterial population by acquiring specific functions that allowed them to outcompete their closest relatives. In conclusion, bacterial species could be defined not only as genomic species but also as ecological species.

Published
2016

12. Analysis of hydroxycinnamic acid degradation in Agrobacterium fabrum reveals a coenzyme A-dependent, beta-oxidative deacetylation pathway

Author

Sébastien Renoud, Cécile Chamignon, Florence Hommais, Jessica Baude, Isabelle Kerzaon, Céline Lavire, Ludovic Vial, Tony Campillo, Xavier Nesme, Floriant Bellvert, Vincent Gaillard, Gilles Comte, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Synthèse et étude de systèmes à intêret biologique (SEESIB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Matériaux Polymères (IMP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Microbiologie, adaptation et pathogénie ( MAP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Ingénierie des Matériaux Polymères - Site INSA Lyon ( IMP ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Lyon, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, EcoGenome project of the French Agence Nationale de la Recherche [ANR-BLAN-08-0090], French Ministere de l'Education Nationale de l'Enseignement Superieur et de la Recherche, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, and École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Coumaric Acids, Agrobacterium, Coenzyme A, [SDV]Life Sciences [q-bio], [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, Genetics and Molecular Biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Applied Microbiology and Biotechnology, Protocatechuic acid, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Ferulic acid, 03 medical and health sciences, chemistry.chemical_compound, Vanillic acid, Caffeic acid, Hydroxybenzoates, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Biotransformation, 030304 developmental biology, chemistry.chemical_classification, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Ecology, biology, 030306 microbiology, Agrobacterium tumefaciens, 15. Life on land, Plants, biology.organism_classification, Hydroxycinnamic acid, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, chemistry, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Metabolic Networks and Pathways, Food Science, Biotechnology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

The soil- and rhizosphere-inhabiting bacterium Agrobacterium fabrum (genomospecies G8 of the Agrobacterium tumefaciens species complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl–CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl–CoA, vanillic acid, and protocatechuic acid. The genes atu1416 , atu1417 , and atu1420 have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genes atu1415 and atu1421 have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)–CoA β-keto-thiolase, respectively. We thus demonstrated that the A. fabrum hydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transform p -coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.

Published
2014

13. Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes

Author

Patrick Wincker, Didier Doillon, Michel Chalot, Laurence Fraissinet-Tachet, Damien Blaudez, Lamia Harfouche, Jessica Baude, Sandrine Perrotto, Corinne Da Silva, Elise David, Roland Marmeisse, Julie Poulain, Laurent Vallon, Jan V. Colpaert, Julie Foulon, Frédéric Lehembre, Christine Oger-Desfeux, and Pierre Richaud

Subjects
Genetics, 0303 health sciences, biology, 030306 microbiology, Saccharomyces cerevisiae, RNA, Sequence alignment, Context (language use), biology.organism_classification, Microbiology, Phenotype, Yeast, 03 medical and health sciences, Genomic library, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

Heavy metals are pollutants which affect all organisms. Since a small number of eukaryotes have been investigated with respect to metal resistance, we hypothesize that many genes that control this phenomenon remain to be identified. This was tested by screening soil eukaryotic metatranscriptomes which encompass RNA from organisms belonging to the main eukaryotic phyla. Soil-extracted polyadenylated mRNAs were converted into cDNAs and 35 of them were selected for their ability to rescue the metal (Cd or Zn) sensitive phenotype of yeast mutants. Few of the genes belonged to families known to confer metal resistance when overexpressed in yeast. Several of them were homologous to genes that had not been studied in the context of metal resistance. For instance, the BOLA ones, which conferred cross metal (Zn, Co, Cd, Mn) resistance may act by interfering with Fe homeostasis. Other genes, such as those encoding 110- to 130-amino-acid-long, cysteine-rich polypeptides, had no homologues in databases. This study confirms that functional metatranscriptomics represents a powerful approach to address basic biological processes in eukaryotes. The selected genes can be used to probe new pathways involved in metal homeostasis and to manipulate the resistance level of selected organisms.

Published
2013

14. Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes

Author

Frédéric, Lehembre, Didier, Doillon, Elise, David, Sandrine, Perrotto, Jessica, Baude, Julie, Foulon, Lamia, Harfouche, Laurent, Vallon, Julie, Poulain, Corinne, Da Silva, Patrick, Wincker, Christine, Oger-Desfeux, Pierre, Richaud, Jan V, Colpaert, Michel, Chalot, Laurence, Fraissinet-Tachet, Damien, Blaudez, and Roland, Marmeisse

Subjects
Gene Expression Profiling, Metals, Heavy, Yeasts, Molecular Sequence Data, Drug Resistance, Eukaryota, Genetic Variation, Soil Pollutants, Soil Microbiology, Gene Library
Abstract

Heavy metals are pollutants which affect all organisms. Since a small number of eukaryotes have been investigated with respect to metal resistance, we hypothesize that many genes that control this phenomenon remain to be identified. This was tested by screening soil eukaryotic metatranscriptomes which encompass RNA from organisms belonging to the main eukaryotic phyla. Soil-extracted polyadenylated mRNAs were converted into cDNAs and 35 of them were selected for their ability to rescue the metal (Cd or Zn) sensitive phenotype of yeast mutants. Few of the genes belonged to families known to confer metal resistance when overexpressed in yeast. Several of them were homologous to genes that had not been studied in the context of metal resistance. For instance, the BOLA ones, which conferred cross metal (Zn, Co, Cd, Mn) resistance may act by interfering with Fe homeostasis. Other genes, such as those encoding 110- to 130-amino-acid-long, cysteine-rich polypeptides, had no homologues in databases. This study confirms that functional metatranscriptomics represents a powerful approach to address basic biological processes in eukaryotes. The selected genes can be used to probe new pathways involved in metal homeostasis and to manipulate the resistance level of selected organisms.

Published
2012

15. Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Author

Daniel Muller, Malek Shams, Céline Lavire, Christine Oger-Desfeux, Xavier Nesme, Jessica Baude, Laurent Guéguen, Ludovic Vial, Denis Costechareyre, Tony Campillo, Danis Abrouk, Vincent Daubin, Florent Lassalle, Florence Hommais, David Chapulliot, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Microbiologie, adaptation et pathogénie (MAP), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Pôle Rhône-Alpin de BioInformatique [Lyon] (PRABI), Université de Lyon-Université de Lyon, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Microbiologie, adaptation et pathogénie ( MAP ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), PRABI, and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
AD-HOC-COMMITTEE, EVOLUTIONARY BIOLOGY, Adaptation, Biological, Agrobacterium, Genome, C58, bacterial species, GENETICS & HEREDITY, Research Articles, Phylogeny, Genetics, bactérie, évolution biologique, 0303 health sciences, biology, TI PLASMIDS, Ecology, Genomovar, Genomics, FAMILY, BACTERIA, Life Sciences & Biomedicine, Species complex, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], GENES, Genetic Speciation, Molecular Sequence Data, linear chromosome, bacterial evolution, Evolution, Molecular, 03 medical and health sciences, 0603 Evolutionary Biology, Bacterial Proteins, phylogénie, ecological niche, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Ecological niche, 0604 Genetics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, écologie microbienne, Science & Technology, 030306 microbiology, biology.organism_classification, EVOLUTION, SP NOV, RHIZOBIUM-LEGUMINOSARUM, Agrobacterium tumefaciens, Hypothetical species, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, FERULIC ACID, Genome, Bacterial, Developmental Biology
Abstract

International audience; The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome--one on the circular chromosome and six on the linear chromosome--suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.

Published
2011

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