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Gopalan-Nair R, Coissac A, Legrand L, Lopez-Roques C, Pécrix Y, Vandecasteele C, Bouchez O, Barlet X, Lanois A, Givaudan A, Brillard J, Genin S, Guidot A. Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution. PLoS Biol 2024; 22:e3002792. [PMID: 39302959 DOI: 10.1371/journal.pbio.3002792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 08/07/2024] [Indexed: 09/22/2024] Open
Abstract
Adaptation is usually explained by beneficial genetic mutations that are transmitted from parents to offspring and become fixed in the adapted population. However, genetic mutation analysis alone is not sufficient to fully explain the adaptive processes, and several studies report the existence of nongenetic (or epigenetic) inheritance that can enable adaptation to new environments. In the present work, we tested the hypothesis of the role of DNA methylation, a form of epigenetic modification, in adaptation of the plant pathogen Ralstonia pseudosolanacearum to the host during experimental evolution. Using SMRT-seq technology, we analyzed the methylomes of 31 experimentally evolved clones obtained after serial passages on 5 different plant species during 300 generations. Comparison with the methylome of the ancestral clone revealed a list of 50 differential methylated sites (DMSs) at the GTWWAC motif. Gene expression analysis of the 39 genes targeted by these DMSs revealed limited correlation between differential methylation and differential expression of the corresponding genes. Only 1 gene showed a correlation, the RSp0338 gene encoding the EpsR regulator protein. The MSRE-qPCR technology, used as an alternative approach for DNA methylation analysis, also found the 2 DMSs upstream RSp0338. Using site-directed mutagenesis, we demonstrated the contribution of these 2 DMSs in host adaptation. As these DMSs appeared very early in the experimental evolution, we hypothesize that such fast epigenetic changes can allow rapid adaptation to the plant stem environment. In addition, we found that the change in DNA methylation upstream RSp0338 remains stable at least for 100 generations outside the host and thus can contribute to long-term adaptation to the host plant. To our knowledge, this is the first study showing a direct link between bacterial epigenetic variation and adaptation to a new environment.
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Affiliation(s)
| | - Aurore Coissac
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Ludovic Legrand
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Yann Pécrix
- PVBMT, Université de La Réunion, CIRAD, Saint-Pierre, Réunion Island, France
| | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRAE, US1426, Castanet-Tolosan, France
| | - Xavier Barlet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Anne Lanois
- DGIMI, Université de Montpellier, INRAE, Montpellier, France
| | - Alain Givaudan
- DGIMI, Université de Montpellier, INRAE, Montpellier, France
| | - Julien Brillard
- DGIMI, Université de Montpellier, INRAE, Montpellier, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alice Guidot
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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Bientz V, Lanois A, Ginibre N, Pagès S, Ogier JC, George S, Rialle S, Brillard J. OxyR is required for oxidative stress resistance of the entomopathogenic bacterium Xenorhabdus nematophila and has a minor role during the bacterial interaction with its hosts. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001481. [PMID: 39058385 PMCID: PMC11281485 DOI: 10.1099/mic.0.001481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024]
Abstract
Xenorhabdus nematophila is a Gram-negative bacterium, mutualistically associated with the soil nematode Steinernema carpocapsae, and this nemato-bacterial complex is parasitic for a broad spectrum of insects. The transcriptional regulator OxyR is widely conserved in bacteria and activates the transcription of a set of genes that influence cellular defence against oxidative stress. It is also involved in the virulence of several bacterial pathogens. The aim of this study was to identify the X. nematophila OxyR regulon and investigate its role in the bacterial life cycle. An oxyR mutant was constructed in X. nematophila and phenotypically characterized in vitro and in vivo after reassociation with its nematode partner. OxyR plays a major role during the X. nematophila resistance to oxidative stress in vitro. Transcriptome analysis allowed the identification of 59 genes differentially regulated in the oxyR mutant compared to the parental strain. In vivo, the oxyR mutant was able to reassociate with the nematode as efficiently as the control strain. These nemato-bacterial complexes harbouring the oxyR mutant symbiont were able to rapidly kill the insect larvae in less than 48 h after infestation, suggesting that factors other than OxyR could also allow X. nematophila to cope with oxidative stress encountered during this phase of infection in insect. The significantly increased number of offspring of the nemato-bacterial complex when reassociated with the X. nematophila oxyR mutant compared to the control strain revealed a potential role of OxyR during this symbiotic stage of the bacterial life cycle.
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Affiliation(s)
| | - Anne Lanois
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France
| | | | - Sylvie Pagès
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France
| | | | - Simon George
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
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Hadchity L, Houard J, Lanois A, Payelleville A, Nassar F, Gualtieri M, Givaudan A, Abi Khattar Z. The AcrAB efflux pump confers self-resistance to stilbenes in Photorhabdus laumondii. Res Microbiol 2023; 174:104081. [PMID: 37196776 DOI: 10.1016/j.resmic.2023.104081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
The Resistance-nodulation-division (RND)-type AcrAB-TolC efflux pump contributes to multidrug resistance in Gram-negative bacteria. Recently, the bacterium Photorhabdus laumondii TT01 has emerged as a goldmine for novel anti-infective drug discovery. Outside plants, Photorhabdus is the only Gram-negative known to produce stilbene-derivatives including 3,5-dihydroxy-4-ethyl-trans-stilbene and 3,5-dihydroxy-4-isopropyl-trans-stilbene (IPS). IPS is a bioactive polyketide which received considerable attention, mainly because of its antimicrobial properties, and is currently in late-stage clinical development as a topical treatment for psoriasis and dermatitis. To date, little is known about how Photorhabdus survives in the presence of stilbenes. We combined genetic and biochemical approaches to assess whether AcrAB efflux pump exports stilbenes in P. laumondii. We demonstrated that the wild-type (WT) exerts an antagonistic activity against its derivative ΔacrA mutant, and that is able to outcompete it in a dual-strain co-culture assay. The ΔacrA mutant also showed high sensitivity to 3,5-dihydroxy-4-ethyl-trans-stilbene and IPS as well as decreased IPS concentrations in its supernatant comparing to the WT. We report here a mechanism of self-resistance against stilbene derivatives of P. laumondii TT01, which enables these bacteria to survive under high concentrations of stilbenes by extruding them out via the AcrAB efflux pump.
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Affiliation(s)
- Linda Hadchity
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon; DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | | | - Anne Lanois
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Amaury Payelleville
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium.
| | - Fida Nassar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
| | | | - Alain Givaudan
- DGIMI, Université Montpellier, INRAE, Montpellier, France.
| | - Ziad Abi Khattar
- Laboratory of Georesources, Geosciences and Environment (L2GE), Microbiology/Tox-Ecotoxicology Team, Faculty of Sciences 2, Lebanese University, P.O.Box 90656, Jdeidet El-Metn, Lebanon.
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Ginibre N, Legrand L, Bientz V, Ogier JC, Lanois A, Pages S, Brillard J. Diverse Roles for a Conserved DNA-Methyltransferase in the Entomopathogenic Bacterium Xenorhabdus. Int J Mol Sci 2022; 23:ijms231911981. [PMID: 36233296 PMCID: PMC9570324 DOI: 10.3390/ijms231911981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022] Open
Abstract
In bacteria, DNA-methyltransferase are responsible for DNA methylation of specific motifs in the genome. This methylation usually occurs at a very high rate. In the present study, we studied the MTases encoding genes found in the entomopathogenic bacteria Xenorhabdus. Only one persistent MTase was identified in the various species of this genus. This MTase, also broadly conserved in numerous Gram-negative bacteria, is called Dam: DNA-adenine MTase. Methylome analysis confirmed that the GATC motifs recognized by Dam were methylated at a rate of >99% in the studied strains. The observed enrichment of unmethylated motifs in putative promoter regions of the X. nematophila F1 strain suggests the possibility of epigenetic regulations. The overexpression of the Dam MTase responsible for additional motifs to be methylated was associated with impairment of two major phenotypes: motility, caused by a downregulation of flagellar genes, and hemolysis. However, our results suggest that dam overexpression did not modify the virulence properties of X. nematophila. This study increases the knowledge on the diverse roles played by MTases in bacteria.
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Affiliation(s)
- Nadège Ginibre
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Ludovic Legrand
- LIPME, Université de Toulouse, INRAE, CNRS, 31320 Castanet-Tolosan, France
| | - Victoria Bientz
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | | | - Anne Lanois
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Sylvie Pages
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Julien Brillard
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
- Correspondence: ; Tel.: +33-467144711
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Jurėnas D, Payelleville A, Roghanian M, Turnbull KJ, Givaudan A, Brillard J, Hauryliuk V, Cascales E. Photorhabdus antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of 23S ribosomal RNA. Nucleic Acids Res 2021; 49:8384-8395. [PMID: 34255843 PMCID: PMC8661411 DOI: 10.1093/nar/gkab608] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/10/2021] [Accepted: 07/01/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteria have evolved sophisticated mechanisms to deliver potent toxins into bacterial competitors or into eukaryotic cells in order to destroy rivals and gain access to a specific niche or to hijack essential metabolic or signaling pathways in the host. Delivered effectors carry various activities such as nucleases, phospholipases, peptidoglycan hydrolases, enzymes that deplete the pools of NADH or ATP, compromise the cell division machinery, or the host cell cytoskeleton. Effectors categorized in the family of polymorphic toxins have a modular structure, in which the toxin domain is fused to additional elements acting as cargo to adapt the effector to a specific secretion machinery. Here we show that Photorhabdus laumondii, an entomopathogen species, delivers a polymorphic antibacterial toxin via a type VI secretion system. This toxin inhibits protein synthesis in a NAD+-dependent manner. Using a biotinylated derivative of NAD, we demonstrate that translation is inhibited through ADP-ribosylation of the ribosomal 23S RNA. Mapping of the modification further showed that the adduct locates on helix 44 of the thiostrepton loop located in the GTPase-associated center and decreases the GTPase activity of the EF-G elongation factor.
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Affiliation(s)
- Dukas Jurėnas
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France
| | - Amaury Payelleville
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France.,DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden
| | | | | | | | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France
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