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Semashko TA, Arzamasov AA, Evsyutina DV, Garanina IA, Matyushkina DS, Ladygina VG, Pobeguts OV, Fisunov GY, Govorun VM. Role of DNA modifications in Mycoplasma gallisepticum. PLoS One 2022; 17:e0277819. [PMID: 36413541 PMCID: PMC9681074 DOI: 10.1371/journal.pone.0277819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022] Open
Abstract
The epigenetics of bacteria, and bacteria with a reduced genome in particular, is of great interest, but is still poorly understood. Mycoplasma gallisepticum, a representative of the class Mollicutes, is an excellent model of a minimal cell because of its reduced genome size, lack of a cell wall, and primitive cell organization. In this study we investigated DNA modifications of the model object Mycoplasma gallisepticum and their roles. We identified DNA modifications and methylation motifs in M. gallisepticum S6 at the genome level using single molecule real time (SMRT) sequencing. Only the ANCNNNNCCT methylation motif was found in the M. gallisepticum S6 genome. The studied bacteria have one functional system for DNA modifications, the Type I restriction-modification (RM) system, MgaS6I. We characterized its activity, affinity, protection and epigenetic functions. We demonstrated the protective effects of this RM system. A common epigenetic signal for bacteria is the m6A modification we found, which can cause changes in DNA-protein interactions and affect the cell phenotype. Native methylation sites are underrepresented in promoter regions and located only near the -35 box of the promoter, which does not have a significant effect on gene expression in mycoplasmas. To study the epigenetics effect of m6A for genome-reduced bacteria, we constructed a series of M. gallisepticum strains expressing EGFP under promoters with the methylation motifs in their different elements. We demonstrated that m6A modifications of the promoter located only in the -10-box affected gene expression and downregulated the expression of the corresponding gene.
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Affiliation(s)
- Tatiana A. Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
- * E-mail:
| | - Alexander A. Arzamasov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Daria V. Evsyutina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
| | - Irina A. Garanina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Daria S. Matyushkina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
| | - Valentina G. Ladygina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Olga V. Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Gleb Y. Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
| | - Vadim M. Govorun
- Research Institute for Systems Biology and Medicine, Moscow, Russian Federation
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Labroussaa F, Baby V, Rodrigue S, Lartigue C. [Whole genome transplantation: bringing natural or synthetic bacterial genomes back to life]. Med Sci (Paris) 2019; 35:761-770. [PMID: 31625898 DOI: 10.1051/medsci/2019154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The development of synthetic genomics (SG) allowed the emergence of several groundbreaking techniques including the synthesis, assembly and engineering of whole bacterial genomes. The successful implantation of those methods, which culminated in the creation of JCVI-syn3.0 the first nearly minimal bacterium with a synthetic genome, mainly results from the use of the yeast Saccharomyces cerevisiae as a transient host for bacterial genome replication and modification. Another method played a key role in the resounding success of this project: bacterial genome transplantation (GT). GT consists in the transfer of bacterial genomes cloned in yeast, back into a cellular environment suitable for the expression of their genetic content. While successful using many mycoplasma species, a complete understanding of the factors governing GT will most certainly help unleash the power of the entire SG pipeline to other genetically intractable bacteria.
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Affiliation(s)
- Fabien Labroussaa
- Institute of Veterinary Bacteriology, University of Bern, PO Box, CH-3001 Bern, Suisse
| | - Vincent Baby
- UMR 1332 Biologie du fruit et pathologie, INRA Bordeaux-Aquitaine, 71 avenue E. Bourlaux, 33882 Villenave d'Ornon, France
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, 2500 boulevard de l'université, Sherbrooke, Québec, Canada
| | - Carole Lartigue
- UMR 1332 Biologie du fruit et pathologie, INRA Bordeaux-Aquitaine, 71 avenue E. Bourlaux, 33882 Villenave d'Ornon, France
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3
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Rideau F, Le Roy C, Sagné E, Renaudin H, Pereyre S, Henrich B, Dordet-Frisoni E, Citti C, Lartigue C, Bébéar C. Random transposon insertion in the Mycoplasma hominis minimal genome. Sci Rep 2019; 9:13554. [PMID: 31537861 PMCID: PMC6753208 DOI: 10.1038/s41598-019-49919-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 08/30/2019] [Indexed: 11/09/2022] Open
Abstract
Mycoplasma hominis is an opportunistic human pathogen associated with genital and neonatal infections. Until this study, the lack of a reliable transformation method for the genetic manipulation of M. hominis hindered the investigation of the pathogenicity and the peculiar arginine-based metabolism of this bacterium. A genomic analysis of 20 different M. hominis strains revealed a number of putative restriction-modification systems in this species. Despite the presence of these systems, a reproducible polyethylene glycol (PEG)-mediated transformation protocol was successfully developed in this study for three different strains: two clinical isolates and the M132 reference strain. Transformants were generated by transposon mutagenesis with an efficiency of approximately 10-9 transformants/cell/µg plasmid and were shown to carry single or multiple mini-transposons randomly inserted within their genomes. One M132-mutant was observed to carry a single-copy transposon inserted within the gene encoding P75, a protein potentially involved in adhesion. However, no difference in adhesion was observed in cell-assays between this mutant and the M132 parent strain. Whole genome sequencing of mutants carrying multiple copies of the transposon further revealed the occurrence of genomic rearrangements. Overall, this is the first time that genetically modified strains of M. hominis have been obtained by random mutagenesis using a mini-transposon conferring resistance to tetracycline.
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Affiliation(s)
- Fabien Rideau
- University of Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France.,INRA, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France
| | - Chloé Le Roy
- University of Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France.,INRA, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France
| | - Eveline Sagné
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | - Hélène Renaudin
- University of Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France.,INRA, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France
| | - Sabine Pereyre
- University of Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France.,INRA, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University, Düsseldorf, Germany
| | | | | | - Carole Lartigue
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, Gironde, France. .,University of Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, Gironde, France.
| | - Cécile Bébéar
- University of Bordeaux, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France. .,INRA, USC-EA3671 Mycoplasmal and Chlamydial Infections in Humans, Bordeaux, France.
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4
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Atack JM, Yang Y, Seib KL, Zhou Y, Jennings MP. A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions. Nucleic Acids Res 2019; 46:3532-3542. [PMID: 29554328 PMCID: PMC5909438 DOI: 10.1093/nar/gky192] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/10/2018] [Indexed: 12/21/2022] Open
Abstract
Many bacteria utilize simple DNA sequence repeats as a mechanism to randomly switch genes on and off. This process is called phase variation. Several phase-variable N6-adenine DNA-methyltransferases from Type III restriction-modification systems have been reported in bacterial pathogens. Random switching of DNA methyltransferases changes the global DNA methylation pattern, leading to changes in gene expression. These epigenetic regulatory systems are called phasevarions — phase-variable regulons. The extent of these phase-variable genes in the bacterial kingdom is unknown. Here, we interrogated a database of restriction-modification systems, REBASE, by searching for all simple DNA sequence repeats in mod genes that encode Type III N6-adenine DNA-methyltransferases. We report that 17.4% of Type III mod genes (662/3805) contain simple sequence repeats. Of these, only one-fifth have been previously identified. The newly discovered examples are widely distributed and include many examples in opportunistic pathogens as well as in environmental species. In many cases, multiple phasevarions exist in one genome, with examples of up to 4 independent phasevarions in some species. We found several new types of phase-variable mod genes, including the first example of a phase-variable methyltransferase in pathogenic Escherichia coli. Phasevarions are a common epigenetic regulation contingency strategy used by both pathogenic and non-pathogenic bacteria.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou 510006, China
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
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Lin Y, Jiang J, Zhang J, You W, Hu Q. Development of a TaqMan real-time PCR for detection of the Mycoplasma mycoides subsp. capri. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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6
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Lin Y, Jiang J, Zhang J, You W, Hu Q. Development of a TaqMan real-time PCR for detection of the Mycoplasma mycoidessubsp. capri. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Phillips ZN, Husna AU, Jennings MP, Seib KL, Atack JM. Phasevarions of bacterial pathogens - phase-variable epigenetic regulators evolving from restriction-modification systems. MICROBIOLOGY-SGM 2019; 165:917-928. [PMID: 30994440 DOI: 10.1099/mic.0.000805] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phase-variable DNA methyltransferases control the expression of multiple genes via epigenetic mechanisms in a wide variety of bacterial species. These systems are called phasevarions, for phase-variable regulons. Phasevarions regulate genes involved in pathogenesis, host adaptation and antibiotic resistance. Many human-adapted bacterial pathogens contain phasevarions. These include leading causes of morbidity and mortality worldwide, such as non-typeable Haemophilus influenzae, Streptococcus pneumoniae and Neisseria spp. Phase-variable methyltransferases and phasevarions have also been discovered in environmental organisms and veterinary pathogens. The existence of many different examples suggests that phasevarions have evolved multiple times as a contingency strategy in the bacterial domain, controlling phenotypes that are important in adapting to environmental change. Many of the organisms that contain phasevarions have existing or emerging drug resistance. Vaccines may therefore represent the best and most cost-effective tool to prevent disease caused by these organisms. However, many phasevarions also control the expression of current and putative vaccine candidates; variable expression of antigens could lead to immune evasion, meaning that vaccines designed using these targets become ineffective. It is therefore essential to characterize phasevarions in order to determine an organism's stably expressed antigenic repertoire, and rationally design broadly effective vaccines.
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Affiliation(s)
- Zachary N Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Asma-Ul Husna
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia
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Baby V, Labroussaa F, Brodeur J, Matteau D, Gourgues G, Lartigue C, Rodrigue S. Cloning and Transplantation of the Mesoplasma florum Genome. ACS Synth Biol 2018; 7:209-217. [PMID: 28893065 DOI: 10.1021/acssynbio.7b00279] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cloning and transplantation of bacterial genomes is a powerful method for the creation of engineered microorganisms. However, much remains to be understood about the molecular mechanisms and limitations of this approach. We report the whole-genome cloning of Mesoplasma florum in Saccharomyces cerevisiae, and use this model to investigate the impact of a bacterial chromosome in yeast cells. Our results indicate that the cloned M. florum genome is subjected to weak transcriptional activity, and causes no significant impact on yeast growth. We also report that the M. florum genome can be transplanted into Mycoplasma capricolum without any negative impact from the putative restriction enzyme encoding gene mfl307. Using whole-genome sequencing, we observed that a small number of mutations appeared in all M. florum transplants. Mutations also arose, albeit at a lower frequency, when the M. capricolum genome was transplanted into M. capricolum recipient cells. These observations suggest that genome transplantation is mutagenic, and that this phenomenon is magnified by the use of genome donor and recipient cell belonging to different species. No difference in efficiency was detected after three successive rounds of genome transplantation, suggesting that the observed mutations were not selected during the procedure. Taken together, our results provide a more accurate picture of the events taking place during bacterial genome cloning and transplantation.
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Affiliation(s)
- Vincent Baby
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Fabien Labroussaa
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Joëlle Brodeur
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Dominick Matteau
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Géraldine Gourgues
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Carole Lartigue
- Université de Bordeaux, INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Sébastien Rodrigue
- Université de Sherbrooke, Département de Biologie, 2500 Boulevard Université, Sherbrooke, Québec J1K 2R1, Canada
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Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi. PLoS One 2016; 11:e0161499. [PMID: 27556252 PMCID: PMC4996451 DOI: 10.1371/journal.pone.0161499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/05/2016] [Indexed: 01/31/2023] Open
Abstract
We examined and compared both the methylomes and the modification-related gene content of four sequenced strains of Bibersteinia trehalosi isolated from the nasopharyngeal tracts of Nebraska cattle with symptoms of bovine respiratory disease complex. The methylation patterns and the encoded DNA methyltransferase (MTase) gene sets were different between each strain, with the only common pattern being that of Dam (GATC). Among the observed patterns were three novel motifs attributable to Type I restriction-modification systems. In some cases the differences in methylation patterns corresponded to the gain or loss of MTase genes, or to recombination at target recognition domains that resulted in changes of enzyme specificity. However, in other cases the differences could be attributed to differential expression of the same MTase gene across strains. The most obvious regulatory mechanism responsible for these differences was slipped strand mispairing within short sequence repeat regions. The combined action of these evolutionary forces allows for alteration of different parts of the methylome at different time scales. We hypothesize that pleiotropic transcriptional modulation resulting from the observed methylomic changes may be involved with the switch between the commensal and pathogenic states of this common member of ruminant microflora.
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