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Carter MQ, Pham A, Huynh S, Parker CT, Miller A, He X, Hu B, Chain PSG. DNA adenine methylase, not the PstI restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli. Food Microbiol 2020; 96:103722. [PMID: 33494894 DOI: 10.1016/j.fm.2020.103722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 01/20/2023]
Abstract
We previously reported a distinct methylome between the two Shiga toxin-producing Escherichia coli (STEC) O145:H28 strains linked to the 2010 U.S. lettuce-associated outbreak (RM13514) and the 2007 Belgium ice cream-associated outbreak (RM13516), respectively. This difference was thought to be attributed to a prophage encoded type II restriction-modification system (PstI R-M) in RM13514. Here, we characterized this PstI R-M system in comparison to DNA adenine methylase (Dam), a highly conserved enzyme in γ proteobacteria, by functional genomics. Deficiency in Dam led to a differential expression of over 1000 genes in RM13514, whereas deficiency in PstI R-M only impacted a few genes transcriptionally. Dam regulated genes involved in diverse functions, whereas PstI R-M regulated genes mostly encoding transporters and adhesins. Dam regulated a large number of genes located on prophages, pathogenicity islands, and plasmids, including Shiga toxin genes, type III secretion system (TTSS) genes, and enterohemolysin genes. Production of Stx2 in dam mutant was significantly higher than in RM13514, supporting a role of Dam in maintaining lysogeny of Stx2-prophage. However, following mitomycin C treatment, Stx2 in RM13514 was significantly higher than that of dam or PstI R-M deletion mutant, implying that both Dam and PstI R-M contributed to maximum Stx2 production.
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Affiliation(s)
- Michelle Qiu Carter
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA.
| | - Antares Pham
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Steven Huynh
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Craig T Parker
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Avalon Miller
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Xiaohua He
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Foodborne Toxin and Detection Research Unit, Albany, CA, USA
| | - Bin Hu
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Patrick S G Chain
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Veisseire P, Bonnet M, Saraoui T, Poupet C, Camarès O, Gachinat M, Callon C, Febvre G, Chassard C, Bornes S. Investigation into In Vitro and In Vivo Caenorhabditis elegans Models to Select Cheese Yeasts as Probiotic Candidates for their Preventive Effects against Salmonella Typhimurium. Microorganisms 2020; 8:microorganisms8060922. [PMID: 32570901 PMCID: PMC7356738 DOI: 10.3390/microorganisms8060922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 12/17/2022] Open
Abstract
The design of multiscale strategies integrating in vitro and in vivo models is necessary for the selection of new probiotics. In this regard, we developed a screening assay based on the investigation of the potential of yeasts from cheese as probiotics against the pathogen Salmonella Typhimurium UPsm1 (ST). Two yeasts isolated from raw-milk cheese (Saccharomyces cerevisiae 16, Sc16; Debaryomyces hansenii 25, Dh25), as well as S. cerevisiae subspecies boulardii (CNCM I-1079, Sb1079), were tested against ST by applying in vitro and in vivo tests. Adherence measurements to Caco-2 and HT29-MTX intestinal cells indicated that the two tested cheese yeasts presented a better adhesion than the probiotic Sb1079 as the control strain. Further, the Dh25 was the cheese yeast most likely to survive in the gastrointestinal tract. What is more, the modulation of the TransEpithelial Electrical Resistance (TEER) of differentiated Caco-2 cell monolayers showed the ability of Dh25 to delay the deleterious effects of ST. The influence of microorganisms on the in vivo model Caenorhabditis elegans was evaluated by measuring the longevity of the worm. This in vivo approach revealed that this yeast increased the worm’s lifespan and protected it against ST infection, confirming that this in vivo model can be useful for screening probiotic cheese yeasts.
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Affiliation(s)
- Philippe Veisseire
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
- Correspondence: ; Tel.: +33-(0)4-43-79-11-28
| | - Muriel Bonnet
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Taous Saraoui
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Cyril Poupet
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Olivier Camarès
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Marylise Gachinat
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Guy Febvre
- Université Clermont Auvergne, Laboratoire Météorologie Physique, CNRS, F-15000 Aurillac, France;
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
| | - Stéphanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, F-15000 Aurillac, France; (M.B.); (T.S.); (C.P.); (O.C.); (M.G.); (C.C.); (C.C.); (S.B.)
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Khan F, Jain S, Oloketuyi SF. Bacteria and bacterial products: Foe and friends to Caenorhabditis elegans. Microbiol Res 2018; 215:102-113. [DOI: 10.1016/j.micres.2018.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/11/2018] [Accepted: 06/24/2018] [Indexed: 02/07/2023]
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Dorati F, Barrett GA, Sanchez-Contreras M, Arseneault T, José MS, Studholme DJ, Murillo J, Caballero P, Waterfield NR, Arnold DL, Shaw LJ, Jackson RW. Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators. Microorganisms 2018; 6:microorganisms6020032. [PMID: 29690522 PMCID: PMC6027264 DOI: 10.3390/microorganisms6020032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/09/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the molecular mechanisms underpinning the ecological success of plant pathogens is critical to develop strategies for controlling diseases and protecting crops. Recent observations have shown that plant pathogenic bacteria, particularly Pseudomonas, exist in a range of natural environments away from their natural plant host e.g., water courses, soil, non-host plants. This exposes them to a variety of eukaryotic predators such as nematodes, insects and amoebae present in the environment. Nematodes and amoeba in particular are bacterial predators while insect herbivores may act as indirect predators, ingesting bacteria on plant tissue. We therefore postulated that bacteria are probably under selective pressure to avoid or survive predation and have therefore developed appropriate coping mechanisms. We tested the hypothesis that plant pathogenic Pseudomonas syringae are able to cope with predation pressure and found that three pathovars show weak, but significant resistance or toxicity. To identify the gene systems that contribute to resistance or toxicity we applied a heterologous screening technique, called Rapid Virulence Annotation (RVA), for anti-predation and toxicity mechanisms. Three cosmid libraries for P. syringae pv. aesculi, pv. tomato and pv. phaseolicola, of approximately 2000 cosmids each, were screened in the susceptible/non-toxic bacterium Escherichia coli against nematode, amoebae and an insect. A number of potential conserved and unique genes were identified which included genes encoding haemolysins, biofilm formation, motility and adhesion. These data provide the first multi-pathovar comparative insight to how plant pathogens cope with different predation pressures and infection of an insect gut and provide a foundation for further study into the function of selected genes and their role in ecological success.
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Affiliation(s)
- Federico Dorati
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
| | - Glyn A Barrett
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
| | | | - Tanya Arseneault
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Research and Development Centre, Quebec, J3B 3E6, Canada.
| | - Mateo San José
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
| | | | - Jesús Murillo
- Instituto de Agrobiotecnología, Universidad Pública de Navarra, 31192 Mutilva, Spain.
| | - Primitivo Caballero
- Instituto de Agrobiotecnología, Universidad Pública de Navarra, 31192 Mutilva, Spain.
| | - Nicholas R Waterfield
- Department of Biology and Biochemistry, University of Bath, Bath, BA1 9BJ, UK.
- Warwick Medical School, University of Warwick, Warwick, CV4 7AL, UK.
| | - Dawn L Arnold
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, BS16 1QY, UK.
| | - Liz J Shaw
- School of Archaeology, Geography and Environmental Science, University of Reading, Reading, RG6 6AX, UK.
| | - Robert W Jackson
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK.
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Adhikari S, Curtis PD. DNA methyltransferases and epigenetic regulation in bacteria. FEMS Microbiol Rev 2016; 40:575-91. [PMID: 27476077 DOI: 10.1093/femsre/fuw023] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Epigenetics is a change in gene expression that is heritable without a change in DNA sequence itself. This phenomenon is well studied in eukaryotes, particularly in humans for its role in cellular differentiation, X chromosome inactivation and diseases like cancer. However, comparatively little is known about epigenetic regulation in bacteria. Bacterial epigenetics is mainly present in the form of DNA methylation where DNA methyltransferases add methyl groups to nucleotides. This review focuses on two methyltransferases well characterized for their roles in gene regulation: Dam and CcrM. Dam methyltransferase in Escherichia coli is important for expression of certain genes such as the pap operon, as well as other cellular processes like DNA replication initiation and DNA repair. In Caulobacter crescentus and other Alphaproteobacteria, the methyltransferase CcrM is cell cycle regulated and is involved in the cell-cycle-dependent regulation of several genes. The diversity of regulatory targets as well as regulatory mechanisms suggests that gene regulation by methylation could be a widespread and potent method of regulation in bacteria.
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Affiliation(s)
- Satish Adhikari
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Patrick D Curtis
- Department of Biology, University of Mississippi, University, MS 38677, USA
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Host-Microbe Interactions in Caenorhabditis elegans. ISRN MICROBIOLOGY 2013; 2013:356451. [PMID: 23984180 PMCID: PMC3747393 DOI: 10.1155/2013/356451] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 07/16/2013] [Indexed: 01/09/2023]
Abstract
A good understanding of how microbes interact with hosts has a direct bearing on our capability of fighting infectious microbial pathogens and making good use of beneficial ones. Among the model organisms used to study reciprocal actions among microbes and hosts, C. elegans may be the most advantageous in the context of its unique attributes such as the short life cycle, easiness of laboratory maintenance, and the availability of different genetic mutants. This review summarizes the recent advances in understanding host-microbe interactions in C. elegans. Although these investigations have greatly enhanced our understanding of C. elegans-microbe relationships, all but one of them involve only one or few microbial species. We argue here that more research is needed for exploring the evolution and establishment of a complex microbial community in the worm's intestine and its interaction with the host.
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Abstract
In prokaryotes, alteration in gene expression was observed with the modification of DNA, especially DNA methylation. Such changes are inherited from generation to generation with no alterations in the DNA sequence and represent the epigenetic signal in prokaryotes. DNA methyltransferases are enzymes involved in DNA modification and thus in epigenetic regulation of gene expression. DNA methylation not only affects the thermodynamic stability of DNA, but also changes its curvature. Methylation of specific residues on DNA can affect the protein-DNA interactions. DNA methylation in prokaryotes regulates a number of physiological processes in the bacterial cell including transcription, DNA mismatch repair and replication initiation. Significantly, many reports have suggested a role of DNA methylation in regulating the expression of a number of genes in virulence and pathogenesis thus, making DNA methlytransferases novel targets for the designing of therapeutics. Here, we summarize the current knowledge about the influence of DNA methylation on gene regulation in different bacteria, and on bacterial virulence.
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Affiliation(s)
- Ritesh Kumar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India,
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Haznedaroglu BZ, Yates MV, Maduro MF, Walker SL. Effects of residual antibiotics in groundwater on Salmonella typhimurium: changes in antibiotic resistance, in vivo and in vitro pathogenicity. ACTA ACUST UNITED AC 2011; 14:41-7. [PMID: 22051852 DOI: 10.1039/c1em10723b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An outbreak-causing strain of Salmonella enterica serovar Typhimurium was exposed to groundwater with residual antibiotics for up to four weeks. Representative concentrations (0.05, 1, and 100 μg L(-1)) of amoxicillin, tetracycline, and a mixture of several other antibiotics (1 μg L(-1) each) were spiked into artificially prepared groundwater (AGW). Antibiotic susceptibility analysis and the virulence response of stressed Salmonella were determined on a weekly basis by using human epithelial cells (HEp2) and soil nematodes (C. elegans). Results have shown that Salmonella typhimurium remains viable for long periods of exposure to antibiotic-supplemented groundwater; however, they failed to cultivate as an indication of a viable but nonculturable state. Prolonged antibiotics exposure did not induce any changes in the antibiotic susceptibility profile of the S. typhimurium strain used in this study. S. typhimurium exposed to 0.05 and 1 μg L(-1) amoxicillin, and 1 μg L(-1) tetracycline showed hyper-virulent profiles in both in vitro and in vivo virulence assays with the HEp2 cells and C. elegans respectively, most evident following 2nd and 3rd weeks of exposure.
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Affiliation(s)
- Berat Z Haznedaroglu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
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Cho BK, Palsson B, Zengler K. Deciphering the regulatory codes in bacterial genomes. Biotechnol J 2011; 6:1052-63. [PMID: 21845736 DOI: 10.1002/biot.201000349] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/30/2011] [Accepted: 07/25/2011] [Indexed: 12/24/2022]
Abstract
Interactions between cis-regulatory elements and trans-acting factors are fundamental for cellular functions such as transcription. With the revolution in microarrays and sequencing technologies, genome-wide binding locations of trans-acting factors are being determined in large numbers. The richness of the genome-scale information has revealed that the nature of the bacterial transcriptome and regulome are considerably more complex than previously expected. In addition, the emerging view of the bacterial transcriptome is revising the concept of the operon organization of the genome. This review describes current advances in the genome-scale analysis of the interaction between cis-regulatory elements and trans-acting factors in microorganisms.
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Affiliation(s)
- Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea.
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Sun K, Jiao XD, Zhang M, Sun L. DNA adenine methylase is involved in the pathogenesis of Edwardsiella tarda. Vet Microbiol 2010; 141:149-54. [DOI: 10.1016/j.vetmic.2009.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 08/23/2009] [Accepted: 09/04/2009] [Indexed: 12/24/2022]
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Fälker S, Schilling J, Schmidt MA, Heusipp G. Overproduction of DNA adenine methyltransferase alters motility, invasion, and the lipopolysaccharide O-antigen composition of Yersinia enterocolitica. Infect Immun 2007; 75:4990-7. [PMID: 17682042 PMCID: PMC2044514 DOI: 10.1128/iai.00457-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA adenine methyltransferase (Dam) not only regulates basic cellular functions but also interferes with the proper expression of virulence factors in various pathogens. We showed previously that for the human pathogen Yersinia enterocolitica, overproduction of Dam results in increased invasion of epithelial cells. Since invasion and motility are coordinately regulated in Y. enterocolitica, we analyzed the motility of a Dam-overproducing (Dam(OP)) strain and found it to be highly motile. In Dam(OP) strains, the operon encoding the master regulator of flagellum biosynthesis, flhDC, is upregulated. We show that the increased invasion is not due to enhanced expression of known and putative Y. enterocolitica invasion and adhesion factors, such as Inv, YadA, Ail, Myf fibrils, Pil, or Flp pili. However, overproduction of Dam no longer results in increased invasion for an inv mutant strain, indicating that Inv is necessary for increased invasion after overproduction of Dam. Since we show that overproduction of Dam results in an increased amount of rough lipopolysaccharide (LPS) molecules lacking O-antigen side chains, this implies that reduced steric hindrance by LPS might contribute to increased invasion by a Y. enterocolitica Dam(OP) strain. Our data add an important new aspect to the various virulence-associated phenotypes influenced by DNA methylation in Y. enterocolitica and indicate that Dam targets regulatory processes modulating the composition and function of the bacterial surface.
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Affiliation(s)
- Stefan Fälker
- Institut für Infektiologie, Zentrum für Molekularbiologie der Entzündung, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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Aloui A, Chatty A, El May A, Landoulsi A. The effect of methylation on DNA replication in Salmonella enterica serovar typhimurium. C R Biol 2007; 330:576-80. [PMID: 17637438 DOI: 10.1016/j.crvi.2007.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2007] [Revised: 06/02/2007] [Accepted: 06/05/2007] [Indexed: 11/22/2022]
Abstract
The DNA adenine methylase of Salmonella typhimurium methylates adenine at GATC sequences. Strains deficient in this methylase are not well transformed by methylated plasmids, but unmethylated plasmids transform them at high frequencies. Hemimethylated daughter molecules accumulate after the transformation of dam(-) strains with fully methylated plasmids, suggesting that hemimethylation prevents DNA replication. It will also be shown that plasmids isolated from dam(-) bacteria are hemimethylated by restriction enzyme digestion. These results may explain why newly formed daughter molecules are not substrates for immediate reinitiation of DNA replication in dam(-) bacteria.
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Affiliation(s)
- Amine Aloui
- Laboratoire de biochimie et biologie moléculaire, Unité de biochimie des lipides et interaction des macromolécules en biologie, 03/UR/0902, faculté des sciences de Bizerte, Zarzouna 7021, Tunisia.
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Abstract
Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.
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Affiliation(s)
- Josep Casadesús
- Departamento de Genética, Universidad de Sevilla, Seville 41080, Spain
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