publication . Article . Other literature type . 2016

Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase.

Ian M. Ehrenreich; Matthew M. Champion; Steven E. Finkel; Lacey L. Westphal; Peter Sauvey;
Open Access
  • Published: 13 Dec 2016 Journal: mSystems, volume 1 (eissn: 2379-5077, Copyright policy)
  • Publisher: American Society for Microbiology
Abstract
ABSTRACT DNA methylation in prokaryotes is widespread. The most common modification of the genome is the methylation of adenine at the N-6 position. In Escherichia coli K-12 and many gammaproteobacteria, this modification is catalyzed by DNA adenine methyltransferase (Dam) at the GATC consensus sequence and is known to modulate cellular processes including transcriptional regulation of gene expression, initiation of chromosomal replication, and DNA mismatch repair. While studies thus far have focused on the motifs associated with methylated adenine (meA), the frequency of meA across the genome, and temporal dynamics during early periods of incubation, here we co...
Subjects
free text keywords: Research Article, Molecular Biology and Physiology, Dam methyltransferase, long-term stationary phase, SMRT, long-term survival, Gene, Methyltransferase, DNA methylation, Sialic acid transport, DNA, chemistry.chemical_compound, chemistry, Biology, RNA-Directed DNA Methylation, Epigenetics, Genetics, Methylation
56 references, page 1 of 4

1.Marinus MG, Løbner-Olesen A 6 12 2014, posting date DNA methylation, p 1–54. EcoSal Plus 2014 doi:10.1128/ecosalplus.ESP-0003-2013. [OpenAIRE] [DOI]

2.Wion D, Casadesús J 2006 N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat Rev Microbiol 4:183–192. doi:10.1038/nrmicro1350.16489347 [OpenAIRE] [PubMed] [DOI]

3.Oshima T, Wada C, Kawagoe Y, Ara T, Maeda M, Masuda Y, Hiraga S, Mori H 2002 Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli. Mol Microbiol 45:673–695. doi:10.1046/j.1365-2958.2002.03037.x.12139615 [OpenAIRE] [PubMed] [DOI]

4.Løbner-Olesen A, Skovgaard O, Marinus MG 2005 Dam methylation: coordinating cellular processes. Curr Opin Microbiol 8:154–160. doi:10.1016/j.mib.2005.02.009.15802246 [OpenAIRE] [PubMed] [DOI]

5.Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee ASN 2012 Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun 3:886. doi:10.1038/ncomms1878.22673913 [OpenAIRE] [PubMed] [DOI]

6.Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y 1997 The complete genome sequence of Escherichia coli K-12. Science 277:1453–1462. doi:10.1126/science.277.5331.1453.9278503 [OpenAIRE] [PubMed] [DOI]

7.Broadbent SE, Balbontin R, Casadesus J, Marinus MG, van der Woude M 2007 YhdJ, a nonessential CcrM-like DNA methyltransferase of Escherichia coli and Salmonella enterica. J Bacteriol 189:4325–4327. doi:10.1128/JB.01854-06.17400740 [OpenAIRE] [PubMed] [DOI]

8.Sánchez-Romero MA, Cota I, Casadesús J 2015 DNA methylation in bacteria: from the methyl group to the methylome. Curr Opin Microbiol 25:9–16. doi:10.1016/j.mib.2015.03.004.25818841 [OpenAIRE] [PubMed] [DOI]

9.Casadesús J, Low DA 2013 Programmed heterogeneity: epigenetic mechanisms in bacteria. J Biol Chem 288:13929–13935. doi:10.1074/jbc.R113.472274.23592777 [OpenAIRE] [PubMed] [DOI]

10.Heusipp G, Fälker S, Schmidt MA 2007 DNA adenine methylation and bacterial pathogenesis. Int J Med Microbiol 297:1–7. doi:10.1016/j.ijmm.2006.10.002.17126598 [OpenAIRE] [PubMed] [DOI]

11.Marinus MG, Casadesus J 2009 Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 33:488–503. doi:10.1111/j.1574-6976.2008.00159.x.19175412 [OpenAIRE] [PubMed] [DOI]

12.Casadesús J, Low D 2006 Epigenetic gene regulation in the bacterial world. Microbiol Mol Biol Rev 70:830–856. doi:10.1128/MMBR.00016-06.16959970 [OpenAIRE] [PubMed] [DOI]

13.Reisenauer A, Kahng LS, McCollu m S, Shapiro L 1999 Bacterial DNA methylation: a cell cycle regulator?J Bacteriol 181:5135–5139.10464180 [OpenAIRE] [PubMed]

14.Donczew R, Zakrzewska-Czerwińska J, Zawilak-Pawlik A 2014 Beyond DnaA: the role of DNA topology and DNA methylation in bacterial replication initiation. J Mol Biol 426:2269–2282. doi:10.1016/j.jmb.2014.04.009.24747048 [OpenAIRE] [PubMed] [DOI]

15.Lu AL, Clark S, Modrich P 1983 Methyl-directed repair of DNA base-pair mismatches in vitro. Proc Natl Acad Sci U S A 80:4639–4643. doi:10.1073/pnas.80.15.4639.6308634 [OpenAIRE] [PubMed] [DOI]

56 references, page 1 of 4
Abstract
ABSTRACT DNA methylation in prokaryotes is widespread. The most common modification of the genome is the methylation of adenine at the N-6 position. In Escherichia coli K-12 and many gammaproteobacteria, this modification is catalyzed by DNA adenine methyltransferase (Dam) at the GATC consensus sequence and is known to modulate cellular processes including transcriptional regulation of gene expression, initiation of chromosomal replication, and DNA mismatch repair. While studies thus far have focused on the motifs associated with methylated adenine (meA), the frequency of meA across the genome, and temporal dynamics during early periods of incubation, here we co...
Subjects
free text keywords: Research Article, Molecular Biology and Physiology, Dam methyltransferase, long-term stationary phase, SMRT, long-term survival, Gene, Methyltransferase, DNA methylation, Sialic acid transport, DNA, chemistry.chemical_compound, chemistry, Biology, RNA-Directed DNA Methylation, Epigenetics, Genetics, Methylation
56 references, page 1 of 4

1.Marinus MG, Løbner-Olesen A 6 12 2014, posting date DNA methylation, p 1–54. EcoSal Plus 2014 doi:10.1128/ecosalplus.ESP-0003-2013. [OpenAIRE] [DOI]

2.Wion D, Casadesús J 2006 N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat Rev Microbiol 4:183–192. doi:10.1038/nrmicro1350.16489347 [OpenAIRE] [PubMed] [DOI]

3.Oshima T, Wada C, Kawagoe Y, Ara T, Maeda M, Masuda Y, Hiraga S, Mori H 2002 Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli. Mol Microbiol 45:673–695. doi:10.1046/j.1365-2958.2002.03037.x.12139615 [OpenAIRE] [PubMed] [DOI]

4.Løbner-Olesen A, Skovgaard O, Marinus MG 2005 Dam methylation: coordinating cellular processes. Curr Opin Microbiol 8:154–160. doi:10.1016/j.mib.2005.02.009.15802246 [OpenAIRE] [PubMed] [DOI]

5.Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee ASN 2012 Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun 3:886. doi:10.1038/ncomms1878.22673913 [OpenAIRE] [PubMed] [DOI]

6.Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y 1997 The complete genome sequence of Escherichia coli K-12. Science 277:1453–1462. doi:10.1126/science.277.5331.1453.9278503 [OpenAIRE] [PubMed] [DOI]

7.Broadbent SE, Balbontin R, Casadesus J, Marinus MG, van der Woude M 2007 YhdJ, a nonessential CcrM-like DNA methyltransferase of Escherichia coli and Salmonella enterica. J Bacteriol 189:4325–4327. doi:10.1128/JB.01854-06.17400740 [OpenAIRE] [PubMed] [DOI]

8.Sánchez-Romero MA, Cota I, Casadesús J 2015 DNA methylation in bacteria: from the methyl group to the methylome. Curr Opin Microbiol 25:9–16. doi:10.1016/j.mib.2015.03.004.25818841 [OpenAIRE] [PubMed] [DOI]

9.Casadesús J, Low DA 2013 Programmed heterogeneity: epigenetic mechanisms in bacteria. J Biol Chem 288:13929–13935. doi:10.1074/jbc.R113.472274.23592777 [OpenAIRE] [PubMed] [DOI]

10.Heusipp G, Fälker S, Schmidt MA 2007 DNA adenine methylation and bacterial pathogenesis. Int J Med Microbiol 297:1–7. doi:10.1016/j.ijmm.2006.10.002.17126598 [OpenAIRE] [PubMed] [DOI]

11.Marinus MG, Casadesus J 2009 Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 33:488–503. doi:10.1111/j.1574-6976.2008.00159.x.19175412 [OpenAIRE] [PubMed] [DOI]

12.Casadesús J, Low D 2006 Epigenetic gene regulation in the bacterial world. Microbiol Mol Biol Rev 70:830–856. doi:10.1128/MMBR.00016-06.16959970 [OpenAIRE] [PubMed] [DOI]

13.Reisenauer A, Kahng LS, McCollu m S, Shapiro L 1999 Bacterial DNA methylation: a cell cycle regulator?J Bacteriol 181:5135–5139.10464180 [OpenAIRE] [PubMed]

14.Donczew R, Zakrzewska-Czerwińska J, Zawilak-Pawlik A 2014 Beyond DnaA: the role of DNA topology and DNA methylation in bacterial replication initiation. J Mol Biol 426:2269–2282. doi:10.1016/j.jmb.2014.04.009.24747048 [OpenAIRE] [PubMed] [DOI]

15.Lu AL, Clark S, Modrich P 1983 Methyl-directed repair of DNA base-pair mismatches in vitro. Proc Natl Acad Sci U S A 80:4639–4643. doi:10.1073/pnas.80.15.4639.6308634 [OpenAIRE] [PubMed] [DOI]

56 references, page 1 of 4
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