Home LiteratureArticle Details
PMID: 26998690 Published · ppublish English Journal Article

A role for the bacterial GATC methylome in antibiotic stress survival.

Nature genetics ·Vol. 48 ·No. 5 ·2016-00-00 ·Pages 581-6

Cohen NR, Ross CA, Jain S, Shapiro RS, Gutierrez A, Belenky P, Li H, Collins JJ

Abstract

Antibiotic resistance is an increasingly serious public health threat. Understanding pathways allowing bacteria to survive antibiotic stress may unveil new therapeutic targets. We explore the role of the bacterial epigenome in antibiotic stress survival using classical genetic tools and single-molecule real-time sequencing to characterize genomic methylation kinetics. We find that Escherichia coli survival under antibiotic pressure is severely compromised without adenine methylation at GATC sites. Although the adenine methylome remains stable during drug stress, without GATC methylation, methyl-dependent mismatch repair (MMR) is deleterious and, fueled by the drug-induced error-prone polymerase Pol IV, overwhelms cells with toxic DNA breaks. In multiple E. coli strains, including pathogenic and drug-resistant clinical isolates, DNA adenine methyltransferase deficiency potentiates antibiotics from the β-lactam and quinolone classes. This work indicates that the GATC methylome provides structural support for bacterial survival during antibiotic stress and suggests targeting bacterial DNA methylation as a viable approach to enhancing antibiotic activity.

MeSH Terms
Adenine/metabolism DNA Methylation DNA, Bacterial/metabolism Drug Resistance, Bacterial/genetics Escherichia coli/drug effects,genetics Stress, Physiological
Chemicals
DNA, Bacterial Adenine
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Cohen Nadia R
Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. | Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. | Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
Ross Christian A
Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Information Technology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA.
Jain Saloni
Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. | Boston University, Boston, Massachusetts, USA.
Shapiro Rebecca S
Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. | Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Gutierrez Arnaud
Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. | Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Belenky Peter
Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA.
Li Hu
Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Information Technology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA.
Collins James J
Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. | Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. | Howard Hughes Medical Institute, Chevy Chase, Maryland, USA. | Boston University, Boston, Massachusetts, USA. | Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. | Harvard-MIT Program in Health Sciences and Technology, Boston, Massachusetts, USA. | Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
References (76)
76 references, click to expand
  1. DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity.
    Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11578-83 PMID: 10500219
  2. Mismatch repair of cis-diamminedichloroplatinum(II)-induced DNA damage.
    Mol Pharmacol. 1985 Jul;28(1):51-5 PMID: 3894930
  3. Eradication of bacterial persisters with antibiotic-generated hydroxyl radicals.
    Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):12147-52 PMID: 22778419
  4. Regulation of finP transcription by DNA adenine methylation in the virulence plasmid of Salmonella enterica.
    J Bacteriol. 2005 Aug;187(16):5691-9 PMID: 16077115
  5. An essential role for DNA adenine methylation in bacterial virulence.
    Science. 1999 May 7;284(5416):967-70 PMID: 10320378
  6. Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production.
    Nat Biotechnol. 2013 Feb;31(2):160-5 PMID: 23292609
  7. Dam methylation: coordinating cellular processes.
    Curr Opin Microbiol. 2005 Apr;8(2):154-60 PMID: 15802246
  8. Mismatch-stimulated killing.
    Proc Natl Acad Sci U S A. 1986 Apr;83(8):2576-8 PMID: 2939453
  9. Inhibitors of RecA activity discovered by high-throughput screening: cell-permeable small molecules attenuate the SOS response in Escherichia coli.
    J Biomol Screen. 2009 Oct;14(9):1092-101 PMID: 19675313
  10. The Epigenomic Landscape of Prokaryotes.
    PLoS Genet. 2016 Feb;12(2):e1005854 PMID: 26870957
  11. Mismatch correction at O6-methylguanine residues in E. coli DNA.
    Nature. 1982 Apr 29;296(5860):868-9 PMID: 7040986
  12. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli.
    Genetics. 2001 May;158(1):41-64 PMID: 11333217
  13. Effects of subinhibitory concentrations of antibiotics on SOS and DNA repair gene expression in Staphylococcus aureus.
    Antimicrob Agents Chemother. 2008 Sep;52(9):3394-7 PMID: 18591271
  14. DinB upregulation is the sole role of the SOS response in stress-induced mutagenesis in Escherichia coli.
    Genetics. 2009 May;182(1):55-68 PMID: 19270270
  15. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.
    Nucleic Acids Res. 2015 Apr 30;43(8):4296-308 PMID: 25845600
  16. SOS response induction by beta-lactams and bacterial defense against antibiotic lethality.
    Science. 2004 Sep 10;305(5690):1629-31 PMID: 15308764
  17. A common mechanism of cellular death induced by bactericidal antibiotics.
    Cell. 2007 Sep 7;130(5):797-810 PMID: 17803904
  18. The mechanism by which DNA adenine methylase and PapI activate the pap epigenetic switch.
    Mol Cell. 2003 Oct;12(4):947-57 PMID: 14580345
  19. Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli.
    Nat Biotechnol. 1998 Jun;16(6):566-71 PMID: 9624689
  20. Entering the era of bacterial epigenomics with single molecule real time DNA sequencing.
    Curr Opin Microbiol. 2013 Apr;16(2):192-8 PMID: 23434113
  21. Approach to antimicrobial prophylaxis for urology procedures in the era of increasing fluoroquinolone resistance.
    Ann Pharmacother. 2014 Mar;48(3):380-6 PMID: 24396088
  22. Envelope instability in DNA adenine methylase mutants of Salmonella enterica.
    Microbiology. 2002 Apr;148(Pt 4):1171-82 PMID: 11932461
  23. The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction.
    J Mol Biol. 2002 Jun 21;319(5):1085-96 PMID: 12079349
  24. Vibrio cholerae triggers SOS and mutagenesis in response to a wide range of antibiotics: a route towards multiresistance.
    Antimicrob Agents Chemother. 2011 May;55(5):2438-41 PMID: 21300836
  25. The developmental origins of chronic physical aggression: biological pathways triggered by early life adversity.
    J Exp Biol. 2015 Jan 1;218(Pt 1):123-33 PMID: 25568459
  26. Mutation as a stress response and the regulation of evolvability.
    Crit Rev Biochem Mol Biol. 2007 Sep-Oct;42(5):399-435 PMID: 17917874
  27. Detection of DNA damage in prokaryotes by terminal deoxyribonucleotide transferase-mediated dUTP nick end labeling.
    Appl Environ Microbiol. 2000 Mar;66(3):1001-6 PMID: 10698764
  28. Epigenetic silencing mediates mitochondria stress-induced longevity.
    Cell Metab. 2013 Jun 4;17(6):954-64 PMID: 23747251
  29. The role of the preserved sequences of Dam methylase.
    Nucleic Acids Res. 1993 Jul 11;21(14):3183-90 PMID: 8341592
  30. Killing by ampicillin and ofloxacin induces overlapping changes in Escherichia coli transcription profile.
    Antimicrob Agents Chemother. 2004 Mar;48(3):890-6 PMID: 14982780
  31. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach.
    Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5977-82 PMID: 16585510
  32. Characterization of DNA adenine methylation mutants of Escherichia coli K12.
    Mutat Res. 1979 Feb;59(2):157-65 PMID: 375073
  33. The cAMP-CRP/CytR nucleoprotein complex in Escherichia coli: two pairs of closely linked binding sites for the cAMP-CRP activator complex are involved in combinatorial regulation of the cdd promoter.
    EMBO J. 1992 Oct;11(10):3635-43 PMID: 1327747
  34. Recombination is essential for viability of an Escherichia coli dam (DNA adenine methyltransferase) mutant.
    J Bacteriol. 2000 Jan;182(2):463-8 PMID: 10629194
  35. Development of rationally designed DNA N6 adenine methyltransferase inhibitors.
    Bioorg Med Chem Lett. 2012 May 1;22(9):3079-82 PMID: 22483584
  36. Novel Inhibitors of E. coli RecA ATPase Activity.
    Curr Chem Genomics. 2010 May 26;4:34-42 PMID: 20648224
  37. Relacin, a novel antibacterial agent targeting the Stringent Response.
    PLoS Pathog. 2012 Sep;8(9):e1002925 PMID: 23028324
  38. Targeting a bacterial stress response to enhance antibiotic action.
    Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14570-5 PMID: 19706543
  39. β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity.
    Nat Commun. 2013;4:1610 PMID: 23511474
  40. Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents.
    Br J Pharmacol. 2013 Jan;168(1):172-88 PMID: 22889062
  41. Epigenetic programming by maternal behavior.
    Nat Neurosci. 2004 Aug;7(8):847-54 PMID: 15220929
  42. DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair.
    FEMS Microbiol Rev. 2012 Nov;36(6):1105-21 PMID: 22404288
  43. Direct detection of DNA methylation during single-molecule, real-time sequencing.
    Nat Methods. 2010 Jun;7(6):461-5 PMID: 20453866
  44. An epigenetic switch involving overlapping fur and DNA methylation optimizes expression of a type VI secretion gene cluster.
    PLoS Genet. 2011 Jul;7(7):e1002205 PMID: 21829382
  45. Error-prone replication for better or worse.
    Trends Microbiol. 2004 Jun;12(6):288-95 PMID: 15165607
  46. Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics.
    Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17025-30 PMID: 12482953
  47. SOS-independent induction of dinB transcription by beta-lactam-mediated inhibition of cell wall synthesis in Escherichia coli.
    J Bacteriol. 2005 Feb;187(4):1515-8 PMID: 15687217
  48. A whole genome approach to in vivo DNA-protein interactions in E. coli.
    Nature. 1992 Dec 10;360(6404):606-10 PMID: 1334233
  49. Bacterial Responses and Genome Instability Induced by Subinhibitory Concentrations of Antibiotics.
    Antibiotics (Basel). 2013 Mar 14;2(1):100-14 PMID: 27029295
  50. Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis.
    Mol Cell. 2010 Feb 12;37(3):311-20 PMID: 20159551
  51. Phasevarions mediate random switching of gene expression in pathogenic Neisseria.
    PLoS Pathog. 2009 Apr;5(4):e1000400 PMID: 19390608
  52. Epigenetic gene regulation in the bacterial world.
    Microbiol Mol Biol Rev. 2006 Sep;70(3):830-56 PMID: 16959970
  53. Stress responses as determinants of antimicrobial resistance in Gram-negative bacteria.
    Trends Microbiol. 2012 May;20(5):227-34 PMID: 22424589
  54. Programmed heterogeneity: epigenetic mechanisms in bacteria.
    J Biol Chem. 2013 May 17;288(20):13929-35 PMID: 23592777
  55. Bile-induced DNA damage in Salmonella enterica.
    Genetics. 2004 Dec;168(4):1787-94 PMID: 15611156
  56. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
    Nat Biotechnol. 2012 Dec;30(12):1232-9 PMID: 23138224
  57. Diverse functions of restriction-modification systems in addition to cellular defense.
    Microbiol Mol Biol Rev. 2013 Mar;77(1):53-72 PMID: 23471617
  58. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.
    Genome Res. 2013 Jan;23(1):129-41 PMID: 23093720
  59. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.
    FEMS Microbiol Rev. 2009 May;33(3):488-503 PMID: 19175412
  60. Viability of Escherichia coli K-12 DNA adenine methylase (dam) mutants requires increased expression of specific genes in the SOS regulon.
    Mol Gen Genet. 1985;201(1):14-9 PMID: 3932821
  61. Epigenetic regulation of stress responses in plants.
    Curr Opin Plant Biol. 2009 Apr;12(2):133-9 PMID: 19179104
  62. Analysis of nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli.
    J Bacteriol. 1994 Jun;176(11):3438-41 PMID: 8195106
  63. Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157:H7.
    J Bacteriol. 2008 Jan;190(1):438-41 PMID: 17981979
  64. Regulation of traJ transcription in the Salmonella virulence plasmid by strand-specific DNA adenine hemimethylation.
    Mol Microbiol. 2005 Sep;57(6):1700-18 PMID: 16135235
  65. Induction of SOS genes in Escherichia coli and mutagenesis in Salmonella typhimurium by fluoroquinolones.
    Mutagenesis. 1990 Jan;5(1):63-6 PMID: 2158613
  66. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy.
    Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4629-34 PMID: 19255432
  67. Inexpensive multiplexed library preparation for megabase-sized genomes.
    PLoS One. 2015;10(5):e0128036 PMID: 26000737
  68. Evolution of the cellular stress proteome: from monophyletic origin to ubiquitous function.
    J Exp Biol. 2003 Sep;206(Pt 18):3119-24 PMID: 12909693
  69. Selective inhibitors of bacterial DNA adenine methyltransferases.
    J Biomol Screen. 2006 Aug;11(5):497-510 PMID: 16760373
  70. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.
    BMC Genomics. 2014;15:1039 PMID: 25432719
  71. DNA methylation and mutator genes in Escherichia coli K-12.
    Mutat Res. 2010 Oct;705(2):71-6 PMID: 20471491
  72. The Escherichia coli methyl-directed mismatch repair system repairs base pairs containing oxidative lesions.
    J Bacteriol. 2003 Mar;185(5):1701-4 PMID: 12591888
  73. DNA mismatch repair.
    Annu Rev Biochem. 2005;74:681-710 PMID: 15952900
  74. Comparison of the changes in global gene expression of Escherichia coli induced by four bactericidal agents.
    J Mol Microbiol Biotechnol. 2003;5(2):105-22 PMID: 12736533
  75. Bacterial stress responses as determinants of antimicrobial resistance.
    J Antimicrob Chemother. 2012 Sep;67(9):2069-89 PMID: 22618862
  76. Antibiotics induce redox-related physiological alterations as part of their lethality.
    Proc Natl Acad Sci U S A. 2014 May 20;111(20):E2100-9 PMID: 24803433
Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.3530
Published
2016-00-00
Epub
2016-00-21
Pages
581-6
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC4848143
Subset
IM
Grants
NIH HHS · DP1 OD003644 · United States
NIGMS NIH HHS · U54 GM114838 · United States
Howard Hughes Medical Institute · United States
External Links
PubMed source DOI: 10.1038/ng.3530 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2