Abstract
In many prokaryotes and eukaryotes, DNA methylation at cis-regulatory sequences determines whether gene expression is on or off. Stable inheritance of these expression states is required in bacterial pathogenesis, cancer and developmental pathways1,2. Here we delineate the factors that control the stability of these states by using the agn43 gene in Escherichia coli as a model system. Systematic disruption of this system shows that a functional switch requires the presence of several, rarely occupied, intermediate states that separate the 'on' and 'off' states. Cells that leave the on and off state enter different intermediate states, where there is a strong bias that drives cells back to their original state. The intermediate states therefore act as buffers that prevent back and forth switching. This mechanism of generating multiple states is an alternative to feedback regulation3,4,5, and its general principle should be applicable to the analysis of other epigenetic switches and the design of synthetic circuits.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33 (Suppl.), 245–254 (2003).
Low, D.A., Weyand, N.J. & Mahan, M.J. Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect. Immun. 69, 7197–7204 (2001).
Gardner, T.S., Cantor, C.R. & Collins, J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).
Isaacs, F.J., Hasty, J., Cantor, C.R. & Collins, J.J. Prediction and measurement of an autoregulatory genetic module. Proc. Natl. Acad. Sci. USA 100, 7714–7719 (2003).
Xiong, W. & Ferrell, J.E., Jr. A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature 426, 460–465 (2003).
Klose, R.J. & Bird, A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci (2006).
Haagmans, W. & van der Woude, M. Phase variation of Ag43 in Escherichia coli: Dam-dependent methylation abrogates OxyR binding and OxyR-mediated repression of transcription. Mol. Microbiol. 35, 877–887 (2000).
Owen, P., Caffrey, P. & Josefsson, L.G. Identification and partial characterization of a novel bipartite protein antigen associated with the outer membrane of Escherichia coli. J. Bacteriol. 169, 3770–3777 (1987).
Henderson, I.R., Meehan, M. & Owen, P. Antigen 43, a phase-variable bipartite outer membrane protein, determines colony morphology and autoaggregation in Escherichia coli K-12. FEMS Microbiol. Lett. 149, 115–120 (1997).
Henderson, I.R. & Owen, P. The major phase-variable outer membrane protein of Escherichia coli structurally resembles the immunoglobulin A1 protease class of exported protein and is regulated by a novel mechanism involving Dam and oxyR. J. Bacteriol. 181, 2132–2141 (1999).
Waldron, D.E., Owen, P. & Dorman, C.J. Competitive interaction of the OxyR DNA-binding protein and the Dam methylase at the antigen 43 gene regulatory region in Escherichia coli. Mol. Microbiol. 44, 509–520 (2002).
Henderson, I.R., Meehan, M. & Owen, P. A novel regulatory mechanism for a novel phase-variable outer membrane protein of Escherichia coli. Adv. Exp. Med. Biol. 412, 349–355 (1997).
Wallecha, A., Munster, V., Correnti, J., Chan, T. & van der Woude, M. Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation. J. Bacteriol. 184, 3338–3347 (2002).
Owen, P., Meehan, M., de Loughry-Doherty, H. & Henderson, I. Phase-variable outer membrane proteins in Escherichia coli. FEMS Immunol. Med. Microbiol. 16, 63–76 (1996).
Correnti, J., Munster, V., Chan, T. & Woude, M. Dam-dependent phase variation of Ag43 in Escherichia coli is altered in a seqA mutant. Mol. Microbiol. 44, 521–532 (2002).
Hasman, H., Schembri, M.A. & Klemm, P. Antigen 43 and type 1 fimbriae determine colony morphology of Escherichia coli K-12. J. Bacteriol. 182, 1089–1095 (2000).
Kullik, I., Toledano, M.B., Tartaglia, L.A. & Storz, G. Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for oxidation and transcriptional activation. J. Bacteriol. 177, 1275–1284 (1995).
Wallecha, A., Correnti, J., Munster, V. & van der Woude, M. Phase variation of Ag43 is independent of the oxidation state of OxyR. J. Bacteriol. 185, 2203–2209 (2003).
Stancheva, I., Koller, T. & Sogo, J.M. Asymmetry of Dam remethylation on the leading and lagging arms of plasmid replicative intermediates. EMBO J. 18, 6542–6551 (1999).
Campbell, J.L. & Kleckner, N. The rate of Dam-mediated DNA adenine methylation in Escherichia coli. Gene 74, 189–190 (1988).
Gerdes, S.Y. et al. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185, 5673–5684 (2003).
Geanacopoulos, M., Vasmatzis, G., Zhurkin, V.B. & Adhya, S. Gal repressosome contains an antiparallel DNA loop. Nat. Struct. Biol. 8, 432–436 (2001).
Oehler, S., Alberti, S. & Muller-Hill, B. Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction. Nucleic Acids Res. 34, 606–612 (2006).
Sun, W. & Hattman, S. Escherichia coli OxyR protein represses the unmethylated bacteriophage Mu mom operon without blocking binding of the transcriptional activator C. Nucleic Acids Res. 24, 4042–4049 (1996).
Urig, S. et al. The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction. J. Mol. Biol. 319, 1085–1096 (2002).
Hopfield, J.J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci. USA 71, 4135–4139 (1974).
Hattman, S. Unusual transcriptional and translational regulation of the bacteriophage Mu mom operon. Pharmacol. Ther. 84, 367–388 (1999).
Hernday, A.D., Braaten, B.A. & Low, D.A. The mechanism by which DNA adenine methylase and PapI activate the pap epigenetic switch. Mol. Cell 12, 947–957 (2003).
Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1–I2 regulatory elements. Nucleic Acids Res. 25, 1203–1210 (1997).
Datsenko, K.A. & Wanner, B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97, 6640–6645 (2000).
Acknowledgements
We thank E.A. Oakenfull for logistical assistance; M. Thattai for discussions and assistance with data analysis; M. van der Woude for bacterial strains and plasmids; R. Lutz and H. Bujard for pZ expression plasmids; and A. Becskei, S.V. Godoy and J.M. Pedraza for suggestions and comments. This work was supported by grants from the National Science Foundation (PHY-0548484) and the National Institutes of Health (R01-GM077183).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Fig. 1
Cis-regulatory deletion strains. (PDF 25 kb)
Supplementary Table 1
Bacterial strains and plasmids. (PDF 85 kb)
Supplementary Table 2
Oligonucleotide sequences. (PDF 32 kb)
Rights and permissions
About this article
Cite this article
Lim, H., van Oudenaarden, A. A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet 39, 269–275 (2007). https://doi.org/10.1038/ng1956
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng1956
This article is cited by
-
Spatially localised expression of the glutamate decarboxylase gadB in Escherichia coli O157:H7 microcolonies in hydrogel matrices
npj Science of Food (2023)
-
Design and validation of a dual-fluorescence reporter system to monitor bacterial gene expression in the gut environment
Applied Microbiology and Biotechnology (2023)
-
Prokaryotic DNA methylation and its functional roles
Journal of Microbiology (2021)
-
Targeted DNA demethylation of the Fgf21 promoter by CRISPR/dCas9-mediated epigenome editing
Scientific Reports (2020)
-
Deciphering bacterial epigenomes using modern sequencing technologies
Nature Reviews Genetics (2019)