A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen
Methylation of DNA is used by numerous organisms to regulate a wide variety of cellular processes, but specific roles for most DNA methyltransferases have not been defined. We studied one such enzyme in Vibrio cholerae, the cholera pathogen, using genome-wide approaches to compare DNA methylation, gene expression, and the sets of genes required or dispensable for growth in bacterial strains that produced or lacked this enzyme. These studies allowed us to identify numerous cellular processes regulated, either directly or indirectly, by this cytosine methyltransferase. In particular, we found that an absence of enzyme activity was associated with reduced levels of a bacterial stress response; consequently, a stress response pathway that is essential in wild type bacteria is not needed for survival of the mutant lacking the methyltransferase. Similar genome-wide analyses can likely to be used to define the cellular roles of many additional uncharacterized DNA methyltransferases.
Vyšlo v časopise:
A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen. PLoS Genet 11(11): e32767. doi:10.1371/journal.pgen.1005666
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005666
Souhrn
Methylation of DNA is used by numerous organisms to regulate a wide variety of cellular processes, but specific roles for most DNA methyltransferases have not been defined. We studied one such enzyme in Vibrio cholerae, the cholera pathogen, using genome-wide approaches to compare DNA methylation, gene expression, and the sets of genes required or dispensable for growth in bacterial strains that produced or lacked this enzyme. These studies allowed us to identify numerous cellular processes regulated, either directly or indirectly, by this cytosine methyltransferase. In particular, we found that an absence of enzyme activity was associated with reduced levels of a bacterial stress response; consequently, a stress response pathway that is essential in wild type bacteria is not needed for survival of the mutant lacking the methyltransferase. Similar genome-wide analyses can likely to be used to define the cellular roles of many additional uncharacterized DNA methyltransferases.
Zdroje
1. Schubeler D. Function and information content of DNA methylation. Nature 2015;517: 321–326, doi: 10.1038/nature14192 25592537
2. Casadesús J. & Low D. Epigenetic gene regulation in the bacterial world. Microbiol Mol Biol Rev 2006;70: 830–856, doi: 10.1128/MMBR.00016-06 16959970
3. Pósfai J., Bhagwat A. S. & Roberts R. J. Sequence motifs specific for cytosine methyltransferases. Gene 1988;74: 261–265. 3248729
4. Timinskas A., Butkus V. & Janulaitis A. Sequence motifs characteristic for DNA [cytosine-N4] and DNA [adenine-N6] methyltransferases. Classification of all DNA methyltransferases. Gene 1995;157: 3–11. 7607512
5. Murray N. E. Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol Mol Biol Rev 2000;64, 412–434. 10839821
6. Wion D. & Casadesús J. N6-methyl-adenine: an epigenetic signal for DNA–protein interactions. Nat Rev Microbiol 2006;4: 183–192, doi: 10.1038/nrmicro1350 16489347
7. Marinus M. G. & Casadesus J. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 2009;33; 488–503, doi: 10.1111/j.1574-6976.2008.00159.x 19175412
8. Lu M., Campbell J. L., Boye E. & Kleckner N. SeqA: a negative modulator of replication initiation in E. coli. Cell 1994;77: 413–426. 8011018
9. Schlagman S. L., Hattman S. & Marinus M. G. Direct role of the Escherichia coli Dam DNA methyltransferase in methylation-directed mismatch repair. J Bacteriol 1986;165: 896–900. 3512529
10. Roberts D., Hoopes B. C., McClure W. R. & Kleckner N. IS10 transposition is regulated by DNA adenine methylation. Cell 1985;43: 117–130, doi:0092-8674(85)90017-0 [pii]. 3000598
11. Peterson S. N. & Reich N. O. Competitive Lrp and Dam assembly at the pap regulatory region: implications for mechanisms of epigenetic regulation. J Mol Biol 2008;383: 92–105, doi: 10.1016/j.jmb.2008.07.086 18706913
12. Collier J., McAdams H. H. & Shapiro L. A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc Natl Acad Sci USA 2007;104; 17111–17116, doi: 10.1073/pnas.0708112104 17942674
13. Militello K. T., Mandarano A. H., Varechtchouk O. & Simon R. D. Cytosine DNA methylation influences drug resistance in Escherichia coli through increased sugE expression. FEMS Microbiol Lett 2014;350: 100–106, doi: 10.1111/1574-6968.12299 24164619
14. Militello K. T. et al. Conservation of Dcm-mediated cytosine DNA methylation in Escherichia coli. FEMS Microbiol Lett 2012;328: 78–85, doi: 10.1111/j.1574-6968.2011.02482.x 22150247
15. Kahramanoglou C. et al. Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun 2012;3: 886, doi: 10.1038/ncomms1878 22673913
16. Srikhanta Y. N. et al. Phasevarions mediate random switching of gene expression in pathogenic Neisseria. PLoS Pathog 2009;5: e1000400, doi: 10.1371/journal.ppat.1000400 19390608
17. Srikhanta Y. N. et al. Phasevarion mediated epigenetic gene regulation in Helicobacter pylori. PLoS ONE 2011;6: e27569, doi: 10.1371/journal.pone.0027569 22162751
18. Roberts R. J., Vincze T., Posfai J. & Macelis D. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2010;38: D234–236, doi: 10.1093/nar/gkp874 doi:gkp874 [pii] 19846593
19. Heidelberg J. F. et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 2000;406: 477–483, doi: 10.1038/35020000 10952301
20. Demarre G. & Chattoraj D. K. DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle. PLoS Genet 2010;6: e1000939, doi: 10.1371/journal.pgen.1000939 20463886
21. Gerding MA, Chao MC, Davis BM, & Waldor MK. Molecular dissection of the essential features of the origin of replication of the second Vibrio cholerae chromosome. mBio 2015;6: e00973–15. doi: 10.1128/mBio.00973-15 26220967
22. Banerjee S. & Chowdhury R. An orphan DNA (cytosine-5-)-methyltransferase in Vibrio cholerae. Microbiology (Reading, Engl) 2006;152: 1055–1062, doi: 10.1099/mic.0.28624–0
23. Chao M. C. et al. High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res 2013;41: 9033–9048, doi: 10.1093/nar/gkt654 23901011
24. Cameron D. E., Urbach J. M. & Mekalanos J. J. A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. Proc Natl Acad Sci USA 2008;105: 8736–8741, doi: 10.1073/pnas.0803281105 18574146
25. Kamp H. D., Patimalla-Dipali B., Lazinski D. W., Wallace-Gadsden F. & Camilli A. Gene fitness landscapes of Vibrio cholerae at important stages of its life cycle. PLoS Pathog 2013;9: e1003800, doi: 10.1371/journal.ppat.1003800 24385900
26. Haberman A., Heywood J. & Meselson M. DNA modification methylase activity of Escherichia coli restriction endonucleases K and P. Proc Natl Acad Sci U S A 1972;69: 3138–3141. 4564204
27. Dalia A. B., Lazinski D. W. & Camilli A. Characterization of undermethylated sites in Vibrio cholerae. J Bacteriol 2013;195: 2389–2399, doi: 10.1128/JB.02112-12 23504020
28. Papenfort K., Forstner K. U., Cong J. P., Sharma C. M. & Bassler B. L. Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation. Proc Natl Acad Sci U S A 2015;112: E766–775, doi: 10.1073/pnas.1500203112 25646441
29. Ades S. E. Regulation by destruction: design of the sigmaE envelope stress response. Curr Opin Microbiol 2008;11: 535–540, doi: 10.1016/j.mib.2008.10.004 18983936
30. De Las Penas A., Connolly L. & Gross C. A. The sigmaE-mediated response to extracytoplasmic stress in Escherichia coli is transduced by RseA and RseB, two negative regulators of sigmaE. Mol Microbiol 1997;24: 373–385. 9159523
31. Missiakas D., Mayer M. P., Lemaire M., Georgopoulos C. & Raina S. Modulation of the Escherichia coli sigmaE (RpoE) heat-shock transcription-factor activity by the RseA, RseB and RseC proteins. Mol Microbiol 1997;24: 355–371. 9159522
32. Campbell E. A. et al. Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA. Mol Cell 2003;11: 1067–1078. 12718891
33. Wilken C., Kitzing K., Kurzbauer R., Ehrmann M. & Clausen T. Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease. Cell 2004;117: 483–494. 15137941
34. Walsh N. P., Alba B. M., Bose B., Gross C. A. & Sauer R. T. OMP peptide signals initiate the envelope-stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain. Cell 2003;113: 61–71. 12679035
35. Chaba R. et al. Signal integration by DegS and RseB governs the σE-mediated envelope stress response in Escherichia coli. Proc Natl Acad Sci U S A 2011;108: 2106–2111, doi: 10.1073/pnas.1019277108 21245315
36. Lima S., Guo M. S., Chaba R., Gross C. A. & Sauer R. T. Dual molecular signals mediate the bacterial response to outer-membrane stress. Science 2013;340: 837–841, doi: 10.1126/science.1235358 23687042
37. Ades S. E., Connolly L. E., Alba B. M. & Gross C. A. The Escherichia coli sigma(E)-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-sigma factor. Genes Dev 1999;13: 2449–2461. 10500101
38. Alba B. M., Leeds J. A., Onufryk C., Lu C. Z. & Gross C. A. DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma(E)-dependent extracytoplasmic stress response. Genes Dev 2002;16: 2156–2168, doi: 10.1101/gad.1008902 12183369
39. Kanehara K., Ito K. & Akiyama Y. YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA. Genes Dev 2002;16: 2147–2155, doi: 10.1101/gad.1002302 12183368
40. Akiyama Y., Kanehara K. & Ito K. RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences. EMBO J 2004;23: 4434–4442, doi: 10.1038/sj.emboj.7600449 15496982
41. Dartigalongue C., Missiakas D. & Raina S. Characterization of the Escherichia coli sigma E regulon. J Biol Chem 2001;276: 20866–20875, doi: 10.1074/jbc.M100464200 11274153
42. Rezuchova B., Miticka H., Homerova D., Roberts M. & Kormanec J. New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system. FEMS Microbiol Lett 2003;225: 1–7. 12900013
43. Rhodius V. A., Suh W. C., Nonaka G., West J. & Gross C. A. Conserved and variable functions of the sigmaE stress response in related genomes. PLoS biology 2006;4: e2, doi: 10.1371/journal.pbio.0040002 16336047
44. Guo M. S. et al. MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein. Genes Dev 2014;28: 1620–1634, doi: 10.1101/gad.243485.114 25030700
45. Thompson K. M., Rhodius V. A. & Gottesman S. SigmaE regulates and is regulated by a small RNA in Escherichia coli. J Bacteriol 2007;189: 4243–4256, doi: 10.1128/JB.00020-07 17416652
46. De Las Penas A., Connolly L. & Gross C. A. SigmaE is an essential sigma factor in Escherichia coli. J Bacteriol 1997;179: 6862–6864. 9352942
47. Davis B. M. & Waldor M. K. High-throughput sequencing reveals suppressors of Vibrio cholerae rpoE mutations: one fewer porin is enough. Nucleic Acids Res 2009;37: 5757–5767, doi: 10.1093/nar/gkp568 19620211
48. Dartigalongue C., Loferer H. & Raina S. EcfE, a new essential inner membrane protease: its role in the regulation of heat shock response in Escherichia coli. EMBO J 2001;20: 5908–5918, doi: 10.1093/emboj/20.21.5908 11689431
49. Alba B. M., Zhong H. J., Pelayo J. C. & Gross C. A. degS (hhoB) is an essential Escherichia coli gene whose indispensable function is to provide sigma (E) activity. Mol Microbiol 2001;40: 1323–1333. 11442831
50. Button J. E., Silhavy T. J. & Ruiz N. A suppressor of cell death caused by the loss of sigmaE downregulates extracytoplasmic stress responses and outer membrane vesicle production in Escherichia coli. J Bacteriol 2007;189: 1523–1530, doi: 10.1128/JB.01534-06 17172327
51. Daimon Y., Narita S. & Akiyama Y. Activation of Toxin-Antitoxin System Toxins Suppresses Lethality Caused by the Loss of sigmaE in Escherichia coli. J Bacteriol 2015;197: 2316–2324, doi: 10.1128/JB.00079-15 25917909
52. Douchin V., Bohn C. & Bouloc P. Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli. J Biol Chem 2006;281: 12253–12259, doi: 10.1074/jbc.M600819200 16513633
53. Mathur J., Davis B. M. & Waldor M. K. Antimicrobial peptides activate the Vibrio cholerae sigmaE regulon through an OmpU-dependent signalling pathway. Mol Microbiol 2007;63: 848–858, doi: 10.1111/j.1365-2958.2006.05544.x 17181782
54. Provenzano D., Lauriano C. M. & Klose K. E. Characterization of the role of the ToxR-modulated outer membrane porins OmpU and OmpT in Vibrio cholerae virulence. J Bacteriol 2001;183: 3652–3662, doi: 10.1128/JB.183.12.3652–3662.2001 11371530
55. Lee K. M. et al. Activation of cholera toxin production by anaerobic respiration of trimethylamine N-oxide in Vibrio cholerae. J Biol Chem 2012;287: 39742–39752, doi: 10.1074/jbc.M112.394932 23019319
56. Klein G., Lindner B., Brabetz W., Brade H. & Raina S. Escherichia coli K-12 Suppressor-free Mutants Lacking Early Glycosyltransferases and Late Acyltransferases: minimal lipopolysaccharide structure and induction of envelope stress response. J Biol Chem 2009;284: 15369–15389, doi: 10.1074/jbc.M900490200 19346244
57. Fukuda A. et al. Aminoacylation of the N-terminal cysteine is essential for Lol-dependent release of lipoproteins from membranes but does not depend on lipoprotein sorting signals. J Biol Chem 2002;277: 43512–43518, doi: 10.1074/jbc.M206816200 12198129
58. Robichon C., Vidal-Ingigliardi D. & Pugsley A. P. Depletion of apolipoprotein N-acyltransferase causes mislocalization of outer membrane lipoproteins in Escherichia coli. J Biol Chem 2005;280: 974–983, doi: 10.1074/jbc.M411059200 15513925
59. Sklar J. G. et al. Lipoprotein SmpA is a component of the YaeT complex that assembles outer membrane proteins in Escherichia coli. Proc Natl Acad Sci U S A 2007;104: 6400–6405, doi: 10.1073/pnas.0701579104 17404237
60. Kredich N. M. Regulation of L-cysteine biosynthesis in Salmonella typhimurium. I. Effects of growth of varying sulfur sources and O-acetyl-L-serine on gene expression. J Biol Chem 1971;246: 3474–3484. 4931306
61. Tam C. & Missiakas D. Changes in lipopolysaccharide structure induce the sigma(E)-dependent response of Escherichia coli. Mol Microbiol 2005;55: 1403–1412, doi: 10.1111/j.1365-2958.2005.04497.x 15720549
62. Chiang S. L. & Rubin E. J. Construction of a mariner-based transposon for epitope-tagging and genomic targeting. Gene 2002;296: 179–185, doi:S0378111902008569 [pii]. 12383515
63. Cameron D. E., Urbach J. M. & Mekalanos J. J. A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. Proc Natl Acad Sci U S A 2008;105: 8736–8741, 0803281105 [pii]. doi: 10.1073/pnas.0803281105 18574146
64. Donnenberg M. S. & Kaper J. B. Construction of an eae deletion mutant of enteropathogenic Escherichia coli by using a positive-selection suicide vector. Infect Immun 1991;59: 4310–4317. 1937792
65. Gibson D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 2009;6: 343–345, doi: 10.1038/nmeth.1318 19363495
66. Pritchard J. R. et al. ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing. PLoS Genet 2014;10: e1004782, doi: 10.1371/journal.pgen.1004782 25375795
67. Miller V. L. & Mekalanos J. J. A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR. J Bacteriol 1988;170: 2575–2583. 2836362
68. Krueger F. & Andrews S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011;27: 1571–1572, doi: 10.1093/bioinformatics/btr167 21493656
69. Mandlik A. et al. RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression. Cell Host Microbe 2011;10: 165–174, S1931-3128(11)00224-1 [pii]. doi: 10.1016/j.chom.2011.07.007 21843873
70. Robinson M. D., McCarthy D. J. & Smyth G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26: 139–140, doi: 10.1093/bioinformatics/btp616 19910308
71. Wang Q. et al. A genome wide screen reveals that Vibrio cholerae phosphoenolpyruvate phosphotransferase system (PTS) modulates virulence gene expression. Infect Immun 2015; doi: 10.1128/IAI.00411-15 26056384
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Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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