References
- Bouzar, H., Jones, J. B., Stall, R. E., Hodge, N. C., Minsavage, G. V., Benedict, A. A. and Alvarez, A. M. 1994. Physiological, chemical, serological, and pathogenic analyses of a worldwide collection of Xanthomonas campestris pv. vesicatoria strains. Phytopathology 84:663-671. https://doi.org/10.1094/Phyto-84-663
- Buttner, D., Noel, L., Thieme, F. and Bonas, U. 2003. Genomic approaches in Xanthomonas campestris pv. vesicatoria allow fishing for virulence genes. J. Biotechnol. 106:203-214. https://doi.org/10.1016/j.jbiotec.2003.07.012
- Camacho, E. M. and Casadesus, J. 2002. Conjugal transfer of the virulence plasmid of Salmonella enterica is regulated by the leucine-responsive regulatory protein and DNA adenine methylation. Mol. Microbiol. 44:1589-1598. https://doi.org/10.1046/j.1365-2958.2002.02981.x
- Casadesus, J. and Low, D. 2006. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70:830-856. https://doi.org/10.1128/MMBR.00016-06
- Chae, J. C., Hung, N. B., Yu, S. M., Lee, H. K. and Lee, Y. H. 2014. Diversity of bacteriophages infecting Xanthomonas oryzae pv. oryzae in paddy fields and its potential to control bacterial leaf blight of rice. J. Microbiol. Biotechnol. 24:740-747. https://doi.org/10.4014/jmb.1402.02013
- Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., Turner, S. W. and Korlach, J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-569. https://doi.org/10.1038/nmeth.2474
- de Jong, A., Pietersma, H., Cordes, M., Kuipers, O. P. and Kok, J. 2012. PePPER: a webserver for prediction of prokaryote promoter elements and regulons. BMC Genomics 13:299. https://doi.org/10.1186/1471-2164-13-299
- Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., Bibillo, A., Bjornson, K., Chaudhuri, B., Christians, F., Cicero, R., Clark, S., Dalal, R., Dewinter, A., Dixon, J., Foquet, M., Gaertner, A., Hardenbol, P., Heiner, C., Hester, K., Holden, D., Kearns, G., Kong, X., Kuse, R., Lacroix, Y., Lin, S., Lundquist, P., Ma, C., Marks, P., Maxham, M., Murphy, D., Park, I., Pham, T., Phillips, M., Roy, J., Sebra, R., Shen, G., Sorenson, J., Tomaney, A., Travers, K., Trulson, M., Vieceli, J., Wegener, J., Wu, D., Yang, A., Zaccarin, D., Zhao, P., Zhongm, F., Korlachm, J. and Turner, S. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323:133-138. https://doi.org/10.1126/science.1162986
- Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J. and Turner, S. W. 2010. Direct detection of DNA methylation during singlemolecule, real-time sequencing. Nat. Methods 7:461-465. https://doi.org/10.1038/nmeth.1459
- Frommer, M., McDonald, L. E., Millar, D. S., Collis, C. M., Watt, F., Grigg, G. W., Molloy, P. L. and Paul, C. L. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. U. S. A. 89:1827-1831. https://doi.org/10.1073/pnas.89.5.1827
- Haagmans, W. and van der Woude, M. 2000. Phase variation of Ag43 in Escherichia coli: Dam-dependent methylation abrogates OxyR binding and OxyR-mediated repression of transcription. Mol. Microbiol. 35:877-887. https://doi.org/10.1046/j.1365-2958.2000.01762.x
- Hong, J. K., Sung, C. H., Kim, D. K., Yun, H. T., Jung, W. and Kim, K. D. 2012. Differential effect of delayed planting on soybean cultivars varying in susceptibility to bacterial pustule and wildfire in Korea. Crop Prot. 42:244-249. https://doi.org/10.1016/j.cropro.2012.07.014
- Kahramanoglou, C., Prieto, A. I., Khedkar, S., Haase, B., Gupta, A., Benes, V., Fraser, G. M., Luscombe, N. M. and Seshasayee, A. S. 2012. Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat. Commun. 3:886. https://doi.org/10.1038/ncomms1878
- Kim, J. G., Choi, S., Oh, J., Moon, J. S. and Hwang, I. 2006. Comparative analysis of three indigenous plasmids from Xanthomonas axonopodis pv. glycines. Plasmid 56:79-87. https://doi.org/10.1016/j.plasmid.2006.03.001
- Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C. and Salzberg, S. L. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12. https://doi.org/10.1186/gb-2004-5-2-r12
- Labrie, S. J., Samson, J. E. and Moineau, S. 2010. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8:317-327. https://doi.org/10.1038/nrmicro2315
- Laird, P. W. 2010. Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet. 11:191-203.
- Lee, J. H., Shin, H., Park, H. J., Ryu, S. and Han, S. W. 2014. Draft genome sequence of Xanthomonas axonopodis pv. glycines 8ra possessing transcription activator-like effectors used for genetic engineering. J. Biotechnol. 179:15-16. https://doi.org/10.1016/j.jbiotec.2014.03.009
- Lee, W. C., Anton, B. P., Wang, S., Baybayan, P., Singh, S., Ashby, M., Chua, E. G., Tay, C. Y., Thirriot, F., Loke, M. F., Goh, K. L., Marshall, B. J., Roberts, R. J. and Vadivelu, J. 2015. The complete methylome of Helicobacter pylori UM032. BMC Genomics 16:424. https://doi.org/10.1186/s12864-015-1585-2
- Low, D. A., Weyand, N. J. and Mahan, M. J. 2001. Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect. Immun. 69:7197-7204. https://doi.org/10.1128/IAI.69.12.7197-7204.2001
- Marinus, M. G. and Casadesus, J. 2009. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol. Rev. 33:488-503. https://doi.org/10.1111/j.1574-6976.2008.00159.x
- Nou, X., Skinner, B., Braaten, B., Blyn, L., Hirsch, D. and Low, D. 1993. Regulation of pyelonephritis-associated pili phasevariation in Escherichia coli: binding of the Papl and the Lrp regulatory proteins is controlled by DNA methylation. Mol. Microbiol. 7:545-553. https://doi.org/10.1111/j.1365-2958.1993.tb01145.x
- Powers, J. G., Weigman, V. J., Shu, J., Pufky, J. M., Cox, D. and Hurban, P. 2013. Efficient and accurate whole genome assembly and methylome profiling of E. coli. BMC Genomics 14:675. https://doi.org/10.1186/1471-2164-14-675
- Razin, A. and Riggs, A. D. 1980. DNA methylation and gene function. Science 210:604-610. https://doi.org/10.1126/science.6254144
- Roberts, R. J., Vincze, T., Posfai, J. and Macelis, D. 2010. REBASE--a database for DNA restriction and modification:enzymes, genes and genomes. Nucleic Acids Res. 38:D234-D236. https://doi.org/10.1093/nar/gkp874
- Ryan, R. P., Vorholter, F. J., Potnis, N., Jones, J. B., Van Sluys, M. A., Bogdanove, A. J. and Dow, J. M. 2011. Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat. Rev. Microbiol. 9:344-355. https://doi.org/10.1038/nrmicro2558
- Sanchez-Romero, M. A., Cota, I. and Casadesus, J. 2015. DNA methylation in bacteria: from the methyl group to the methylome. Curr. Opin. Microbiol. 25:9-16. https://doi.org/10.1016/j.mib.2015.03.004
- Seemann, T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068-2069. https://doi.org/10.1093/bioinformatics/btu153
- Skarstad, K. and Katayama, T. 2013. Regulating DNA replication in bacteria. Cold Spring Harb. Perspect. Biol. 5:a012922.
- Thieme, F., Koebnik, R., Bekel, T., Berger, C., Boch, J., Buttner, D., Caldana, C., Gaigalat, L., Goesmann, A., Kay, S., Kirchner, O., Lanz, C., Linke, B., McHardy, A. C., Meyer, F., Mittenhuber, G., Nies, D. H., Niesbach-Klosgen, U., Patschkowski, T., Ruckert, C., Rupp, O., Schneiker, S., Schuster, S. C., Vorholter, F. J., Weber, E., Puhler, A., Bonas, U., Bartels, D. and Kaiser, O. 2005. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J. Bacteriol. 187:7254-7266. https://doi.org/10.1128/JB.187.21.7254-7266.2005
- Varela-alvarez, E., Andreakis, N., Lago-Leston, A., Pearson, G. A., Serrao, E. A., Procaccini, G., Duarte, C. M. and Marba, M. 2006. Genomic DNA isolation from green and brown algae (caulerpales and fucales) for microsatellite library construction. J. Phycol. 42:741-745. https://doi.org/10.1111/j.1529-8817.2006.00218.x
- Wengelnik, K. and Bonas, U. 1996. HrpXv, an AraC-type regulator, activates expression of five of the six loci in the hrp cluster of Xanthomonas campestris pv. vesicatoria. J. Bacteriol. 178:3462-3469. https://doi.org/10.1128/jb.178.12.3462-3469.1996
- Yu, Y. J. and Yang, M. T. 2007. A novel restriction-modification system from Xanthomonas campestris pv. vesicatoria encodes a m4C-methyltransferase and a nonfunctional restriction endonuclease. FEMS Microbiol. Lett. 272:83-90. https://doi.org/10.1111/j.1574-6968.2007.00738.x
- Zautner, A. E., Goldschmidt, A. M., Thurmer, A., Schuldes, J., Bader, O., Lugert, R., Gross, U., Stingl, K., Salinas, G. and Lingner, T. 2015. SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs. BMC Genomics 16:1088. https://doi.org/10.1186/s12864-015-2317-3
- Zhang, W., Sun, Z., Menghe, B. and Zhang, H. 2015. Short communication: Single molecule, real-time sequencing technology revealed species- and strain-specific methylation patterns of 2 Lactobacillus strains. J. Dairy Sci. 98:3020-3024. https://doi.org/10.3168/jds.2014-9272
- Zhu, L., Zhong, J., Jia, X., Liu, G., Kang, Y., Dong, M., Zhang, X., Li, Q., Yue, L., Li, C., Fu, J., Xiao, J., Yan, J., Zhang, B., Lei, M., Chen, S., Lv, L., Zhu, B., Huang, H. and Chen, F. 2016. Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio singlemolecule real-time (SMRT) technology. Nucleic Acids Res. 44:730-743. https://doi.org/10.1093/nar/gkv1498
Cited by
- spp. Cultured in Minimal and Rich Media vol.17, pp.23-24, 2017, https://doi.org/10.1002/pmic.201700142
- N6-Methyladenine DNA modification in Xanthomonas oryzae pv. oryzicola genome vol.8, pp.1, 2018, https://doi.org/10.1038/s41598-018-34559-5
- The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines vol.8, pp.1, 2018, https://doi.org/10.1038/s41598-018-30620-5
- Functional characterization of a putative DNA methyltransferase, EadM, in Xanthomonas axonopodis pv. glycines by proteomic and phenotypic analyses vol.9, pp.1, 2019, https://doi.org/10.1038/s41598-019-38650-3