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http://dx.doi.org/10.5423/PPJ.FT.10.2016.0216

Methylome Analysis of Two Xanthomonas spp. Using Single-Molecule Real-Time Sequencing  

Seong, Hoon Je (Department of Systems Biotechnology, Chung-Ang University)
Park, Hye-Jee (Department of Integrative Plant Science, Chung-Ang University)
Hong, Eunji (Department of Life Science (BK21 Program), Chung-Ang University)
Lee, Sung Chul (Department of Life Science (BK21 Program), Chung-Ang University)
Sul, Woo Jun (Department of Systems Biotechnology, Chung-Ang University)
Han, Sang-Wook (Department of Integrative Plant Science, Chung-Ang University)
Publication Information
The Plant Pathology Journal / v.32, no.6, 2016 , pp. 500-507 More about this Journal
Abstract
Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv. glycines (Xag) strain 8ra and X. campestris pv. vesicatoria (Xcv) strain 85-10. We identified $N^6$-methyladenine (6mA) and $N^4$-methylcytosine (4mC) modification in both genomes. In addition, we assigned putative DNA methylation motifs including previously unreported methylation motifs via REBASE and MotifMaker, and compared methylation patterns in both species. Although Xag and Xcv belong to the same genus, their methylation patterns were dramatically different. The number of 4mC DNA bases in Xag (66,682) was significantly higher (29 fold) than in Xcv (2,321). In contrast, the number of 6mA DNA bases (4,147) in Xag was comparable to the number in Xcv (5,491). Strikingly, there were no common or shared motifs in the 10 most frequently methylated motifs of both strains, indicating they possess unique species- or strain-specific methylation motifs. Among the 20 most frequent motifs from both strains, for 9 motifs at least 1% of the methylated bases were located in putative promoter regions. Methylome analysis by SMRT sequencing technology is the first step toward understanding the biology and functions of DNA methylation in this genus.
Keywords
methylome; single-molecule real-time sequencing; Xanthomonas;
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1 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.   DOI
2 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.   DOI
3 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.   DOI
4 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.   DOI
5 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.   DOI
6 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.   DOI
7 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.   DOI
8 Laird, P. W. 2010. Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet. 11:191-203.
9 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.   DOI
10 Labrie, S. J., Samson, J. E. and Moineau, S. 2010. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8:317-327.   DOI
11 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.   DOI
12 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.   DOI
13 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.   DOI
14 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.   DOI
15 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.   DOI
16 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.   DOI
17 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.   DOI
18 Razin, A. and Riggs, A. D. 1980. DNA methylation and gene function. Science 210:604-610.   DOI
19 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.   DOI
20 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.   DOI
21 Seemann, T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068-2069.   DOI
22 Skarstad, K. and Katayama, T. 2013. Regulating DNA replication in bacteria. Cold Spring Harb. Perspect. Biol. 5:a012922.
23 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.   DOI
24 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.   DOI
25 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.   DOI
26 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.   DOI
27 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.   DOI
28 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.   DOI
29 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.   DOI
30 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.   DOI
31 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.   DOI
32 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.   DOI
33 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.   DOI
34 Casadesus, J. and Low, D. 2006. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70:830-856.   DOI
35 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.   DOI
36 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.   DOI