Abstract
DNA N6-methyladenine (6mA) modifications expand the information capacity of DNA and have long been known to exist in bacterial genomes. Xanthomonas oryzae pv. Oryzicola (Xoc) is the causative agent of bacterial leaf streak, an emerging and destructive disease in rice worldwide. However, the genome-wide distribution patterns and potential functions of 6mA in Xoc are largely unknown. In this study, we analyzed the levels and global distribution patterns of 6mA modification in genomic DNA of seven Xoc strains (BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8 and RS105). The 6mA modification was found to be widely distributed across the seven Xoc genomes, accounting for percent of 3.80, 3.10, 3.70, 4.20, 3.40, 2.10, and 3.10 of the total adenines in BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8, and RS105, respectively. Notably, more than 82% of 6mA sites were located within gene bodies in all seven strains. Two specific motifs for 6 mA modification, ARGT and AVCG, were prevalent in all seven strains. Comparison of putative DNA methylation motifs from the seven strains reveals that Xoc have a specific DNA methylation system. Furthermore, the 6 mA modification of rpfC dramatically decreased during Xoc infection indicates the important role for Xoc adaption to environment.
Highlights
DNA methylation, a base modification, does not alter the underlying DNA sequence, but adds additional information to bases through the addition of a methyl group
The density (6 mA/A) is about 2.1% to 4.2% of the total adenines in the Xanthomonas oryzae pv. oryzicola (Xoc) genomic DNA (Table 1), which was close to the strain Xcv 85–10 of Xanthomonas campestris pv. vesicatoria (3.84%)[25] and the Hesseltinella vesiculosa (2.8%)12,but higher than those in Caenorhabditis elegans (~0.7%)[8], Chlamydomonas (~0.4%)[7], Drosophila (0.07%)[9], Human (0.051%) and Arabidopsis thaliana (0.048%)[4]
The atlas of m6A modification sites have been elucidated in several bacteria strains by using Single molecule real-time (SMRT) sequencing, which opened up a new direction for epigenetics research[22,23,24,25]
Summary
DNA methylation, a base modification, does not alter the underlying DNA sequence, but adds additional information to bases through the addition of a methyl group. The development of high throughput sequencing has greatly promoted the research and identification of 6 mA in fungi, plants, animals and humans[4,7,8,9,10,11,12], which can further reveal the genome-wide distribution patterns of 6 mA modifications as well as different functions in biological processes among organisms. DNA 6 mA modification is ubiquitous in microbial genomes and plays an important role in regulating the biological processes in bacteria. We measured the levels and global distribution patterns of 6 mA in genomic DNA of seven Xoc strains (BLS256, BLS279, CFBP2286, CFBP7331, CFBP7341, L8 and RS105), and compared DNA methylation motifs among seven strains
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