부산대학교 도서관

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.bbrc.2007.09.055 Byline: Hiroyuki Ichida (a)(b), Kazuyuki Maeda (c), Hisashi Ichise (c), Tomoki Matsuyama (d), Tomoko Abe (b), Katsuyoshi Yoneyama (c), Takato Koba (a) Keywords: Xanthomonas oryzae pathovar oryzae MAFF 311018; In silico RLGS; DNA adenine methylation Abstract: We have developed a restriction landmark genome scanning (RLGS) system in silico, involving two-dimensional electrophoretic analysis of DNA by computer simulation that is based on the availability of whole-genome sequences for specific organisms. We applied the technique to the analysis of the Xanthomonas oryzae pathovar oryzae (Xoo) MAFF 311018, which causes bacterial blight in rice. The coverage that was found to be achievable using RLGS in silico, as a percentage of the genomic regions that could be detected, ranged from 44.5% to 72.7% per image. However, this reached a value of 96.7% using four images that were obtained with different combinations of landmark restriction enzymes. Interestingly, the signal intensity of some of the specific spots obtained was significantly lower than that of other surrounding spots when MboI, which cleaves unmethylated 5'-GATC-3' sites, was used. DNA gel blot analysis with both DNA adenine methylase (Dam)-sensitive and -insensitive isoschizomers (MboI and Sau3AI) revealed that Dam-mediated DNA adenine methylation had indeed occurred at these particular sites. These results suggest that a significant portion of the 5'-GATC-3' sites within the Xoo genome is stably methylated by Dam. Author Affiliation: (a) Graduate School of Science and Technology, Chiba University, Matsudo, Chiba 271-8510, Japan (b) Accelerator Applications Research Group, Nishina Center for Accelerator-Based Science, RIKEN, Wako, Saitama 351-0198, Japan (c) Faculty of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan (d) Cellular Biochemistry Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama 351-0198, Japan Article History: Received 11 September 2007