title: In silico restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018.
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.
authors: Graduate School of Science and Technology, Chiba University, Matsudo, Chiba 271-8510, Japan. ichida@riken.jp
authors: Hiroyuki
authors: H
authors: Ichida
authors: Kazuyuki
authors: K
authors: Maeda
authors: Hisashi
authors: H
authors: Ichise
authors: Tomoki
authors: T
authors: Matsuyama
authors: Tomoko
authors: T
authors: Abe
authors: Katsuyoshi
authors: K
authors: Yoneyama
authors: Takato
authors: T
authors: Koba
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D016680:Genome, Bacterial; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000378:metabolism; D012984:Software; D014974:Xanthomonas / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; C058693:Dam methyltransferase; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); D015252:Deoxyribonucleases, Type II Site-Specific; C024405:GATC-specific type II deoxyribonucleases