Publication in refereed journal
香港中文大学研究人员 ( 现职)
| 关海山教授 (生命科学学院) |
| 张文杰先生 (食品研究中心) |
全文
| 数位物件识别号 (DOI) http://dx.doi.org/10.1371/journal.pone.0033759 |
引用次数
Web of Sciencehttp://aims.cuhk.edu.hk/converis/portal/Publication/6WOS source URL
其它资讯
摘要Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of "alien" elements which probably undergo special temporal-spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these "exotic" regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased "non-optimal" codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for "alien" regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions.
着者Huang QL, Cheng XJ, Cheung MK, Kiselev SS, Ozoline ON, Kwan HS
期刊名称PLoS ONE
出版年份2012
月份3
日期20
卷号7
期次3
出版社PUBLIC LIBRARY SCIENCE
国际标準期刊号1932-http://aims.cuhk.edu.hk/converis/portal/Publication/6203
语言英式英语
Web of Science 学科类别Multidisciplinary Sciences; MULTIDISCIPLINARY SCIENCES; Science & Technology - Other Topics
