Das Soumita, Chaudhuri Keya
Human Genetics and Genomics Group, Indian Institute of Chemical Biology, Calcutta, India.
In Silico Biol. 2003;3(3):287-300.
Previously using global transcription profile approach, the icmF gene of V. cholerae was identified as an in vivo induced gene involved in the regulation of motility, adherence to intestinal epithelial cells. The present report shows that icmF has 27 homologues in the finished and unfinished microbial genome sequences available in the database and among them only Legionella pneumophila IcmF has been partially characterized. We first identified a gene cluster containing 15 genes surrounding IcmF and designated as IcmF associated homologous protein (IAHP), present in nine gram-negative proteo-bacteria that need an intimate contact with the eukaryotic host cells. Only in P. aeruginosa the cluster is present in three different regions of the genome. In Y. pestis CO92 the cluster is in the same orientation as that of V. cholerae. But in E. coli O157:H7 VT2 Sakai, E. coli O157:H7 EDL933 and Y. pestis KIM, the cluster is in the opposite orientation to that of V. cholerae though the relative position of respective ORFs are the same. In other proteobacteria like M. loti, A. tumefaciens, P. aeruginosa and S. typhimurum, the genes are reshuffled indicating the frequent rearrangement in microbial genomes. Annotation, motif and domain prediction suggested a role of the proteins of IAHP cluster in cell surface architecture or secretion. Phylogenetic analysis of each protein belonging to the cluster present in all the nine organisms showed that only E. coli O157:H7 VT2 Sakai, E. coli O157:H7 EDL933, Y. pestis KIM and Y. pestis CO92 are closer to the V. cholerae and this pattern was similar for all proteins in the cluster. Presence of low G + C regions before and after the gene cluster in V. cholerae and both of the E. coli O157: H7 strains provide possibility of transfer of the gene cluster from a foreign source. From our finding it can be speculated that both of the E. coli O157:H7 strains and V. cholerae has a common ancestor, but the other organism where the cluster is reshuffled has undergone a long term of evolution.
此前采用全转录谱方法，霍乱弧菌的icmF基因被鉴定为一个体内诱导基因，参与调控运动性以及对肠道上皮细胞的黏附。本报告显示，icmF在数据库中已完成和未完成的微生物基因组序列中有27个同源物，其中只有嗜肺军团菌的IcmF已得到部分表征。我们首先鉴定出一个包含15个基因的基因簇，该基因簇围绕icmF，被命名为icmF相关同源蛋白（IAHP），存在于9种需要与真核宿主细胞密切接触的革兰氏阴性变形菌中。仅在铜绿假单胞菌中，该基因簇存在于基因组的三个不同区域。在鼠疫耶尔森菌CO92中，该基因簇与霍乱弧菌的方向相同。但在大肠杆菌O157:H7 VT2阪崎株、大肠杆菌O157:H7 EDL933和鼠疫耶尔森菌KIM中，尽管各个开放阅读框的相对位置相同，但该基因簇与霍乱弧菌的方向相反。在其他变形菌如百脉根根瘤菌、根癌土壤杆菌、铜绿假单胞菌和鼠伤寒沙门氏菌中，这些基因发生了重排，表明微生物基因组中频繁发生重排。注释、基序和结构域预测表明，IAHP基因簇的蛋白质在细胞表面结构或分泌中发挥作用。对所有9种生物中该基因簇的每种蛋白质进行系统发育分析表明，只有大肠杆菌O157:H7 VT2阪崎株、大肠杆菌O157:H7 EDL933、鼠疫耶尔森菌KIM和鼠疫耶尔森菌CO92与霍乱弧菌关系较近，并且该基因簇中所有蛋白质的这种模式都是相似的。霍乱弧菌以及两种大肠杆菌O157:H7菌株的基因簇前后存在低G + C区域，这为该基因簇从外源转移提供了可能性。从我们的研究结果可以推测，两种大肠杆菌O157:H7菌株和霍乱弧菌有一个共同的祖先，但该基因簇发生重排的其他生物经历了长期的进化。
