The chromosome of Shigella flexneri bacteriophage Sf6:: Complete nucleotide sequence, genetic mosaicism, and DNA packaging
The chromosome of Shigella flexneri bacteriophage Sf6:: Complete nucleotide sequence, genetic mosaicism, and DNA packaging
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DOI：
10.1016/j.jmb.2004.03.068
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发表时间：
2004-05-28
影响因子：
5.6
通讯作者：
Clark, AJ
中科院分区：
文献类型：
--
作者：
Casjens, S;Winn-Stapley, DA;Clark, AJ
福氏志贺菌温和噬菌体Sf6是感兴趣的，部分原因是其原噬菌体表达oac基因，该基因改变其宿主细菌的表面O-抗原多糖的抗原特性。我们已经确定了其39，044 bp基因组的完整序列。该序列显示Sf6是典型的类噬菌体群的成员，并且像这种类型的其他噬菌体一样具有高度嵌合的基因组。它的染色体区域编码的蛋白质与至少15种不同的先前表征的拟谷氨酰胺和前噬菌体>80%相同，但43%的基因组，包括病毒体组装基因，与一种噬菌体HK 620的基因组同源。对Sf6和HK 620之间核苷酸差异的分析表明，即使这些相似的区域也是高度嵌合的。这种镶嵌现象暗示了病毒体结构蛋白可能相互作用的方式。Sf6早期操纵子的排列方式类似于典型的类噬菌体，在“代谢”基因组结构域的功能模块之间经常发现“边界序列”。由于编码基因及其DNA靶位点的高度相似性，我们预测Sf6的整合酶、早期转录抗终止子、CI和Cro阻遏物以及CII蛋白具有与分别由HPK 620、λ、434和P22编码的同源蛋白非常相似的DNA结合特异性。晚期操纵子包含两个tRNA基因。Sf6末端酶基因是不寻常的。DNA包装系列的体内起始分析表明，识别用于包装的DNA的Sf6装置似乎在包括可能的pac位点的约1800 bp的大区域内的许多位点切割用于包装系列起始的DNA。这与先前表征的噬菌体包装机制不同。(C)2004 Elsevier Ltd.保留所有权利。
Shigella flexneri temperate bacteriophage Sf6 is of interest in part because its prophage expresses the oac gene that alters the antigenic properties of the surface O-antigen polysaccharide of its host bacterium. We have determined the complete sequence of its 39,044 bp genome. The sequence shows that Sf6 is a member of the canonical lambdoid phage group, and like other phages of this type has a highly mosaic genome. It has chromosomal regions that encode proteins >80% identical with at least 15 different previously characterized lambdoid phages and prophages, but 43% of the genome, including the virion assembly genes, is homologous to the genome of one phage, HK620. An analysis of the nucleotide differences between Sf6 and HK620 indicates that even these similar regions are highly mosaic. This mosaicism suggests ways in which the virion structural proteins might interact with each other. The Sf6 early operons are arranged like a typical lambdoid phage, with "boundary sequences" often found between functional modules in the "metabolic" genome domain. By virtue of high degree of similarity in the encoding genes and their DNA target sites, we predict that the integrase, early transcription anti-terminator, CI and Cro repressors, and CII protein of Sf6 have DNA binding specificities very similar to the homologous proteins encoded by phages HK620,lambda, 434 and P22, respectively. The late operon contains two tRNA genes. The Sf6 terminase genes are unusual. Analysis of in vivo initiation of the DNA packaging series showed that the Sf6 apparatus that recognizes DNA for packaging appears to cleave DNA for initiation of packaging series at many sites within a large region of about 1800 bp that includes a possible pac site. This is unlike previously characterized phage packaging mechanisms. (C) 2004 Elsevier Ltd. All rights reserved.