【作者】 王建斌；

【导师】 胡松年； 杨焕明；

【作者基本信息】 浙江大学 ， 生物信息学， 2006， 博士

【摘要】 我们测序和分析了一株从深海中分离的耐冷耐压希瓦氏菌Shewanella sp.wp3、一株具有高度致病性和抗药性的人猪致病沙门氏菌Salmonella Enterica Serovar Choleraesuis SC-B67和一株以肠道细菌为宿主的噬菌体bacteriophage T5的全基因组,它们都是来自于或侵染gamma变形菌纲的物种。Shewanella sp.wp3基因组由5,396,476个碱基对(bp)组成,共有4,944个开放阅读框(ORF)。我们将S.sp.wp3基因组和一株分离自温暖湖里的希瓦氏菌Shewanella oneidensis的基因组进行了比较。结果表明S.sp.wp3基因组显著地扩张过,它包括了更多的与各种代谢途径相关的基因,而可移动的原件则相对较少。基因的复制是造成这种扩张的最主要原因,因为我们在基因组中没有找到很明显的基因横向转移的迹象,但是却找到证据表明正在进行中的基因复制事件的发生。基因组的这种扩张被认为是对极端环境的一种适应,因为它为细菌带来了更多的选择,帮助细菌渡过各种难关。我们的分析结果为将来更好地理解希瓦氏菌的生物学和进化提供了框架,也为深入研究深海中的生命,尤其是深海细菌提供了指导。 S.Choleraesuis SC-B67基因组和其它已经测序的沙门氏菌的基因组十分相似。通过在基因组水平对三株已测序的沙门氏菌比较发现,与S.Typhimurium LT2相比,S.Choleraesuis SC-B67和S.Typhi CT18具有更多的删除事件的发生。S.Choleraesuis具有151个假基因,其中由那些与细菌趋向相关的信号转导途径中转变而来的假基因的比例,在这三株已测序的沙门氏菌基因组中是最多的。在这些基因中的突变将会导致细菌能更加自由地游动,使得它们得以更有效地与宿主细胞发生作用而形成侵染。一个TetR/AcrR家族中调控基因acrR由于在其基因中产生了终止密码子而失去了活性,导致与环丙沙星抗性相关的基因AcrAB的过量表达。基因的横向转移为不同血清型的沙门氏菌在宿主中不断开辟新的生存空更多还原

【Abstract】 A deep-sea piezotolerant and psychrotolerant Shewanella sp. wp3, a highly invasive and multidrug-resistant swine and human pathogen Salmonella Enterica Serovar Choleraesuis SC-B67 and an enterobacteria phage T5 were completely sequenced and analyzed. All of these organisms are from or infect gammaproteobacteria. The genome sequence of 5. sp. wp3 consists of 5,396,476 base pair (bp), with 4,944 open reading frames (ORPs). S. sp. wp3 genome was compared to the genome of Shewanella oneidensis, a bacteria from warm-lake. Comparative results revealed S. sp. wp3 genome has been significantly expanded, it contains more genes for versatile pathways but fewer for mobile elements;gene duplication is believed to be main contributor for this expansion, as there is no obvious sign for horizontal gene transfer, but evidence for ongoing duplication events in its genome. The expanded genome is an adaptation to extreme life, as it brings more alternatives. All these results provide a framework for future studies to understand shewanella evolution and the biological basics of life at depth.S. Choleraesuis SC-B67 genome is highly similar to the already sequenced Salmonella. Genome-wide comparison of three sequenced Salmonella genomes revealed that more deletion events occurred in S. Choleraesuis SC-B67 and S. Typhi CT18 relative to S. Typhimurium LT2. S. Choleraesuis has 151 pseudogenes, which, among the three Salmonella genomes, include the highest percentage of pseudogenes arising from the genes involved in bacterial chemotaxis signal-transduction pathways. Mutations in these genes may increase smooth swimming of the bacteria, potentially allowing more effective interactions with and invasion of host cells to occur. A key regulatory gene of TetR/AcrR family, acrR, was inactivated through the introduction of an internal stop codon resulting in overexpression of AcrAB that appears to be associated with ciprofloxacin resistance. While lateral gene transfer providing basic functions to allow niche expansion in the host and environment is maintained duringthe evolution of different serovars of Salmonella, genes providing little overall selective benefit may be lost rapidly. Our findings suggest that the formation of pseudogenes may provide a simple evolutionary pathway that complements gene acquisition to enhance virulence and antimicrobial resistance in S. Choleraesuis.Comparative analysis of two 50-kb virulence plasmids of Salmonella enterica serovar Choleraesuis strains SC-B67 (pSCV50) and RF-1 (pKDSC50) were also carried out. The two plasmids share over 99% sequence similarity. Ninety-two nucleotide variations at 42 sites were detected between the two plasmids. Two regions in pSCV50 appeared to be more susceptible to changes: one is the non-virulence-associated transfer region (27.5-33.0 Kb) and the other a function-unknown region (9.0-10.5 Kb). The results indicate that virulence-related genes on the 50-Kb plasmid are under negative selection, suggesting that they play important roles in the expression of virulence during the process of infection, while other genes in this plasmid tend to evolve neutrally.Bacteriophage T5 is of 121,752 bp, with large direct terminal repeats of 10,139 bp (8.3%) at both ends. The genome structure is consistently arranged according to its lytic life cycle. Of the 168 potential open reading frames (ORFs), 61 were annotated;these annotated ORFs are mainly enzymes involved in phage DNA replication, repair, and nucleotide metabolism. At least five endonucleases that believed to help inducing nicks in T5 genomic DNA were identified, also found is a separated DNA ligase. Analysis of T5 early promoters suggests a probable motif AAA{3, 4 T}nTTGCTT{17, 18 n}TATAATA{12, 13 W}{10 R} for strong promoters that may strengthen the step modification of host RNA polymerase, and thus control transcription of phage DNA. The distinct protein domain profile and a mosaic genome structure suggest an origin from the common genetic pool.更多还原