Complete Genome Sequence And Analysis Of The Deep-sea Piezotolerant And Psychrotolerant Shewanella Sp. Wp3, The Swine Pathogen Salmonella Enterica Serovar Choleraesuis SC-B67 And The Bacteriophage T5

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.