What genetic features set Salmonella serotypes apart from closely related organisms such as E. coli? Comparison of bacterial genomes shows that Salmonella-specific DNA regions encode many of the biological properties that distinguish Salmonella serotypes from other members of the family Enterobacteriaceae. An alignment of the chromosomes of S. enterica serotype Typhimurium and E.coli K-12 provided the first evidence that their collinear genetic maps are interrupted by large DNA segments that are present in only one of these organisms [2, 3]. Highresolution global analysis of these genetic differences was initiated with the completion of the S. enterica serotype Typhimurium LT2 genome sequence . McClelland and coworkers used genomic subtraction to identify 935 genes present in S. enterica serotype Typhimurium (LT2), but absent from E. coli (K-12 and O157:H7), and from sample sequences of Klebsiella pneumoniae (MGH 78578) and Yersinia pestis (CO92) [5, 6]. Of these 935 genes, 224 were never scored as absent when genomic DNA of 22 Salmonella serotypes was hybridized to an LT2 microar-ray containing 4483 of the 4596 annotated S. Typhimurium ORFs . Furthermore, 56 of these 224 genes were reliably identified as being present in all 22 Salmonella serotypes by microarray and were designated Salmonella "signature" genes. In a similar study, Falkow and coworkers hybridized genomic DNA from 18 different Salmonella serotypes to a S. enterica serotype Typhimurium strain LT2 microarray containing 4169 ORFs. This work revealed a list of 2244 genes shared by all members of the genus . Some 1931 of these genes are also present in the genome of E. coli K-12, thus leaving a list of some 313 Salmonella signature genes.
For Salmonella signature genes whose functions are known it seems clear that their presence explains many of the biological features that distinguish Salmonella serotypes from closely related enterobacteria such as E. coli. One important biochemical property for differentiating Salmonella serotypes from E. coli or Shigella serotypes is their ability to produce hydrogen sulfide. This biochemical reaction is part of a complex pathway (involving 88 genes) that allows Salmonella serotypes to utilize 1,2-propanediol and ethanolamine as carbon sources under anaerobic conditions . Genes required for degradation of ethanolamine are encoded by the eutSPQTDMNEJGHABCLK operon whose expression is controlled by the adjacent eutR regulatory gene [9, 10]. Genes required for degradation of 1,2-propane-diol are encoded by a gene cluster consisting of porR, pduF, and the pduABC-DEGHJKLMNOPQSTUVWX operon . The degradation of 1,2-propanediol and ethanolamine furthermore requires the cofactor cobalamin (vitamin B12), whose biosynthesis involves genes encoded by the cobCD operon, cysG, and the cobl operon (cbiABCDETFGHJKLMNQOPUST) . Cobalamin biosynthesis occurs only anaerobically in Salmonella serotypes [13, 14]. The only known electron acceptor supporting anaerobic growth of Salmonella serotypes with 1,2-propanediol or ethanolamine as carbon source is tetrathionate . The genes involved in using tetrathionate as a terminal respiratory electron acceptor are encoded by the divergently described operons ttrSR and ttrBCA . During anaerobic growth on 1,2-propanediol or ethanolamine, Salmonella serotypes reduce tetrathionate to thiosulfate, which is then further reduced to hydrogen sulfide by enzymes encoded by the asrABC operon  and phsABC operon . Although the cbiABCDETFGHJKLMNQOPUST operon, the cobCD operon, the porR pduF pduABCDEGHJKLMNOPQSTUVWX gene cluster, the ttrSR ttrBCA gene cluster, the asrABC operon, and the phsABC operon are located at different map positions on the S. Typhimurium genome, each operon contains Salmonella signature genes identified by microarray analysis (Fig. 6.1) , while only the eut operon and cysG are also present in E. coli. Despite the fact that these operons act in concert during 1,2-propanediol and ethanolamine respiration, their map position and phylogenetic distribution suggests that each was either independently acquired by horizontal gene transfer in the genus Salmonella or lost by deletion from E. coli during divergence of their lineages. 1,2-Propanediol is produced by the fermentation of the common plant sugar rhamnose , suggesting that its utilization may contribute to intestinal colonization of Salmonella serotypes.
A second characteristic that differentiates Salmonella serotypes from E. coli is the ability to cause invasive enteric infections resulting in an inflammatory diarrhea . The genes important for invasion of the intestinal epithelium and the elicitation of an inflammatory response in the intestine are among the Salmonella signature genes identified by microarray analysis [5, 7]. Invasion of intestinal epithelial cells is mediated by a type III secretion system (T3SS-1) encoded by 31 genes located on Salmonella pathogenicity island 1 (SPI1) (Fig. 6.1) . With the exception of the avrA gene , T3SS1 genes located on SPI1 are present in all Salmonella serotypes but absent from the genomes of related enterobacteria . The T3SS-1 translocates effector proteins into the host cell cytosol. Seven T3SS-1 translocated effector proteins are encoded by genes located outside SPI1, including sopA , sopB (sigD) (located on SPI5) , sopD , sopE , sopE2 , slrP , and sspH1 . The genes sipA, sopB, sopD, and sopE2 are present in all phylo-genetic lineages of the genus Salmonella  and are required for bacterial invasion . The different map positions of SPI1, SPI5, sopA, sopD, and sopE2 imply that individual components of the invasion machinery were acquired independently during the divergence of the genus Salmonella from the E. coli lineage by horizontal gene transfer.
The above considerations suggest that some 97 Salmonella signature genes determine two important characteristics that distinguish the genus from closely related enterobacteria, namely the ability to invade and cause inflammation in the intestinal mucosa and the ability to use 1,2-propanediol anaerobically as carbon source (Fig. 6.1). Interestingly, transcriptional profiling using a S. Typhimurium LT2 microarray shows that both groups of genes are coordinately regulated by the CsrA protein . That is, a csrA mutant expresses the pdu operon, the eut operon, the cob operon, the phs operon, the sopE2 gene, the sopA gene, the SPI5 invasion genes, and the SPI1 invasion genes at markedly reduced levels compared to the S. enterica serotype Typhimurium wild type. CsrA may thus be a global regulator of a large subset of Salmonella signature genes involved in the intestinal phase of infection.
Several additional Salmonella signature genes may be critical for interaction of Salmonella serotypes with their vertebrate hosts. Some of these Salmonella signature genes are organized in operons involved in the biosynthesis of fimbrial adhesions, including bcfABCDEFG and sthABCDE [7, 32]. Other Salmonella signature genes involved in host pathogen interaction encode functions allowing bacteria to evade killing by macrophages, a property important for bacterial survival in intestinal tissue upon T3SS-1-mediated penetration of the epithelium. These genes include the magnesium transporters mgtBC encoded by SPI3  and genes encoding a second type III secretion system (T3SS-2) encoded by SPI2 . However, while microarray analysis shows that some SPI2 genes (i.e., sseB, sscA, sscB, ssaNQ and yscR) seem to be conserved in S. bongori , large parts of SPI2 appear to be absent or highly divergent in S. bongori by hybridization analysis [35, 36]. SPI2 is, however, highly conserved among serotypes of S. enterica. In summary, as many as 121 Salmonella signature genes may encode functions that allow Salmonella serotypes to adhere, utilize carbon sources, invade, and subsequently survive in tissue during intestinal colonization of their vertebrate hosts.
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