Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the <i>Salmonella</i> pathogenicity islands

Vernikos, Georgios S.; Parkhill, Julian

doi:10.1093/bioinformatics/btl369

Cited by 383 publications

(405 citation statements)

References 28 publications

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“…SPI-6 varies markedly in size in all the other sequenced Salmonella, including S. Typhi (McClelland et al 2001(McClelland et al , 2004Parkhill et al 2001;Chiu et al 2005). Of the other known SPIs, are absent from S. Enteritidis PT4 Vernikos and Parkhill 2006). Conversely, SPI-17 is present in S. Enteritidis PT4 but absent from S. Typhimurium LT2.…”

Section: Resultsmentioning

confidence: 99%

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Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Thomson

Clayton

Windhorst³

et al. 2008

Genome Res.

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We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis. Significantly, the genome of S. Gallinarum has undergone extensive degradation through deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those identified previously in other host-adapted bacteria reveals the loss of many common functional traits and provides insights into possible mechanisms of host and tissue adaptation. We propose that experimental analysis in chickens and mice of S. Enteritidis–harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica.

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Section: Resultsmentioning

confidence: 99%

“…Conversely, SPI-17 is present in S. Enteritidis PT4 but absent from S. Typhimurium LT2. The S. Enteritidis PT4 SPI-17 is a degenerate prophage encoding CDS known to be involved in O-antigen conversion in other systems (Vernikos and Parkhill 2006).…”

Section: Resultsmentioning

confidence: 99%

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Thomson

Clayton

Windhorst³

et al. 2008

Genome Res.

Self Cite

398

511

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“…Putative genes from horizontal gene transfer (HGT) were identified using Alien_hunter (Vernikos and Parkhill, 2006) using a threshold of 12.015 and a window size of 5000 nt. BLASTX search of the output identified 357 open reading frames.…”

Section: Genome Annotation and Analysismentioning

confidence: 99%

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

et al. 2014

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Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49 T and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49 T to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49 T relies on the relatively abundant r-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49 T to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques.

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“…These gene blocks are often inserted near a tRNA gene and generally display distinct codon usage and a different overall base composition from the core bacterial chromosome, suggesting that they were acquired from a foreign source. Thus far, 15 SPIs have been identified in Typhi [1,14]. SPI-1 and SPI-2, which are present in all S. enterica serovars, represent 2 major pathogenesis determinants that encode type III secretion systems (T3SS).…”

Section: Salmonella Pathogenicity Islands (Spi)mentioning

confidence: 99%

Typhi genes expressed during infection or involved in pathogenesis

Daigle

2008

J Infect Dev Ctries

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Salmonella enterica serovar Typhi (Typhi), the aetiologic agent of typhoid fever, is a human restricted pathogen. Elucidation of the interactions between the infected host and this pathogen is critical to understand infectious diseases but is deterred by a lack of in vivo infection assays, since Typhi uniquely infects humans and there is no suitable animal model. Macrophages can be used as an alternative model, as the ability to survive and replicate within these cells is thought to be one of the major pathogenesis determinants for Salmonella. Typhi genes that are expressed within human macrophages have been identified, as well as Typhi immunogenic proteins expressed in humans with typhoid. Known virulence factors of Salmonella are expressed during infection of macrophages, such as SPI-2 encoded genes, supporting the validity of the model; however, many genes of unknown functions are also expressed. The importance of these genes should be investigated during future studies aimed at elucidating the intracellular lifestyle of this human-specific pathogen. This review describes Typhi genes expressed during infection or involved in cell interaction.

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Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 383 publications

References 28 publications

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

Typhi genes expressed during infection or involved in pathogenesis

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