Christopher Medway edited Results and Discussion.tex  over 8 years ago

Commit id: 73d9084d32a638f88e20011351f5e420dbb7756e

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Another genomic feature of Yersinia that deliniates pathogenic and non-pathogenic biovars in the 'high-pathogenicity island' (HPI) \cite{11418330}. The HPI is present in highly pathogenic yersinia (pestis, pseudotuberculosis III amd enterocolitica 1B) and absent in mildly- and non-pathogenic biovars \cite{11418330}. Although the arcitecture of the HPI differs between yersinia species, there is a common repertoise of yersiniabactin genes. The HPI found in \textit{Y.enterocolitica}, HPI_Yen, is approximatly 44kbp, larger than the HPI_Yps (36.8kbp) found in other pathogenic Yersinia \cite{15493818}. Yersiniabactin is a sidophore pivitol for the harnessing and trafficking iron, an essential cofactor in many enzymatic reactions. HPI_Yen comprises of \textit{irp1-9}, textit{YbtA} and \textit{fyuA}, in adittion to insertion sequennces; IS1328 and IS1400. Genes known to flank the HPI, glycosyl hydrolases locus on one flank, and the citrate synthase locus on the other, were present in a single 157kbp contig in our query sequence. However none of the yersiniabactin machinery is found in our Y.enterocolitica sample. Compared to a reference Y.enterocolitica biovar 1B (GenBank: AM286415.1), which does contain the HPI, the distance between flanking loci was 32kbp shorter in our query sequence. Furthermore, interrogating the ISfinder database did not reveal any of the repetative sequences (IS1328, IS1329 and IS1400) charateristic of a pathogenic biovar.  \subsection{Metabolism and Functional Pathways}  The metabolic flexibility of \textit{Y.enterocolitica} biovars is known to the highly heterogeneous, with biovar 1A displaying the least flexability broadest metabolic potential \cite{Reuter}. Several metabolic pathways are known to be specific to certain Yersinia linieges; cobalamine biosynthesis, 1,2-propanediol utilisation, tetrathionate respiration, hydrogenase complexes and cellulose biosynthesis  \cite{Reuter}. Comparison of all functional catagories between our query \textit{Y.enterocolitica} biovar and a 'reference pathogenic' Y.enterocolitica strain 8081 (a 1B biovar) isolates a number of exclusive functional domains. Most strikingly, the pathogenic reference is enriched for; i) membrane transport protein, particularly of the type-III sectreation system, and ii) iron-aquasition and metabolism proteins.  Our query strain has a number of metabolic/functional catagories not found in the pathogenic reference; i) Coenzyme B12 biosynthesis ?? (\textit{pduO}), ii) RTX toxin cluster, iii) beta-Fimbriae (type VII secretion system), iv) Choloylglycine hydrolase and bile hydrolysis, v) Central meta-cleavage pathway of aromatic compound degradation, vi) D-galactonate catabolism, vii) Aldehyde dehydrogenase B, viii) L-fucose utilization**, ix) N-Acetyl-Galactosamine and Galactosamine Utilization**, x) Phage packaging machinery, Phage replication and Phage tail proteins and xi)Xanthosine utilization (xap region).  \cite{21798805}  Taken together, the phylogenetic analysis and genome annotation suggest that the query sequence is of a non-pathogenic strain (1A) of \textit{Y.enterocolitica}. Whilst not carrying any of the established markers of pathogenicity, the presence of several novel virulance features may confeer upon it a degree of pathogenic potential.