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Comparative genomics to investigate genome function and adaptations in the newly sequenced Brachyspira hyodysenteriae and Brachyspira pilosicoli

Wanchanthuek, Phatthanaphong (2009) Comparative genomics to investigate genome function and adaptations in the newly sequenced Brachyspira hyodysenteriae and Brachyspira pilosicoli. PhD thesis, Murdoch University.

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Brachyspira hyodysenteriae and Brachyspira pilosicoli are anaerobic intestinal spirochaetes that are the aetiological agents of swine dysentery and intestinal spirochaetosis, respectively. As part of this PhD study the genome sequence of B. hyodysenteriae strain WA1 and a near complete sequence of B. pilosicoli strain 95/1000 were obtained, and subjected to comparative genomic analysis. The B. hyodysenteriae genome consisted of a circular 3.0 Mb chromosome, and a 35,940 bp circular plasmid that has not previously been described. The incomplete genome of B. pilosicoli contained 4 scaffolds. There were 2,652 and 2,297 predicted ORFs in the B. hyodysenteriae and B. pilosicoli strains, respectively. Of the predicted ORFs, more had similarities to proteins of the enteric Clostridium species than they did to proteins of other spirochaetes. Many of these genes were associated with transport and metabolism, and they may have been gradually acquired through horizontal gene transfer in the environment of the large intestine.

A reconstruction of central metabolic pathways of the Brachyspira species identified a complete set of coding sequences for glycolysis, gluconeogenesis, a non-oxidative pentose phosphate pathway, nucleotide metabolism and a respiratory electron transport chain. A notable finding was the presence of rfb genes on the B. hyodysenteriae plasmid, and their apparent absence from B. pilosicoli. As these genes are involved in rhamnose biosynthesis it is likely that the composition of the B. hyodysenteriae lipooligosaccharide O-sugars is different from that of B. pilosicoli. O-antigen differences in these related species could be associated with differences in their specific niches, and/or with their disease specificity. Overall, comparison of B. hyodysenteriae and B. pilosicoli protein content and analysis of their central metabolic pathways showed that they have diverged markedly from other spirochaetes in the process of adapting to their habitat in the large intestine.

The presence of overlapping genes in the two spirochaetes and in other spirochaete species also was investigated. The number of overlapping genes in the 12 spirochaete genomes examined ranged from 11-45%. Of these, 80% were unidirectional. Overlapping genes were found irregularly distributed within the Brachyspira genomes such that 70-80% of them occurred on the same strand (unidirectional, ->->/<-<-), with 16-28% occurring on opposite DNA strands (divergent, <-->). The remaining 4-6% of overlapping genes were convergent (-><-). The majority of the unidirectional overlap regions were relatively short, with >50% of the total observations overlapping by >4 bp. A small number of overlapping gene-pairs were duplicated within each genome and there were some triplet overlapping genes. Unique orthologous overlapping genes were identified within the various spirochaete genera. Over 75% of the overlapping genes in the Brachyspira species were in the same or related metabolic pathway. This finding suggests that overlapping genes are not only likely to be the result of functional constraints but also are constrained from a metabolomic context. Of the remaining 25% overlapping genes, 50% contained one hypothetical gene with unknown function. In addition, in one of the orthologous overlapping genes in the Brachyspira species, a promoter was shared, indicating the presence of a novel class of overlapping gene operon in these intestinal spirochaetes.

Item Type: Thesis (PhD)
Murdoch Affiliation: Centre for Comparative Genomics
Supervisor(s): Bellgard, Matthew
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