Bellgard, M.

Hampson, D.

Wanchanthuek, P.

English

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Comparison of Brachyspira central metabolism pathways using genomic sequence data Phatthanaphong Wanchanthuek1,3      David J. Hampson2         pwnach@ccg.murdoch.edu.au            D.Hampson@murdoch.edu.au  Matthew Bellgard1 mbellgard@ccg.murdoch.edu.au 1 Centre for Comparative Genomics, Murdoch University, South Street, Murdoch, WA 6150, Australia 2  School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia 3  Faculty of Informatics, Mahasarakham University, Kantarawichai District, Mahasarakham 44150, Thailand  1  Introduction   The Brachyspira hyodysenteriae and B. pilosicoli are anaerobic spirochaetes that colonize the large intestine and cause diarrhea. We recently sequenced the 3.0 and 2.6 Mb genomes of B. hyodysenteriae and B. pilosicoli, respectively. The complete genome sequences were analyzed, and putative biological functions were assigned to 1,829 (69%) of the 1,685 (73%) predicted protein-encoding genes. Annotation of the genome, however, is only the first step toward understanding the function of genes. To understand biological function, individual genes have to be placed into a biological context, including the context of metabolic pathways. Reconstruction of metabolic pathways therefore will assist in our understanding in silico predictions of gene function and the metabolic (potential) capabilities of an organism. Many databases and tools that aid metabolic reconstruction can be found on the World Wide Web (1). We have used genomic information to construct the major metabolic pathways of B. hyodysenteriae and B. pilosicoli and performed a comparative analysis of the metabolic genes and pathways of B. hyodysenteriae and B. pilosicoli. Overall, the metabolic pathways of B. hyodysenteriae were similar to B. pilosicoli, but there were notable differences in several pathways including nucleotidesugar metabolism, lipopolysaccharide biosynthesis and the synthesis of cell wall components. Our results provide a useful guide to the post-genomic analysis of B. hyodysenteriae and B. pilosicoli and lead to a better understanding of the predicted structure and functional of these spirochaetes.    2  Materials and Methods  2.1  Organisms  The complete genomic sequences of B. hyodysenteriae WA-1 and a draft of the genome sequence of B. pilosicoli 95/1000 were recently obtained and annotated at the Centre for Comparative Genomics (CCG), Murdoch University.  2.2  Prediction and annotation of protein coding sequences   Metabolic and genetic analysis of B. hyodysenteriae and B. pilosicoli was based on previous published annotation data. Annotation of COGs of putative functional genes was further confirmed by performing a BLAST search against the COG database (e-value >1-5, multiple assignments per protein allowed) (7). Metabolic pathways were subsequently analyzed using the Kyoto encyclopedia of genes and genomes (KEGGs) metabolic database (2, 4). Each gene that was implicated in a metabolic pathway was manually confirmed by a BLAST search of KEGG genes using BLASTP program (e-value >1-5).  3  Results  Analysis of the genome sequences provided a global view of the metabolic potential of B. hyodysenteriae and B. pilosicoli (Fig. 1). Of the 2,652 (B. hyodysenteriae) and 2,297 (B. pilosicoli) predicted proteins, 801 (30%) and 781 (34%) predicted proteins were indentified as enzymes, of which 375 (14%) and 365 (15%) were assigned Enzyme Commission (EC) numbers. This is considerably fewer than the roughly one-quarter to one-third of the genes in bacterial and archeal genomes that can be mapped to KEGG pathway diagrams (3). This suggests either that B. hyodysenteriae and B. pilosicoli have a similar proportion of its genome devoted to enzymes, or that enzymes are more difficult to identify in B. hyodysenteriae and B. pilosicoli by sequence similarity methods. However, many biochemical pathways could be reconstructed in their entirety, suggesting that this similarity-searching approach was for the most part successful, and that the relative paucity of enzymes in B. hyodysenteriae and B. pilosicoli may relate to their life-style in large intestine.   Figure 1. Key metabolic pathways in B. hyodysenteriae and B. pilosicoli  Genome sequence analysis revealed that the enzymes of these pathways are present in B. hyodysenteriae and B. pilosicoli. The central metabolic pathways are a glycolytic pathway and non-oxidative pentose phosphate pathway (Fig. 1). Briefly, the central carbon metabolic pathway in B. hyodysenteriae and B. pilosicoli are most similar to that in Leptospira. B. hyodysenteriae and B. pilosicoli have a complete glycolysis pathway and pentose phosphate pathway, but an incomplete TCA cycle. This incomplete reductive type of cycle probably functions primarily in carbon assimilation and the generation of precursor metabolites for biosynthesis (5). Some of the previously identified metabolic characteristics of Brachyspira, such as the absence of the TCA (6), were confirmed by genomic analysis. A complete set of genes for glycolysis, nucleotide metabolism and lipopolysaccharide biosynthesis, and respiratory electron transport chain were identified in B. hyodysenteriae and B. pilosicoli (Fig. 1). This was consistent with the notion that the organisms generate ATP by oxidative phosphorylation.   References  [1] Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R. & Palsson, B. O. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences of the United States of America 104, 1777-1782. [2] Kanehisa, M. & Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28, 27-30. [3] Kanehisa, M. (2002). The KEGG database. Novartis Foundation symposium 247, 91-101; discussion 101-103, 119-128, 244-152. [4] Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. (2002). The KEGG databases at GenomeNet. Nucleic Acids Research, 30, 42-46. [5] Romano, A. H. & Conway, T. (1996). Evolution of carbohydrate metabolic pathways. Research in Microbiology, 147, 448-455. [6] Stanton, T. B. (1989). Glucose metabolism and NADH recycling by Treponema hyodysenteriae, the agent of swine dysentery. Applied and Environmental Microbiology, 55, 2365-2371. [7] Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. (2000). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research, 28, 33-36.   

Comparison of Brachyspira central metabolism pathways

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Comparison of Brachyspira central metabolism pathways

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