The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production
Article first published online: 12 MAY 2010
© 2010 Society for Applied Microbiology and Blackwell Publishing Ltd
Special Issue: Symbiosis. Editors: Professors Paola Bonfante, Karen Visick, and Moriya Ohkuma
Volume 12, Issue 8, pages 2289–2301, August 2010
How to Cite
Sieber, J. R., Sims, D. R., Han, C., Kim, E., Lykidis, A., Lapidus, A. L., McDonnald, E., Rohlin, L., Culley, D. E., Gunsalus, R. and McInerney, M. J. (2010), The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environmental Microbiology, 12: 2289–2301. doi: 10.1111/j.1462-2920.2010.02237.x
- Issue published online: 4 AUG 2010
- Article first published online: 12 MAY 2010
- Received 18 January, 2010; accepted 5 March, 2010.
Fig. S1. Phylogeny of S. wolfei. A maximum likelihood dendrogram of syntrophic and non-syntrophic species was generated using near full-length, aligned 16S rRNA genes downloaded from the Greengenes database (DeSantis et al., 2006). A bootstrapped (100 reps) maximum likelihood dendrogram was generated using the RAxML algorithm (Stamatakis et al., 2008) as implemented online by the CIPRES Portal (Miller et al., 2009).
Fig. S2. Circular representation of the S. wolfei genome. The concentric circles (from outside to inside) indicate: ORFs on the forward (circle 1) and reverse (circle 2) strands (each coloured by COG categories); RNA genes (tRNA genes in green, sRNA genes in red and other RNA genes in black) (circle 3); G + C content (circle 4); and G + C skew (circle 5). Key genes are shown on the outside, hydrogenases and formate dehydrogenases in green, β-oxidation genes in blue, genes potentially involved in reverse electron transport in pink, and ATPase and HDR in black.
Fig. S3. Ribosomal RNA gene clusters of S. wolfei. The enlargement below shows the alignment of the initial portions of the three 16S rRNA genes.
Fig. S4. Best reciprocal protein hits for S. wolfei ORFs with other genomes.
Fig. S5. Best blast hit distribution of S. wolfei ORFs with other genomes.
Fig. S6. Phylogenetic analysis of predicted coding sequences of the membrane-bound FeS oxidoreductase potentially involved in reverse electron transport in S. wolfei. Similar protein coding genes of interest were identified, translated and downloaded from the Integrated Microbial Genomes (IMG) database. Amino acid sequences were aligned using ProbCons (Do et al., 2005) and databases were created using ARB (Ludwig et al., 2004). Sequences were exported and maximum likelihood trees were created (using the Jones–Taylor–Thornton probability model) and bootstrapped 100 times using the phylip phylogenetic package (Felsenstein, 1989). Bootstrap values are given above each node only for values greater than 50%.
Table S1. General features of the S. wolfei genome in comparison with genomes of select members of the Firmicutes and other bacteria capable of syntrophic metabolism.
Table S2. List of genes involved in key metabolic step in S. wolfei.
Table S3. List of genes involved in electron transfer and formation of ion gradients and those predicted to have transmembrane helices in S. wolfei.
Table S4. List of genes involved in transport in S. wolfei.
Table S5. List of sigma factor genes in S. wolfei.
Table S6. List of genes involved in motility and chemotaxis in S. wolfei.
Table S7. List of genes involved in sporulation in S. wolfei.
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