Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co-culture with Sedimentibacter sp.
Article first published online: 31 AUG 2012
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Environmental Microbiology Reports
Volume 4, Issue 6, pages 604–616, December 2012
How to Cite
Maphosa, F., van Passel, M. W. J., de Vos, W. M. and Smidt, H. (2012), Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co-culture with Sedimentibacter sp. Environmental Microbiology Reports, 4: 604–616. doi: 10.1111/j.1758-2229.2012.00376.x
- Issue published online: 14 NOV 2012
- Article first published online: 31 AUG 2012
- Accepted manuscript online: 7 AUG 2012 08:36AM EST
- Manuscript Accepted: 28 JUL 2012
- Manuscript Received: 24 JUL 2012
- Ecogenomics Project of the Netherlands Genomics Initiative
- Netherlands Organization for Scientific Research(NWO)
Fig. S1. Hierarchical clustering of the normalized genome dissimilarity scores for the 4 largest contigs of each of Dehalobacter and Sedimentibacter. The Dehalococcoides mccartyi 195 genome sequence was included in the comparison as external reference. Depicted in solid and dashed circles are the Dehalobacter and Sedimentibacter contigs respectively, indicating they have similar genome signatures.
Fig. S2. General protein coding features of the Dehalobacter genome. Hypothetical – no significant similarity to any other sequenced gene. Conserved unknown – conserved hypothetical protein with sequence similarity to a translation of an ORF in another organism; however, there is no experimental evidence for its protein production. Unknown function – significant sequence similarity to a named protein for which no specific function is currently assigned.
Fig. S3. Classification of Sedimentibacter small contigs (< 1000 bp) with high G + C (60–80%) based on functional clustering as implemented in MG-RAST.
Fig. S4. Partial primary sequence alignment of predicted reductive dehalogenase homologues in Dehalobacter sp. E1 and characterized proteins from other OHRB. Deduced amino acid sequences were aligned with ClustalW (Thompson et al., 1994). Conserved sequence motifs including two iron sulfur cluster binding motifs and the twin arginine signal sequence (C2-C6, FeS1, FeS2 and RR) are indicated. (AAW39060 – TceA, Dehalococcoides mccartyi 195; CAD28790 – PceA, Dehalobacter restrictus; AAQ54585 – CprA5, Desulfitobacterium hafniense PCP1; AAW80323 – PceA, Desulfitobacterium hafniense Y51; AAD44542 – CprA, Desulfitobacterium dehalogenans).
Fig. S5. Comparison of the pceABCT cluster on Contig00022 of the Dehalobacter E1 genome sequence to the gene cluster of Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense strains TCE1 and Y51. tnp – transposase-like elements, mcpA – methyl accepting chemotaxis gene, IS represents an insertion sequence element of the IS3/IS911 family, ACR an uncharacterized Archaeal Conserved Region (COG2078) and PFLA a putative pyruvate-formate lyase-activating enzyme.
Table S1. Reductive dehalogenase homologue encoding genes identified in the Dehalobacter genome.
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