Additional Supporting Information may be found in the online version of this article:
Genome circle. Circles (from outside to inside): 1, the outer circle gives the location of all genes of the C1 pathway (red), the heterodisulfide reductase activities (blue) and the methylviologen non-reducing hydrogenase activities (green). Arrows above indicate the orientation of the marked genes with respect to the deduced origin of replication; 2, scale circle in Mbp; 3, the third ring gives the location of all ORFs on the leading and the lagging strand, classified and colour-stained as given by the C
lusters of O
roups of proteins (COG) (http://www.ncbi.nlm.nih.gov/COG/grace/fiew.cgi
); 4, all genes that differ significantly from the standard codon usage of Db. autotrophicum
HRM2 and therefore represent putative foreign genes are marked in green; 5, on the fifth ring all transposase/putative transposonrelated genes (dark blue), or recombinase/invertase genes (orange) are marked; arrows above indicate the orientation of the given genes with respect to the origin of replication; 6, the GC content (red) is given with marked average value (black); 7, translational components are given: rDNA clusters (green), incomplete rDNAs (red) and all tRNAs (blue); arrows above indicate the orientation of the marked genes with respect to the origin of replication.
Mummer plot. Comparison of the Db. autotrophicum
HRM2 chromosome with the chromosomes of the closely related δ-proteobacteria Dt. psychrophila
LSv54, Dv. vulgaris
Hildenborough, Dv. desulfuricans
G20, G. sulfurreducens
PCA and the sulfate-reducing archaeon A. fulgidus
VC-16. Red dots indicate colinear similarities, green dots indicate inverted similarities. The chromosome of Db. autotrophicum
HRM2 completely lacks synteny with the compared chromosomes. In contrast, a mummer plot of a comparison of Dv. vulgaris
Hildenborough and Dv. desulfuricans
G20 reveals genome synteny. All comparisons were performed with the programs from the MUMmer software package as described in the documentation for distantly related sequences (http://mummer.sourceforge.net/
Fig. S3. Protein domain alignment of heterodisulfide reductases (Hdrs) from Db. autotrophicum HRM2 and experimentally characterized Hdr reference proteins. A multiple protein domain alignment of all Hdrs from Db. autotrophicum HRM2 and experimentally characterized reference proteins revealed the four distinct Hdr groups A, L, D and F. The alignment is based on colour-coded Pfam domain scans. Each protein group contains at least one selenocysteine-containing and one non-selenocysteine-containing paralogue of the enzyme. In many cases Db. autotrophicum HRM2 encodes the protein domains necessary to form an Hdr by two or more colocalized genes. It is remarkable that in each case the order of the Hdr domains is conserved in the order of the encoding genes and is colinear to the order of domains within the reference proteins. Group A contains four Hdrs of Db. autotrophicum HRM2 with similarities to HdrA of the archaea M. mazei and A. fulgidus. HdrA1 to HdrA3 are encoded by two and three genes, respectively, which contain all Pfam domains found in the single polypeptides of the reference proteins. For HdrA4 no protein encoding the MvhD domain could be identified. Group L contains three members, HdrL1 to HdrL3, each colocalized with a MvhD protein. The group L proteins are newly found in Db. autotrophicum HRM2. Group D contains HdrD1 to HdrD5 from Db. autotrophicum HRM2. The members of this group align with the domains of HdrD1 from A. fulgidus. HdrD is a paralogue of HdrD from HdrDE from M. mazei and A. fulgidus, which are encoded by one protein in the case of A. fulgidus and two proteins in the case of M. mazei respectively. An orthologue of HdrE could not be identified within the Db. autotrophicum HRM2 genome. Group F consists of three members HdrF1 to HdrF3. HdrF1/F1′ is encoded by two genes whereas HdrF2 and HdrF3 are encoded by one gene. Group F represents, as group L, a newly found type of Hdrs from Db. autotrophicum HRM2.
Table S1. Bidirectional blast comparisons of 4947 protein sequences from Db. autotrophicum HRM2 and 700 whole genome protein data sets.
Table S2. Repeat analysis of sulfate- or sulfur-reducing prokaryotes.
Table S3. Selenocysteine-containing proteins.
Table S4. Pfam domain occurrence in two-component systems from Db. autotrophicum HRM2.
Table S5. Sequence of used primers.
Please note: Wiley-Blackwell are not responsible for the content or functionality of any supporting materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.