Figure 1.
Genomic Organization of C. hydrogenoformans
From the outside inward the circles show: (1, 2) predicted protein-coding regions on the plus and minus strands (colors were assigned according to the color code of functional classes; (3) prophage (orange) and CRISPR (pink) regions; (4) χ2-square score of tri-nucleotide composition; (5) GC skew (blue indicates a positive value and red a negative value); (6) tRNAs (green); (7) rRNAs (blue) and structural RNAs (red).
Table 1.
General Features of the C. hydrogenoformans Genome
Figure 2.
Genome Tree of Representatives of Firmicutes
A maximum likelihood tree was built from concatenated protein sequences of 31 universal housekeeping genes and rooted by two outgroup Actinobacteria (high GC Gram-positives) species: Corynebacterium glutamicum and Streptomyces coelicolor. Bootstrap support values (out of 100 runs) for branches of interest are shown beside them. Each species' ability to sporulate and its number of putative orthologs of the 175 known B. subtilis sporulation genes are also shown.
Figure 3.
Genome Locations of Genes Predicted to Encode Five CODH Complexes
The genome locations of the genes encoding the five CooS homologs (labelled CooS I-V) are shown. Also shown are neighboring genes that are predicted to encode the five distinct CODH complexes (CODH I-V) with each CooS homolog. Possible cellular roles for four of the five CODH complexes are indicated.
Figure 4.
Phylogenetic Tree of CooS Homologs
The figure shows a maximum-likelihood tree of CooS homologs. The tree indicates the five CooS homologs in C. hydrogenoformans are not the result of recent duplications but instead are from distinct subfamilies. The other CooS homologs included in the tree were obtained from the NCBI nr database and include some from incomplete genome sequences generated by United States Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/).
Figure 5.
Predicted Complete Acetyl-CoA Pathway of Carbon Fixation in C. hydrogenoformans
Genes predicted to encode each step in the acetyl-CoA pathway of carbon fixation were identified in the genome. The locus numbers are indicated on the figure.
Table 2.
Orthologs of Known Bacillus subtilis Sporulation Genes in C. hydrogenoformans
Figure 6.
An Electron Micrograph of a C. hydrogenoformans Endospore
The finding of homologs of many genes involved in sporulation in other species led us to test whether C. hydrogenoformans also could form an endospore. Under stressful growth conditions, endospore-like structures form. We note that even though homologs could not be found in the genome for many genes that in other species are involved in protective outer-layer (cortex, coat, and exosporium) formation, those structures seem to be visible and intact.
Figure 7.
Phylogenetic Profile Analysis of Sporulation in C. hydrogenoformans
For each protein encoded by the C. hydrogenoformans genome, a profile was created of the presence or absence of orthologs of that protein in the predicted proteomes of all other complete genome sequences. Proteins were then clustered by the similarity of their profiles, thus allowing the grouping of proteins by their distribution patterns across species. Examination of the groupings showed one cluster consisting of mostly homologs of sporulation proteins. This cluster is shown with C. hydrogenoformans proteins in rows (and the prediced function and protein ID indicated on the right) and other species in columns with presence of a ortholog indicated in red and absence in black. The tree to the left represents the portion of the cluster diagram for these proteins. Note that most of these proteins are found only in a few species represented in red columns near the center of the diagram. The species corresponding to these columns are indicated. We also note that though most of the proteins in this cluster, for which functions can be predicted, are predicted to be involved in sporulation and some have no predictable functions (highlighted in blue). This indicates that functions of these proteins' homologs have not been characterized in other species. Since these proteins show similar distribution patterns to so many proteins with roles in sporulation, we predict that they represent novel sporulation functions.
Table 3.
Selenoproteins Identified in C. hydrogenoformans Genome