Phylogenetic Tree of CooS Homologs

<p>The figure shows a maximum-likelihood tree of CooS homologs. The tree indicates the five CooS homologs in <i>C. hydrogenoformans</i> 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 (<a href="http://www.jgi.doe.gov/" target="_blank">http://www.jgi.doe.gov/</a>).</p

Genomic Organization of <i>C. hydrogenoformans</i>

<p>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).</p

An Electron Micrograph of a <i>C. hydrogenoformans</i> Endospore

<p>The finding of homologs of many genes involved in sporulation in other species led us to test whether <i>C. hydrogenoformans</i> 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.</p

Genome Locations of Genes Predicted to Encode Five CODH Complexes

<p>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.</p

Genome Tree of Representatives of Firmicutes

<p>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: <i>Corynebacterium glutamicum</i> and <i>Streptomyces coelicolor.</i> 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 <i>B. subtilis</i> sporulation genes are also shown.</p

Predicted Complete Acetyl-CoA Pathway of Carbon Fixation in <i>C. hydrogenoformans</i>

<p>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.</p

Phylogenetic Analysis and Frequency Distribution of Protein Percent Identity

<p>Concensus maximum-likelihood trees are depicted using multiple alignments of 16S rRNA (A) or 12 concatenated protein datasets (B). The numbers along the branches denote percent occurrence of nodes among 100 bootstrap replicates. The scale bar represents the number of nucleotide (A) or amino acid (B) substitutions.</p

Whole-Genome Comparison of Five <i>Campylobacter</i> Strains

<p>Line figures depict the results of PROmer analysis. Colored lines denote percent identity of protein translations and are plotted according to the location in the reference (C. jejuni RM1221, x-axis) and query genomes (C. jejuni NCTC 11168 [upper y-axis] and C. coli RM2228 [lower y-axis]) (A). The Venn diagrams show the number of proteins shared (black) or unique (red) within a particular relationship for all five <i>Campylobacter</i> strains (B) and for members of the sequenced ε-Proteobacteria compared in this study (C). Protein sequences binned as “unique” are unique within the context of the genomes plotted and the cutoffs used to parse the BLASTP data. The pie charts plot the number of protein sequences by main functional role categories for C. jejuni RM1221 ORFs. A frequency distribution of protein percent identity (D) was computed: specifically, the number of protein sequences within class intervals of 5% amino acid identity from 35% to 100% that match C. jejuni RM1221 reference sequences were plotted.</p

Linear Representations of Prophage Regions

<p>Regions are (from top to bottom): CMLP1, CJIE2, CJIE4, CLIE1, and CUIE1. Colors of ORFs are indicated in the key by putative phage function. Connecting lines represent those ORFs whose protein sequences match at a BLASTP of 30% identity or better. These lines do not indicate the coordinates of match, merely that there is a match.</p

Phage Alignments and Neighboring Genes

<p>Conserved gene order between the WO phage in <i>Wolbachia</i> sp. <i>w</i>Kue and prophage regions of <i>w</i>Mel. Putative proteins in <i>w</i>Kue (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020069#pbio-0020069-Masui2" target="_blank">Masui et al. 2001</a>) were searched using TBLASTN against the <i>w</i>Mel genome. Matches with an <i>E</i>-value of less than 1e⁻¹⁵ are linked by connecting lines. CDSs are colored as follows: brown, phage structural or replication genes; light blue, conserved hypotheticals; red, hypotheticals; magenta, transposases or reverse transcriptases; blue, ankyrin repeat genes; light gray, <i>radC</i>; light green, paralogous genes; gold, others. The regions surrounding the phage are shown because they have some unusual features relative to the rest of the genome. For example, WO-A and WO-B are each flanked on one side by clusters of genes in two paralogous families that are distantly related to phage repressors. In each of these clusters, a homolog of the <i>radC</i> gene is found. A third <i>radC</i> homolog (WD1093) in the genome is also flanked by a member of one of these gene families (WD1095). While the connection between <i>radC</i> and the phage is unclear, the multiple copies of the <i>radC</i> gene and the members of these paralogous families may have contributed to the phage rearrangements described above.</p