An alternative to the accepted phylogeny of purple bacteria based on 16S rRNA: Analyses of the amino acid sequences of cytochromes C2 and C556 from Rhodobacter (Rhodovulum) sulfidophilus

It is becoming increasingly apparent from complete genome sequences that 16 S rRNA data, as currently interpreted, does not provide an unambiguous pict ure of bacterial phylogeny, In contrast, we have found that analysis of ins ertions and deletions in the amino acid sequences of cytochrome c(2) has so me advantages in establishing relationships and that this approach may have broad utility in acquiring a better understanding of bacterial relationshi ps. The amino acid sequences of cytochromes c(2) and c556 have been determi ned in whole or in part from four strains of Rhodobacter sulfidophilus. The cytochrome c(2) contains three- and eight-residue insertions as well as a single-residue deletion in common with the large cytochromes c(2) but in co ntrast to the small cytochromes c(2) and mitochondrial cytochromes. In addi tion, the Rb. sulfidophilus protein shares a rare six- to seven-residue ins ertion with other Rhodobacter cytochromes c(2). The cytochrome c556 is a lo w-spin class II cytochrome c homologous to the greater family of cytochrome s c', which are usually high-spin. The similarity of cytochrome c556 to oth er species of class II cytochromes is consistent with the relationships ded uced from comparisons of cytochromes c,. Thus, our results do not support p lacement of Rb. sulfidophilus in a separate genus, Rhodovulum, which was pr oposed primarily on the basis of 16S rRNA sequences. Instead, the Rhodobact er cytochromes c, are distinct from those of other genera and species of pu rple bacteria and show a different pattern of relationships among species t han reported for 16S rRNA. (C) 2001 Academic Press.