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
Rp. Ambler et al., 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, ARCH BIOCH, 388(1), 2001, pp. 25-33
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.