Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene

Abstract

Genes from Pseudomonas fluorescens, Chromatium vinosum, Micrococcus luteus, Deinococcus radiodurans, and Thermotoga maritima with homology to the Escherichia coli rho gene were cloned and sequenced, and their sequences were compared with other available sequences. The species for all of the compared sequences are members of five bacterial phyla, including Thermotogales, the most deeply diverged phylum. This suggests that a rho-like gene is ubiquitous in the Bacteria and was present in their common ancestor. The comparative analysis revealed that the Rho homologs are highly conserved, exhibiting a minimum identity of 50% of their amino acid residues in pairwise comparisons. The ATP-binding domain had a particularly high degree of conservation, consisting of some blocks with sequences of residues that are very similar to segments of the a and , subunits of Fl-ATPase and of other blocks with sequences that are unique to Rho. The RNA-binding domain is more diverged than the ATP-binding domain. However, one of its most highly conserved segments includes a RNP1-like sequence, which is known to be involved in RNA binding. Overall, the degree of similarity is lowest in the first 50 residues (the first half of the RNA-binding domain), in the putative connector region between the RNA-binding and the ATP-binding domains, and in the last 50 residues of the polypeptide. Since functionally defective mutants for E. coli Rho exist in all three of these segments, they represent important parts of Rho that have undergone adaptive evolution. More recently, a gene with a sequence similar to that of E. coli rho was identified for B. subtilis (38). This suggested that the rho gene may not be confined to close relatives of E. coli.To help resolve the question of the universality of Rho homologs, we undertook the identification, isolation, and sequence characterization of genes with homology to the E. coli rho gene from evolutionarily diverged bacteria. Since mutations occur naturally and will accumulate over a long period of time, the sequences of diverged homolog genes can be used to determine the parts of Rho in which the residues are constrained to maintain the structure and function of the protein and the parts in which the residues are able to diverge. Thus, the finding of diverged homolog genes would also contribute to an understanding of the structural organization of Rho protein.We report here the sequences of rho gene homologs from five bacteria, two from the same subphylum as E. coli, and three from highly diverged phyla. These sequences along with recently reported sequences of rho gene homologs from three other diverged organisms and along with that of the E. coli rho gene are analyzed with respect to evolutionary relatedness and to the positions of conserved and diverged residues. The results indicate that a gene with homology to E. coli rho is widespread in the Bacteria, that it probably existed when the Bacteria diverged from the progenitor that also gave rise to the Archaea and the Eukarya, and that it encodes a protei...

Phyletic distribution and conservation of the bacterial transcription termination factor Rho

“…Species containing rho belong to nearly all bacterial phyla with the noticeable exceptions of Tenericutes and Cyanobacteria (see below), which confirms previous observations (Opperman & Richardson, 1994;Washburn et al, 2001). Analysis of published data also indicates that Rho proteins are expressed in representative species across phyla (Table S2).…”

“…5; see also below). Overall, Rho's CTD appears more conserved than that of NTD, which confirms previous observations (Opperman & Richardson, 1994). Of particular notice is the fact that most Rho factors from Actinobacteria and Bacteroidetes, a significant fraction of Rho factors from Firmicutes and a few additional Rho factors from other phyla contain large insertion domains between the NHB and CSD-like RBD regions (Fig.…”

“…tuberculosis), BSU37080 (Bacillus subtilis), HMPREF9087_1232 (Enterococcus casseliflavus), sce7932 (Sorangium cellulosum) and Hprae_1978 (Halanaerobium praevalen). Consistent with long-known homology (Opperman & Richardson, 1994), usually the best PSI-BLAST hits for rho-less species were ATP synthase subunits with 40-60 % coverage (corresponding to Rho's CTD) and 20-30 % identity scores.…”

“…Interestingly, genomes containing rho sequence(s) tend to be larger and GC-richer than rho-less genomes, suggesting a link between Rho function and the complexity of genome structure (or expression) and/or lifestyle of the bacterial species. Overall, our work significantly extends early phylogenetic analyses (Opperman & Richardson, 1994;Washburn et al, 2001) that were performed with limited sets of bacterial sequences and before detailed structural information on Rho became available, thereby providing a comprehensive framework for future analyses of this central regulatory factor.…”

“…The rationale for this simple rule is, however, not firmly established. Notably, the phyletic distribution and structural conservation of Rho within living organisms were inferred more than a decade ago from very limited sets of DNA sequences (Opperman & Richardson, 1994;Washburn et al, 2001). Hence, the fractions of bacteria devoid of rho genes or containing Rho factors whose function may be unaffected by BCM are not known.…”