The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species

Abstract

The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the α, β, γ, δ, and ε Proteobacteria, cyanobacteria, high-GC grampositives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positives species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with the RecAs of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences, phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.

Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant

“…Moreover, large-scale phylogenies of recA in the Bacteria as a whole have been found to be consistent with the corresponding rRNA gene sequence-based phylogenies (Eisen, 1995;Young, 1998).…”

Highly Solvent Tolerance in Serratia marcescens IBBPo15

“…bacteria examined, this gene was proposed as a phylogenetic marker for distantly related species 33 . The expression of recA gene in bacteria is inducible by agents which cause DNA damage 11 .…”

Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis.

“…Resolving deeper branches of prokaryotic phylogeny with rRNA is notoriously difficult (Pace, 1997). Affinity between cyanobacteria and high-GjC Grampositives has been observed in the case of RecA, though not for rRNA from the same species (Eisen, 1995). Affinity between cyanobacteria and Grampositives is also observed in phylogenies of Hsp70, though not specifically to either high-or low-GjC groups (Gupta, 1998).…”