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 - PubMed (original) (raw)

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

J A Eisen. J Mol Evol. 1995 Dec.

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 alpha, beta, gamma, delta, epsilon proteobacteria, cyanobacteria, high-GC gram-positives, 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-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those 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.

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Figures

Figure 1

Figure 1

Alignment of complete RecA sequences. The alignment was generated using the clustalw multiple sequence alignment program. Dashes (-) represent alignment gaps. Three insertions that are present in only one sequence each (Myb.t, Myb.l, and Tg.m) and the first 80 aa of the A. thaliana protein are left out for space reasons and are indicated by a ••. Conservation of alignment positions as determined by the clustalw program is indicated by * (identical aa in all) and. (similar aa in all). The alignment positions used in phylogenetic analysis are indicated by the sequence mask (1=used, 0=not used). Sequence abbreviations are described in Table 1.

Figure 1

Figure 1

Alignment of complete RecA sequences. The alignment was generated using the clustalw multiple sequence alignment program. Dashes (-) represent alignment gaps. Three insertions that are present in only one sequence each (Myb.t, Myb.l, and Tg.m) and the first 80 aa of the A. thaliana protein are left out for space reasons and are indicated by a ••. Conservation of alignment positions as determined by the clustalw program is indicated by * (identical aa in all) and. (similar aa in all). The alignment positions used in phylogenetic analysis are indicated by the sequence mask (1=used, 0=not used). Sequence abbreviations are described in Table 1.

Figure 2

Figure 2

Comparison of consensus trees for RecA and SS-rRNA. Strict-rule consensus trees representing the phylogenetic patterns found in all trees generated by multiple methods for each molecule are shown. The RecA consensus (A) was generated from the PAUP, protpars, Fitch-Margoliash, De Soete and neighbor-joining trees (see Methods). The SS-rRNA consensus (B) was generated from the dnapars, Fitch-Margoliash, De Soete and neighbor-joining trees. Comparable species are aligned in the middle and species are ordered to minimize branch crossing (note two crossed branches in SS-rRNA tree). Consensus clades are shaded for each molecule.

Figure 3

Figure 3

Fitch-Margoliash trees for RecA (A) and SS-rRNA (B). Trees were generated from the multiple sequence alignments by the method of Fitch and Margoliash. Regions of ambiguous alignment and indels were excluded from the analysis (see Methods). For the RecA tree, distances were calculated using the protdist program of PHYLIP with a PAM-matrix based distance correction. For the SS-rRNA tree, distances were calculated using the dnadist program of PHYLIP and the Kimura-2-parameter distance correction. Consensus clades representing groups found in all phylogenetic methods are highlighted. Branch lengths and scale bars correspond to estimated evolutionary distance. Bootstrap values when over 40 are indicated.

Figure 3

Figure 3

Fitch-Margoliash trees for RecA (A) and SS-rRNA (B). Trees were generated from the multiple sequence alignments by the method of Fitch and Margoliash. Regions of ambiguous alignment and indels were excluded from the analysis (see Methods). For the RecA tree, distances were calculated using the protdist program of PHYLIP with a PAM-matrix based distance correction. For the SS-rRNA tree, distances were calculated using the dnadist program of PHYLIP and the Kimura-2-parameter distance correction. Consensus clades representing groups found in all phylogenetic methods are highlighted. Branch lengths and scale bars correspond to estimated evolutionary distance. Bootstrap values when over 40 are indicated.

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