Phylogenomics and signature proteins for the alpha proteobacteria and its main groups

Abstract

Background: Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known.

Results: We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several alpha-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all alpha-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and many families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae). Many other proteins that are present at different phylogenetic depths in alpha-proteobacteria provide important information regarding their evolution. The evolutionary relationships among alpha-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within alpha-proteobacteria have diverged in the following order: (Rickettsiales(Rhodospirillales (Sphingomonadales (Rhodobacterales (Caulobacterales-Parvularculales (Rhizobiales)))))). We also describe two conserved inserts in DNA Gyrase B and RNA polymerase beta subunit that are distinctive characteristics of the Sphingomonadales and Rhodosprilllales species, respectively. The results presented here also provide support for the grouping of Hyphomonadaceae and Parvularcula species with the Caulobacterales and the placement of Stappia aggregata with the Rhizobiaceae group.

Conclusion: The alpha-proteobacteria-specific proteins and indels described here provide novel and powerful means for the taxonomic, biochemical and molecular biological studies on these bacteria. Their functional studies should prove helpful in identifying novel biochemical and physiological characteristics that are unique to these bacteria.

Figure 1

A neighbour-joining distance tree based on concatenated sequences for 12 conserved proteins. The numbers on the nodes indicate bootstrap scores (out of 100) observed in the neighbour-joining (NJ), maximum parsimony (MP) and maximum-likelihood (ML) analyses (NJ/MP/ML). The species marked with * are presently not part of the Caulobacterales order, but the results of phylogenetic and phylogenomic studies presented here suggest their placement in this group.

Figure 2

Character compatibility cliques showing the two largest cliques of mutually compatible characters based on the two states sites in the concatenated sequence alignment for 12 conserved proteins. The cliques consisted of 350 mutually compatible characters. The numbers of characters that distinguished different clades are indicated on the nodes. Rooting was done using the sequences for Helicobacter pylori and Campylobacter jejuni. *, as in Figure 1.

Figure 3

Summary of the phylogenomic analyses showing the species distribution of various α-proteobacteria-specific proteins and the suggested evolutionary stages where the genes for these proteins have likely evolved. The genes IDs for some proteins described in earlier work are indicated [17]. The information for all other proteins can be found in the indicated Tables or Additional files. A large numbers of conserved indels that are specific for different groups or clades within α-proteobacteria shown here have also been identified in our earlier work [16] (not shown here). The branching order of α-proteobacteria relative to other bacteria has been established in earlier work [32,58].

Figure 4

Partial sequence alignments of DNA Gyrase B showing a 4 aa insert that is mainly specific for the Sphingomonadales species. A 4–5 aa insert present in some other α-proteobacteria could be due to either LGTs or taxonomic anomalies. The dashes (-) denote identity with the amino acid on the top line. Sequence information for other groups of bacteria (which do not contain this insert) is not shown.

Figure 5

Partial sequence alignments of RNA polymerase β subunit (RpoB) showing a large insert (boxed) that is a distinctive characteristic of various Rhodospirillales species and not found in any other bacteria. There are two homologs of RpoB in Magentospirillum (Mag.) magneticum and only one of these contains the insert. The dashes (-) denote identity with the amino acid on the top line.