The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes

Abstract

The evolutionary relationships of proteobacteria, which comprise the largest and phenotypically most diverse division among prokaryotes, are examined based on the analyses of available molecular sequence data. Sequence alignments of different proteins have led to the identification of numerous conserved inserts and deletions (referred to as signature sequences), which either are unique characteristics of various proteobacterial species or are shared by only members from certain subdivisions of proteobacteria. These signature sequences provide molecular means to define the proteobacterial phyla and their various subdivisions and to understand their evolutionary relationships to the other groups of eubacteria as well as the eukaryotes. Based on signature sequences that are present in different proteins it is now possible to infer that the various eubacterial phyla evolved from a common ancestor in the following order: low-G+C Gram-positive-->high-G+C Gram-positive-->Deinococcus-Thermus (green nonsulfur bacteria)-->cyanobacteria-->Spirochetes-->Chlamydia-Cytophaga-Aquifex -green sulfur bacteria-->Proteobacteria-1 (epsilon and delta)-->Proteobacteria-2 (alpha)-->Proteobacteria-3 (beta)-->Proteobacteria-4 (gamma). An unexpected but important aspect of the relationship deduced here is that the main eubacterial phyla are related to each other linearly rather than in a tree-like manner, suggesting that the major evolutionary changes within Bacteria have taken place in a directional manner. The identified signatures permit placement of prokaryotes into different groups/divisions and could be used for determinative purposes. These signatures generally support the origin of mitochondria from an alpha-proteobacterium and provide evidence that the nuclear cytosolic homologs of many genes are also derived from proteobacteria.

Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology

“…(1) the generation of Gram-negative bacteria from symbiosis between an archaea and a Gram-positive bacterium (Gupta, 1998(Gupta, , 2000 and (2) the generation of the first eukaryotic cell from symbiosis between an archaea and a Gram-negative bacterium (Gupta, 2000;Rivera & Lake, 2004;Horiike et al, 2001Horiike et al, , 2004Embley & Martin, 2006). If we think about how these important events might have occurred at the molecular level, we have to recognize the tremendous challenges presented by the need to integrate separate genomes, metabolisms, envelopes and external structures into a viable cell.…”

Microarrays for microbiologists

“…Phylogenetic classification based on rRNA\rDNA and signature sequences is usually able to provide an accurate classification of micro-organisms above the species level (Gupta, 2000). However, it has become evident that lateral gene transfer is an important mechanism of evolution for prokaryotes, complicating phylogenetic analysis based on a small number of genes.…”

Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces a aThe GenBank accession numbers for the sequences reported in this paper are indicated in the text.

“…Chlamydial signatures were identified in these alignments by visual inspection, where a conserved indel was uniquely present in this group of species. To qualify as a useful signature, any identified indel was required to be flanked on both sides by regions of high sequence conservation, ensuring that the observed indel was not due to sequencing errors or alignment artefacts (Gupta, 1998(Gupta, , 2000b. PCR amplification and sequencing.…”

“…We have recently described a new approach based on shared conserved insertion and deletions (indels) in various proteins that has proven very useful in identifying main groups within the domain Bacteria and in understanding their relationship to each other (Gupta, 1998(Gupta, , 2000a. By tracking the presence or absence of specific indels in various proteins in different phyla, this approach allows the logical deduction of the relative branching order of different groups from a common ancestor (Gupta, 1998(Gupta, , 2000bGriffiths & Gupta, 2001). The use of this approach indicates that the Chlamydiaceae branch is in a similar position to the large, diverse Cytophaga-Flavobacterium-Bacteroides group which has been placed between the Spirochaetes and the δ,ε-Proteobacteria (Gupta, 2000b).…”

“…By tracking the presence or absence of specific indels in various proteins in different phyla, this approach allows the logical deduction of the relative branching order of different groups from a common ancestor (Gupta, 1998(Gupta, , 2000bGriffiths & Gupta, 2001). The use of this approach indicates that the Chlamydiaceae branch is in a similar position to the large, diverse Cytophaga-Flavobacterium-Bacteroides group which has been placed between the Spirochaetes and the δ,ε-Proteobacteria (Gupta, 2000b). The present work describes a number of conserved indels in various proteins which provide specific molecular markers for the chlamydial group of species, and can unambiguously define and identify this group from all other groups of bacteria.…”