The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins

The presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerfulmeans for understanding the evolutionary relationships among the Bacteria. Using such indels, all of the main groups within the Bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: Low G+C Gram-positive → High G+C Gram-positive → Deinococcus–Thermus → Cyanobacteria → Spirochetes → Aquifex–Chlamydia–Cytophaga → Proteobacteria-1 (ε, δ) → Proteobacteria-2 (α) → Proteobacteria-3 (β) → Proteobacteria-4 (γ). The usefulness of this approach for understanding bacterialphyl ogeny was examined here using sequence data from various completed bacterial genomes. By using 12 indels in highly conserved and widely represented proteins, the species from all 41 completed bacterial genomes were assigned to different groups; and the observed distribution of these indels in different species was then compared with that predicted by the signature sequence model. The presence or absence of these indels in various proteins in different bacteria followed the pattern exactly as predicted; and, in more than 450 observations, no exceptions or contradictions in the placement of indels were observed. These results provide strong evidence that lateral gene transfer events have not affected the genes containing these indels to any significant extent. The phylogenetic placement of bacteria into different groups based on signature sequences also showed an excellent correlation with the 16 S rRNA with 39 of the 41 species assigned to the same group by both methods. These results strongly vindicate the usefulness of the signature sequence approach to understanding phylogeny within the Bacteria and show that it provides a reliable and internally consistent means for the placement of bacterialspecies into different groups and for determining the relative branching order of the groups

Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes

The prokaryotic organisms can be divided into two main groups depending upon whether their cell envelopes contain one membrane (monoderms) or two membranes (diderms). It is important to understand how these and other variations that are observed in the cell envelopes of prokaryotic organisms have originated. In 2009, James Lake proposed that cells with two membranes (primarily Gram-negative bacteria) originated from an ancient endosymbiotic event involving an Actinobacteria and a Clostridia (Lake 2009). However, this Perspective argues that this proposal is based on a number of incorrect assumptions and the data presented in support of this model are also of questionable nature. Thus, there is no reliable evidence to support the endosymbiotic origin of double membrane bacteria. In contrast, many observations suggest that antibiotic selection pressure was an important selective force in prokaryotic evolution and that it likely played a central role in the evolution of diderm (Gram-negative) bacteria. Some bacterial phyla, such as Deinococcus-Thermus, which lack lipopolysaccharide (LPS) and yet contain some characteristics of the diderm bacteria, are postulated as evolutionary intermediates (simple diderms) in the transition between the monoderm bacterial taxa and the bacterial groups that have the archetypal LPS-containing outer cell membrane found in Gram-negative bacteria. It is possible to distinguish the two stages in the evolution of diderm-LPS cells (viz. monoderm bacteria → simple diderms lacking LPS → LPS containing archetypal diderm bacteria) by means of conserved inserts in the Hsp70 and Hsp60 proteins. The insert in the Hsp60 protein also distinguishes the traditional Gram-negative diderm bacterial phyla from atypical taxa of diderm bacteria (viz. Negativicutes, Fusobacteria, Synergistetes and Elusimicrobia). The Gram-negative bacterial phyla with an LPS-diderm cell envelope, as defined by the presence of the Hsp60 insert, are indicated to form a monophyletic clade and no loss of the outer membrane from any species from this group seems to have occurred. This argues against the origin of monoderm prokaryotes from diderm bacteria by loss of outer membrane

Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum

The members of the Deinococcus-Thermus phylum, which include many species that are resistant to extreme radiation, as well as several thermophiles, have been recognized solely on the basis of their branching patterns in 16S rRNA and other phylogenetic trees. No biochemical or physiological characteristic is currently known that is unique to this group of species. To identify genes/proteins that are exclusive of this group of species, systematic protein basic local alignment tool (Blastp) searches were carried out on each open reading frame (ORF) in the genome of Deinococcus radiodurans. These studies identified 65 proteins that were only found in all three sequenced Deinococcus-Thermus genomes (viz. D. radiodurans, D. geothermalis and Thermus thermophilus), but not in any other bacteria. In addition, these studies also identified 206 proteins that are exclusively found in the two Deinocococci species, and 399 proteins that are unique to D. radiodurans. The identified proteins, which represent a genetic repertoire distinctive to the Deinococcus-Thermus group, or to Deinococci species, provide novel molecular markers for their identification and characterization. The cellular functions of most of these proteins are not known and their studies should prove useful in identifying novel biochemical and physiological characteristics that are exclusive of these groups of bacteria and also those responsible for the extreme radiation resistance of Deinococci. [Int Microbiol 2007; 10(3):201-208

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

<p>Abstract</p> <p>Background</p> <p>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. <it>Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales </it>and <it>Caulobacterales</it>), very few or no distinctive molecular or biochemical characteristics are known.</p> <p>Results</p> <p>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 α-proteobacteria (viz. <it>Bradyrhizobium japonicum</it>, <it>Brucella suis</it>, <it>Caulobacter crescentus</it>, <it>Gluconobacter oxydans</it>, <it>Mesorhizobium loti</it>, <it>Nitrobacter winogradskyi</it>, <it>Novosphingobium aromaticivorans</it>, <it>Rhodobacter sphaeroides </it>2.4.1, <it>Silicibacter sp</it>. TM1040, <it>Rhodospirillum rubrum </it>and <it>Wolbachia </it>(<it>Drosophila</it>) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all α-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. <it>Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales </it>and <it>Caulobacterales</it>) and many families (viz. <it>Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae </it>and <it>Bartonellaceae</it>). Many other proteins that are present at different phylogenetic depths in α-proteobacteria provide important information regarding their evolution. The evolutionary relationships among α-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 α-proteobacteria have diverged in the following order: (<it>Rickettsiales</it>(<it>Rhodospirillales </it>(<it>Sphingomonadales </it>(<it>Rhodobacterales </it>(<it>Caulobacterales-Parvularculales </it>(<it>Rhizobiales</it>)))))). We also describe two conserved inserts in DNA Gyrase B and RNA polymerase beta subunit that are distinctive characteristics of the <it>Sphingomonadales </it>and <it>Rhodosprilllales </it>species, respectively. The results presented here also provide support for the grouping of <it>Hyphomonadacea</it>e and <it>Parvularcula </it>species with the <it>Caulobacterales </it>and the placement of <it>Stappia aggregata </it>with the <it>Rhizobiaceae </it>group.</p> <p>Conclusion</p> <p>The α-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.</p

Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

<p>Abstract</p> <p>Background</p> <p>The <it>Bacteroidetes </it>and <it>Chlorobi </it>species constitute two main groups of the <it>Bacteria </it>that are closely related in phylogenetic trees. The <it>Bacteroidetes </it>species are widely distributed and include many important periodontal pathogens. In contrast, all <it>Chlorobi </it>are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them.</p> <p>Results</p> <p>Systematic blast searches were performed on each open reading frame in the genomes of <it>Porphyromonas gingivalis </it>W83, <it>Bacteroides fragilis </it>YCH46, <it>B. thetaiotaomicron </it>VPI-5482, <it>Gramella forsetii KT0803, Chlorobium luteolum </it>(formerly <it>Pelodictyon luteolum</it>) DSM 273 and <it>Chlorobaculum tepidum </it>(formerly <it>Chlorobium tepidum</it>) TLS to search for proteins that are uniquely present in either all or certain subgroups of <it>Bacteroidetes </it>and <it>Chlorobi</it>. These studies have identified > 600 proteins for which homologues are not found in other organisms. This includes 27 and 51 proteins that are specific for most of the sequenced <it>Bacteroidetes </it>and <it>Chlorobi </it>genomes, respectively; 52 and 38 proteins that are limited to species from the <it>Bacteroidales </it>and <it>Flavobacteriales </it>orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the <it>Bacteroides </it>genus. Additionally, 6 proteins that are uniquely shared by species from the <it>Bacteroidetes </it>and <it>Chlorobi </it>phyla (one of them also present in the <it>Fibrobacteres</it>) have also been identified. This work also describes two large conserved inserts in DNA polymerase III (DnaE) and alanyl-tRNA synthetase that are distinctive characteristics of the <it>Chlorobi </it>species and a 3 aa deletion in ClpB chaperone that is mainly found in various <it>Bacteroidales, Flavobacteriales </it>and <it>Flexebacteraceae</it>, but generally not found in the homologs from other organisms. Phylogenetic analyses of the <it>Bacteroidetes </it>and <it>Chlorobi </it>species is also reported based on concatenated sequences for 12 conserved proteins by different methods including the character compatibility (or clique) approach. The placement of <it>Salinibacter ruber </it>with other <it>Bacteroidetes </it>species was not resolved by other phylogenetic methods, but this affiliation was strongly supported by the character compatibility approach.</p> <p>Conclusion</p> <p>The molecular signatures described here provide novel tools for identifying and circumscribing species from the <it>Bacteroidetes </it>and <it>Chlorobi </it>phyla as well as some of their main groups in clear terms. These results also provide strong evidence that species from these two phyla (and also possibly <it>Fibrobacteres</it>) are specifically related to each other and they form a single superphylum. Functional studies on these proteins and indels should aid in the discovery of novel biochemical and physiological characteristics that are unique to these groups of bacteria.</p

Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

BACKGROUND: The Archaea are highly diverse in terms of their physiology, metabolism and ecology. Presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. The evolutionary relationships among different groups within the Euryarchaeota branch are also not clearly understood. RESULTS: We have carried out comprehensive analyses on each open reading frame (ORFs) in the genomes of 11 archaea (3 Crenarchaeota – Aeropyrum pernix, Pyrobaculum aerophilum and Sulfolobus acidocaldarius; 8 Euryarchaeota – Pyrococcus abyssi, Methanococcus maripaludis, Methanopyrus kandleri, Methanococcoides burtonii, Halobacterium sp. NCR-1, Haloquadratum walsbyi, Thermoplasma acidophilum and Picrophilus torridus) to search for proteins that are unique to either all Archaea or for its main subgroups. These studies have identified 1448 proteins or ORFs that are distinctive characteristics of Archaea and its various subgroups and whose homologues are not found in other organisms. Six of these proteins are unique to all Archaea, 10 others are only missing in Nanoarchaeum equitans and a large number of other proteins are specific for various main groups within the Archaea (e.g. Crenarchaeota, Euryarchaeota, Sulfolobales and Desulfurococcales, Halobacteriales, Thermococci, Thermoplasmata, all methanogenic archaea or particular groups of methanogens). Of particular importance is the observation that 31 proteins are uniquely present in virtually all methanogens (including M. kandleri) and 10 additional proteins are only found in different methanogens as well as A. fulgidus. In contrast, no protein was exclusively shared by various methanogen and any of the Halobacteriales or Thermoplasmatales. These results strongly indicate that all methanogenic archaea form a monophyletic group exclusive of other archaea and that this lineage likely evolved from Archaeoglobus. In addition, 15 proteins that are uniquely shared by M. kandleri and Methanobacteriales suggest a close evolutionary relationship between them. In contrast to the phylogenomics studies, a monophyletic grouping of archaea is not supported by phylogenetic analyses based on protein sequences. CONCLUSION: The identified archaea-specific proteins provide novel molecular markers or signature proteins that are distinctive characteristics of Archaea and all of its major subgroups. The species distributions of these proteins provide novel insights into the evolutionary relationships among different groups within Archaea, particularly regarding the origin of methanogenesis. Most of these proteins are of unknown function and further studies should lead to discovery of novel biochemical and physiological characteristics that are unique to either all archaea or its different subgroups

Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales

The Aquificales species are presently believed to be the earliest branching lineage within Bacteria. However, the branching order of this group in different phylogenetic trees is highly variable and not resolved. In the present work, the phylogenetic placement of Aquificales was examined by means of a cladistic approach based on the shared presence or absence of definite signature sequences (consisting of conserved inserts or deletions) in many highly conserved and important proteins, e.g. RNA polymerase β(RpoB), RNA polymerase β´(RpoC), alanyl-tRNA synthetase (AlaRS), CTP synthase, inorganic pyrophosphatase (PPase), Hsp70 and Hsp60. For this purpose, fragments of the above genes that contained the signature regions were cloned from different Aquificales, species (Calderobacterium hydrogenophilum, Hydrogenobacter marinus, and Thermocrinis ruber) and the sequence data were compared with those available from all other species. The presence in Aquificales species of distinctive inserts in Hsp70 and Hsp60 that are not found in any Firmicutes, Actinobacteria, or Thermotoga-Clostridium species excluded them from these groups of Bacteria. The shared presence of prominent indels in the RpoB (>100 amino acids), RpoC (>100 amino acids) and AlaRS (4 amino acids) proteins, which are only found in the various Aquificales species, the Chlamydiae, the CFBG (Cytophaga- Flavobacteria-Bacteroides-green sulfur bacteria) group, and Proteobacteria, strongly suggests their placement within these groups of Bacteria. A specific relationship between Proteobacteria and Aquificales is suggested by the presence in inorganic pyrophosphatase of a 2-amino-acid insert that is uniquely found in these phyla. However, the Aquificales species lacked a number of other protein signatures (e.g. indels in CTP synthase and Hsp70) that are characteristic of Proteobacteria, indicating that they constitute a distinct phylum related to Proteobacteria. These results provide strong and consistent evidence that the Aquificales diverged after the branching of Firmicutes, Actinobacteria, Thermotoga, Deinococcus-Thermus, green nonsulfur bacteria, Cyanobacteria, Spirochetes, Chlamydiae, and CFBG group, but before the emergence of the Proteobacteria. [Int Microbiol 2004; 7(1):41–52

Signature proteins that are distinctive of alpha proteobacteria

BACKGROUND: The alpha (α) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16S rRNA trees, with no known molecular characteristic that is unique to this group. The genomes of three α-proteobacteria, Rickettsia prowazekii (RP), Caulobacter crescentus (CC) and Bartonella quintana (BQ), were analyzed in order to search for proteins that are unique to this group. RESULTS: Blast analyses of protein sequences from the above genomes have led to the identification of 61 proteins which are distinctive characteristics of α-proteobacteria and are generally not found in any other bacteria. These α-proteobacterial signature proteins are generally of hypothetical functions and they can be classified as follows: (i) Six proteins (CC2102, CC3292, CC3319, CC1887, CC1725 and CC1365) which are uniquely present in most sequenced α-proteobacterial genomes; (ii) Ten proteins (CC1211, CC1886, CC2245, CC3470, CC0520, CC0365, CC0366, CC1977, CC3010 and CC0100) which are present in all α-proteobacteria except the Rickettsiales; (iii) Five proteins (CC2345, CC3115, CC3401, CC3467 and CC1021) not found in the intracellular bacteria belonging to the order Rickettsiales and the Bartonellaceae family; (iv) Four proteins (CC1652, CC2247, CC3295 and CC1035) that are absent from various Rickettsiales as well as Rhodobacterales; (v) Three proteins (RP104, RP105 and RP106) that are unique to the order Rickettsiales and four proteins (RP766, RP192, RP030 and RP187) which are specific for the Rickettsiaceae family; (vi) Six proteins (BQ00140, BQ00720, BQ03880, BQ12030, BQ07670 and BQ11900) which are specific to the order Rhizobiales; (vii) Four proteins (BQ01660, BQ02450, BQ03770 and BQ13470) which are specific for the order Rhizobiales excluding the family Bradyrhizobiaceae; (viii) Nine proteins (BQ12190, BQ11460, BQ11450, BQ11430, BQ11380, BQ11160, BQ11120, BQ11100 and BQ11030 which are distinctive of the Bartonellaceae family;(ix) Six proteins (CC0189, CC0569, CC0331, CC0349, CC2323 and CC2637) which show sporadic distribution in α-proteobacteria, (x) Four proteins (CC2585, CC0226, CC2790 and RP382) in which lateral gene transfers are indicated to have occurred between α-proteobacteria and a limited number of other bacteria. CONCLUSION: The identified proteins provide novel means for defining and identifying the α-proteobacteria and many of its subgroups in clear molecular terms and in understanding the evolution of this group of species. These signature proteins, together with the large number of α-proteobacteria specific indels that have recently been identified , provide evidence that all species from this diverse group share many unifying and distinctive characteristics. Functional studies on these proteins should prove very helpful in the identification of such characteristics

Signature proteins for the major clades of Cyanobacteria

<p>Abstract</p> <p>Background</p> <p>The phylogeny and taxonomy of cyanobacteria is currently poorly understood due to paucity of reliable markers for identification and circumscription of its major clades.</p> <p>Results</p> <p>A combination of phylogenomic and protein signature based approaches was used to characterize the major clades of cyanobacteria. Phylogenetic trees were constructed for 44 cyanobacteria based on 44 conserved proteins. In parallel, Blastp searches were carried out on each ORF in the genomes of <it>Synechococcus WH8102, Synechocystis PCC6803, Nostoc PCC7120, Synechococcus JA-3-3Ab, Prochlorococcus MIT9215 </it>and <it>Prochlor. marinus subsp. marinus CCMP1375 </it>to identify proteins that are specific for various main clades of cyanobacteria. These studies have identified 39 proteins that are specific for all (or most) cyanobacteria and large numbers of proteins for other cyanobacterial clades. The identified signature proteins include: (i) 14 proteins for a deep branching clade (Clade A) of <it>Gloebacter violaceus </it>and two diazotrophic <it>Synechococcus </it>strains (JA-3-3Ab and JA2-3-B'a); (ii) 5 proteins that are present in all other cyanobacteria except those from Clade A; (iii) 60 proteins that are specific for a clade (Clade C) consisting of various marine unicellular cyanobacteria (viz. <it>Synechococcus </it>and <it>Prochlorococcus</it>); (iv) 14 and 19 signature proteins that are specific for the Clade C <it>Synechococcus </it>and <it>Prochlorococcus </it>strains, respectively; (v) 67 proteins that are specific for the Low B/A ecotype <it>Prochlorococcus </it>strains, containing lower ratio of <it>chl b/a</it>₂and adapted to growth at high light intensities; (vi) 65 and 8 proteins that are specific for the <it>Nostocales </it>and <it>Chroococcales </it>orders, respectively; and (vii) 22 and 9 proteins that are uniquely shared by various <it>Nostocales </it>and <it>Oscillatoriales </it>orders, or by these two orders and the <it>Chroococcales</it>, respectively. We also describe 3 conserved indels in flavoprotein, heme oxygenase and protochlorophyllide oxidoreductase proteins that are specific for either Clade C cyanobacteria or for various subclades of <it>Prochlorococcus</it>. Many other conserved indels for cyanobacterial clades have been described recently.</p> <p>Conclusions</p> <p>These signature proteins and indels provide novel means for circumscription of various cyanobacterial clades in clear molecular terms. Their functional studies should lead to discovery of novel properties that are unique to these groups of cyanobacteria.</p