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

Gupta RS, Lorenzini E - BMC Evol. Biol. (2007)

Bottom Line: These studies have identified > 600 proteins for which homologues are not found in other organisms.This work also describes two large conserved inserts in DNA polymerase III (DnaE) and alanyl-tRNA synthetase that are distinctive characteristics of the Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms.These results also provide strong evidence that species from these two phyla (and also possibly Fibrobacteres) are specifically related to each other and they form a single superphylum.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada. gupta@mcmaster.ca

ABSTRACT

Background: The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi 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.

Results: Systematic blast searches were performed on each open reading frame in the genomes of Porphyromonas gingivalis W83, Bacteroides fragilis YCH46, B. thetaiotaomicron VPI-5482, Gramella forsetii KT0803, Chlorobium luteolum (formerly Pelodictyon luteolum) DSM 273 and Chlorobaculum tepidum (formerly Chlorobium tepidum) TLS to search for proteins that are uniquely present in either all or certain subgroups of Bacteroidetes and Chlorobi. 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 Bacteroidetes and Chlorobi genomes, respectively; 52 and 38 proteins that are limited to species from the Bacteroidales and Flavobacteriales orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the Bacteroides genus. Additionally, 6 proteins that are uniquely shared by species from the Bacteroidetes and Chlorobi phyla (one of them also present in the Fibrobacteres) 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 Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms. Phylogenetic analyses of the Bacteroidetes and Chlorobi 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 Salinibacter ruber with other Bacteroidetes species was not resolved by other phylogenetic methods, but this affiliation was strongly supported by the character compatibility approach.

Conclusion: The molecular signatures described here provide novel tools for identifying and circumscribing species from the Bacteroidetes and Chlorobi 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 Fibrobacteres) 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.

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Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins. The tree was rooted using sequences for Deinococcus-Thermus species and numbers on the nodes indicate bootstrap scores in the NJ and maximum-likelihood analyses (NJ/MP). The branching position of G. forsetii, which became available after this analysis was completed, is not shown. However, our analysis of a smaller dataset indicates that it exhibits closest affinity for the flavobacteria Psychrobacter torquis (results not shown).
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Figure 1: Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins. The tree was rooted using sequences for Deinococcus-Thermus species and numbers on the nodes indicate bootstrap scores in the NJ and maximum-likelihood analyses (NJ/MP). The branching position of G. forsetii, which became available after this analysis was completed, is not shown. However, our analysis of a smaller dataset indicates that it exhibits closest affinity for the flavobacteria Psychrobacter torquis (results not shown).

Mentions: Phylogenetic trees were constructed using the neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) methods [51]. The results of these analyses for the NJ and ML methods are presented in Fig. 1. The trees were rooted using the sequences for Deinococcus-Thermus species. The tree in both cases consisted of two well-resolved clades (100% bootstrap scores by both treeing methods), one comprising of various Chlorobi species and the other containing various Cytophaga-Flavobacteria-Bacteroides (CFB) species. In these trees, S. ruber appeared as a deep branching outgroup of the Chlorobi clade, but in view of the low bootstrap score of the node indicating this relationship and the long branch that separated them, this relationship was not reliable. The topology of various species in the MP tree was very similar, except that in this tree S. ruber formed the outgroup of Chlorobi as well as various other CFB group of bacteria (results not shown). In addition to the uncertain position of S. ruber, different species belonging to the genus Flavobacterium did not form a coherent phylogenetic group (Fig. 1). For most other Bacteroidetes species, sequence information for multiple species from the same genera was not available.


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

Gupta RS, Lorenzini E - BMC Evol. Biol. (2007)

Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins. The tree was rooted using sequences for Deinococcus-Thermus species and numbers on the nodes indicate bootstrap scores in the NJ and maximum-likelihood analyses (NJ/MP). The branching position of G. forsetii, which became available after this analysis was completed, is not shown. However, our analysis of a smaller dataset indicates that it exhibits closest affinity for the flavobacteria Psychrobacter torquis (results not shown).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1887533&req=5

Figure 1: Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins. The tree was rooted using sequences for Deinococcus-Thermus species and numbers on the nodes indicate bootstrap scores in the NJ and maximum-likelihood analyses (NJ/MP). The branching position of G. forsetii, which became available after this analysis was completed, is not shown. However, our analysis of a smaller dataset indicates that it exhibits closest affinity for the flavobacteria Psychrobacter torquis (results not shown).
Mentions: Phylogenetic trees were constructed using the neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) methods [51]. The results of these analyses for the NJ and ML methods are presented in Fig. 1. The trees were rooted using the sequences for Deinococcus-Thermus species. The tree in both cases consisted of two well-resolved clades (100% bootstrap scores by both treeing methods), one comprising of various Chlorobi species and the other containing various Cytophaga-Flavobacteria-Bacteroides (CFB) species. In these trees, S. ruber appeared as a deep branching outgroup of the Chlorobi clade, but in view of the low bootstrap score of the node indicating this relationship and the long branch that separated them, this relationship was not reliable. The topology of various species in the MP tree was very similar, except that in this tree S. ruber formed the outgroup of Chlorobi as well as various other CFB group of bacteria (results not shown). In addition to the uncertain position of S. ruber, different species belonging to the genus Flavobacterium did not form a coherent phylogenetic group (Fig. 1). For most other Bacteroidetes species, sequence information for multiple species from the same genera was not available.

Bottom Line: These studies have identified > 600 proteins for which homologues are not found in other organisms.This work also describes two large conserved inserts in DNA polymerase III (DnaE) and alanyl-tRNA synthetase that are distinctive characteristics of the Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms.These results also provide strong evidence that species from these two phyla (and also possibly Fibrobacteres) are specifically related to each other and they form a single superphylum.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada. gupta@mcmaster.ca

ABSTRACT

Background: The Bacteroidetes and Chlorobi species constitute two main groups of the Bacteria that are closely related in phylogenetic trees. The Bacteroidetes species are widely distributed and include many important periodontal pathogens. In contrast, all Chlorobi 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.

Results: Systematic blast searches were performed on each open reading frame in the genomes of Porphyromonas gingivalis W83, Bacteroides fragilis YCH46, B. thetaiotaomicron VPI-5482, Gramella forsetii KT0803, Chlorobium luteolum (formerly Pelodictyon luteolum) DSM 273 and Chlorobaculum tepidum (formerly Chlorobium tepidum) TLS to search for proteins that are uniquely present in either all or certain subgroups of Bacteroidetes and Chlorobi. 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 Bacteroidetes and Chlorobi genomes, respectively; 52 and 38 proteins that are limited to species from the Bacteroidales and Flavobacteriales orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the Bacteroides genus. Additionally, 6 proteins that are uniquely shared by species from the Bacteroidetes and Chlorobi phyla (one of them also present in the Fibrobacteres) 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 Chlorobi species and a 3 aa deletion in ClpB chaperone that is mainly found in various Bacteroidales, Flavobacteriales and Flexebacteraceae, but generally not found in the homologs from other organisms. Phylogenetic analyses of the Bacteroidetes and Chlorobi 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 Salinibacter ruber with other Bacteroidetes species was not resolved by other phylogenetic methods, but this affiliation was strongly supported by the character compatibility approach.

Conclusion: The molecular signatures described here provide novel tools for identifying and circumscribing species from the Bacteroidetes and Chlorobi 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 Fibrobacteres) 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.

Show MeSH
Related in: MedlinePlus