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

• Main Authors: Lorenzini Emily, Gupta Radhey S
• Format: Article
• Language: English
• Published: BMC 2007-05-01
• Series: BMC Evolutionary Biology
• Online Access: http://www.biomedcentral.com/1471-2148/7/71

<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>