Signature proteins that are distinctive of alpha proteobacteria

<p>Abstract</p> <p>Background</p> <p>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, <it>Rickettsia prowazekii </it>(RP), <it>Caulobacter crescentus </it>(CC) and <it>Bartonella quintana </it>(BQ), were analyzed in order to search for proteins that are unique to this group.</p> <p>Results</p> <p>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 <it>Rickettsiales</it>; (iii) Five proteins (CC2345, CC3115, CC3401, CC3467 and CC1021) not found in the intracellular bacteria belonging to the order <it>Rickettsiales </it>and the <it>Bartonellaceae </it>family; (iv) Four proteins (CC1652, CC2247, CC3295 and CC1035) that are absent from various <it>Rickettsiales </it>as well as <it>Rhodobacterales</it>; (v) Three proteins (RP104, RP105 and RP106) that are unique to the order <it>Rickettsiales </it>and four proteins (RP766, RP192, RP030 and RP187) which are specific for the <it>Rickettsiaceae </it>family; (vi) Six proteins (BQ00140, BQ00720, BQ03880, BQ12030, BQ07670 and BQ11900) which are specific to the order <it>Rhizobiales</it>; (vii) Four proteins (BQ01660, BQ02450, BQ03770 and BQ13470) which are specific for the order <it>Rhizobiales </it>excluding the family <it>Bradyrhizobiaceae</it>; (viii) Nine proteins (BQ12190, BQ11460, BQ11450, BQ11430, BQ11380, BQ11160, BQ11120, BQ11100 and BQ11030 which are distinctive of the <it>Bartonellaceae </it>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.</p> <p>Conclusion</p> <p>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 <url>http://www.bacterialphylogeny.com</url>, 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.</p>