Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the deinococcus-thermus phylum.
The Deinococcus-Thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16S rRNA trees. No unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. In this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the Deinococcus-Thermus phylum but are not found in any other group of bacteria. The identified signatures include a 7-amino-acid (aa) insert in threonyl-tRNA synthetase, 1- and 3-aa inserts in the RNA polymerase beta' subunit, a 5-aa deletion in signal recognition particle (Ffh/SR54), a 2-aa insert in major sigma factor 70 (sigma70), a 2-aa insert in seryl-tRNA synthetase (SerRS), a 1-aa insert in ribosomal protein L1, and a 2-aa insert in UvrA homologs. By using PCR primers for conserved regions, fragments of these genes were amplified from a number of Deinococcus-Thermus species, and all such fragments (except SerRS in Deinococcus proteolyticus) were found to contain the indicated signatures. The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group. The signature in SerRS, which is absent in D. proteolyticus, was likely introduced after the branching of this species. Phylogenetic studies as well as the nature of the inserts in some of these proteins (viz., sigma70 and SerRS) also support a sister group relationship between the Thermus and the Meiothermus genera. The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group.
Griffiths
Emma
E
Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5.
Gupta
Radhey S
RS
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry; D034301:Deinococcus / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D012808:Sigma Factor / Q000737:chemistry; D018271:Signal Recognition Particle / Q000737:chemistry; D013914:Threonine-tRNA Ligase / Q000737:chemistry
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C082931:Ffh protein, E coli; D012808:Sigma Factor; D018271:Signal Recognition Particle; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D013914:Threonine-tRNA Ligase