Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria

Abstract

Gram-positive bacteria with a high G+C content are currently recognized as a distinct phylum, Actinobacteria, on the basis of their branching in 16S rRNA trees. Except for an insert in the 23S rRNA, there are no unique biochemical or molecular characteristics known at present that can distinguish this group from all other bacteria. In this work, three conserved indels (i.e. inserts or deletions) are described in three widely distributed proteins that are distinctive characteristics of the Actinobacteria and are not found in any other groups of bacteria. The identified signatures are a 2 aa deletion in cytochrome-c oxidase subunit 1 (Cox1), a 4 aa insert in CTP synthetase and a 5 aa insert in glutamyl-tRNA synthetase (GluRS). Additionally, the actinobacterial specificity of the large insert in the 23S rRNA was also tested. Using primers designed for conserved regions flanking these signatures, fragments of most of these genes were amplified from 23 actinobacterial species, covering many different families and orders, for which no sequence information was previously available. All the 61 sequenced fragments, except two in GluRS, were found to contain the indicated signatures. The presence of these signatures in various species from 20 families within this phylum provides evidence that they are likely distinctive characteristics of the entire phylum, which were introduced in a common ancestor of this group. The absence of all four of these signatures in Symbiobacterium thermophilum suggests that this species, which is distantly related to other actinobacteria in 16S rRNA and CTP synthetase trees, may not be a part of the phylum Actinobacteria. The identified signatures provide novel molecular means for defining and circumscribing the phylum Actinobacteria. Functional studies on them should prove helpful in understanding novel biochemical and physiological characteristics of this group of bacteria.Abbreviations: Cox1, cytochrome-c oxidase subunit 1; GluRS, glutamyl-tRNA synthetase.The GenBank/EMBL/DDBJ accession numbers for the novel sequences described in this paper are indicated in Figs 1-4. Full Cox1, CTP synthetase and GluRS alignments and accession numbers of 16S rRNA gene and CTP synthetase gene sequences used are available as supplementary material in IJSEM Online.

Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)

“…The presence of these Clostridium-specific signatures in these species would provide a strong case for their transfer to the genus Clostridium. Because all of the conserved indels described here are found in highly conserved regions, it should be possible to obtain sequence information for these signatures from other species by using degenerate PCR primers flanking the indel-containing regions, as described in our other work (Griffiths et al, 2005;Gao & Gupta, 2005).…”

“…Multiple sequence alignments for these and many other proteins that have been created in our earlier work (Griffiths & Gupta, 2004;Gao & Gupta, 2005) were visually inspected to identify any conserved indel that was restricted to either all or specific groups of the clostridia.…”

“…The maximum-likelihood (ML) analysis was carried out using the WAG+F model with gamma distribution of evolutionary rates with four categories using the TREE-PUZZLE program with 10 000 puzzling steps (Schmidt et al, 2002). Maximum-parsimony (MP) trees based on 1000 bootstrap replicates were computed using the MEGA 4.1 program (Tamura et al, 2007).Identification of conserved indels specific to the clostridia.Multiple sequence alignments for these and many other proteins that have been created in our earlier work (Griffiths & Gupta, 2004;Gao & Gupta, 2005) were visually inspected to identify any conserved indel that was restricted to either all or specific groups of the clostridia. …”

Genome beginnings: rooting the tree of life

“…The GyrA protein contains an indel (Gao & Gupta 2005) that is ideal for determining whether the root is Review. Rooting the tree of life J.…”

An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa

“…Besides the phylogeny of the 16S rRNA gene, some conserved indels in 23S rRNA and protein (e.g. cytochrome-c oxidase I, CTP synthetase and glutamyl-tRNA synthetase) sequences support the distinctness of members of the class from all other bacteria (Gao & Gupta, 2005). The initial hierarchical classification system of the Actinobacteria embraced 95 genera, belonging to 30 families and 10 suborders.…”