Comprehensive phylogenetic analysis of bacterial reverse transcriptases

PLoS One. 2014 Nov 25;9(11):e114083. doi: 10.1371/journal.pone.0114083. eCollection 2014.

Abstract

Much less is known about reverse transcriptases (RTs) in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center) platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity) per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs), Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L), and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actinobacteria / enzymology*
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Phylogeny*
  • RNA-Directed DNA Polymerase / classification
  • RNA-Directed DNA Polymerase / metabolism*

Substances

  • RNA-Directed DNA Polymerase

Grant support

This work was supported by the CSD 2009-0006 for the Consolider-Ingenio program, including ERDF (European Regional Development Funds), and BIO2011-24401 from the Spanish Ministerio de Ciencia e Innovación, which has been renamed the Ministerio de Economía y Competitividad. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.