Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

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.

Transposons: the agents of antibiotic resistance in bacteria

“…RTns are often found in the eukaryotes genome . Bacterial retrotranscriptase has been found in retrons, diversity‐generating retroelements (DGRs), and group Π introns .…”

Mobile Group II Introns as Ancestral Eukaryotic Elements

“…Evolutionary connections between RT-containing elements (right) (based on [26, 28] with modifications). Group II introns are related to all other RT-containing elements found in prokaryotes and eukaryotes (left) (based on [21] with modifications).…”

“…Intron subclasses based on RNA structure characteristics are indicated in parenthesis (IIA–IIC). Although the number of known group II introns is steadily growing, the evolutionary relationship between major lineages of introns remain unresolved [1, 5, 26, 28]. …”

“…Bacterial group II introns are highly variable in abundance and diversity even between closely related species and strains [20, 25, 26, 28]. Most bacterial genomes harbor only a few introns [25, 26, 29], which represent a minuscule fraction of the genome when compared to other bacterial mobile elements [30].…”

“…Most bacterial genomes harbor only a few introns [25, 26, 29], which represent a minuscule fraction of the genome when compared to other bacterial mobile elements [30]. This paucity of group II introns likely reflects host-cell defense mechanisms against intron proliferation [31].…”