Identification and classification of reverse transcriptases in bacterial genomes and metagenomes

Abstract

Reverse transcriptases (RTs) are found in different systems including group II introns, Diversity Generating Retroelements (DGRs), retrons, CRISPR-Cas systems, and Abortive Infection (Abi) systems in prokaryotes. Different classes of RTs can play different roles, such as template switching and mobility in group II introns, spacer acquisition in CRISPR-Cas systems, mutagenic retrohoming in DGRs, programmed cell suicide in Abi systems, and recently discovered phage defense in retrons. While some classes of RTs have been studied extensively, others remain to be characterized. There is a lack of computational tools for identifying and characterizing various classes of RTs. In this study, we built a tool (called myRT) for identification and classification of prokaryotic RTs. In addition, our tool provides information about the genomic neighborhood of each RT, providing potential functional clues. We applied our tool to predict RTs in all complete and draft bacterial genomes, and created a collection that can be used for exploration of putative RTs and their associated protein domains. Application of myRT to metagenomes showed that gut metagenomes encode proportionally more RTs related to DGRs, outnumbering retron-related RTs, as compared to the collection of reference genomes. MyRT is both available as a standalone software (https://github.com/mgtools/myRT) and also through a website (https://omics.informatics.indiana.edu/myRT/).

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

“…Of these 5022 representative sequences, 325 belong to previously undescribed groups (Figure 1 and Supplementary Table S1 ). It is worth mentioning that by following this methodology, we did not obtain any representative sequence of the UG11 group, consistent with the fact that recent analyses ( 5 , 74 ) highlighted that UG11 does not belong to the UG/Abi lineage, but to the retron lineage. To investigate the relationships between these novel sequences, we performed a phylogenetic reconstruction of the RT domain present in all UG/Abi RT representative sequences, increasing from 28 to 39 the number of well-supported UG RT groups and revealing the presence of three main clades (Figure 1 ).…”

“…This is the example of UG23 (some sequences present in this group have clustered within the UG33 group), UG13 (subdivided in UG13a and UG13b) or UG39 (now including 15 sequences previously clustered within UG28). Some of these changes were already anticipated by Sharifi and Ye ( 74 ), who also pointed out that the 15 sequences within UG28 constituted a new clade that was named UG28b. However, evolutionary analyses indicate that this group is phylogenetically independent and is specifically associated with the protein cluster 64 (VirE + PriCT-2 domains).…”

Phages and their satellites encode hotspots of antiviral systems

“…The gop gene product was shown to be toxic in the absence of β ( Ghisotti et al., 1990 ), suggesting that the system may form a toxin-antitoxin system functioning through abortive infection. We also identified a RT from unknown group 5 ( Sharifi and Ye, 2021 ; Toro and Nisa-Martínez, 2014 ) with a C-terminal nitrilase domain ( Table S3 ) that is associated with a transmembrane effector. This system is reminiscent of a recently described anti-phage system called type-I DRT ( Gao et al., 2020 ), although the RT belongs to a different clade.…”

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

“…Toxin and Antitoxin (TA) genes were identified based on specific domains of TA systems using Metafisher (https://github.com/JeanMainguy/MeTAfisher). Reverse transcriptases (RTs) were predicted and classified through the myRT web-server (https://omics.informatics.indiana.edu/myRT/) 14 .…”

“…In line with antagonistic co-evolution of viruses and their hosts 9,10 , viruses have developed efficient and robust counter-defense systems, such as antirestriction, anti-CRISPR and other counter-defense proteins 11,12 . Diversity-generating retroelements (DGRs) containing reverse transcriptase (RT) are another important diversification mechanism for driving sustained amino acid-level diversification of their target domains 13,14 . Viruses also encode DGRs to produce many mutations in specific regions of host target genes through error-prone reverse transcription [15][16][17] .…”