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 and classify RTs in all complete and draft bacterial genomes, and created a collection that can be used for exploration of putative RTs. Application of myRT to gut 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 and also through a website.

Ribovirus classification by a polymerase barcode sequence

“…We created a consolidated set of non-RdRP sequences ( ) to aid the development and validation of , including the following amino acid sequences clustered at 97% identity: UniProt proteomes for human ( ), yeast ( ), E. coli ( ); all retroviral and DNA-viral sequences from GenBank; and ; the training set of validated RT developed for ( Sharifi & Ye, 2021 ), and disordered proteins from ( Hatos et al, 2020 ). Manual inspection of the following 10 sequences identified as high-confidence RdRP by were confirmed by InterPro ( Hunter et al, 2009 ) and ( Altschul et al, 1997 ) to be RdRP and discarded: , , , , , , , , , and .…”

Ribovirus classification by a polymerase barcode sequence

“…We created a consolidated set of non-RdRP sequences () to aid the development and validation of , including the following amino acid sequences clustered at 97% identity: UniProt proteomes for human (), yeast (), E. coli (); all retroviral and DNA-viral sequences from GenBank; and ; the training set of validated RT developed for (Sharifi and Ye 2021), and disordered proteins from https://disprot.org (Hatos et al 2020). Manual inspection of the following ten sequences identified as high-confidence RdRP by were confirmed by InterPro (Hunter et al 2009) and (Altschul et al 1997) to be RdRP and discarded: , , , , , , , , , and .…”