Abstract
Reverse transcriptases (RTs) closely related to those encoded by group II introns but lacking the intron RNA structure have been found associated with type III clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems, a prokaryotic immune system against invading viruses and foreign genetic elements. Two models have been proposed to explain the origin and evolutionary relationships of these RTs: (i) the “single point of origin” model, according to which these RTs originated from a single acquisition event in bacterial, with the various protein domains (RT, RT-Cas1, and Cas6-RT-Cas1 fusions) corresponding to single points in evolution; and (ii) the “various origins” model, according to which, independent acquisition events in different evolutionary episodes led to these fusions. We tested these alternative hypotheses, by analyzing and integrating published datasets of RT sequences associated with CRISPR-Cas systems and inferring phylogenetic trees by maximum likelihood (ML) methods. The RTs studied could be grouped into 13 clades, mostly in bacteria, in which they probably evolved. The various clades appear to form three independent lineages in bacteria and a recent lineage in archaea. Our data show that the Cas6 domain was acquired twice, independently, through RT-Cas1 fusion, in the bacterial lineages. Taken together, there more evidence to support the “various origins” hypothesis.
Highlights
Phylogenetic analyses have shown that bacterial Reverse transcriptases (RTs) can be classified into 17 main groups, and that over 50% of these enzymes, which can be used to generate complementary DNA from an RNA template, are encoded by group II introns (Toro and Nisa-Martínez, 2014; Zimmerly and Wu, 2015)
RTs closely related to those encoded by group II introns but lacking a recognizable intron RNA structure have been identified, and some of these RTs are associated with type III clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems, adjacent or fused at the C-terminus to Cas1 (Kojima and Kanehisa, 2008; Simon and Zimmerly, 2008; Toro and Nisa-Martínez, 2014; Silas et al, 2016, 2017a; Toro et al, 2017; Shmakov et al, 2018)
We used MUSCLE software (Edgar, 2004) to align 21 RT-like sequences from the identified branches 7, 8, and 9 reported by Silas et al (2017a) absent from our previous study against our dataset (Toro et al, 2017) comprising 537 sequences and encompassing RT domains (0–7) including 414 sequences of the known group II intron RT classes, three RTs from the closely related G2L4 group (Toro and NisaMartínez, 2014) with no recognizable group II intron structure, two RT sequences related to the archaeal RTs associated with CRISPR-Cas systems of clade 1, and 118 RT sequences associated with CRISPR-cas loci
Summary
Phylogenetic analyses have shown that bacterial Reverse transcriptases (RTs) can be classified into 17 main groups, and that over 50% of these enzymes, which can be used to generate complementary DNA (cDNA) from an RNA template, are encoded by group II introns (Toro and Nisa-Martínez, 2014; Zimmerly and Wu, 2015). These introns act as ribozymes and mobile retroelements (Michel et al, 1989; Ferat and Michel, 1993; Toro et al, 2007; Lambowitz and Zimmerly, 2011). Attention has recently focused on these RTs associated with CRISPRCas systems because, in a CRISPR-Cas type III-B displaying transcription-dependent DNA interference (Silas et al, 2017b) harbored by the marine bacterium Marinomonas mediterranea (MMB-1), the associated RT-Cas fusion has been shown to facilitate the RT-dependent acquisition of RNA spacers in vivo through a mechanism resembling group II intron retrohoming (Silas et al, 2016)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
