Pervasive Suicidal Integrases in Deep-Sea Archaea

Abstract

Mobile genetic elements (MGEs) often encode integrases which catalyze the site-specific insertion of their genetic information into the host genome and the reverse reaction of excision. Hyperthermophilic archaea harbor integrases belonging to the SSV-family which carry the MGE recombination site within their open reading frame. Upon integration into the host genome, SSV integrases disrupt their own gene into two inactive pseudogenes and are termed suicidal for this reason. The evolutionary maintenance of suicidal integrases, concurring with the high prevalence and multiples recruitments of these recombinases by archaeal MGEs, is highly paradoxical. To elucidate this phenomenon, we analyzed the wide phylogenomic distribution of a prominent class of suicidal integrases which revealed a highly variable integration site specificity. Our results highlighted the remarkable hybrid nature of these enzymes encoded from the assembly of inactive pseudogenes of different origins. The characterization of the biological properties of one of these integrases, IntpT26-2 showed that this enzyme was active over a wide range of temperatures up to 99 °C and displayed a less-stringent site specificity requirement than comparable integrases. These observations concurred in explaining the pervasiveness of these suicidal integrases in the most hyperthermophilic organisms. The biochemical and phylogenomic data presented here revealed a target site switching system operating on highly thermostable integrases and suggested a new model for split gene reconstitution. By generating fast-evolving pseudogenes at high frequency, suicidal integrases constitute a powerful model to approach the molecular mechanisms involved in the generation of active genes variants by the recombination of proto-genes.

Archaeal tyrosine recombinases

“…26-2 plasmid pT26-2 (Badel et al . 2020 ) were uncovered in the Euryarchaeota phylum as well. Remarkably, recombinases that disrupt their own gene are found exclusively in the archaeal domain and were named suicidal integrases (Badel et al .…”

“…Remarkably, recombinases that disrupt their own gene are found exclusively in the archaeal domain and were named suicidal integrases (Badel et al . 2020 ). It would be logical to assume such MGEs would remain irreversibly integrated into their host genome.…”

“… 2017 ; Badel et al . 2019 , 2020 ). Partial sequences <150 residues were eliminated from the initial dataset and redundancy was reduced using the UCLUST program (Edgar 2010 ) to eliminate sequences sharing >90% identity (Fig.…”

“…In a previous report, we successfully used a different methodology based on protein similarity networks to establish relationships between different archaeal integrase families (Badel et al . 2020 ). A similar approach was conducted on the present archaeal integrase dataset using the SiLiX program (Miele, Penel and Duret 2011 ) in order to define families sharing 25% identity covering at least 60% of the protein.…”

“… 2018 ; Badel et al . 2020 ). A similar large clade of archaeal integrases from pNOB8, pT26-2, SNJ2, pTN3 and SSV was previously observed by phylogenetic analysis (Wang et al .…”