Archaeal tyrosine recombinases

Abstract

The integration of mobile genetic elements into their host chromosome influences the immediate fate of cellular organisms and gradually shapes their evolution. Site-specific recombinases catalyzing this integration have been extensively characterized both in bacteria and eukarya. More recently, a number of reports provided the in-depth characterization of archaeal tyrosine recombinases and highlighted new particular features not observed in the other two domains. In addition to being active in extreme environments, archaeal integrases catalyze reactions beyond site-specific recombination. Some of these integrases can catalyze low sequence specificity recombination reactions with the same outcome as homologous recombination events generating deep rearrangements of their host genome. A large proportion of archaeal integrases are termed suicidal due to the presence of a specific recombination target within their own gene. The paradoxical maintenance of integrases which disrupt their gene upon integration implies novel mechanisms for their evolution. In this review, we assess the diversity of the archaeal tyrosine recombinases using a phylogenomic analysis based on an exhaustive similarity network. We outline the biochemical, ecological and evolutionary properties of these enzymes in the context of the families we identified and emphasize similarities and differences between archaeal recombinases and their bacterial and eukaryal counterparts.

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

“…5A; Table 2). Tandem integrations have been previously described for euryarchaeal and thaumarchaeal iMGEs, including viruses, plasmids and casposons (Krupovic and Bamford, 2008; Krupovic et al ., 2019), and it has been suggested that recombination between such tandemly integrated elements promotes their modular genome evolution (Badel et al ., 2021).…”

“…shibatae iMGEs encode both types of integrases, but all have integrated into the genome by recombining with the 3′‐distal regions of diverse tRNA genes (Table 2). Although protein‐coding genes and intergenic regions are also known to serve as integration sites for archaeal viruses and plasmids (Krupovic et al ., 2010a; Krupovic et al ., 2010b; Kazlauskas et al ., 2018; Krupovic et al ., 2019), the tRNA genes are by far the most common att sites (Badel et al ., 2021). Notably, we found that the SSV1 genome occupied not only the previously reported tRNA‐Arg (CCG) gene (Reiter et al ., 1989; Schleper et al ., 1992) but was also integrated into a secondary target site, tRNA‐Arg (TCG).…”

Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon

“…This protein family is known to be important for the integration and excision of mobile genetic elements into the host chromosome and the post-replicative segregation of plasmids and circular chromosomes in bacteria, eukaryotes and archaea [ 33 ]. Recently, new particular features were highlighted for archaeal tyrosine recombinases as catalysing reactions beyond site-specific recombination such as low-sequence specificity recombination reactions with the same outcome as homologous recombination events [ 34 ]. These low-sequence specificity recombinations might be the reason why selected mutants sometimes lose their plasmid but stay puromycin resistant by introducing the pac gene into their chromosome.…”

Genome Enrichment of Rare, Unknown Species from Complicated Microbiome by Nanopore Selective Sequencing

“…These GIs were always missing in previously genomes assembled by short reads due to the defective resolving of repetitive fragments flanking the exogenous genetic island 33,34 . In the largest GIs of 36 Kbp, we identified six copies of Tyrosine recombinase ( xerA, xerC , or xerD ), which had previously been reported to facilitate the insertion of gene islands into the host chromosome by catalyzing site-specific, energy-independent DNA recombination 34,36 . Additionally, we identified a heat shock protein, HtpX , that may contribute to the heat shock response facilitating the cell’s survival in a thermophilic environment.…”