Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs

Abstract

Homologous recombination is a key in contributing to bacteriophages genome repair, circularization and replication. No less than six kinds of recombinase genes have been reported so far in bacteriophage genomes, two (UvsX and Gp2.5) from virulent, and four (Sak, Redβ, Erf and Sak4) from temperate phages. Using profile–profile comparisons, structure-based modelling and gene-context analyses, we provide new views on the global landscape of recombinases in 465 bacteriophages. We show that Sak, Redβ and Erf belong to a common large superfamily adopting a shortcut Rad52-like fold. Remote homologs of Sak4 are predicted to adopt a shortcut Rad51/RecA fold and are discovered widespread among phage genomes. Unexpectedly, within temperate phages, gene-context analyses also pinpointed the presence of distant Gp2.5 homologs, believed to be restricted to virulent phages. All in all, three major superfamilies of phage recombinases emerged either related to Rad52-like, Rad51-like or Gp2.5-like proteins. For two newly detected recombinases belonging to the Sak4 and Gp2.5 families, we provide experimental evidence of their recombination activity in vivo. Temperate versus virulent lifestyle together with the importance of genome mosaicism is discussed in the light of these novel recombinases. Screening for these recombinases in genomes can be performed at http://biodev.extra.cea.fr/virfam.

Mgm101 Is a Rad52-related Protein Required for Mitochondrial DNA Recombination

“…The Rad52-type proteins are widespread among bacteriophages. Based on structure-based modeling, these viral recombination proteins are grouped into the Rad52-, RecA/ Rad51-, and Gp2.5-type subfamilies (37). The Rad52 family proteins are structurally characterized by a typical ␤-␤-␤-␣ fold, despite very limited similarity in their primary sequences.…”

“…Although the Rad52-type recombination proteins are only conserved at the tertiary and quaternary structural levels rather than at primary sequences (37), close orthologs of Mgm101 are readily identified in lower animals (e.g., Nematostella venctensis) and in Dictyostelium discoideum (see supplemental Fig. S5).…”

“…It is evolutionarily related to a highly diverged superfamily of recombination proteins that are widely present in temperate bacteriophages (35)(36)(37). These viral proteins, as exemplified by Red␤, Erf, and Sak, have single strand annealing (SSA) activity.…”

A standardized workflow for surveying recombinases expands bacterial genome‐editing capabilities

“…Isothermal/Gibson assembly was carried out according to procedures outlined in (Gibson et al ., 2009; Gibson, 2011). ssDNA binding proteins with potential recombineering activity were selected from the NCBI non‐redundant (nr) protein sequence database: drawing from a recent survey of bacteriophage genomes for homologues to Rad52, Rad51 and Gp2.5 superfamily recombinases (Lopes et al ., 2010), homologues from the major recombinase families were identified on Pseudomonas phage genomes. We designated the following proteins belonging to ERF, GP2.5, Sak and Sak4 families as sequence references for a subsequent sequence similarity search: ERF recombinase from P. aeruginosa phage D3 (GenBank no.…”

Preparation of the Mgm101 Recombination Protein by MBP-based Tagging Strategy

“…Rad52 belongs to a diverse group of recombination proteins that are widespread among bacteriophages 11 . These proteins are also known as Single Strand Annealing Proteins (SSAPs), based on their activity in promoting the annealing of homologous single stranded DNA molecules.…”