InterPro domain: IPR006641

The YqgF domain family is described as RNase H-like and typified by the Escherichia coli protein YqgF [ 1 ].YqgF domain-containing proteins are predicted to be ribonucleases or resolvases based on homology to RuvC Holliday junction resolvases.

The group of proteins containing this domain are found primarily in the low-GC Gram-positive bacteria Holliday junction resolvases (HJRs) and in eukaryote orthologs. The RuvC HJRs are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma urealyticum( Q9PQY7 , [ 2 ]). Furthermore, loss of function ruvC mutants of Escherichia coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase [ 2 ]. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [ 3 ].

The functions of eukaryotic proteins having this domain are less well described. In Saccharomyces cerevisiae (Baker's yeast) Spt6p and its orthologues, the catalytic residues are substituted indicating that they lack the enzymatic function of resolvases [ 3 ]. Spt6p has been implicated in transcription initiation [ 3 ] and in maintaining normal chromatin structure during transcription elongation [ 4 ].

Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes.

The YqgF domain is also found in Tex proteins, where maintains the core structural elements and aligns especially well with RuvC nucleases, although Tex does not appear to possess nuclease activity [ 4 ]. Tex (toxin expression) is a highly conserved bacterial protein involved in expression of critical toxin genes [ 5 ].

1. SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res. 28, 3417-32
2. Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. J. Mol. Biol. 257, 561-73
3. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301, 1096-9
4. Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. J. Mol. Biol. 377, 1460-73
5. A new gene locus of Bordetella pertussis defines a novel family of prokaryotic transcriptional accessory proteins. J. Bacteriol. 178, 4445-52