The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Abstract

Ribonuclease H-like (RNHL) superfamily, also called the retroviral integrase superfamily, groups together numerous enzymes involved in nucleic acid metabolism and implicated in many biological processes, including replication, homologous recombination, DNA repair, transposition and RNA interference. The RNHL superfamily proteins show extensive divergence of sequences and structures. We conducted database searches to identify members of the RNHL superfamily (including those previously unknown), yielding >60 000 unique domain sequences. Our analysis led to the identification of new RNHL superfamily members, such as RRXRR (PF14239), DUF460 (PF04312, COG2433), DUF3010 (PF11215), DUF429 (PF04250 and COG2410, COG4328, COG4923), DUF1092 (PF06485), COG5558, OrfB_IS605 (PF01385, COG0675) and Peptidase_A17 (PF05380). Based on the clustering analysis we grouped all identified RNHL domain sequences into 152 families. Phylogenetic studies revealed relationships between these families, and suggested a possible history of the evolution of RNHL fold and its active site. Our results revealed clear division of the RNHL superfamily into exonucleases and endonucleases. Structural analyses of features characteristic for particular groups revealed a correlation between the orientation of the C-terminal helix with the exonuclease/endonuclease function and the architecture of the active site. Our analysis provides a comprehensive picture of sequence-structure-function relationships in the RNHL superfamily that may guide functional studies of the previously uncharacterized protein families.

R-loop: an emerging regulator of chromatin dynamics

“…Overexpression of RNase H has been shown to partially complement the growth defect of DNA topoisomerase I mutants in Escherichia coli by reducing R-loops formation [3,30]. This mechanism is evolutionary conserved and found in yeast and mammals [31].…”

Resilience of biochemical activity in protein domains in the face of structural divergence

“…A classic example are the tRNA synthetases, all of which catalyze the same basic reaction (ATP-dependent ligation of the acyl group of an amino acid of the 2’ or 3’ hydroxyl of the cognate tRNA), but belong to two distinct protein superfamilies with structurally unrelated folds [5]. On the other hand, structural studies also revealed that divergent evolution is rampant among protein domains – enzymatic domains, which were originally considered to be unrelated, such as actin, hexokinase, RNase H, PIWI, and diverse integrases of transposons and retroviruses were shown to contain a common fold (the RNase H fold) with comparable active site residues [6]. Discovery of divergent relationships via structural comparisons has provided a robust framework for understanding the evolutionary “exploration” of substrate space, wherein certain folds have been utilized as platforms for extensive biochemical diversification [7-9].…”

Characterization of the C-Terminal Nuclease Domain of Herpes Simplex Virus pUL15 as a Target of Nucleotidyltransferase Inhibitors

“…11–13 Thus, a structurally related HSV enzyme seems to be a plausible HSV target. As an example, infected cell protein 8 (ICP8), a DNA binding protein required for HSV replication, belongs to the superfamily of NTases sharing an “RNase H-like” fold, 14 and Yan et al have shown that raltegravir, an inhibitor of HIV-1 integrase (IN), another NTase, blocks replication of alpha-, beta-, and gammaherpesviruses. 15 A second HSV candidate, pUL15, is a component of the terminase molecular motor complex that is responsible for mobilizing viral DNA into the capsid.…”