Structural and Functional Divergence of MutS2 from Bacterial MutS1 and Eukaryotic MSH4-MSH5 Homologs

Abstract

MutS homologs, identified in nearly all bacteria and eukaryotes, include the bacterial proteins MutS1 and MutS2 and the eukaryotic MutS homologs 1 to 7, and they often are involved in recognition and repair of mismatched bases and small insertion/deletions, thereby limiting illegitimate recombination and spontaneous mutation. To explore the relationship of MutS2 to other MutS homologs, we examined conserved protein domains. Fundamental differences in structure between MutS2 and other MutS homologs suggest that MutS1 and MutS2 diverged early during evolution, with all eukaryotic homologs arising from a MutS1 ancestor. Data from MutS1 crystal structures, biochemical results from MutS2 analyses, and our phylogenetic studies suggest that MutS2 has functions distinct from other members of the MutS family. A mutS2 mutant was constructed in Helicobacter pylori, which lacks mutS1 and mismatch repair genes mutL and mutH. We show that MutS2 plays no role in mismatch or recombinational repair or deletion between direct DNA repeats. In contrast, MutS2 plays a significant role in limiting intergenomic recombination across a range of donor DNA tested. This phenotypic analysis is consistent with the phylogenetic and biochemical data suggesting that MutS1 and MutS2 have divergent functions.MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes (16,19,23). The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis (1, 64). All members of the MutS family contain the highly conserved Walker A/B ATPase domain (16), and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange (27,45,49,64).The function of the second prokaryotic homolog, MutS2, is unknown. Sequence analyses reveal fundamental differences between MutS2 and other MutS family members (19). MutS2 proteins contain a conserved C-terminal domain of ϳ250 amino acid residues not found in other MutS homologs and lack the conserved N-terminal region present in most of the other MutS family members (43). According to one hypothesis, MutS2 is more closely related to the meiotic recombination proteins MSH4 and MSH5, while MutS1 is more closely related to MSH2,. This hypothesis suggests a gene duplication event early in the evolution of MutS, resulting in the two main MutS lineages, with MSH4 and MSH5 branching with MutS2 and MSH2, -3, and -6 branching with MutS1. Consistent with this hypothesis, MutS2 has been shown to not play a role in mismatch repair (13,59,69). However, arguing against this hypothesis is the lack of homology between MutS2 and MSH4-MSH5. According to another hypothesis, all eukaryotic MutS homologs evolved from one ancesto...

Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Suppression

“…3A). This result indicates that ttMutS2 is involved in the suppression of homologous recombination like H. pylori MutS2 (8,9). We examined the effect of ttmutS2 disruption on the resistance to mitomycin-C (MMC), which induces both DNA intrastrand and, to a greater extent, interstrand cross-links.…”

“…Recent studies have shown that bacterial and plant MutS2 proteins are candidate anti-recombination enzymes (8,9). MutS2 is a paralogue of Escherichia coli MutS, which recognizes a mismatched base pair and induces the mismatch repair (MMR) 2 pathway ( Fig.…”

“…It had been reported that eukaryotic MSH4 and MSH5 promote homologous recombination (13)(14)(15). In contrast, the disruption of Helicobacter pylori mutS2 increases the frequency of homologous recombination, indicating that H. pylori MutS2 suppresses homologous recombination (8,9). Moreover, it has been shown that purified H. pylori MutS2 binds to a DNA structure mimicking the Holliday junction and interferes with the strand-exchange reaction mediated by RecA in vitro (8).…”

DprB Facilitates Inter- and Intragenomic Recombination in Helicobacter pylori

“…A DprAfamily protein encoded by HP0333 plays roles in high-frequency uptake and translocation of exogenous DNA (4, 62, 63), and RecA (HP0153) is required for the homologous recombination inherent in H. pylori transformation (55, 70). Expression of H. pylori natural competence genes can be induced by DNA damage, further increasing transformation frequency (TF) and gene exchange (20).In H. pylori, natural transformation is suppressed by the DNA helicases RuvB and RecG (30,32). Holliday junctions (HJs), fourway branched DNA intermediates produced at the last step of homologous recombination, are recognized by Holliday junction resolvases (HJRs), specialized DNA-binding proteins that are required to complete recombination (59).…”

Change Is Good: Variations in Common Biological Mechanisms in the Epsilonproteobacterial GeneraCampylobacterandHelicobacter

“…As a whole, the MutS family of proteins is often involved in the recognition and repair of mismatched DNA base pairs (220,442). However, in H. pylori, MutS2 is not involved in mismatch repair and actually inhibits intergenomic recombination (309,487). This suppression of homologous recombination may provide H. pylori with another means to control genetic diversity or to aid in the recognition of illegitimate recombination events (307,487).…”