Molecular basis for the functions of a bacterial MutS2 in DNA repair and recombination

Abstract

Bacterial MutS2 proteins, consisting of functional domains for ATPase, DNA-binding, and nuclease activities, play roles in DNA recombination and repair. Here we observe a mechanism for generating MutS2 expression diversity in the human pathogen Helicobacter pylori, and identify a unique MutS2 domain responsible for specific DNA-binding. H. pylori strains differ in mutS2 expression due to variations in the DNA upstream sequence containing short sequence repeats. Based on Western blots, mutS2 in some strains appears to be co-translated with the upstream gene, but in other strains (e.g. UA948) such translational coupling does not occur. Accordingly, strain UA948 had phenotypes similar to its ΔmutS2 derivative, whereas expression of MutS2 at a separate locus in UA948 (the genetically complemented strain) displayed a lower mutation rate and lower transformation frequency than did ΔmutS2. A series of truncated HpMutS2 proteins were purified and tested for their specific abilities to bind 8-oxoG-containing DNA (GO:C) and Holiday Junction structures (HJ). The specific DNA binding domain was localized to an area adjacent to the Smr nuclease domain, and it encompasses 30-amino-acid-residues containing a “KPPKNKFKPPK” motif. Gel shift assays and competition assays supported that a truncated version of HpMutS2-C12 (~12 kDa protein containing the specific DNA-binding domain) has much greater capacity to bind to HJ or GO:C DNA than to normal double stranded DNA. By studying the in vivo roles of the separate domains of HpMutS2, we observed that the truncated versions were unable to complement the ΔmutS2 strain, suggesting the requirement for coordinated function of all the domains in vivo.

A bacterial DNA repair pathway specific to a natural antibiotic

“…We recently investigated the mismatch repair homolog MutS2 and arrived at a similar conclusion—MutS2 has been adapted to the specific DNA repair needs of different organisms. MutS2 in B. subtilis promotes homologous recombination (Burby and Simmons, ), whereas MutS2 in several other organisms inhibits homologous recombination (Pinto et al ., ; Fukui et al ., ; Damke et al ., ; Wang and Maier, ). The reality that distantly related organisms have adapted their genetic repertoire inherited from the most recent common ancestor would seem obvious.…”

Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression

“…MutS2 has been shown to play an important role in repairing oxidative DNA damage and it has anti-recombination activity in Helicobacter pylori . MutS2 maintains the integrity of the genome by suppressing homologous and homoeologous DNA recombination [37, 38].…”

An atypical CRISPR-Cas locus in Symbiobacterium thermophilum flanked by a transposase, a reverse transcriptase, the endonuclease MutS2 and a putative Cas9-like protein

“…Also, though MutS2 was mentioned in the protocol for 'CRISPR/Cas9 Editing of the Bacillus subtilis Genome', there is no indication that its CRISPR-like endonuclease activity was discussed. Another study emphasized the requirement of all domains of this protein for its functionality [42]. The considerable sequence homology to other MutS2 proteins expectedly translates into significant structural homology (Fig 2a) on a predicted structures, and will help in identifying domains/active sites [43] and other promiscuous functions, if they exist [44].…”