Short-patch correction of C/C mismatches in human cells

Alleviation of C⋅C Mismatches in DNA by the Escherichia coli Fpg Protein

DNA polymerase III mis-insertion may, where not corrected by its 3′→ 5′ exonuclease or the mismatch repair (MMR) function, result in all possible non-cognate base pairs in DNA generating base substitutions. The most thermodynamically unstable base pair, the cytosine (C)⋅C mismatch, destabilizes adjacent base pairs, is resistant to correction by MMR in Escherichia coli, and its repair mechanism remains elusive. We present here in vitro evidence that C⋅C mismatch can be processed by base excision repair initiated by the E. coli formamidopyrimidine-DNA glycosylase (Fpg) protein. The k_cat for C⋅C is, however, 2.5 to 10 times lower than for its primary substrate 8-oxoguanine (oxo⁸G)⋅C, but approaches those for 5,6-dihydrothymine (dHT)⋅C and thymine glycol (Tg)⋅C. The K_M values are all in the same range, which indicates efficient recognition of C⋅C mismatches in DNA. Fpg activity was also exhibited for the thymine (T)⋅T mismatch and for N⁴- and/or 5-methylated C opposite C or T, Fpg activity being enabled on a broad spectrum of DNA lesions and mismatches by the flexibility of the active site loop. We hypothesize that Fpg plays a role in resolving C⋅C in particular, but also other pyrimidine⋅pyrimidine mismatches, which increases survival at the cost of some mutagenesis.

Effects of the loss of mismatch repair genes on single-strand annealing between divergent sequences in Saccharomyces cerevisiae

Eukaryotic genomes contain many duplicated genes closely located with each other, such as the hexose transporter (HXT) genes in Saccharomyces cerevisiae. They can potentially recombine via single-strand annealing (SSA) pathway. SSA between highly divergent sequences generates heteroduplex DNA intermediates with many mismatches, which can be corrected by mismatch repair (MMR), resulting in recombinant sequences with a single junction point. In this report, we demonstrate that SSA between HXT1 and HXT4 genes in MMR-deficient yeast cells produces recombinant genes with multiple-junctions resulting from alternating HXT1 and HXT4 tracts. The mutations in MMR genes had differential effects on SSA frequencies; msh6Δ mutation significantly stimulated SSA events, whereas msh2Δ and msh3Δ slightly suppressed it. We set up an assay that can identify a pair of recombinant genes derived from a single heteroduplex DNA. As a result, the recombinant genes with multiple-junctions were found to accompany genes with single-junctions. Based on the results presented here, a model was proposed to generate multiple-junctions in SSA pathway involving an alternative short-patch repair system.

Eliminating both canonical and short-patch mismatch repair in Drosophila melanogaster suggests a new meiotic recombination model

In most meiotic systems, recombination is essential to form connections between homologs that ensure their accurate segregation from one another. Meiotic recombination is initiated by DNA double-strand breaks that are repaired using the homologous chromosome as a template. Studies of recombination in budding yeast have led to a model in which most early repair intermediates are disassembled to produce noncrossovers. Selected repair events are stabilized so they can proceed to form double-Holliday junction (dHJ) intermediates, which are subsequently resolved into crossovers. This model is supported in yeast by physical isolation of recombination intermediates, but the extent to which it pertains to animals is unknown. We sought to test this model in Drosophila melanogaster by analyzing patterns of heteroduplex DNA (hDNA) in recombination products. Previous attempts to do this have relied on knocking out the canonical mismatch repair (MMR) pathway, but in both yeast and Drosophila the resulting recombination products are complex and difficult to interpret. We show that, in Drosophila, this complexity results from a secondary, short-patch MMR pathway that requires nucleotide excision repair. Knocking out both canonical and short-patch MMR reveals hDNA patterns that reveal that many noncrossovers arise after both ends of the break have engaged with the homolog. Patterns of hDNA in crossovers could be explained by biased resolution of a dHJ; however, considering the noncrossover and crossover results together suggests a model in which a two-end engagement intermediate with unligated HJs can be disassembled by a helicase to a produce noncrossover or nicked by a nuclease to produce a crossover. While some aspects of this model are similar to the model from budding yeast, production of both noncrossovers and crossovers from a single, late intermediate is a fundamental difference that has important implications for crossover control.

During meiosis, breaks are introduced into the DNA, then repaired to give either crossovers between homologous chromosomes (these help to ensure correct segregation of these chromosomes from one another), or non-crossover products. Meiotic break repair mechanisms have been best studied in budding yeast, leading to detailed molecular models. Technical limitations have prevented directly testing these models in multi-cellular organisms. One approach that has been tried is to map segments of DNA that are mismatched, since different models predict different arrangements. Mismatches are usually repaired quickly, so analyzing these patterns requires eliminating mismatch repair processes. Although others have knocked out the primary mismatch repair system, we have now, for the first time in an animal, identified the secondary repair pathway and eliminated it and the primary pathway simultaneously. We then analyzed mismatches produced during meiosis. Though the results can be fit to the most popular current model from yeast, if some modifications are made, we also consider a simpler model that incorporates elements of the current model and of earlier models.

Versatile protection from mutagenic DNA lesions conferred by bipartite recognition in nucleotide excision repair

Nucleotide excision repair is a cut-and-patch pathway that eliminates potentially mutagenic DNA lesions caused by ultraviolet light, electrophilic chemicals, oxygen radicals and many other genetic insults. Unlike antigen recognition by the immune system, which employs billions of immunoglobulins and T-cell receptors, the nucleotide excision repair complex relies on just a few generic factors to detect an extremely wide range of DNA adducts. This molecular versatility is achieved by a bipartite strategy initiated by the detection of abnormal strand fluctuations, followed by the localization of injured residues through an enzymatic scanning process coupled to DNA unwinding. The early recognition subunits are able to probe the thermodynamic properties of nucleic acid substrates but avoid direct contacts with chemically altered bases. Only downstream subunits of the bipartite recognition process interact more closely with damaged bases to delineate the sites of DNA incision. Thus, consecutive factors expand the spectrum of deleterious genetic lesions conveyed to DNA repair by detecting distinct molecular features of target substrates.

Removal of deoxyinosine from the Escherichia coli chromosome as studied by oligonucleotide transformation

Deoxyinosine (dI) is produced in DNA by the hydrolytic or nitrosative deamination of deoxyadenosine. It is excised in a repair pathway that is initiated by endonuclease V, the product of the nfi gene. The repair was studied in vivo using high-efficiency oligonucleotide transformation mediated by the Beta protein of bacteriophage lambda in a mismatch repair-deficient host. Escherichia coli was transformed with oligonucleotides containing a selectable A-G base substitution mutation. When the mutagenic dG was replaced by a dI in the oligonucleotide, it lost 93-99% of its transforming ability in an nfi(+) cell, but it remained fully functional in an nfi mutant. Therefore, endonuclease V is responsible for most of the removal of deoxyinosine from DNA. New nfi mutants were isolated based on the strong selection provided by their tolerance for transformation by dI-containing DNA. The repair patch for dI was then measured by determining how close to the transforming dG residue a dI could be placed in the oligonucleotide before it interferes with transformation. At the endonuclease V cleavage site, three nucleotides were preferentially removed from the 3' end and two nucleotides were removed from the 5' end. dI:dT and dI:dC base pairs gave the same results. Caveats include possible interference by Beta protein and by mispaired bases. Thus, oligonucleotide transformation can be used to determine the relative importance of redundant repair pathways, to isolate new DNA repair mutants, and to determine with high precision the sizes of repair tracts in intact cells.

Accurate homologous recombination is a prominent double-strand break repair pathway in mammalian chromosomes and is modulated by mismatch repair protein Msh2

We designed DNA substrates to study intrachromosomal recombination in mammalian chromosomes. Each substrate contains a thymidine kinase (tk) gene fused to a neomycin resistance (neo) gene. The fusion gene is disrupted by an oligonucleotide containing the 18-bp recognition site for endonuclease I-SceI. Substrates also contain a "donor" tk sequence that displays 1% or 19% sequence divergence relative to the tk portion of the fusion gene. Each donor serves as a potential recombination partner for the fusion gene. After stably transfecting substrates into mammalian cell lines, we investigated spontaneous recombination and double-strand break (DSB)-induced recombination following I-SceI expression. No recombination events between sequences with 19% divergence were recovered. Strikingly, even though no selection for accurate repair was imposed, accurate conservative homologous recombination was the predominant DSB repair event recovered from rodent and human cell lines transfected with the substrate containing sequences displaying 1% divergence. Our work is the first unequivocal demonstration that homologous recombination can serve as a major DSB repair pathway in mammalian chromosomes. We also found that Msh2 can modulate homologous recombination in that Msh2 deficiency promoted discontinuity and increased length of gene conversion tracts and brought about a severalfold increase in the overall frequency of DSB-induced recombination.

Trypanosoma brucei homologous recombination is dependent on substrate length and homology, though displays a differential dependence on mismatch repair as substrate length decreases

Homologous recombination functions universally in the maintenance of genome stability through the repair of DNA breaks and in ensuring the completion of replication. In some organisms, homologous recombination can perform more specific functions. One example of this is in antigenic variation, a widely conserved mechanism for the evasion of host immunity. Trypanosoma brucei, the causative agent of sleeping sickness in Africa, undergoes antigenic variation by periodic changes in its variant surface glycoprotein (VSG) coat. VSG switches involve the activation of VSG genes, from an enormous silent archive, by recombination into specialized expression sites. These reactions involve homologous recombination, though they are characterized by an unusually high rate of switching and by atypical substrate requirements. Here, we have examined the substrate parameters of T. brucei homologous recombination. We show, first, that the reaction is strictly dependent on substrate length and that it is impeded by base mismatches, features shared by homologous recombination in all organisms characterized. Second, we identify a pathway of homologous recombination that acts preferentially on short substrates and is impeded to a lesser extent by base mismatches and the mismatch repair machinery. Finally, we show that mismatches during T. brucei recombination may be repaired by short-patch mismatch repair.

Impact of the loss of AtMSH2 on double-strand break-induced recombination between highly diverged homeologous sequences in Arabidopsis thaliana germinal tissues

We experimented a novel reporter system to analyze intrachromosomal recombination between homeologous sequences in Arabidopsis germ cell lineages. The recombination substrates used are the BAR and PAT genes which diverge by about 13% at the nucleotide level and confer resistance to the herbicide glufosinate. DNA double-strand breaks (DSBs) were generated by the I-Sce1 endonuclease to induce recombination. Loss of AtMSH2 induces a 3-fold increase of the frequency of recombination events indicating that AtMSH2 is involved in the anti-recombination activity that prevents exchange between highly diverged sequences in Arabidopsis. Molecular analysis of recombined alleles indicates that in wild type plants the single strand annealing (SSA) pathway can process more efficiently homologous 3' ends than 3' ends generated by resection of non-homologous overhangs. The loss of AtMSH2 disturbs this process, leading to a modification of the distribution of the BAR/PAT junctions and therefore showing that the MSH2 function is also involved in determining the structure of the recombined alleles. In addition, conversion tracts were observed in some alleles. They are shorter in MSH2 deficient plants than in wild-type, suggesting that a short-patch mismatch repair, not controlled by MSH2, could exist in Arabidopsis.