Methyl-directed Repair of Mismatched Small Heterologous Sequences in Cell Extracts from Escherichia coli

Fang, Wen‐Hsien; Wu, Jiun-Yi; Su, Ming-Jang

doi:10.1074/jbc.272.36.22714

Cited by 29 publications

(33 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, the MutHSL mismatch repair system can repair minus one frameshift mismatches and G:T and C:A mismatches formed by PolIII during DNA replication, aˆnding consistent with other studies (9,37). This result was consistent with in vitro MutHSL enzyme activity that e‹ciently corrected the transition G-T mismatch (38,39) and 1-3 base insertion/deletion heteroduplexes as e‹ciently as base pair mismatches (40). The minus frameshifts and transitions in the mutS strain were located at speciˆc hotspots (14).…”

Section: Dna Sequence Alteration In E Coli Mutator Strainssupporting

confidence: 79%

Spontaneous Mutagenesis in Escherichia coli and Saccharomyces cerevisiae

Imai

Tago

Endo

et al. 2006

Genes and Environment

View full text Add to dashboard Cite

In this article, we described the spontaneously occurring mutation speciˆcities of defects that are involved in translesion polymerase, mutS mismatch correction and polA mismatch correction in Escherichia coli. We argue that 1) there is no contribution of translesion polymerase to E. coli chromosomal mutation, 2) mutS system recognizes and corrects transition and frameshift mismatches and 3) polA system recognizes and corrects deletion, frameshift and transition mismatches. We also characterized the genetic alterations that inactivate either the CAN1 gene of Saccharomyces cerevisiae haploid cells or heterozygously situated in diploid cells. The characteristics of mutation in haploid yeast are essentially consistent with those in E. coli, suggesting that similar mechanisms are operating to form spontaneous mutation. CAN1 ＋ /can1 -(Can S ) to can1 -/can1 -(Can R ) mutations in diploid cells could occur through recombination, mainly allelic crossover and gene conversion.

show abstract

Section: Dna Sequence Alteration In E Coli Mutator Strainssupporting

confidence: 79%

Spontaneous Mutagenesis in Escherichia coli and Saccharomyces cerevisiae

Imai

Tago

Endo

et al. 2006

Genes and Environment

View full text Add to dashboard Cite

show abstract

“…However, how large a DNA loop can be processed by MMR was not clear. In E. coli, it has been documented that MMR can correct unpaired heteroduplexes containing no more than 7 nucleotides (8,10,11,34,35). In yeast, the upper limit of the loop size increases to 13 nucleotides (18,19).…”

Section: Discussionmentioning

confidence: 99%

Bi-directional Processing of DNA Loops by Mismatch Repair-dependent and -independent Pathways in Human Cells

McCulloch¹,

Gu²,

Li³

2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

Previous work has shown that small DNA loop heterologies are repaired not only through the mismatch repair (MMR) pathway but also via an MMR-independent pathway in human cells. However, how DNA loop repair is partitioned between these pathways and how the MMR-independent repair is processed are not clear. Using a novel construct that completely and specifically inhibits MMR in HeLa extracts, we demonstrate here that although MMR is capable of bi-directionally processing DNA loops of 2, 4, 5, 8, 10, or 12 nucleotides in length, the repair activity decreases with the increase of the loop size. Evidence is presented that the largest loop that the MMR system can process is 16 nucleotides. We also show that strand-specific MMR-independent loop repair occurs for all looped substrates tested and rigorously demonstrate that this repair is bi-directional. Analysis of repair intermediates generated by the MMRindependent pathway revealed that although the processing of looped substrates with a strand break 5 to the heterology occurred similarly to MMR (i.e. excision is conducted by exonucleases from the pre-existing strand break to the heterology), the processing of the heterology in substrates with a 3 strand break is consistent with the involvement of endonucleases.DNA insertion/deletion heterologies (also called DNA loops) are formed during normal DNA metabolism, particularly within simple repetitive sequences (1). These DNA loop structures are mutagenic if they are not corrected. It is known that the DNA mismatch repair (MMR) 1 system in both prokaryotes and eukaryotes is capable of correcting small DNA loops (for reviews, see Refs. 2-7). The Escherichia coli MMR system can efficiently process DNA insertion/deletion heterologies up to 7 unpaired nucleotides (8 -11). Gel-shift analyses using mismatch recognition complexes purified from both yeast and human cells have demonstrated that MutS␣ (a heterodimer of MSH2 and MSH6) can bind to small DNA loops with 1-4 nucleotides, whereas MutS␤ (a heterodimer of MSH2 and MSH3) can interact with DNA loops up to 24 nucleotides (12)(13)(14)(15)(16)(17). Genetic studies in yeast suggest that the yeast MMR system may be capable of correcting DNA loops up to 13 unpaired nucleotides (18,19). Functional in vitro MMR assays have shown that the human MMR can repair DNA loops with at least 8 unpaired nucleotides (20 -22). However, the upper limits of loop size that can be processed by the human MMR system have not been adequately defined.There is accumulating evidence suggesting that DNA loop repair can be conducted in a manner independent of MMR (21-26). First, in vitro functional repair assays have been used to demonstrate that human cells have a pathway or pathways that can carry out strand-specific repair of looped heterologies using an MMR-independent mechanism. Umar et al. (21) and Littman et al. (24) have identified a vigorous 5Ј-nick-directed loop repair activity of this type using MMR-deficient extracts and DNA substrates containing 5-16 (21) or Ն27 (24) nucleotides in the loop. ...

show abstract

“…The Escherichia coli mismatch repair pathway will correct loops up to about 7 unpaired nucleotides, but larger heterologies are poorly processed by this system (11)(12)(13)(14). A similar specificity is characteristic of the human mismatch repair system, which can correct loops up to about 10 unpaired nucleotides (15-17).…”

mentioning

confidence: 92%

“…Materials-E. coli strains NM522, RS5033, GM3773 (mutH471::Tn5), GM2931 (mutL25), RK1517 (mutS201::Tn5), and bacteriophage M13mp18 were as described (14). E. coli DNA ligase, ATP-dependent DNase, T4 polynucleotide kinase, calf intestinal alkaline phosphatase, and restriction endonucleases were obtained from New England Biolabs or Amersham Biosciences.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

DNA Loop Repair by Escherichia coli Cell Extracts

Fang

Wang

et al. 2003

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The nick-directed DNA repair efficiency of a set of M13mp18-derived heteroduplexes containing 8-, 12-, 16-, 22-, 27-, 45-, and 429-nucleotide loops was determined by in vitro assay. Unpaired nucleotides of each heteroduplex reside within overlapping recognition sites for two restriction endonucleases, permitting independent evaluation of repair occurring on either DNA strand. Our results show that a strand break located either 3 or 5 to the loop is sufficient to direct heterology repair to the nicked strand in Escherichia coli extracts. Strandspecific repair by this system requires Mg 2؉ and the four dNTPs and is equally efficient on insertions and deletions. This activity is distinct from the MutHLS mismatch repair pathway. Strand specificity and repair efficiency are largely independent of the GATC methylation state of the DNA and presence of the products of mismatch repair genes mutH, mutL, and mutS. This study provides evidence for a loop repair pathway in E. coli that is distinct from conventional mismatch repair.DNA mispairs can occur within the DNA helix as a consequence of DNA biosynthetic errors or as a result of recombinational strand transfer between nonidentical sequences (1-4). Such pairing errors may take the form of base-base mismatches or loops, in which one strand contains one or more unpaired nucleotides. Strand-specific correction of base-base and loop mismatches produced during DNA biosynthesis plays an important role in mutation avoidance (2, 5, 6), and mismatch repair within the recombination heteroduplex has been implicated in gene conversion (3,4,7,8).Base-base mispairs are subject to strand-specific correction by the mismatch repair system of both prokaryotes and eukaryotes (5, 6, 9, 10), but action of this system on loop mispairs is limited to fairly small heterologies. The Escherichia coli mismatch repair pathway will correct loops up to about 7 unpaired nucleotides, but larger heterologies are poorly processed by this system (11)(12)(13)(14). A similar specificity is characteristic of the human mismatch repair system, which can correct loops up to about 10 unpaired nucleotides (15-17).There is evidence that eukaryotes can rectify large unpaired heterologies by a pathway distinct from the mismatch repair system. Available evidence suggests that specificities of the eukaryotic mismatch repair and large loop repair systems partially overlap. When transformed into Saccharomyces cerevisiae, plasmids harboring 8-or 12-base heterologies undergo loop correction (18), and repair is partially reduced but not eliminated by inactivation in the mismatch repair gene PMS1 (19). 21) found that heteroduplexes containing loops of 16, 27, and 216 bases were repaired both in vivo and in vitro by mismatch repair-deficient yeast strains.Transformation of monkey cells with heteroduplex DNAs containing unpaired single-stranded loops has indicated that mammalian cells can rectify such structures (22)(23)(24)(25). In vitro experiments have also indicated that human cells possess a system distinct from the mism...

show abstract

Methyl-directed Repair of Mismatched Small Heterologous Sequences in Cell Extracts from Escherichia coli

Cited by 29 publications

References 41 publications

Spontaneous Mutagenesis in Escherichia coli and Saccharomyces cerevisiae

Spontaneous Mutagenesis in Escherichia coli and Saccharomyces cerevisiae

Bi-directional Processing of DNA Loops by Mismatch Repair-dependent and -independent Pathways in Human Cells

DNA Loop Repair by Escherichia coli Cell Extracts

Contact Info

Product

Resources

About