• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of molcellbPermissionsJournals.ASM.orgJournalMCB ArticleJournal InfoAuthorsReviewers
Mol Cell Biol. May 1997; 17(5): 2859–2865.
PMCID: PMC232138

Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants.


Homonucleotide runs in coding sequences are hot spots for frameshift mutations and potential sources of genetic changes leading to cancer in humans having a mismatch repair defect. We examined frameshift mutations in homonucleotide runs of deoxyadenosines ranging from 4 to 14 bases at the same position in the LYS2 gene of the yeast Saccharomyces cerevisiae. In the msh2 mismatch repair mutant, runs of 9 to 14 deoxyadenosines are 1,700-fold to 51,000-fold, respectively, more mutable for single-nucleotide deletions than are runs of 4 deoxyadenosines. These frameshift mutations can account for up to 99% of all forward mutations inactivating the 4-kb LYS2 gene. Based on results with single and double mutations of the POL2 and MSH2 genes, both DNA polymerase epsilon proofreading and mismatch repair are efficient for short runs while only the mismatch repair system prevents frameshift mutations in runs of > or = 8 nucleotides. Therefore, coding sequences containing long homonucleotide runs are likely to be at risk for mutational inactivation in cells lacking mismatch repair capability.

Full Text

The Full Text of this article is available as a PDF (201K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Araki H, Ropp PA, Johnson AL, Johnston LH, Morrison A, Sugino A. DNA polymerase II, the probable homolog of mammalian DNA polymerase epsilon, replicates chromosomal DNA in the yeast Saccharomyces cerevisiae. EMBO J. 1992 Feb;11(2):733–740. [PMC free article] [PubMed]
  • Bebenek K, Beard WA, Casas-Finet JR, Kim HR, Darden TA, Wilson SH, Kunkel TA. Reduced frameshift fidelity and processivity of HIV-1 reverse transcriptase mutants containing alanine substitutions in helix H of the thumb subdomain. J Biol Chem. 1995 Aug 18;270(33):19516–19523. [PubMed]
  • Beckman JS, Weber JL. Survey of human and rat microsatellites. Genomics. 1992 Apr;12(4):627–631. [PubMed]
  • Bhattacharyya NP, Ganesh A, Phear G, Richards B, Skandalis A, Meuth M. Molecular analysis of mutations in mutator colorectal carcinoma cell lines. Hum Mol Genet. 1995 Nov;4(11):2057–2064. [PubMed]
  • Bhattacharyya NP, Skandalis A, Ganesh A, Groden J, Meuth M. Mutator phenotypes in human colorectal carcinoma cell lines. Proc Natl Acad Sci U S A. 1994 Jul 5;91(14):6319–6323. [PMC free article] [PubMed]
  • Branch P, Hampson R, Karran P. DNA mismatch binding defects, DNA damage tolerance, and mutator phenotypes in human colorectal carcinoma cell lines. Cancer Res. 1995 Jun 1;55(11):2304–2309. [PubMed]
  • Budd M, Campbell JL. Temperature-sensitive mutations in the yeast DNA polymerase I gene. Proc Natl Acad Sci U S A. 1987 May;84(9):2838–2842. [PMC free article] [PubMed]
  • Budd ME, Campbell JL. DNA polymerases required for repair of UV-induced damage in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Apr;15(4):2173–2179. [PMC free article] [PubMed]
  • Campos RV, Zhang L, Drucker DJ. Differential expression of RNA transcripts encoding unique carboxy-terminal sequences of human parathyroid hormone-related peptide. Mol Endocrinol. 1994 Dec;8(12):1656–1666. [PubMed]
  • Chattoo BB, Palmer E, Ono B, Sherman F. Patterns of Genetic and Phenotypic Suppression of lys2 Mutations in the Yeast SACCHAROMYCES CEREVISIAE. Genetics. 1979 Sep;93(1):67–79. [PMC free article] [PubMed]
  • Chattoo BB, Sherman F, Azubalis DA, Fjellstedt TA, Mehnert D, Ogur M. Selection of lys2 Mutants of the Yeast SACCHAROMYCES CEREVISIAE by the Utilization of alpha-AMINOADIPATE. Genetics. 1979 Sep;93(1):51–65. [PMC free article] [PubMed]
  • Eshleman JR, Lang EZ, Bowerfind GK, Parsons R, Vogelstein B, Willson JK, Veigl ML, Sedwick WD, Markowitz SD. Increased mutation rate at the hprt locus accompanies microsatellite instability in colon cancer. Oncogene. 1995 Jan 5;10(1):33–37. [PubMed]
  • Eshleman JR, Markowitz SD. Microsatellite instability in inherited and sporadic neoplasms. Curr Opin Oncol. 1995 Jan;7(1):83–89. [PubMed]
  • Eshleman JR, Markowitz SD, Donover PS, Lang EZ, Lutterbaugh JD, Li GM, Longley M, Modrich P, Veigl ML, Sedwick WD. Diverse hypermutability of multiple expressed sequence motifs present in a cancer with microsatellite instability. Oncogene. 1996 Apr 4;12(7):1425–1432. [PubMed]
  • Feng G, Tsui HC, Winkler ME. Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells. J Bacteriol. 1996 Apr;178(8):2388–2396. [PMC free article] [PubMed]
  • Freund AM, Bichara M, Fuchs RP. Z-DNA-forming sequences are spontaneous deletion hot spots. Proc Natl Acad Sci U S A. 1989 Oct;86(19):7465–7469. [PMC free article] [PubMed]
  • Greene CN, Jinks-Robertson S. Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins. Mol Cell Biol. 1997 May;17(5):2844–2850. [PMC free article] [PubMed]
  • Hess P, Aquilina G, Dogliotti E, Bignami M. Spontaneous mutations at aprt locus in a mammalian cell line defective in mismatch recognition. Somat Cell Mol Genet. 1994 Sep;20(5):409–421. [PubMed]
  • Huang J, Papadopoulos N, McKinley AJ, Farrington SM, Curtis LJ, Wyllie AH, Zheng S, Willson JK, Markowitz SD, Morin P, et al. APC mutations in colorectal tumors with mismatch repair deficiency. Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):9049–9054. [PMC free article] [PubMed]
  • Johnson RE, Kovvali GK, Prakash L, Prakash S. Requirement of the yeast MSH3 and MSH6 genes for MSH2-dependent genomic stability. J Biol Chem. 1996 Mar 29;271(13):7285–7288. [PubMed]
  • Johnson RE, Kovvali GK, Prakash L, Prakash S. Requirement of the yeast RTH1 5' to 3' exonuclease for the stability of simple repetitive DNA. Science. 1995 Jul 14;269(5221):238–240. [PubMed]
  • Kat A, Thilly WG, Fang WH, Longley MJ, Li GM, Modrich P. An alkylation-tolerant, mutator human cell line is deficient in strand-specific mismatch repair. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6424–6428. [PMC free article] [PubMed]
  • Kinzler KW, Vogelstein B. Lessons from hereditary colorectal cancer. Cell. 1996 Oct 18;87(2):159–170. [PubMed]
  • Kroutil LC, Register K, Bebenek K, Kunkel TA. Exonucleolytic proofreading during replication of repetitive DNA. Biochemistry. 1996 Jan 23;35(3):1046–1053. [PubMed]
  • Kunkel TA. Frameshift mutagenesis by eucaryotic DNA polymerases in vitro. J Biol Chem. 1986 Oct 15;261(29):13581–13587. [PubMed]
  • Kunkel TA, Patel SS, Johnson KA. Error-prone replication of repeated DNA sequences by T7 DNA polymerase in the absence of its processivity subunit. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):6830–6834. [PMC free article] [PubMed]
  • Levinson G, Gutman GA. High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucleic Acids Res. 1987 Jul 10;15(13):5323–5338. [PMC free article] [PubMed]
  • Loeb LA. Mutator phenotype may be required for multistage carcinogenesis. Cancer Res. 1991 Jun 15;51(12):3075–3079. [PubMed]
  • Longerich S, Galloway AM, Harris RS, Wong C, Rosenberg SM. Adaptive mutation sequences reproduced by mismatch repair deficiency. Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12017–12020. [PMC free article] [PubMed]
  • Malkhosyan S, McCarty A, Sawai H, Perucho M. Differences in the spectrum of spontaneous mutations in the hprt gene between tumor cells of the microsatellite mutator phenotype. Mutat Res. 1996 May;316(5-6):249–259. [PubMed]
  • Markowitz S, Wang J, Myeroff L, Parsons R, Sun L, Lutterbaugh J, Fan RS, Zborowska E, Kinzler KW, Vogelstein B, et al. Inactivation of the type II TGF-beta receptor in colon cancer cells with microsatellite instability. Science. 1995 Jun 2;268(5215):1336–1338. [PubMed]
  • Marsischky GT, Filosi N, Kane MF, Kolodner R. Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair. Genes Dev. 1996 Feb 15;10(4):407–420. [PubMed]
  • Martin TJ, Moseley JM, Gillespie MT. Parathyroid hormone-related protein: biochemistry and molecular biology. Crit Rev Biochem Mol Biol. 1991;26(3-4):377–395. [PubMed]
  • Modrich P, Lahue R. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu Rev Biochem. 1996;65:101–133. [PubMed]
  • Morrison A, Bell JB, Kunkel TA, Sugino A. Eukaryotic DNA polymerase amino acid sequence required for 3'----5' exonuclease activity. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9473–9477. [PMC free article] [PubMed]
  • Morrison A, Johnson AL, Johnston LH, Sugino A. Pathway correcting DNA replication errors in Saccharomyces cerevisiae. EMBO J. 1993 Apr;12(4):1467–1473. [PMC free article] [PubMed]
  • Morrison A, Sugino A. The 3'-->5' exonucleases of both DNA polymerases delta and epsilon participate in correcting errors of DNA replication in Saccharomyces cerevisiae. Mol Gen Genet. 1994 Feb;242(3):289–296. [PubMed]
  • Morrison A, Sugino A. DNA polymerase II, the epsilon polymerase of Saccharomyces cerevisiae. Prog Nucleic Acid Res Mol Biol. 1993;46:93–120. [PubMed]
  • Parsons R, Myeroff LL, Liu B, Willson JK, Markowitz SD, Kinzler KW, Vogelstein B. Microsatellite instability and mutations of the transforming growth factor beta type II receptor gene in colorectal cancer. Cancer Res. 1995 Dec 1;55(23):5548–5550. [PubMed]
  • Pribnow D, Sigurdson DC, Gold L, Singer BS, Napoli C, Brosius J, Dull TJ, Noller HF. rII cistrons of bacteriophage T4. DNA sequence around the intercistronic divide and positions of genetic landmarks. J Mol Biol. 1981 Jul 5;149(3):337–376. [PubMed]
  • Prolla TA, Christie DM, Liskay RM. Dual requirement in yeast DNA mismatch repair for MLH1 and PMS1, two homologs of the bacterial mutL gene. Mol Cell Biol. 1994 Jan;14(1):407–415. [PMC free article] [PubMed]
  • Reenan RA, Kolodner RD. Characterization of insertion mutations in the Saccharomyces cerevisiae MSH1 and MSH2 genes: evidence for separate mitochondrial and nuclear functions. Genetics. 1992 Dec;132(4):975–985. [PMC free article] [PubMed]
  • Ripley LS, Clark A, deBoer JG. Spectrum of spontaneous frameshift mutations. Sequences of bacteriophage T4 rII gene frameshifts. J Mol Biol. 1986 Oct 20;191(4):601–613. [PubMed]
  • Schaaper RM, Dunn RL. Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc Natl Acad Sci U S A. 1987 Sep;84(17):6220–6224. [PMC free article] [PubMed]
  • Schaaper RM, Dunn RL. Spontaneous mutation in the Escherichia coli lacI gene. Genetics. 1991 Oct;129(2):317–326. [PMC free article] [PubMed]
  • Shcherbakova PV, Pavlov YI. 3'-->5' exonucleases of DNA polymerases epsilon and delta correct base analog induced DNA replication errors on opposite DNA strands in Saccharomyces cerevisiae. Genetics. 1996 Mar;142(3):717–726. [PMC free article] [PubMed]
  • Sia EA, Kokoska RJ, Dominska M, Greenwell P, Petes TD. Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes. Mol Cell Biol. 1997 May;17(5):2851–2858. [PMC free article] [PubMed]
  • Southby J, Murphy LM, Martin TJ, Gillespie MT. Cell-specific and regulator-induced promoter usage and messenger ribonucleic acid splicing for parathyroid hormone-related protein. Endocrinology. 1996 Apr;137(4):1349–1357. [PubMed]
  • Souza RF, Appel R, Yin J, Wang S, Smolinski KN, Abraham JM, Zou TT, Shi YQ, Lei J, Cottrell J, et al. Microsatellite instability in the insulin-like growth factor II receptor gene in gastrointestinal tumours. Nat Genet. 1996 Nov;14(3):255–257. [PubMed]
  • Strand M, Earley MC, Crouse GF, Petes TD. Mutations in the MSH3 gene preferentially lead to deletions within tracts of simple repetitive DNA in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1995 Oct 24;92(22):10418–10421. [PMC free article] [PubMed]
  • Strand M, Prolla TA, Liskay RM, Petes TD. Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature. 1993 Sep 16;365(6443):274–276. [PubMed]
  • Streisinger G, Okada Y, Emrich J, Newton J, Tsugita A, Terzaghi E, Inouye M. Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol. 1966;31:77–84. [PubMed]
  • Streisinger G, Owen J. Mechanisms of spontaneous and induced frameshift mutation in bacteriophage T4. Genetics. 1985 Apr;109(4):633–659. [PMC free article] [PubMed]
  • Thomas DC, Umar A, Kunkel TA. Microsatellite instability and mismatch repair defects in cancer. Mutat Res. 1996 Feb 19;350(1):201–205. [PubMed]
  • Tran H, Degtyareva N, Gordenin D, Resnick MA. Altered replication and inverted repeats induce mismatch repair-independent recombination between highly diverged DNAs in yeast. Mol Cell Biol. 1997 Feb;17(2):1027–1036. [PMC free article] [PubMed]
  • Tran HT, Degtyareva NP, Koloteva NN, Sugino A, Masumoto H, Gordenin DA, Resnick MA. Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes. Mol Cell Biol. 1995 Oct;15(10):5607–5617. [PMC free article] [PubMed]
  • Tran HT, Gordenin DA, Resnick MA. The prevention of repeat-associated deletions in Saccharomyces cerevisiae by mismatch repair depends on size and origin of deletions. Genetics. 1996 Aug;143(4):1579–1587. [PMC free article] [PubMed]
  • Umar A, Buermeyer AB, Simon JA, Thomas DC, Clark AB, Liskay RM, Kunkel TA. Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell. 1996 Oct 4;87(1):65–73. [PubMed]
  • Wang J, Sun L, Myeroff L, Wang X, Gentry LE, Yang J, Liang J, Zborowska E, Markowitz S, Willson JK, et al. Demonstration that mutation of the type II transforming growth factor beta receptor inactivates its tumor suppressor activity in replication error-positive colon carcinoma cells. J Biol Chem. 1995 Sep 15;270(37):22044–22049. [PubMed]
  • Williamson MS, Game JC, Fogel S. Meiotic gene conversion mutants in Saccharomyces cerevisiae. I. Isolation and characterization of pms1-1 and pms1-2. Genetics. 1985 Aug;110(4):609–646. [PMC free article] [PubMed]
  • Yasuda T, Banville D, Hendy GN, Goltzman D. Characterization of the human parathyroid hormone-like peptide gene. Functional and evolutionary aspects. J Biol Chem. 1989 May 5;264(13):7720–7725. [PubMed]

Articles from Molecular and Cellular Biology are provided here courtesy of American Society for Microbiology (ASM)


Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...