The search for the right partner: Homologous pairing and DNA strand exchange proteins in eukaryotes (original) (raw)

References

  1. Aboussekhra, A., Chanet, R., Adjiri, A., and Fabre, F., Semidominant suppressors of Srs2 helicase mutations of_Saccharomyces cerevisiae_ map in the_RAD51_ gene, whose sequence predicts a protein with similarities to procaryotic RecA proteins. Molec. cell. Biol.12 (1992) 3224–3234.
    CAS PubMed PubMed Central Google Scholar
  2. Arai, N., Kawasaki, K., and Shibata, T., A multi-component protein of a fission yeast which promotes joint molecule formation from homologous DNAs. J. biol. Chem.267 (1992) 3514–3522.
    Article CAS PubMed Google Scholar
  3. Bähler, J., Hagens, G., Holzinger, G., Scherthan, H., and Heyer, W.-D.,Saccharomyces cerevisiae cells lacking the homologous pairing protein p175_SEP1_ arrest at pachytene during meiotic prophase. Chromosoma. In press.
  4. Basile, G., Aker, M., and Mortimer, R. K., Nucleotide sequence and transcriptional regulation of the yeast recombinational repair gene_RAD51_. Molec. cell. Biol.12 (1992) 3235–3246.
    CAS PubMed PubMed Central Google Scholar
  5. Bezzubova, O., Shinohara, A., Mueller, R. G., Ogawa, H., and Buerstedde, J.-M., A chicken_RAD51_ homologue is expressed at high levels in lymphoid and reproductive organs. Nucl. Acids Res.21 (1993) 1577–1580.
    Article CAS PubMed PubMed Central Google Scholar
  6. Bishop, D. K., Park, D., Xu, L., and Kleckner, N.,DMC1, A meiosis-specific yeast homolog of_E. coli_ recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell_69_ (1992) 439–456.
    Article CAS PubMed Google Scholar
  7. Bollag, R. J., Elwood, D. R., Tobin, E. D., Godwin, A. R., and Liskay, R. M., Formation of heteroduplex DNA during mammalian intra-chromosomal gene conversion. Molec. cell. Biol.12 (1992) 1546–1552.
    CAS PubMed PubMed Central Google Scholar
  8. Bortner, C., Hernandez, T. R., Lehman, I. R., and Griffith, J., Herpes simplex virus 1 single-stranded DNA-binding protein (ICP8) will promote homologous pairing and strand transfer. J. molec. Biol.231 (1993) 241–250.
    Article CAS PubMed Google Scholar
  9. Cerutti, H., Osman, M., Grandoni, P., and Jagendorf, A. T., A homolog of_Escherichia coli_ RecA protein in plastids of higher plants. Proc. natl Acad. Sci. USA_89_ (1992) 8068–8072.
    Article CAS PubMed PubMed Central Google Scholar
  10. Cerutti, H., and Jagendorf, A. T., DNA strand transfer activity in Pea (Pisum sativum L.) chloroplasts. Plant Physiol.102 (1993) 145–153.
    Article CAS PubMed PubMed Central Google Scholar
  11. Cerutti, H., Ibrahim, H. Z., and Jagendorf, A. T., Treatment of Pea (Pisum sativum L.) protoplasts with DNA-damaging agents induces a 39-kilodalton chloroplast protein immunologically related to_Escherichia coli_ RecA. Plant Physiol.102 (1993) 155–163.
    Article CAS PubMed PubMed Central Google Scholar
  12. Cheng, R., Baker, T. I., Cords, C. E., and Radloff, R. J.,mei-3, a recombination and repair gene of_Neurospora crassa_, encodes a RecA-like protein. Mutation Res.294 (1993) 223–234.
    Article CAS PubMed Google Scholar
  13. Clark, A. B., Dykstra, C. C., and Sugino, A., Isolation, DNA sequence, and regulation of a_Saccharomyces cerevisiae_ gene that encodes DNA strand transfer protein α. Molec. cell. Biol.11 (1991) 2576–2582.
    CAS PubMed PubMed Central Google Scholar
  14. Dykstra, C. C., Hamatake, R. K., and Sugino, A., DNA strand transfer protein β from yeast mitotic cells differs from strand transfer protein α from meiotic cells. J. biol. Chem.265 (1990) 10968–10973.
    Article CAS PubMed Google Scholar
  15. Dykstra, C. C., Kitada, K., Clark, A. B., Hamatake, R. K., and Sugino, A., Cloning and characterization of DST2, the gene for DNA strand transfer protein β from_Saccharomyces cerevisiae_. Molec. cell. Biol.11 (1991) 2583–2592.
    CAS PubMed PubMed Central Google Scholar
  16. Egelman, E. H., What do X-ray crystallographic and electron microscopic structural studies of the RecA protein tell us about recombination? Curr. Opin. in struct. Biol.3 (1993) 189–197
    Article CAS Google Scholar
  17. Eggleston, A. K., and Kowalczykowski, S. C., An overview of homologous pairing and DNA strand exchange proteins. Biochimie_73_ (1991) 163–176.
    Article CAS PubMed Google Scholar
  18. Fields, S., and Song, O.-K., A novel genetic system to detect protein: protein interactions. Nature_340_ (1989) 245–246.
    Article CAS PubMed Google Scholar
  19. Fishel, R. A., Detmer, K., and Rich, A., Identification of homologous pairing and strand-exchange activity from a human tumor cell line based on Z-DNA affinity chromatography. Proc. natl Acad. Sci. USA_85_ (1988) 36–40.
    Article CAS PubMed PubMed Central Google Scholar
  20. Fisher, C., Parks, R. J., Lanzon, M. L., and Evans, D. H., Heteroduplex DNA formation is associated with replication and recombination in poxvirus infected cells. Genetics_129_ (1991) 7–18.
    Article CAS PubMed PubMed Central Google Scholar
  21. Fotheringham, S., and Holloman, W. K., Extrachromosomal recombination is deranged in the_rec2_ mutant of_Ustilago maydis_. Genetics_129_ (1991) 1053–1060.
    Article CAS PubMed Central Google Scholar
  22. Friedberg, E. C., Deoxyribonucleic acid repair in the yeast_Saccharomyces cerevisiae_. Microbiol. Rev.52 (1988) 70–102.
    Article CAS PubMed PubMed Central Google Scholar
  23. Gao, M., and Knipe, D. M., Genetic evidence for multiple nuclear functions of the herpes simplex virus ICP8 DNA binding protein. J. Virol.63 (1989) 5258–5267.
    Article CAS PubMed PubMed Central Google Scholar
  24. Goyon, C., and Lichten, M., Timing of molecular events in meiosis in_Saccharomyces cerevisiae_: Stable heteroduplex DNA is formed in meiotic prophase. Molec. cell. Biol.13 (1993) 373–382.
    CAS PubMed PubMed Central Google Scholar
  25. Griffith, J. D., and Harris, L. D., DNA strand exchanges. CRC crit. Rev. Biochem.23 (1988) S43-S86.
    Article PubMed Google Scholar
  26. Gu, L., Huang, S.-M., and Sander, M., Drosophila Rrp1 complements_E. coli xth nfo_ mutants: Protection against both oxidative and alkylation-induced DNA damage. Nucl. Acids Res.21 (1993) 4788–4795.
    Article CAS PubMed PubMed Central Google Scholar
  27. Halbrook, J., and McEntee, K., Purification and characterization of a DNA-pairing and strand transfer activity from mitotic_Saacharomyces cerevisiae_. J. biol. Chem.264 (1989) 21403–21412.
    Article CAS PubMed Google Scholar
  28. Hall, S. D., Kane, M. F., and Kolodner, R. D., Identification and characterization of the_Escherichia coli_ recT protein, a protein encoded by the recE region that promotes renaturation of homologous single-stranded DNA. J. Bact.175 (1993) 277–287.
    Article CAS PubMed PubMed Central Google Scholar
  29. Heyer, W.-D., and Kolodner, R. D., Enzymology of homologous recombination in_Saccharomyces cerevisiae_. Prog. nucl. Acid Res. molec. Biol.46 (1993) 221–271.
    Article CAS Google Scholar
  30. Hinnebusch, A. G., and Liebman, S. W., Protein synthesis and translational control in_Saccharomyces cerevisiae_, in: The Molecular and Cellular Biology of the Yeast Saccharomyces. Genome Dynamics, Protein Synthesis, and Energetics, pp. 627–735. Eds. J. R. Broach, J. Pringle and E. Jones, CSHL Press, Cold Spring Harbor 1992.
    Google Scholar
  31. Holden, D. W., Spanos, A., and Banks, G. R., Nucleotide sequence of the_REC1_ gene of_Ustilago maydis_. Nucl. Acids Res.17 (1989) 10489.
    Article CAS PubMed PubMed Central Google Scholar
  32. Holliday, R., Altered recombination frequencies in radiation sensitive strains of_Ustilago_. Mutation Res.4 (1967) 275–288.
    Article CAS PubMed Google Scholar
  33. Howard-Flanders, P., West, S. C., and Stasiak, A., Role of RecA protein spiral filaments in genetic recombination. Nature_309_ (1984) 215–220.
    Article CAS PubMed Google Scholar
  34. Hsieh, P., Meyn, M. S., and Camerini-Otero, R. D., Partial purification and characterization of a recombinase from human cells. Cell_44_ (1986) 885–894.
    Article CAS PubMed Google Scholar
  35. Hsu, C. L., and Stevens, A., Yeast cells lacking 5′–3′ exoribonuclease I contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Molec. cell. Biol.13 (1993) 4826–4835.
    CAS PubMed PubMed Central Google Scholar
  36. Huang, K. N., and Symington, L. S., A 5′–3′ exonuclease from_Saccharomyces cerevisiae_ is required for_in vitro_ recombination between linear DNA molecules with overlapping homology. Molec. cell. Biol.13 (1993) 3125–3134.
    CAS PubMed PubMed Central Google Scholar
  37. Johnson, A. W., and Kolodner, R. D., Strand exchange protein I from_Saccharomyces cerevisiae_: a novel multifunctional protein that contains DNA strand exchange and exonuclease activites. J. biol. Chem.266 (1991) 14046–14054.
    Article CAS PubMed Google Scholar
  38. Johnson, A. W., and Kolodner, R. D., Characterization of the interaction of_Saccharomyces cerevisiae_ strand exchange protein I with DNA. J. biol. Chem. In press.
  39. Johnson, A. W., and Kolodner, R. D., The activity of the_Saccharomyces cerevisiae_ strand exchange protein 1 intrinsic exonuclease during joint molecule formation. J. biol. Chem. In press.
  40. Kaus, J. A., and Mortimer, R. K., Nucleotide sequence of the_RAD57_ gene of_Saccharomyces cerevisiae_. Gene_105_ (1991) 139–140.
    Article Google Scholar
  41. Kawasaki, I., Sugano, S., and Ikeda, H., Calf thymus histone H1 is a recombinase that catalyzes ATP-independent DNA strand transfer. Proc. natl Acad. Sci. USA_86_ (1989) 5281–5285.
    Article CAS PubMed PubMed Central Google Scholar
  42. Kawasaki, I., Sugano, S., and Ikeda, H., Calf thymus histone H1 is a recombinase that catalyzes ATP-independent DNA strand transfer. Proc. natl Acad. Sci. USA_87_ (1989) 6128.
    Google Scholar
  43. Kearsey, S., and Kipling, D., Recombination and RNA processing: a common strand? T Cell Biol.1 (1991) 110–112.
    Article CAS Google Scholar
  44. Kim, J., Genes controlling conjugation and mitotic cell division in yeast_Saccharomyces cerevisiae_. Ph. D. thesis (1988) Massachusetts Institute of Technology.
  45. Kim, J., Ljungdahl, P. O., and Fink, G. R.,kem mutations affect nuclear fusion in_Saccharomyces cerevisiae_. Genetics_126_ (1990) 799–812.
    Article CAS PubMed PubMed Central Google Scholar
  46. Kipling, D., and Kearsey, S. E., TFIIS and strand-transfer proteins. Nature_353_ (1991) 509.
    Article CAS PubMed Google Scholar
  47. Kleckner, N., Padmore, R., and Bishop, D. K., Meiotic chromosome metabolism: one view. Cold Spring Harb. Symp. quant. Biol.56 (1991) 729–743.
    Article CAS PubMed Google Scholar
  48. Kmiec, E., and Holloman, W. K., Homologous pairing of DNA molecules promoted by a protein from_Ustilago_. Cell_29_ (1982) 367–374.
    Article CAS PubMed Google Scholar
  49. Kobayashi, T., Hotta, Y., and Tabata, S., Isolation and characterization of a yeast gene that is homologous with a meiosisspecific cDNA from a plant. Molec. gen. Genet.237 (1993) 225–232.
    Article CAS PubMed Google Scholar
  50. Kolodner, R., Evans, D. H., and Morrison, P. T., Purification and characterization of an activity from_Saccharomyces cerevisiae_ that catalyzes homologous pairing and strand exchange. Proc. natl Acad. Sci. USA_84_ (1987) 5560–5564.
    Article CAS PubMed PubMed Central Google Scholar
  51. Kowalczykowski, S. C., Biochemistry of genetic recombination: Energetics and mechanism of DNA strand exchange. A. Rev. Biophys. biophys. Chem.20 (1991) 539–575.
    Article CAS Google Scholar
  52. Lovett, S., and Mortimer, R. K., Characterization of null mutants of the_rad55_ gene of_Saccharomyces cerevisiae_: effects of temperature, osmotic strength, and mating type. Genetics_116_ (1987) 547–533.
    Article CAS PubMed PubMed Central Google Scholar
  53. Lovett, S. T., Sequence of the RAD55 gene of_Saccharomyces cerevisiae_: similarity of RAD55 to prokaryotic RecA and other RecA-like proteins. Gene. In press.
  54. Lowenhaupt, K., Sander, M., Hauser, C., and Rich, A., Drosophila melanogaster strand transferase. J. biol. Chem.264 (1989) 20568–20575.
    Article CAS PubMed Google Scholar
  55. McCarthy, J. G., Sander, M., Lowenhaupt, K., and Rich, A., Sensitive homologous recombination strand transfer assay: Partial purification of a_Drosophila melanogaster_ enzyme and detection of sequence effects on the strand transfer activity of RecA protein. Proc. natl Acad. Sci. USA_85_ (1988) 5854–5858.
    Article CAS PubMed PubMed Central Google Scholar
  56. Meselson, M. S., and Radding, C. R., A general model for genetic recombination. Proc. natl Acad. Sci. USA_72_ (1975) 358–361.
    Article CAS PubMed PubMed Central Google Scholar
  57. Milne, G. T., and Weaver, D. T., Dominant negative alleles of_RAD52_ reveal a DNA repair/recombination complex including Rad51 and Rad52. Genes Dev.7 (1993) 1755–1765.
    Article CAS PubMed Google Scholar
  58. Moore, S. P., and Fishel, R., Purification and characterization of a protein from human cells which promotes homologous pairing of DNA. J. biol. Chem.265 (1990) 11108–11117.
    Article CAS PubMed Google Scholar
  59. Moore, S. P., Erdile, L., Kelly, T., and Fishel, R., The human homologous pairing protein HPP-1 is specifically stimulated by the cognate single-stranded binding protein hRP-A. Proc. natl Acad. Sci. USA_88_ (1991) 9067–9071.
    Article CAS PubMed PubMed Central Google Scholar
  60. Morita, T., Yoshimura, Y., Yamamoto, A., Murata, K., Mori, M., Yamamoto, H., and Matsuhiro, A., A mouse homolog of the_Escherichia coli recA_ and_Saccharomyces cerevisiae Rad51_ genes. Proc. natl Acad. Sci. USA_90_ (1993) 6577–6580.
    Article CAS PubMed PubMed Central Google Scholar
  61. Morrison, D. P., and Hastings, P. J., Characterization of the mutator mutation_mut 5-1_. Molec. gen. Genet.175 (1979) 57–65.
    Article CAS PubMed Google Scholar
  62. Muris, D. F. R., Vreken, K., Carr, A. M., Broughton, B. C., Lehmann, A. R., Lohman, P. H. M., and Pastink, A., Cloning of_RAD51_ homolog of_Schizosaccharomyces pombe_. Nucl. Acids Res.21 (1993) 4586–4591.
    Article CAS PubMed PubMed Central Google Scholar
  63. Nag, D. K., and Petes, T. D., Physical detection of heteroduplexes during meiotic recombination in the yeast_Saccharomyces cerevisiae_. Molec. cell. Biol.13 (1993) 2324–2331.
    CAS PubMed PubMed Central Google Scholar
  64. Nugent, M., Huang, S.-M., and Sander, M., Characterization of the apurinic endonuclease activity of Drosophila Rrpl. Biochemistry_32_ (1993) 11445–11452.
    Article CAS PubMed Google Scholar
  65. Ogawa, T., Shinohara, A., Ogawa, H., and Tomizawa, J., Functional structure of the RecA protein found by chimera analysis. J. molec. Biol.226 (1992) 651–660.
    Article CAS PubMed Google Scholar
  66. Ogawa, T., Yu, X., Shinohara, A., and Egelman, E. H., Similarity of the yeast Rad51 filament to the bacterial RecA filament. Science_259_ (1993) 1896–1899.
    Article CAS PubMed Google Scholar
  67. Ogawa, T., Shinohara, A., Nabetani, A., Ikeya, T., Yu, X., Egelman, E. H., and Ogawa, H., RecA-like recombination proteins in Eukaryotes: functions of_Rad51_ and_Rad52_ genes of_Saccharomyces cerevisiae_. Cold Spring Harb. Symp. quant. Biol. In press.
  68. Pang, Q., Hays, J. B., and Rajagopal, I., A plant cDNA that partially complements_Escherichia coli_ recA mutations predicts a polypeptide not strongly homologous to RecA proteins. Proc. natl Acad. Sci. USA_89_ (1992) 8073–8077.
    Article CAS PubMed PubMed Central Google Scholar
  69. Panyutin, I. G., and Hsieh, P., Formation of a single base mismatch impedes spontaneous DNA branch migration. J. molec. Biol.230 (1993) 413–424.
    Article CAS PubMed Google Scholar
  70. Petes, T. D., Malone, R. E., and Symington, L. S., Recombination in Yeast. In: The Molecular and Cellular Biology of the Yeast Saccharomyces. Genome Dynamics, Protein Synthesis, and Energetics. pp. 407–521. Eds J. R. Broach, J. Pringle, E. Jones. CSHL Press, Cold Spring Harbor 1992.
    Google Scholar
  71. Radding, C. M., Helical interactions in homologous pairing and strand exchange driven by RecA protein. J. biol. Chem.266 (1991) 5355–5358.
    Article CAS PubMed Google Scholar
  72. Roca, A. I., and Cox, M. M., The RecA protein: Structure and function. CRC crit. Rev.25 (1990) 415–456.
    Article CAS Google Scholar
  73. Saeki, T., Machida, I., and Nakai, S., Genetic control of diploid recovery after γ-irradiation in the yeast_Saccharomyces cerevisiae_. Mutation Res.73 (1980) 251–265.
    Article CAS PubMed Google Scholar
  74. Sander, M., Lowenhaupt, K., Lane, W. S., and Rich, A., Cloning and characterization of Rrpl, the gene encoding Drosophila strand transferase: carboxy-terminal homology to DNA repair endo/exonucleases. Nucl. Acids Res.19 (1991) 4523–4529.
    Article CAS PubMed PubMed Central Google Scholar
  75. Sander, M., Lowenhaupt, K., and Rich, A., Drosophila Rrpl protein: An apurinic endonuclease with homologous recombination activities. Proc. natl Acad. Sci. USA_88_ (1991) 6780–6784.
    Article CAS PubMed PubMed Central Google Scholar
  76. Shinohara, A., Ogawa, H., and Ogawa, T., Rad51 protein involved in repair and recombination in_S. cerevisiae_ is a RecA-like protein. Cell_69_ (1992) 457–470.
    Article CAS PubMed Google Scholar
  77. Shinohara, A., Ogawa, H., Hatsuda, Y., Ushio, N., Ikeo, K., and Ogawa, T., Cloning of human, mouse and fission yeast recombination genes homologous to Rad51 and recA. Nature Genet.4 (1993) 239–243.
    Article CAS PubMed Google Scholar
  78. Shuster, E. O., and Byers, B., Pachytene arrest and other meiotic effects of the Start mutations in_Saccharomyces cerevisiae_. Genetics_123_ (1989) 29–43.
    Article CAS PubMed PubMed Central Google Scholar
  79. Sikorav, J.-L., and Church, G. M., Complementary recognition in condensed DNA: accelerated DNA renaturation. J. molec. Biol.222 (1991) 1085–1108.
    Article CAS PubMed Google Scholar
  80. Silberstein, Z., Shalit, M., and Cohen, A., Heteroduplex strand-specificity in restriction-stimulated recombination by the RecE pathway of_Escherichia coli_. Genetics_133_ (1993) 439–448.
    Article CAS PubMed PubMed Central Google Scholar
  81. Smith, G. R., Homologous recombination in procaryotes. Microbiol. Rev.52 (1988) 1–28.
    Article CAS PubMed PubMed Central Google Scholar
  82. Stasiak, A., Three-stranded DNA structure: is this thesecret of DNA homologous recognition? Molec. Microbiol.6 (1992) 3267–3276.
    Article CAS Google Scholar
  83. Stevens, A., and Maupin, M. K., A 5′−3′ exoribonuclease of_Saccharomyces cerevisiae_: size and novel substrate specificity. Archs Biochem. Biophys.252 (1987) 339–347.
    Article CAS Google Scholar
  84. Story, R. M., Weber, I. T., and Steitz, T. A., The structure of the_E. coli_ recA protein monomer and polymer. Nature_355_ (1992) 318–325.
    Article CAS PubMed Google Scholar
  85. Story, R. M., and Steitz, T. A., Structure of the recA protein-ADP complex. Nature_355_ (1992) 374–376.
    Article CAS PubMed Google Scholar
  86. Story, R. M., Bishop, D. K., Kleckner, N., and Steitz T. A., Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast. Science_259_ (1993) 1892–1896.
    Article CAS PubMed Google Scholar
  87. Sugino, A., Nitiss, J., and Resnick, M. A., ATP-independent DNA strand transfer catalyzed by protein(s) from meiotic cells of the yeast_Saccharomyces cerevisiae_. Proc. natl Acad. Sci. USA_85_ (1988) 3683–3687.
    Article CAS PubMed PubMed Central Google Scholar
  88. Svaren, J., Inagami, K., Lovegren, E., and Chalkley, R., DNA denatures upon drying after ethanol precipitation. Nucl. Acids Res.15 (1987) 8739–8754.
    Article CAS PubMed PubMed Central Google Scholar
  89. Szankasi, P., and Smith, G. R., A single-stranded DNA exonuclease from_Schizosaccharomyces pombe_. Biochemistry_31_ (1992) 6769–6773.
    Article CAS PubMed Google Scholar
  90. Szostak, J. W., Orr-Weaver, T. L., Rothstein, R. J., and Stahl, F. W., The double-strand-break repair model for recombination. Cell_33_ (1983) 25–35.
    Article CAS PubMed Google Scholar
  91. Tartof, K. D., and Henikoff, S., Trans-sensing effects from Drosophila to humans. Cell_65_ (1991) 201–203.
    Article CAS PubMed Google Scholar
  92. Tishkoff, D., Johnson, A. W., and Kolodner, R. D., Molecular and genetic analysis of the gene encoding the_Saccharomyces cerevisiae_ strand exchange protein SEP1. Molec. cell. Biol.11 (1991) 2593–2608.
    CAS PubMed PubMed Central Google Scholar
  93. Walker, J. E., Saraste, M., Runswick, M. J., and Gay, N. J., Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and the other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J.1 (1982) 945–951.
    Article CAS PubMed PubMed Central Google Scholar
  94. West, S. C., Enzymes and molecular mechanisms of genetic recombination. A. Rev. Biochem.61 (1992) 603–640.
    Article CAS Google Scholar
  95. Zhang, W., and Evans, D. H., DNA strand exchange catalyzed by proteins from vaccinia virus-infected cells. J. Virol.67 (1993) 204–212.
    Article CAS PubMed PubMed Central Google Scholar
  96. Yoshimura, Y., Morita, T., Yamamoto, A., and Matsuhiro, A., Cloning sequence of the human RecA-like gene cDNA. Nucl. Acids Res.21 (1993) 1665.
    Article CAS PubMed PubMed Central Google Scholar

Download references