Homology requirements for double-strand break-mediated recombination in a phage λ-td intron model system

Genetics

Volumn 143, Issue 3, 1996, Pages 1057-1068

  Parker, Monica M ^a   Court, Deborah A ^a,c   Preiter, Karen ^a   Belfort, Marlene ^a,b  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b WADSWORTH CENTER   (United States)

^c UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE DNA;

ARTICLE; BACTERIOPHAGE LAMBDA; CONTROLLED STUDY; DNA RECOMBINATION; DNA SEQUENCE; DNA STRAND BREAKAGE; EXON; GENETIC MODEL; INTRON; NONHUMAN; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

BACTERIOPHAGE LAMBDA; DNA, VIRAL; EXONS; EXONUCLEASES; INTRONS; MODELS, GENETIC; RECOMBINATION, GENETIC;

BACTERIOPHAGE LAMBDA;

EID: 0030014294     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (45)

1. BELFORT, M., 1990 Phage T4 introns: self-splicing and mobility. Annu. Rev. Genet. 24: 363-385.
2. BELFORT, M., and P. S. PERLMAN, 1995 Mechanisms of intron mobility. J. Biol. Chem. 270: 30237-30240.
3. BELFORT, M., M. E. REABAN, T. COETZEE and J. Z. DALGAARD, 1995 Prokaryotic introns and inteins: a panoply of form and function. J. Bacteriol. 177: 3897-3903.
4. BELL-PEDERSEN, D., S. M. QUIRK, M. AUBREY and M. BELFORT, 1989 A site-specific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4. Gene 82: 119-126.
5. BELL-PEDERSEN, D., S. QUIRK, J. CLYMAN and M. BELFORT, 1990 Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications. Nucleic Acids Res. 18: 3763-3770.
6. BRYK, M., S. M. QUIRK, J. E. MUELLER, N. LOIZOS, C. LAWRENCE et al., 1993 The td intron endonuclease makes extensive sequence tolerant contacts across the minor groove of its DNA target. EMBO J. 12: 2141-2149.
7. BRYK, M., M. BELISLE, J. E. MUELLER and M. BELFORT, 1995 Selection of a remote cleavage site by I-TevI, the td intron-encoded endonuclease. J. Mol. Biol. 247: 197-210.
8. CASSUTO, E., and C. M. RADDING, 1971 Mechanism for the action of lambda exonuclease in genetic recombination. Nature New Biol. 229: 13-16.
9. CHANDRY, P. S., and M. BELFORT, 1987 Activation of a cryptic 5′ splice site in the upstream exon of the phage T4 td transcript: exon context, missplicing, and mRNA deletion in a fidelity mutant. Genes Dev. 1: 1028-1037.
10. CHANG, A. C. Y., and S. N. COHEN, 1978 Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134: 1141-1156.
11. CHENG, S., B. VAN HOUTEN, H. B. GAMPER, A. SANCAR and J. E. HEARST, 1988 Use of psoralen-modified oligonucleotides to trap three-stranded RecA-DNA complexes and repair of these cross-linked complexes by ABC excinuclease. J. Biol. Chem. 263: 15110-15117.
12. CLYMAN, J., and M. BELFORT, 1992 Trans and cis requirements for intron mobility in a prokaryotic system. Genes Dev. 6: 1269-1279.
13. DAVIS, R. W., D. BOTSTEIN and J. R. ROTH, 1980 Advanced Bacterial Genetics, A Manual for Genetic Engineering. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
14. DUJON, B., 1989 Group I introns as mobile genetic elements: facts and mechanistic speculations - a review. Gene 82: 91-114.
15. FENTON, A. C., and A. R. POTEETE, 1984 Genetic analysis of the erf region of the bacteriophage P22 chromosome. Virology 134: 148-160.
16. FORMOSA, T., and B. M. ALBERTS, 1986 DNA synthesis dependent on genetic recombination: characterization of a reaction catalyzed by purified bacteriophage T4 proteins. Cell 47: 793-806.
17. GONDA, D. K., and C. M. RADDING, 1983 By searching processively RecA protein pairs DNA molecules that share a limited stretch of homology. Cell 34: 647-654.
18. HSIEH, P., C. S. CAMERINI-OTERO and R. D. CAMERINI-OTERO, 1992 The synapsis event in the homologous pairing of DNAs: RecA recognizes and pairs less than one helical repeat of DNA. Proc. Natl. Acad. Sci. USA 89: 6492-6496.
19. JEONG-YU, S., and D. CARROLL, 1992 Effect of terminal nonhomologies on homologous recombination in Xenopus laevis oocytes. Mol. Cell. Biol. 12: 5426-5437.
20. KING, S. R., and J. P. RICHARDSON, 1986 Role of homology and pathway specificity for recombination between plasmids and bacteriophage lambda. Mol. Gen. Genet. 204: 141-147.
21. KOWALCZYKOWSKI, S. C., and A. K. EGGLESTON, 1994 Homologous pairing and DNA strand-exchange proteins. Annu. Rev. Biochem. 63: 991-1043.
22. LAMBOWITZ, A. M., and M. BELFORT, 1993 Introns as mobile genetic elements. Annu. Rev. Biochem. 62: 587-622.
23. LUISI-DELUCA, C., and R. D. KOLODNER, 1992 Effect of terminal non- homology on intramolecular recombination of linear plasmid substrates in Escherichia coli. J. Mol. Biol. 227: 72-80.
24. MARYON, E., and D. CARROLL, 1991 Involvement of single-stranded tails in homologous recombination of DNA injected into Xenopus laevis oocyte nuclei. Mol. Cell. Biol. 11: 3268-3277.
25. MUELLER, J. E., M. BRYK, N. LOIZOS and M. BELFORT, 1993 Homing endonucleases, pp. 111-143 in Nucleases, Ed. 2, edited by S. M. LINN, R. S. LLOYD and R. J. ROBERTS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. MUELLER, J. E., J. CLYMAN, Y.-J. HUANG, M. M. PARKER and M. BELFORT, 1996 Intron mobility in phage T4 occurs in the context of recombination-dependent DNA replication by multiple pathways. Genes Dev. 10: 351-364.
27. PRASHAD, N., and J. HOSODA, 1972 Role of genes 46 and 47 in bacteriophage T4 reproduction. II. Formation of gaps on parental DNA of polynucleotide ligase defective mutants. J. Mol. Biol. 70: 617-635.
28. QUIRK, S. M., D. BELL-PEDERSEN and M. BELFORT, 1989 Intron mobility in the T-Even phages: high frequency inheritance of group I introns promoted by intron open reading frames. Cell 56: 455-465.
29. ROTH, D. B., and J. H. WILSON, 1986 Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol. Cell. Biol. 6: 4295-4304.
30. SAKAKI, Y., A. E. KARU, S. LINN and H. ECHOLS, 1973 Purification and properties of the γ-protein specified by bacteriophage λ: an inhibitor of the host RecBC recombination enzyme. Proc. Natl. Acad. Sci. USA 70: 2215-2219.
31. SALINAS, F., H. JIANG and T. KODADEK, 1995 Homology dependence of UvsX protein-catalyzed joint molecule formation. J. Biol. Chem. 270: 5181-5186.
32. SAMBROOK, J., E. F. FRITSCH and T. MANIATIS, 1989 Molecular Cloning. A Laboratory Manual, Ed. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. SCHIESTL, R. H., and T. D. PETES, 1991 Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 88: 7585-7589.
34. SHAH, D. B., and H. BERGER, 1971 Replication of gene 46-47 amber mutants of bacteriophage T4D. J. Mol. Biol. 57:17-34.
35. SHALITIN, C., and Y. NAOT, 1971 Role of gene 46 in bacteriophage T4 deoxyribonucleic acid synthesis. J. Virol. 8: 142-153.
36. SHEN, P., and H. V. HUANG, 1986 Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 112: 441-457.
37. SHINOHARA, A., and T. OGAWA, 1995 Homologous recombination and the roles of double-strand breaks. Trends Biochem. 20: 387-391.
38. SINGER, B. S., L. GOLD, P. GAUSS and D. H. DOHERTY, 1982 Determination of the amount of homology required for recombination in bacteriophage T4. Cell 31: 25-33.
39. SUGAWARA, N., and J. E. HABER, 1992 Characterization of double-strand break-induced recombination: homology requirements and single-stranded DNA formation. Mol. Cell. Biol. 12: 563-575.
40. SUN, H., D. TRECO and J. W. SZOSTAK, 1991 Extensive 3′-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site. Cell 64: 1155-1161.
41. THALER, D. S., M. M. STAHL and F. S. STAHL, 1987a Tests of the double-strand-break repair model for Red-mediated recombination of phage λ and plasmid λdv. Genetics 116: 501-511.
42. THALER, D. S., M. M. STAHL and F. S. STAHL, 1987b Double-chaincut sites are recombination hotspots in the Red pathway of phage λ. J. Mol. Biol. 195: 75-87.
43. WHITE, C. I., and J. E. HABER, 1990 Intermediates of recombination during mating type switching in Saccharomyces cerevisiae. EMBO J. 9: 663-673.
44. ZHANG, W., C. READING and A. B. DEISSEROTH, 1992 Improved PCR sequencing with formamide. Trends Genet. 8: 332
45. ZISSLER, J., E. SIGNER and F. SCHAFFER, 1971 The role of recombination in growth of bacteriophage lambda. II. Inhibition of growth by prophage P2, pp. 469-475 in The Bacteriophage Lambda, edited by A. D. HERSHEY. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.