Chapter 22 : Recombination Machinery: Holliday Junction-Resolving Enzymes

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Recombination Machinery: Holliday Junction-Resolving Enzymes, Page 1 of 2

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Holliday junctions are resolved into recombinant duplex DNA species by a class of structure-specific endonucleases known as the Holliday junction-resolving enzymes. The primary cellular resolving enzyme in bacteria is RuvC, which is the main focus of this chapter. The author also talks about the RusA protein, which may act as an alternative to RuvC in some bacterial species, and attempts to place RuvC in a wider context based on our knowledge of other junction-resolving enzymes. The first cellular Holliday junction-resolving enzyme identified was RuvC from . Homologous recombination is ubiquitous among cellular life forms and many prokaryotic and eukaryotic viruses, and wherever Holliday junctions are formed, junction-resolving enzymes can be confidently expected. Resolving enzymes recognize the branched structure of the Holliday junction and introduce paired phosphodiester bond cleavages in opposing strands to collapse the junction, releasing nicked duplex DNA products. The study of homologous recombination and the Holliday junction was for many years the realm of geneticists. Holliday junction migration work has largely been driven by studies of the RuvABC resolvasome, emphasizing the continuing utility of bacteria as a model system to study some of the most interesting problems in biology.

Citation: White M. 2005. Recombination Machinery: Holliday Junction-Resolving Enzymes, p 405-412. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch22

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DNA Polymerase I
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Image of Figure 1
Figure 1

Sequence alignment of a diverse selection of RuvC homologues: ECOLI (, Swiss-Prot database accession number P24239), YERPE (, Q8ZEU7), VIBCH (, Q9KR00), NEIMA (, Q9JTU3), TREPA (, O83530), RHILO (, Q98F72), THEMA (, Q9WZ45), DEIRA (, Q9RX75), STRCO (, Q9L289), ANASP ( sp., O52751), HELPY (, O25544), CAMJE (, Q9PLU8), MYCLE (, P40834), and SYNY3 ( sp., Q55506).

Citation: White M. 2005. Recombination Machinery: Holliday Junction-Resolving Enzymes, p 405-412. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch22
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Image of Figure 2
Figure 2

Sequence alignment of a selection of cellular and viral RusA homologues: AQUAE (, Swiss-Prot database accession number O67766), LEGPN (, Q9AKY6), BACSU (, Q8X556), ECOLI (, P40116), CP9330 (phage CP-933O from O157:H7, AAL89445), CP933X (phage CP-933X from O157:H7, Q8X707), and BP82 (phage BP-82, Q37873).

Citation: White M. 2005. Recombination Machinery: Holliday Junction-Resolving Enzymes, p 405-412. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch22
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1. Aravind, L.,, K. S. Makarova,, and E. V. Koonin. 2000. Survey and summary: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res. 28:34173432.
2. Ariyoshi, M.,, D. G. Vassylyev,, H. Iwasaki,, H. Nakamura,, H. Shinagawa,, and K. Morikawa. 1994. Atomic structure of the RuvC resolvase: a Holliday junction-specific endonuclease from E. coli. Cell 78:10631072.
3. Beese, L. S.,, and T. A. Steitz. 1991. Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J. 10:2533.
4. Bennett, R. J.,, H. J. Dunderdale,, and S. C. West. 1993. Resolution of Holliday junctions by RuvC resolvase: cleavage specificity and DNA distortion. Cell 74:10211031.
5. Bennett, R. J.,, and S. C. West. 1996. Resolution of Holliday junctions in genetic recombination: RuvC protein nicks DNA at the point of strand exchange. Proc. Natl. Acad. Sci. USA 93:1221712222.
6. Bennett, R. J.,, and S. C. West. 1995. Structural analysis of the RuvC-Holliday junction complex reveals an unfolded junction. J. Mol. Biol. 252:213226.
7. Bolt, E. L.,, G. J. Sharples,, and R. G. Lloyd. 1999. Identification of three aspartic acid residues essential for catalysis by the RusA Holliday junction resolvase. J. Mol. Biol. 286:403415.
8. Ceschini, S.,, A. Keeley,, M. S. McAlister,, M. Oram,, J. Phelan,, L. H. Pearl,, I. R. Tsaneva,, and T. E. Barrett. 2001. Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2. EMBO J. 20:66016611.
9. Connolly, B.,, C. Parsons,, F. Benson,, H. Dunderdale,, R. Lloyd,, and S. West. 1991. Resolution of Holliday junctions in vitro requires the Escherichia coli ruvC gene product. Proc. Natl. Acad. Sci. USA 88:60636067.
10. Connolly, B.,, and S. C. West. 1990. Genetic recombination in Escherichia coli: Holliday junctions made by RecA protein are resolved by fractionated cell-free extracts. Proc. Natl. Acad. Sci. USA 87:84768480.
11. Constantinou, A.,, A. A. Davies,, and S. C. West. 2001. Branch migration and Holliday junction resolution catalyzed by activities from mammalian cells. Cell 104:259268.
12. Declais, A. C.,, and D. M. Lilley. 2000. Extensive central disruption of a four-way junction on binding CCE1 resolving enzyme. J. Mol. Biol. 296:421433.
13. de Massey, B.,, R. A. Weisberg,, and F. W. Studier. 1987. Gene 3 endonuclease of bacteriophage T7 resolves conformationally branched structures in double-stranded DNA. J. Mol. Biol. 193:359376.
14. Dunderdale, H. J.,, F. E. Benson,, C. A. Parsons,, G. J. Sharples,, R. G. Lloyd,, and S. C. West. 1991. Formation and resolution of recombination intermediates by E. coli RecA and RuvC proteins. Nature 354:506510.
15. Eggleston, A. K.,, A. H. Mitchell,, and S. C. West. 1997. In vitro reconstitution of the late steps of genetic recombination in E. coli. Cell 89:607617.
16. Fogg, J.,, M. J. Schofield,, M. F. White,, and D. M. J. Lilley. 1999. Sequence and functional-group specificity for cleavage of DNA junctions by RuvC of Escherichia coli. Biochemistry 38:1134911358.
17. Fogg, J. M.,, M. Kvaratskhelia,, M. F. White,, and D. M. Lilley. 2001. Distortion of DNA junctions imposed by the binding of resolving enzymes: a fluorescence study. J. Mol. Biol. 313:751764.
18. Fogg, J. M.,, and D. M. Lilley. 2000. Ensuring productive resolution by the junction-resolving enzyme RuvC: large enhancement of the second-strand cleavage rate. Biochemistry 39:1612516134.
19. Garcia, A. D.,, L. Aravind,, E. Koonin,, and B. Moss. 2000. Bacterial-type DNA Holliday junction resolvases in eukaryotic viruses. Proc. Natl. Acad. Sci. USA 97:89268931.
20. Giraud-Panis, M. J.,, and D. M. Lilley. 1998. Structural recognition and distortion by the DNA junction-resolving enzyme RusA. J. Mol. Biol. 278:117133.
21. Goedken, E. R.,, and S. Marqusee. 2001. Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site. J. Biol. Chem. 276:72667271.
22. Holliday, R. 1964. A mechanism for gene conversion in fungi. Genet. Res. 5:282304.
23. Ichiyanagi, K.,, H. Iwasaki,, T. Hishida,, and H. Shinagawa. 1998. Mutational analysis on structure-function relationship of a Holliday junction specific endonuclease RuvC. Genes Cells 3:575586.
24. Iwasaki, H.,, M. Takahagi,, T. Shiba,, A. Nakata,, and H. Shinagawa. 1991. Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. EMBO J. 10:43814389.
25. Katayanagi, K.,, M. Miyagawa,, M. Matsuchima,, M. Ishikawa,, S. Kanaya,, H. Nakamura,, M. Ikehara,, T. Matsuzaki,, and K. Morikawa. 1992. Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J. Mol. Biol. 223:10291052.
26. Kemper, B., 1997. Branched DNA resolving enzymes (X-solvases), p. 179204. In J. A. Nickoloff, and M. Hoekstra (ed.), DNA Damage and Repair: Biochemistry, Genetics and Cell Biology. Humana Press, Ottawa, Ontario, Canada.
27. Kemper, B.,, and D. T. Brown. 1976. Function of gene 49 of bacteriophage T4. II. Analysis of intracellular development and the structure of very fast sedimenting DNA. J. Virol. 18:10001015.
28. Kemper, B.,, and E. Janz. 1976. Function of gene 49 of bacteriophage T4. 1. Isolation and biochemical charcterisation of very fast sedimenting DNA. J. Virol. 18:992999.
29. Kvaratskhelia, M.,, S. George,, A. Cooper,, and M. F. White. 1999. Quantitation of binding of metal ions and DNA junctions by the Holliday junction resolving enzyme Cce1. Biochemistry 38:1661316619.
30. Kvaratskhelia, M.,, B. N. Wardleworth,, D. G. Norman,, and M. F. White. 2000. A conserved nuclease domain in the archaeal Holliday junction resolving enzyme Hjc. J. Biol. Chem. 275:2554025546.
31. Lilley, D. M.,, and D. G. Norman. 1999. The Holliday junction is finally seen with crystal clarity. Nat. Struct. Biol. 6:897899.
32. Lilley, D. M. J.,, and M. F. White. 2001. The junction-resolving enzymes. Nat. Rev. Mol. Cell. Biol. 2:433443.
33. Lilley, D. M. J.,, and M. F. White. 2000. Resolving the relationships of resolving enzymes. Proc. Natl. Acad. Sci. USA 97:93519353.
34. Lloyd, R. G.,, F. E. Benson,, and C. E. Shurvington. 1984. Effect of ruv mutations on recombination and DNA repair in Escherichia coli K12. Mol. Gen. Genet. 194:303309.
35. Lloyd, R. G.,, and G. J. Sharples. 1993. Dissociation of synthetic Holliday junctions by E. coli RecG protein. EMBO J. 12:1722.
36. Mahdi, A. A.,, G. J. Sharples,, T. N. Mandal,, and R. G. Lloyd. 1996. Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. J. Mol. Biol. 257:561573.
37. Mandal, T.,, A. Mahdi,, G. Sharples,, and R. Lloyd. 1993. Resolution of Holliday intermediates in recombination and DNA repair: indirect suppression of ruvA, ruvB, and ruvC mutations. J. Bacteriol. 175:43254334.
38. Michel, B.,, G. D. Recchia,, M. Penel-Colin,, S. D. Ehrlich,, and D. J. Sherratt. 2000. Resolution of Holliday junctions by RuvABC prevents dimer formation in rep mutants and UV-irradiated cells. Mol. Microbiol. 37:180191.
39. Nishimoto, H.,, M. Takayama,, and T. Minagawa. 1979. Purification and some properties of a deoxyribonuclease whose synthesis is controlled by gene 49 of bacteriophage T4. J. Biochem. 100:433440.
40. Rice, P.,, and K. Mizuuchi. 1995. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell 82:209220.
41. Saito, A.,, H. Iwasaki,, M. Ariyoshi,, K. Morikawa,, and H. Shinagawa. 1995. Identification of four acidic amino acids that constitute the catalytic centre of the RuvC Holliday junction resolvase. Proc. Natl. Acad. Sci. USA 92:74707474.
42. Schofield, M. J.,, D. M. J. Lilley,, and M. F. White. 1998. Dissection of the sequence specificity of the Holliday junction endonuclease CCE1. Biochemistry 37:77337740.
43. Shah, R.,, R. J. Bennett,, and S. C. West. 1994. Genetic recombination in E. coli: RuvC protein cleaves Holliday junctions at resolution hotspots in vitro. Cell 79:853864.
44. Shah, R.,, R. Cosstick,, and S. C. West. 1997. The RuvC protein dimer resolves Holliday junctions by a dual incision mechanism that involves base-specific contacts. EMBO J. 16:14641472.
45. Sharples, G. J. 2001. The X philes: structure-specific endonucleases that resolve Holliday junctions. Mol. Microbiol. 39:823834.
46. Sharples, G. J.,, F. E. Benson,, G. T. Iling,, and R. G. Lloyd. 1990. Molecular and functional analysis of the ruv region of Escherichia coli K-12 reveals three genes involved in DNA repair and recombination. Mol. Gen. Genet. 221:219226.
47. Sharples, G. J.,, E. L. Bolt,, and R. G. Lloyd. 2002. RusA proteins from the extreme thermophile Aquifex aeolicus and lactococcal phage r1t resolve Holliday junctions. Mol. Microbiol. 44:549559.
48. Sharples, G. J.,, S. N. Chan,, A. A. Mahdi,, M. C. Whitby,, and R. G. Lloyd. 1994. Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions. EMBO J. 13:61336142.
49. Sharples, G. J.,, and R. G. Lloyd. 1991. Resolution of Holliday junctions in Escherichia coli: identification of the ruvC gene product as a 19-kilodalton protein. J. Bacteriol. 173:77117715.
50. Stuart, D.,, K. Ellison,, K. Graham,, and G. McFadden. 1992. In vitro resolution of poxvirus replicative intermediates into linear minichromosomes with hairpin termini by a virally induced Holliday junction endonuclease. J. Virol. 66:15511563.
51. Takahagi, M.,, H. Iwasaki,, A. Nakata,, and H. Shinagawa. 1991. Molecular analysis of the Escherichia coli ruvC gene, which encodes a Holliday junction-specific endonuclease. J. Bacteriol. 173:57475753.
52. Tsujimoto, Y.,, and H. Ogawa. 1978. Intermediates in genetic recombination of bacteriophage T7 DNA. Biological activity and the roles of gene 3 and gene 5. J. Mol. Biol. 125:255273.
53. van Gool, A. J.,, N. M. Hajibagheri,, A. Stasiak,, and S. C. West. 1999. Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of Holliday junction resolution. Genes Dev. 13:18611870.
54. van Gool, A. J.,, R. Shah,, C. Mezard,, and S. C. West. 1998. Functional interactions between the Holliday junction resolvase and the branch migration motor of Escherichia coli. EMBO J. 17:18381845.
55. Whitby, M. C.,, E. L. Bolt,, S. N. Chan,, and R. G. Lloyd. 1996. Interactions between RuvA and RuvC at Holliday junctions: inhibition of junction cleavage and formation of a RuvA- RuvC-DNA complex. J. Mol. Biol. 264:878890.
56. Whitby, M. C.,, L. Ryder,, and R. G. Lloyd. 1993. Reverse branch migration of Holliday junctions by RecG protein—a new mechanism for resolution of intermediates in recombination and DNA repair. Cell 75:341350.
57. White, M. F.,, M.-J. E. Giraud-Panis,, J. R. G. Pohler,, and D. M. J. Lilley. 1997. Recognition and manipulation of branched DNA structures by junction resolving enzymes. J. Mol. Biol. 269:647664.
58. White, M. F.,, and D. M. Lilley. 1998. Interaction of the resolving enzyme YDC2 with the four-way DNA junction. Nucleic Acids Res. 26:56095616.
59. White, M. F.,, and D. M. Lilley. 1997. The resolving enzyme CCE1 of yeast opens the structure of the four-way DNA junction. J. Mol. Biol. 266:122134.
60. Yoshikawa, M.,, H. Iwasaki,, K. Kinoshita,, and H. Shinagawa. 2000. Two basic residues, Lys-107 and Lys-118, of RuvC resolvase are involved in critical contacts with the Holliday junction for its resolution. Genes Cells 5:803813.
61. Yoshikawa, M.,, H. Iwasaki,, and H. Shinagawa. 2001. Evidence that phenylalanine 69 in Escherichia coli RuvC resolvase forms a stacking interaction during binding and destabilization of a Holliday junction DNA substrate. J. Biol. Chem. 276:1043210436.

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