1887
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.

Phage-encoded Serine Integrases and Other Large Serine Recombinases

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Buy this Microbiology Spectrum Article
Price Non-Member $15.00
  • Author: Margaret C. M. Smith1
  • Editors: Phoebe Rice2, Nancy Craig3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biology, University of York, York, United Kingdom; 2: University of Chicago, Chicago, IL; 3: Johns Hopkins University, Baltimore, MD
  • Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
  • Received 09 October 2014 Accepted 24 October 2014 Published 02 July 2015
  • Maggie Smith, maggie.smith@york.ac.uk
image of Phage-encoded Serine Integrases and Other Large Serine Recombinases
    Preview this microbiology spectrum article:
    Zoom in
    Zoomout

    Phage-encoded Serine Integrases and Other Large Serine Recombinases, Page 1 of 2

    | /docserver/preview/fulltext/microbiolspec/3/4/MDNA3-0059-2014-1.gif /docserver/preview/fulltext/microbiolspec/3/4/MDNA3-0059-2014-2.gif
  • Abstract:

    The large serine recombinases (LSRs) are a family of enzymes, encoded in temperate phage genomes or on mobile elements, that precisely cut and recombine DNA in a highly controllable and predictable way. In phage integration, the LSRs act at specific sites, the site in the phage and the site in the host chromosome, where cleavage and strand exchange leads to the integrated prophage flanked by the recombinant sites and . The prophage can excise by recombination between and but this requires a phage-encoded accessory protein, the recombination directionality factor (RDF). Although the LSRs can bind specifically to all the recombination sites, only specific integrase-bound sites can pair in a synaptic complex prior to strand exchange. Recent structural information has led to a breakthrough in our understanding of the mechanism of the LSRs, notably how the LSRs bind to their substrates and how LSRs display this site-selectivity. We also understand that the RDFs exercise control over the LSRs by protein–protein interactions. Other recent work with the LSRs have contributed to our understanding of how all serine recombinases undergo strand exchange subunit rotation, facilitated by surfaces that resemble a molecular bearing.

  • Citation: Smith M. 2015. Phage-encoded Serine Integrases and Other Large Serine Recombinases. Microbiol Spectrum 3(4):MDNA3-0059-2014. doi:10.1128/microbiolspec.MDNA3-0059-2014.

Key Concept Ranking

Clostridium difficile
0.50946736
0.50946736

References

1. Grindley NDF, Whiteson KL, Rice PA. 2006. Mechanisms of site-specific recombination. Annu Rev Biochem 75:567–605. [PubMed][CrossRef]
2. Smith MCM, Thorpe HM. 2002. Diversity in the serine recombinases. Mol Microbiol 44:299–307. [PubMed][CrossRef]
3. Thorpe HM, Smith MCM. 1998. In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family. Proc Natl Acad Sci USA 95:5505–5510. [PubMed][CrossRef]
4. Kim AI, Ghosh P, Aaron MA, Bibb LA, Jain S, Hatfull GF. 2003. Mycobacteriophage Bxb1 integrates into the Mycobacterium smegmatis groEL1 gene. Mol Microbiol 50:463–473. [PubMed][CrossRef]
5. Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne GD. 2013. Attachment site recognition and regulation of directionality by the serine integrases. Nucleic Acids Res 41:8341–8356. [PubMed][CrossRef]
6. Van Duyne GD, Rutherford K. 2013. Large serine recombinase domain structure and attachment site binding. Crit Rev Biochem Molec Biol 48:476–491. [PubMed][CrossRef]
7. Rutherford K, Van Duyne GD. 2014. The ins and outs of serine integrase site-specific recombination. Curr Opin Struct Biol 24:125–131. [PubMed][CrossRef]
8. Adams V, Lyras D, Farrow KA, Rood JI. 2002. The clostridial mobilisable transposons. Cell Mol Life Sci 59:2033–2043. [PubMed][CrossRef]
9. Mullany P, Roberts AP, Wang H. 2002. Mechanism of integration and excision in conjugative transposons. Cell Mol Life Sci 59:2017–2022. [PubMed][CrossRef]
10. Hanssen AM, Ericson Sollid JU. 2006. SCCmec in staphylococci: genes on the move. FEMS Immunol Med Microbiol 46:8–20. [PubMed][CrossRef]
11. Campbell AM. 1962. Episomes, p 101–145. In Caspari EW, Thoday JM (ed), Advances in Genetics. Academic Press, New York, NY.
12. Lewis JA, Hatfull GF. 2001. Control of directionality in integrase-mediated recombination: examination of recombination directionality factors (RDFs) including Xis and Cox proteins. Nucleic Acids Res 29:2205–2216. [PubMed][CrossRef]
13. Smith MCM, Brown WR, McEwan AR, Rowley PA. 2010. Site-specific recombination by phiC31 integrase and other large serine recombinases. Biochem Soc Trans 38:388–394. [PubMed][CrossRef]
14. Misiura A, Pigli YZ, Boyle-Vavra S, Daum RS, Boocock MR, Rice PA. 2013. Roles of two large serine recombinases in mobilizing the methicillin-resistance cassette SCCmec. Mol Microbiol 88:1218–1229. [PubMed][CrossRef]
15. Combes P, Till R, Bee S, Smith MCM. 2002. The streptomyces genome contains multiple pseudo-attB sites for the ɸC31-encoded site-specific recombination system. J Bacteriol 184:5746–5752. [PubMed][CrossRef]
16. Bibb LA, Hancox MI, Hatfull GF. 2005. Integration and excision by the large serine recombinase phiRv1 integrase. Mol Microbiol 55:1896–1910. [PubMed][CrossRef]
17. Ito T, Katayama Y, Asada K, Mori N, Tsutsumimoto K, Tiensasitorn C, Hiramatsu K. 2001. Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 45:1323–1336. [PubMed][CrossRef]
18. Singh S, Rockenbach K, Dedrick RM, VanDemark AP, Hatfull GF. 2014. Cross-talk between diverse serine integrases. J Mol Biol 426:318–331. [PubMed][CrossRef]
19. Carrasco CD, Ramaswamy KS, Ramasubramanian TS, Golden JW. 1994. Anabaena xisF gene encodes a developmentally regulated site-specific recombinase. Genes Dev 8:74–83. [PubMed][CrossRef]
20. Sato T, Samori Y, Kobayashi Y. 1990. The cisA cistron of Bacillus subtilis sporulation gene spoIVC encodes a protein homologus to a site-sepcific recombinase. J Bacteriol 172:1092–1098. [PubMed]
21. Stragier P, Kunkel B, Kroos L, Losick R. 1989. Chromosomal rearrangement generating a composite gene for a developmental transcription factor. Science 243:507–512. [PubMed][CrossRef]
22. Golden JW, Mulligan ME, Haselkorn R. 1987. Different recombination site specificity of two developmentally regulated genome rearrangements. Nature 327:526–529. [PubMed][CrossRef]
23. Carrasco CD, Buettner JA, Golden JW. 1995. Programmed DNA rearrangement of a cyanobacteria hupL gene in heterocysts. Proc Natl Acad Sci USA 92:791–795. [PubMed][CrossRef]
24. Ramaswamy KS, Carrasco CD, Fatma T, Golden JW. 1997. Cell-type specificity of the Anabaena fdxN-element rearrangement requires xisH and xisI. Mol Microbiol 23:1241–1249. [PubMed][CrossRef]
25. Kunkel B, Losick R, Stragier P. 1990. The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene. Genes Dev 4:525–535. [PubMed][CrossRef]
26. Popham DL, Stragier P. 1992. Binding of the Bacillus subtilis spoIVCA product to the recombination sites of the element interrupting the sigma-K encoding gene. Proc Natl Acad Sci USA 89:5991–5995. [PubMed][CrossRef]
27. Loessner MJ, Inman RB, Lauer P, Calendar R. 2000. Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. Mol Microbiol 35:324–340. [PubMed][CrossRef]
28. Rabinovich L, Sigal N, Borovok I, Nir-Paz R, Herskovits AA. 2012. Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence. Cell 150:792–802. [PubMed][CrossRef]
29. Claverys JP, Prudhomme M, Martin B. 2006. Induction of competence regulons as a general response to stress in gram-positive bacteria. Annu Rev Microbiol 60:451–475. [PubMed][CrossRef]
30. Bannam TL, Crellin PK, Rood JI. 1995. Molecular genetics of the chloramphenicol-resistance transposon Tn4451 from Clostridium perfringens: the TnpX site-specific recombinase excises a circular transposon molecule. Mol Microbiol 16:535–551. [PubMed][CrossRef]
31. Crellin PK, Rood JI. 1997. The resolvase/invertase domain of the site-specific recombinase TnpX is functional and recognizes a target sequence that resembles the junction of the circular form of the Clostridium perfringens transposon Tn4451. J Bacteriol 179:5148–5156. [PubMed]
32. Wang H, Mullany P. 2000. The large resolvase TndX is required and sufficient for integration and excision of derivatives of the novel conjugative transposon Tn5397. J Bacteriol 182:6577–6583. [PubMed][CrossRef]
33. Lyras D, Rood JI. 2000. Transposition of Tn4451 and Tn4453 involves a circular intermediate that forms a promoter for the large resolvase, TnpX. Mol Microbiol 38:588–601. [PubMed][CrossRef]
34. Wang H, Smith MCM, Mullany P. 2006. The conjugative transposon Tn5397 has a strong preference for integration into its Clostridium difficile target site. J Bacteriol 188:4871–4878. [PubMed][CrossRef]
35. Katayama Y, Ito T, Hiramatsu K. 2000. A new class of genetic element, staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 44:1549–1555. [PubMed][CrossRef]
36. Wang L, Archer GL. 2010. Roles of CcrA and CcrB in excision and integration of staphylococcal cassette chromosome mec, a Staphylococcus aureus genomic island. J Bacteriol 192:3204–3212. [PubMed][CrossRef]
37. Ito T, Katayama Y, Hiramatsu K. 1999. Cloning and nucleotide sequence determination of the entire mec DNA of pre-methicillin-resistant Staphylococcus aureus N315. Antimicrob Agents Chemother 43:1449–1458. [PubMed]
38. Scharn CR, Tenover FC, Goering RV. 2013. Transduction of staphylococcal cassette chromosome mec elements between strains of Staphylococcus aureus. Antimicrob Agents Chemother 57:5233–5238. [PubMed][CrossRef]
39. Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA. 2005. Structure of a synaptic gamma-delta resolvase tetramer covalently linked to two cleaved DNAs. Science 309:1210–1215. [PubMed][CrossRef]
40. Yang W, Steitz TA. 1995. Crystal-structure of the site-specific recombinase gamma-delta resolvase complexed with a 34bp cleavage site. Cell 82:193–207. [PubMed][CrossRef]
41. Yuan P, Gupta K, Van Duyne GD. 2008. Tetrameric structure of a serine integrase catalytic domain. Structure 16:1275–1286. [PubMed][CrossRef]
42. Ghosh P, Kim AI, Hatfull GF. 2003. The orientation of mycobacteriophage Bxb1 integration is solely dependent on the central dinucleotide of attP and attB. Mol Cell 12:1101–1111. [PubMed][CrossRef]
43. Ghosh P, Pannunzio NR, Hatfull GF. 2005. Synapsis in phage Bxb1 integration: selection mechanism for the correct pair of recombination sites. J Mol Biol 349:331–348. [PubMed][CrossRef]
44. Smith MCA, Till R, Brady K, Soultanas P, Thorpe H, Smith MCM. 2004. Synapsis and DNA cleavage in ɸC31 integrase-mediated site-specific recombination. Nucleic Acids Res 32:2607–2617. [PubMed][CrossRef]
45. Zhang L, Wang L, Wang J, Ou X, Zhao G, Ding X. 2010. DNA cleavage is independent of synapsis during Streptomyces phage ɸBT1 integrase-mediated site-specific recombination. J Mol Cell Biol 2:264–275. [PubMed][CrossRef]
46. Smith MCA, Till R, Smith MCM. 2004. Switching the polarity of a bacteriophage integration system. Mol Microbiol 51:1719–1728. [PubMed][CrossRef]
47. Thorpe HM, Wilson SE, Smith MCM. 2000. Control of directionality in the site-specific recombination system of the Streptomyces phage ɸC31. Mol Microbiol 38:232–241. [PubMed][CrossRef]
48. Rowley PA, Smith MCA, Younger E, Smith MCM. 2008. A motif in the C-terminal domain of ɸC31 integrase controls the directionality of recombination. Nucleic Acids Res 36:3879–3891. [PubMed][CrossRef]
49. Breuner A, Brondsted L, Hammer K. 1999. Novel organisation of genes involved in prophage excision identified in the temperate lactococcal bacteriophage TP901-1. J Bacteriol 181:7291–7297. [PubMed]
50. Zhang L, Ou X, Zhao G, Ding X. 2008. Highly efficient in vitro site-specific recombination system based on Streptomyces phage ɸBT1 integrase. J Bacteriol 190:6392–6397. [PubMed][CrossRef]
51. Ghosh P, Bibb LA, Hatfull GF. 2008. Two-step site selection for serine-integrase-mediated excision: DNA-directed integrase conformation and central dinucleotide proofreading. Proc Natl Acad Sci USA 105:3238–3243. [PubMed][CrossRef]
52. Ghosh P, Wasil LR, Hatfull GF. 2006. Control of phage Bxb1 excision by a novel recombination directionality factor. PLoS Biol 4:e186. [PubMed][CrossRef]
53. Khaleel T, Younger E, McEwan AR, Varghese AS, Smith MCM. 2011. A phage protein that binds ɸC31 integrase to switch its directionality. Mol Microbiol 80:1450–1463. [PubMed][CrossRef]
54. Matsuura M, Noguchi T, Yamaguchi D, Aida T, Asayama M, Takahashi H, Shirai M. 1996. The sre gene (ORF469) encodes a site-specific recombinase responsible for integration of the R4 phage genome. J Bacteriol 178:3374–3376. [PubMed]
55. Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA. 2008. Architecture of a serine recombinase-DNA regulatory complex. Mol Cell 30:145–155. [PubMed][CrossRef]
56. Adams V, Lucet IS, Lyras D, Rood JI. 2004. DNA binding properties of TnpX indicate that different synapses are formed in the excision and integration of the Tn4451 family. Mol Microbiol 53:1195–1207. [PubMed][CrossRef]
57. Mandali S, Dhar G, Avliyakulov NK, Haykinson MJ, Johnson RC. 2013. The site-specific integration reaction of Listeria phage A118 integrase, a serine recombinase. Mobile DNA 4:2. [PubMed][CrossRef]
58. Rowley PA, Smith MCM. 2008. Role of the N-terminal domain of ɸC31 integrase in attB-attP synapsis. J Bacteriol 190:6918–6921. [PubMed][CrossRef]
59. McEwan AR, Raab A, Kelly SM, Feldmann J, Smith MCM. 2011. Zinc is essential for high-affinity DNA binding and recombinase activity of ɸC31 integrase Nucleic Acids Res 39:6137–6147. [PubMed][CrossRef]
60. McEwan AR, Rowley PA, Smith MCM. 2009. DNA binding and synapsis by the large C-terminal domain of ɸC31 integrase. Nucleic Acids Res 37:4764–4773. [PubMed][CrossRef]
61. Lucet IS, Tynan FE, Adams V, Rossjohn J, Lyras D, Rood JI. 2005. Identification of the structural and functional domains of the large serine recombinase TnpX from Clostridium perfringens. J Biol Chem 280:2503–2511. [PubMed][CrossRef]
62. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. 2014. Pfam: the protein families database. Nucleic Acids Res 42:D222–D230. [PubMed][CrossRef]
63. Gupta M, Till R, Smith MCM. 2007. Sequences in attB that affect the ability of ɸC31 integrase to synapse and to activate DNA cleavage. Nucleic Acids Res 35:3407–3419. [PubMed][CrossRef]
64. Singh S, Ghosh P, Hatfull GF. 2013. Attachment site selection and identity in Bxb1 serine integrase-mediated site-specific recombination. PLoS Genet 9:e1003490. [PubMed][CrossRef]
65. Bibb LA, Hatfull GF. 2002. Integration and excision of the Mycobacterium tuberculosis prophage-like element, ɸRv1. Mol Microbiol. 45:1515–1526. [PubMed][CrossRef]
66. Zhang L, Zhu B, Dai R, Zhao G, Ding X. 2013. Control of directionality in Streptomyces phage ɸBT1 integrase-mediated site-specific recombination. PloS One 8:e80434. [PubMed][CrossRef]
67. Lyras D, Adams V, Lucet I, Rood JI. 2004. The large resolvase TnpX is the only transposon-encoded protein required for transposition of the Tn4451/3 family of integrative mobilizable elements. Mol Microbiol 51:1787–1800. [PubMed][CrossRef]
68. Olorunniji FJ, Buck DE, Colloms SD, McEwan AR, Smith MCM, Stark WM, Rosser SJ. 2012. Gated rotation mechanism of site-specific recombination by ɸC31 integrase. Proc Natl Acad Sci USA 109:19661–19666. [PubMed][CrossRef]
69. Kuhstoss S, Rao RN. 1991. Analysis of the integration function of the streptomycete bacteriophage phic31. J Mol Biol 222:897–908. [PubMed][CrossRef]
70. Kuhstoss S, Richardson MA, Rao RN. 1991. Plasmid cloning vectors that integrate site-specifically in Streptomyces spp. Gene 97:143–146. [PubMed][CrossRef]
71. St-Pierre F, Cui L, Priest DG, Endy D, Dodd IB, Shearwin KE. 2013. One-step cloning and chromosomal integration of DNA. ACS Synth Biol 2:537–541. [PubMed][CrossRef]
72. Fogg PC, Colloms S, Rosser S, Stark M, Smith MCM. 2014. New applications for phage integrases. J Mol Biol 426:2703–2716. [PubMed][CrossRef]
73. Groth AC, Calos MP. 2004. Phage integrases: biology and applications. J Mol Biol 335:667–678. [PubMed][CrossRef]
74. Groth AC, Olivares EC, Thyagarajan B, Calos MP. 2000. A phage integrase directs efficient site-specific integration in human cells. Proc Natl Acad Sci USA 97:5995–6000. [PubMed][CrossRef]
75. Zhang L, Zhao G, Ding X. 2011. Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination. Sci Rep 1:141. [PubMed][CrossRef]
76. Colloms SD, Merrick CA, Olorunniji FJ, Stark WM, Smith MCM, Osbourn A, Keasling JD, Rosser SJ. 2013. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res 42:e23. [PubMed][CrossRef]
77. Bonnet J, Subsoontorn P, Endy D. 2012. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci USA 109:8884–8889. [PubMed][CrossRef]
78. Bonnet J, Yin P, Ortiz ME, Subsoontorn P, Endy D. 2013. Amplifying genetic logic gates. Science 340:599–603. [PubMed][CrossRef]
79. Smith MCM. 2013. Conservative site-specific recombination, p 555–561. In Lennarz W (ed), The Encyclopedia of Biological Chemistry, vol 1. Academic Press, Waltham, MA. [CrossRef]
80. Christiansen B, Johnsen MG, Stenby E, Vogensen FK, Hammer K. 1994. Characterization of the lactococcal temperate phage TP901-1 and its site-specific integration. J Bacteriol 176:1069–1076. [PubMed]
81. Gregory MA, Till R, Smith MCM. 2003. Integration site for Streptomyces phage ɸBT1 and the development of novel site-specific integrating vectors. J Bacteriol 185:5320–5323. [PubMed][CrossRef]
82. Shirai M, Nara H, Sato A, Aida T, Takahashi H. 1991. Site-specific integration of the actinophage R4 genome into the chromosome of Streptomyces parvulus upon lysogenization. J Bacteriol 173:4237–4239. [PubMed]
83. Morita K, Yamamoto T, Fusada N, Komatsu M, Ikeda H, Hirano N, Takahashi H. 2009. The site-specific recombination system of actinophage TG1. FEMS Microbiol Lett 297:234–240. [PubMed][CrossRef]
84. Park MO, Lim KH, Kim TH, Chang HI. 2007. Characterization of site-specific recombination by the integrase MJ1 from enterococcal bacteriophage ɸFC1. J Microbiol Biotechnol 17:342–347. [PubMed]
85. Rashel M, Uchiyama J, Ujihara T, Takemura I, Hoshiba H, Matsuzaki S. 2008. A novel site-specific recombination system derived from bacteriophage ɸMR11. Biochem Biophys Res Commun 368:192–198. [PubMed][CrossRef]
86. Fayed B, Younger E, Taylor G, Smith MCM. 2014. A novel Streptomyces spp. integration vector derived from the S. venezuelae phage, SV1. BMC Biotechnol 14:51. [PubMed][CrossRef]
87. Kilcher S, Loessner MJ, Klumpp J. 2010. Brochothrix thermosphacta bacteriophages feature heterogeneous and highly mosaic genomes and utilize unique prophage insertion sites. J Bacteriol 192:5441–5453. [PubMed][CrossRef]
88. Lazarevic V, Dusterhoft A, Soldo B, Hilbert H, Mauel C, Karamata D. 1999. Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPβc2. Microbiology 145(Pt 5):1055–1067. [PubMed][CrossRef]
89. Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, Shvartsbeyn A, Vamathevan JJ, Tallon L, Althoff R, Arbogast TS, Fadrosh DW, Read TD, Gill SR. 2006. Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry. J Bacteriol 188:3402–3408. [PubMed][CrossRef]
90. Canchaya C, Desiere F, McShan WM, Ferretti JJ, Parkhill J, Brussow H. 2002. Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370. Virology 302:245–258. [PubMed][CrossRef]
microbiolspec.MDNA3-0059-2014.citations
cm/3/4
content/journal/microbiolspec/10.1128/microbiolspec.MDNA3-0059-2014
Loading

Citations loading...

Loading

Article metrics loading...

/content/journal/microbiolspec/10.1128/microbiolspec.MDNA3-0059-2014
2015-07-02
2017-09-19

Abstract:

The large serine recombinases (LSRs) are a family of enzymes, encoded in temperate phage genomes or on mobile elements, that precisely cut and recombine DNA in a highly controllable and predictable way. In phage integration, the LSRs act at specific sites, the site in the phage and the site in the host chromosome, where cleavage and strand exchange leads to the integrated prophage flanked by the recombinant sites and . The prophage can excise by recombination between and but this requires a phage-encoded accessory protein, the recombination directionality factor (RDF). Although the LSRs can bind specifically to all the recombination sites, only specific integrase-bound sites can pair in a synaptic complex prior to strand exchange. Recent structural information has led to a breakthrough in our understanding of the mechanism of the LSRs, notably how the LSRs bind to their substrates and how LSRs display this site-selectivity. We also understand that the RDFs exercise control over the LSRs by protein–protein interactions. Other recent work with the LSRs have contributed to our understanding of how all serine recombinases undergo strand exchange subunit rotation, facilitated by surfaces that resemble a molecular bearing.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Role of large serine recombinases in (A) phage integration and excision and (B) movement by mobile elements. Black and blue double lines represent the host and phage/mobile element DNA, respectively. Triangles are the / sites (blue) or host sites (black). The hybrid and sites are mixed. Figure adapted from Smith ( 79 ) with permission from Elsevier Press. doi:10.1128/microbiolspec.MDNA3-0059-2014.f1

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

The recombination pathway by large serine recombinases (LSRs). (i) Diagram of the domain structure of the LSRs; the N-terminal domain (NTD; green) is the catalytic domain; αE (green line) is the long alpha helix that connects the NTD to the recombinase domain (RD; red). The short linker between the RD and the zinc ribbon domain (ZD) is indicated by the arrow. The coiled-coil (CC) motif is depicted by rectangular projections. (ii) The LSRs in the unbound state are likely to be compact and globular ( 6 ). (iii) The LSRs binding to (gray) and (black). The relative positions of the ZD domains are different on and and these have consequences for the positions of the CC motifs. The CC motifs are either flared and dark, indicating they are projecting out of the paper or not flared and light, where they project into the paper. The scissile phosphates are located flanking the two nucleotide crossover sites shown as two white vertical lines. Bound to and , the CC to CC motifs can begin to interact and initiate synapsis. (iv) A synaptic complex is formed that requires interactions between the CC motifs as well as through the NTD tetrameric interface ( 41 ). Conformational changes occur in the NTDs to generate a flat interface for subunit rotation. (v) DNA cleavage occurs with concomitant formation of the phosphoseryl bonds. (vi) Subunit rotation swaps half sites, in this case B′ and P′. (vii) Joining of the recombinant products leads to a closed conformation of LSRs on the and sites and conformation changes in the NTDs. Figure adapted from Rutherford and van Duyne ( 6 ) with permission from Elsevier Press. doi:10.1128/microbiolspec.MDNA3-0059-2014.f2

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Structures of the integrase C-terminal domain (CTD) bound to the A118 half site. Four views are shown to illustrate two different trajectories of the coiled-coil (CC) motif. (A) (i) A schematic of a dimer of a large serine recombinase bound to an site. The structures shown in (ii) and (iii) relate to the boxed area in (i) and display two different trajectories of the CC motif as described in Rutherford . ( 5 ). (B) (i) The schematic indicates that the views in (ii) and (iii), which show the same structures as in (A)(ii) and (A)(iii), are looking down through the DNA. Domains are color-coded: green is the C-terminal end of αE from the N-terminal domain (NTD), Red is the recombinases domain (RD), blue is the zinc ribbon domain (ZD) and the light blue region within ZD is the CC motif. The NTDs, which are absent in the structures, would connect to the αE helix (green) to bind to the opposite side of the DNA from the CTDs. Figures were constructed using the PDP file 4KIS. doi:10.1128/microbiolspec.MDNA3-0059-2014.f3

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4
FIGURE 4

Binding motifs in the attachment sites for (LI) integrase, Bxb1, and ɸC31 integrases. Numbering of the bases is outwards from the crossover dinucleotide (00) to the left (minus) and the right (plus). The red and blue boxes indicate the recombinase domain (RD) and zinc ribbon domain (ZD) binding motifs,respectively. The three base pairs recognized by the RD-ZD linker in the sites are shown in pink. Highlighted orange are bases that are mutational sensitive and yellow is the discriminatory base described in Singh . ( 64 ). doi:10.1128/microbiolspec.MDNA3-0059-2014.f4

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5
FIGURE 5

Structural models of a large serine recombinase bound to a full site (A) and a full site (B) adapted from Rutherford . ( 5 ) with permission from Oxford University Press and redrawn by Dr. Greg van Duyne. The domains are colored using the same scheme as in Fig. 3 . ZD, zinc ribbon domain; RD, recombinases domain; NTD, N-terminal domain. doi:10.1128/microbiolspec.MDNA3-0059-2014.f5

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6
FIGURE 6

Site-selectivity explained by the geometry of the CC motifs bound to the attachment sites. (A) The three panels show the hypothetical assembly of synaptic complexes by integrase bound to two sites (left panel), two sites (middle panel), and an and site (right panel). The integrase subunits are colored red if bound to P or P′ and blue on B or B′. Line 1 in each panel shows an integrase dimer bound to an attachment site and the dimer is viewed from the perspective of zinc ribbon domain (ZD) and recombinase domain (RD) and looking down towards the N-terminal domain (NTD) bound to the opposite face of the DNA (black line). Line 2 is a second dimer bound to an attachment site but viewed the other way, that is, from the NTD and looking down towards the RD and ZD domains underneath. Line 3 shows what happens when the dimer from line 1 is superimposed on the dimer from line 2 to generate an integrase tetramer and line 4 is where this complex is rotated by 90°. In line 4, the CC motifs are flared and dark where they project out of the page and pale and thin where they project into the page. The CC motifs project in opposite directions from dimers bound to two sites or two sites but are proposed to be close enough to interact between integrase dimers bound to and site. (B) Possible pathway for assembly of the excision synapse with so-called complementary interactions between the integrase subunits is shown on the left ( 48 ). The and sites are proposed to be in a closed conformation with respect to the CC motif in the absence of the recombination directionality factor (RDF). Addition of the RDF might bind to the ZD domain to change the trajectory of the CC motifs so that they are in a more open conformation. As the CC motifs in the dimers bound to and project in the same direction (here projecting out of the page), there is an opportunity for them to interact, but only in the presence of the RDF. If one of the or sites aligns in the opposite orientation as shown by the tetramer synapse on the right, the CC motifs cannot interact as they are projecting in different directions, possibly explaining noncomplementary interaction and the bias against this type of synaptic complex in excision ( 48 ). doi:10.1128/microbiolspec.MDNA3-0059-2014.f6

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 7
FIGURE 7

The role of the central dinucleotide in site polarity. The central dinucleotide determines the polarity of the and sites and the identity of the and sites. (A) The wild type recombination sites for ɸC31 integrase have a nonpalindromic 5′TT at the crossover dinucleotides that after cleavage and strand exchange by subunit rotation [indicated by arrow (i)] can base pair in the recombinants allowing joining of the DNA backbone [indicated by arrow (ii)]. (B) Any sites that have a mismatch at the dinucleotide cannot join after DNA cleavage and one round of strand exchange by subunit rotation. Strand exchange can either reverse or the rotation iterates to regenerate the substrates [indicated by arrows (iii)]. The recombination pathway can then begin again. (C) Fifty percent of synaptic complexes assemble with and in an antiparallel orientation such that cutting of the substrates yields dinucleotides at the crossover that cannot base pair in the recombinants leading to reversal or iteration of strand exchange (iii). In excision, and do not normally assemble an antiparallel synapse as this would require noncomplementary interactions between integrases bound to two P type (or two B type) half sites. However, × (or × ) can form a synapse with the permitted complementary interactions by integrase subunits but joining of the products is prevented. doi:10.1128/microbiolspec.MDNA3-0059-2014.f7

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014
Permissions and Reprints Request Permissions
Download as Powerpoint

Tables

Generic image for table
TABLE 1

Location of sites

Source: microbiolspec July 2015 vol. 3 no. 4 doi:10.1128/microbiolspec.MDNA3-0059-2014

Supplemental Material

No supplementary material available for this content.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error