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Breaking and joining single-stranded DNA: the HUH endonuclease superfamily

Nature Reviews Microbiology volume 11, pages 525–538 (2013)Cite this article

Subjects

Key Points

  • HUH endonucleases contain the characteristic HUH motif (in which U represents a hydrophobic residue) and a Y motif, containing either one or two Tyr residues.

  • HUH endonucleases catalyse breakage and joining of single-stranded DNA (ssDNA) by a unique mechanism using a Y motif Tyr to create a 5′ intermediate covalent bond with the ssDNA substrate.

  • Many HUH endonucleases recognize and bind DNA hairpin structures in a sequence- or structure-specific way.

  • Rep (replication) proteins are HUH endonucleases that mediate rolling circle replication in phages, plasmids and viruses.

  • Relaxases use the HUH mechanism to catalyse plasmid replication and conjugation.

  • Transposases are HUH endonucleases that mediate ssDNA transposition — for example, for the IS91 family and IS200–IS605 family insertion sequences, for insertion sequences with a common region (ISCRs) and for Helitrons.

  • HUH endonucleases use the same catalytic motifs to mediate a diverse array of reactions, and this versatility has led to the widespread adoption of the HUH mechanism.

Abstract

HUH endonucleases are numerous and widespread in all three domains of life. The major function of these enzymes is processing a range of mobile genetic elements by catalysing cleavage and rejoining of single-stranded DNA using an active-site Tyr residue to make a transient 5′-phosphotyrosine bond with the DNA substrate. These enzymes have a key role in rolling-circle replication of plasmids and bacteriophages, in plasmid transfer, in the replication of several eukaryotic viruses and in various types of transposition. They have also been appropriated for cellular processes such as intron homing and the processing of bacterial repeated extragenic palindromes. Here, we provide an overview of these fascinating enzymes and their functions, using well-characterized examples of Rep proteins, relaxases and transposases, and we explore the molecular mechanisms used in their diverse activities.

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Figure 1: Reaction mechanism and organization of selected HUH proteins.
Figure 2: Structures of various HUH enzymes with their substrate DNAs.
Figure 3: Rolling-circle replication.
Figure 4: Rolling hairpin replication of adeno-associated virus.
Figure 5: Rolling-circle replication-mediated conjugation.
Figure 6: Single-strand transposons.

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References

  1. Kornberg, A. & Baker, T. A. DNA Replication 2nd edn (Freeman, 1992).

    Google Scholar 

  2. Ilyina, T. V. & Koonin, E. V. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 20, 3279–3285 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Koonin, E. V. & Ilyina, T. V. Computer-assisted dissection of rolling circle DNA replication. Biosystems 30, 241–268 (1993). References 2 and 3 are the first bioinformatic analyses of HUH endonucleases.

    Article  CAS  PubMed  Google Scholar 

  4. Kapitonov, V. V. & Jurka, J. Rolling-circle transposons in eukaryotes. Proc. Natl Acad. Sci. USA 98, 8714–8719 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Garcillan-Barcia, M. P., Bernales, I., Mendiola, M. V. & De la Cruz, F. in Mobile DNA Vol. II (eds Craig, N. L., Craigie, R., Gellert, M., & Lambowitz, A.) 891–904 (ASM Press, 2002).

    Google Scholar 

  6. Ton-Hoang, B. et al. Transposition of ISHp608, member of an unusual family of bacterial insertion sequences. EMBO J. 24, 3325–3338 (2005). A description of IS 608 and its behaviour.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Ronning, D. R. et al. Active site sharing and subterminal hairpin recognition in a new class of DNA transposases. Mol. Cell 20, 143–154 (2005).

    Article  CAS  PubMed  Google Scholar 

  8. Toleman, M. A., Bennett, P. M. & Walsh, T. R. ISCR elements: novel gene-capturing systems of the 21st century? Microbiol. Mol. Biol. Rev. 70, 296–316 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Garcillan-Barcia, M. P., Francia, M. V. & de la Cruz, F. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol. Rev. 33, 657–687 (2009). A discussion of the diversity of relaxases and their classification.

    Article  CAS  PubMed  Google Scholar 

  10. Gruss, A. & Ehrlich, S. D. The family of highly interrelated single-stranded deoxyribonucleic acid plasmids. Microbiol. Rev. 53, 231–241 (1989).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Rosario, K., Duffy, S. & Breitbart, M. A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch. Virol. 157, 1851–1871 (2012).

    Article  CAS  PubMed  Google Scholar 

  12. Curcio, M. J. & Derbyshire, K. M. The outs and ins of transposition: from Mu to Kangaroo. Nature Rev. Mol. Cell Biol. 4, 865–877 (2003).

    Article  CAS  Google Scholar 

  13. Odegrip, R. & Haggard-Ljungquist, E. The two active-site tyrosine residues of the A protein play non-equivalent roles during initiation of rolling circle replication of bacteriophage p2. J. Mol. Biol. 308, 147–163 (2001).

    Article  CAS  PubMed  Google Scholar 

  14. Grindley, N. D., Whiteson, K. L. & Rice, P. A. Mechanisms of site-specific recombination. Annu. Rev. Biochem. 75, 567–605 (2006).

    Article  CAS  PubMed  Google Scholar 

  15. Hickman, A. B. et al. DNA recognition and the precleavage state during single-stranded DNA transposition in D. radiodurans. EMBO J. 29, 3840–3852 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Boer, R. et al. Unveiling the molecular mechanism of a conjugative relaxase: the structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. J. Mol. Biol. 358, 857–869 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Boer, D. R. et al. Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains. EMBO J. 28, 1666–1678 (2009). The multimeric structure of the Rep protein from plasmid pMV158.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Datta, S., Larkin, C. & Schildbach, J. F. Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Structure 11, 1369–1379 (2003).

    Article  CAS  PubMed  Google Scholar 

  19. Larkin, C. et al. Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the F factor relaxase. Structure 13, 1533–1544 (2005).

    Article  CAS  PubMed  Google Scholar 

  20. Edwards, J. S. et al. Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus. Proc. Natl Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1219701110 (2013).

  21. Dyda, F. & Hickman, A. B. A Mob of Reps. Structure 11, 1310–1311 (2003).

    Article  CAS  PubMed  Google Scholar 

  22. Guasch, A. et al. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nature Struct. Biol. 10, 1002–1010 (2003). The structure of the TrwC relaxase complexed with its DNA substrate.

    Article  CAS  PubMed  Google Scholar 

  23. Hickman, A. B., Ronning, D. R., Perez, Z. N., Kotin, R. M. & Dyda, F. The nuclease domain of adeno-associated virus Rep coordinates replication initiation using two distinct DNA recognition interfaces. Mol. Cell 13, 403–414 (2004). A description of the different binding modes of AAV Rep from a structural point of view.

    Article  CAS  PubMed  Google Scholar 

  24. Clerot, D. & Bernardi, F. DNA helicase activity is associated with the replication initiator protein Rep of tomato yellow leaf curl geminivirus. J. Virol. 80, 11322–11330 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Odegrip, R., Schoen, S., Haggard-Ljungquist, E., Park, K. & Chattoraj, D. K. The interaction of bacteriophage P2 B protein with Escherichia coli DnaB helicase. J. Virol. 74, 4057–4063 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Petit, M. A. et al. PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication. Mol. Microbiol. 29, 261–273 (1998).

    Article  CAS  PubMed  Google Scholar 

  27. Bruand, C. & Ehrlich, S. D. UvrD-dependent replication of rolling-circle plasmids in Escherichia coli. Mol. Microbiol. 35, 204–210 (2000).

    Article  CAS  PubMed  Google Scholar 

  28. Chang, T. L. et al. Biochemical characterization of the Staphylococcus aureus PcrA. helicase and its role in plasmid rolling circle replication. J. Biol. Chem. 277, 45880–45886 (2002).

    Article  CAS  PubMed  Google Scholar 

  29. Brister, J. R. & Muzyczka, N. Rep-mediated nicking of the adeno-associated virus origin requires two biochemical activities, DNA helicase activity and transesterification. J. Virol. 73, 9325–9336 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Im, D. S. & Muzyczka, N. The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity. Cell 61, 447–457 (1990).

    Article  CAS  PubMed  Google Scholar 

  31. Brister, J. R. & Muzyczka, N. Mechanism of Rep-mediated adeno-associated virus origin nicking. J. Virol. 74, 7762–7771 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ton-Hoang, B. et al. Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences. Nucleic Acids Res. 40, 3596–3609 (2012). The identification and structure of TnpA(REP), and an analysis of the activity of this enzyme.

    Article  CAS  PubMed  Google Scholar 

  33. Messing, S. A. et al. The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease. Nucleic Acids Res. 40, 9964–9979 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Orozco, B. M. & Hanley-Bowdoin, L. A. DNA structure is required for geminivirus replication origin function. J. Virol. 70, 148–158 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. del Solar, G., Giraldo, R., Ruiz-Echevarria, M. J., Espinosa, M. & Diaz-Orejas, R. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434–464 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Bikard, D., Loot, C., Baharoglu, Z. & Mazel, D. Folded DNA in action: hairpin formation and biological functions in prokaryotes. Microbiol. Mol. Biol. Rev. 74, 570–588 (2011).

    Article  CAS  Google Scholar 

  37. Larkin, C., Datta, S., Nezami, A., Dohm, J. A. & Schildbach, J. F. Crystallization and preliminary X-ray characterization of the relaxase domain of F factor TraI. Acta Crystallogr. D Biol. Crystallogr. 59, 1514–1516 (2003).

    Article  PubMed  CAS  Google Scholar 

  38. Ruiz-Maso, J. A., Lurz, R., Espinosa, M. & del Solar, G. Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication. Nucleic Acids Res. 35, 1230–1244 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Gilbert, W. & Dressler, D. DNA replication: the rolling circle model. Cold Spring Harb. Symp. Quant. Biol. 33, 473–484 (1968).

    Article  CAS  PubMed  Google Scholar 

  40. Khan, S. A. Plasmid rolling-circle replication: recent developments. Mol. Microbiol. 37, 477–484 (2000).

    Article  CAS  PubMed  Google Scholar 

  41. Brown, D. R. et al. DNA structures required for ϕX174 A-protein-directed initiation and termination of DNA replication. Cold Spring Harb. Symp. Quant. Biol. 47, 701–715 (1983).

    Article  PubMed  Google Scholar 

  42. Brown, D. R., Schmidt-Glenewinkel, T., Reinberg, D. & Hurwitz, J. DNA sequences which support activities of the bacteriophage φX174 gene A protein. J. Biol. Chem. 258, 8402–8412 (1983).

    Article  CAS  PubMed  Google Scholar 

  43. Roth, M. J., Brown, D. R. & Hurwitz, J. Analysis of bacteriophage ϕX174 gene A protein-mediated termination and reinitiation of ϕX DNA synthesis. II. Structural characterization of the covalent ϕX A protein-DNA complex. J. Biol. Chem. 259, 10556–10568 (1984).

    Article  CAS  PubMed  Google Scholar 

  44. Hanai, R. & Wang, J. C. The mechanism of sequence-specific DNA cleavage and strand transfer by ϕX174 gene A* protein. J. Biol. Chem. 268, 23830–23836 (1993).

    Article  CAS  PubMed  Google Scholar 

  45. van Mansfeld, A. D., van Teeffelen, H. A., Baas, P. D. & Jansz, H. S. Two juxtaposed tyrosyl-OH groups participate in ϕX174 gene A protein catalysed cleavage and ligation of DNA. Nucleic Acids Res. 14, 4229–4238 (1986). A demonstration of the importance of two Tyr residues in the φX174 Rep protein for catalysis.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Barabas, O. et al. Mechanism of IS200/IS605 family DNA transposases: activation and transposon-directed target site selection. Cell 132, 208–220 (2008). The structural model for single-strand transposition of IS 608 and other IS 200 –IS 605 family members.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Noirot-Gros, M. F. & Ehrlich, S. D. Change of a catalytic reaction carried out by a DNA replication protein. Science 274, 777–780 (1996).

    Article  CAS  PubMed  Google Scholar 

  48. Novick, R. P. Contrasting lifestyles of rolling-circle phages and plasmids. Trends Biochem. Sci. 23, 434–438 (1998).

    Article  CAS  PubMed  Google Scholar 

  49. Moscoso, M., Eritja, R. & Espinosa, M. Initiation of replication of plasmid pMV158: mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein. J. Mol. Biol. 268, 840–856 (1997).

    Article  CAS  PubMed  Google Scholar 

  50. Tattersall, P. & Ward, D. C. Rolling hairpin model for replication of parvovirus and linear chromosomal DNA. Nature 263, 106–109 (1976).

    Article  CAS  PubMed  Google Scholar 

  51. James, J. A. et al. Crystal structure of the SF3 helicase from adeno-associated virus type 2. Structure 11, 1025–1035 (2003).

    Article  CAS  PubMed  Google Scholar 

  52. Smith, R. H. & Kotin, R. M. The Rep52 gene product of adeno-associated virus is a DNA helicase with 3′-to-5′ polarity. J. Virol. 72, 4874–4881 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Maggin, J. E., James, J. A., Chappie, J. S., Dyda, F. & Hickman, A. B. The amino acid linker between the endonuclease and helicase domains of adeno-associated virus type 5 Rep plays a critical role in DNA-dependent oligomerization. J. Virol. 86, 3337–3346 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Zarate-Perez, F. et al. The interdomain linker of AAV-2 Rep68 is an integral part of its oligomerization domain: role of a conserved SF3 helicase residue in oligomerization. PLoS Pathog. 8, e1002764 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Hickman, A. B., Ronning, D. R., Kotin, R. M. & Dyda, F. Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep. Mol. Cell 10, 327–337 (2002).

    Article  CAS  PubMed  Google Scholar 

  56. King, J. A., Dubielzig, R., Grimm, D. & Kleinschmidt, J. A. DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids. EMBO J. 20, 3282–3291 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Campos-Olivas, R., Louis, J. M., Clerot, D., Gronenborn, B. & Gronenborn, A. M. The structure of a replication initiator unites diverse aspects of nucleic acid metabolism. Proc. Natl Acad. Sci. USA 99, 10310–10315 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Vega-Rocha, S., Gronenborn, B., Gronenborn, A. M. & Campos-Olivas, R. Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures. Biochemistry 46, 6201–6212 (2007).

    Article  CAS  PubMed  Google Scholar 

  59. Vega-Rocha, S., Byeon, I. J., Gronenborn, B., Gronenborn, A. M. & Campos-Olivas, R. Solution structure, divalent metal and DNA binding of the endonuclease domain from the replication initiation protein from porcine circovirus 2. J. Mol. Biol. 367, 473–487 (2007).

    Article  CAS  PubMed  Google Scholar 

  60. Oke, M. et al. A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for the Rep mechanism and viral replication. J. Virol. 85, 925–931 (2011).

    Article  CAS  PubMed  Google Scholar 

  61. Noirot-Gros, M. F., Bidnenko, V. & Ehrlich, S. D. Active site of the replication protein of the rolling circle plasmid pC194. EMBO J. 13, 4412–4420 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Rasooly, A. & Rasooly, R. S. How rolling circle plasmids control their copy number. Trends Microbiol. 5, 440–446 (1997).

    Article  CAS  PubMed  Google Scholar 

  63. Laufs, J. et al. Geminivirus replication: genetic and biochemical characterization of Rep protein function, a review. Biochimie 77, 765–773 (1995).

    Article  CAS  PubMed  Google Scholar 

  64. Lederberg, J. & Tatum, E. L. Sex in bacteria; genetic studies, 1945–1952. Science 118, 169–175 (1953).

    Article  CAS  PubMed  Google Scholar 

  65. de la Cruz, F., Frost, L. S., Meyer, R. J. & Zechner, E. L. Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol. Rev. 34, 18–40 (2010).

    Article  CAS  PubMed  Google Scholar 

  66. Guglielmini, J., Quintais, L., Garcillan-Barcia, M. P., de la Cruz, F. & Rocha, E. P. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet. 7, e1002222 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Burrus, V., Pavlovic, G., Decaris, B. & Guedon, G. Conjugative transposons: the tip of the iceberg. Mol. Microbiol. 46, 601–610 (2002).

    Article  CAS  PubMed  Google Scholar 

  68. Guerillot, R., Da Cunha, V., Sauvage, E., Bouchier, C. & Glaser, P. Modular evolution of TnGBSs, a new family of integrative and conjugative elements associating insertion sequence transposition, plasmid replication, and conjugation for their spreading. J. Bacteriol. 195, 1979–1990 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Smyth, D. S. & Robinson, D. A. Integrative and sequence characteristics of a novel genetic element, ICE6013, in Staphylococcus aureus. J. Bacteriol. 191, 5964–5975 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Rocco, J. M. & Churchward, G. The integrase of the conjugative transposon Tn916 directs strand- and sequence-specific cleavage of the origin of conjugal transfer, oriT, by the endonuclease Orf20. J. Bacteriol. 188, 2207–2213 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Lee, C. A., Babic, A. & Grossman, A. D. Autonomous plasmid-like replication of a conjugative transposon. Mol. Microbiol. 75, 268–279 (2010).

    Article  CAS  PubMed  Google Scholar 

  72. Draper, O., Cesar, C. E., Machon, C., de la Cruz, F. & Llosa, M. Site-specific recombinase and integrase activities of a conjugative relaxase in recipient cells. Proc. Natl Acad. Sci. USA 102, 16385–16390 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Kingsman, A. & Willetts, N. The requirements for conjugal DNA synthesis in the donor strain during F lac transfer. J. Mol. Biol. 122, 287–300 (1978).

    Article  CAS  PubMed  Google Scholar 

  74. Nash, R. P., Habibi, S., Cheng, Y., Lujan, S. A. & Redinbo, M. R. The mechanism and control of DNA transfer by the conjugative relaxase of resistance plasmid pCU1. Nucleic Acids Res. 38, 5929–5943 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Monzingo, A. F., Ozburn, A., Xia, S., Meyer, R. J. & Robertus, J. D. The structure of the minimal relaxase domain of MobA at 2.1 Å resolution. J. Mol. Biol. 366, 165–178 (2007).

    Article  CAS  PubMed  Google Scholar 

  76. Larkin, C., Haft, R. J. F., Harley, M. J., Traxler, B. & Schildbach, J. F. Roles of active site residues and the HUH motif of the F plasmid TraI relaxase. J. Biol. Chem. 282, 33707–33713 (2007).

    Article  CAS  PubMed  Google Scholar 

  77. Gonzalez-Perez, B. et al. Analysis of DNA processing reactions in bacterial conjugation by using suicide oligonucleotides. EMBO J. 26, 3847–3857 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Dostal, L., Shao, S. & Schildbach, J. F. Tracking F plasmid TraI relaxase processing reactions provides insight into F plasmid transfer. Nucleic Acids Res. 39, 2658–2670 (2011).

    Article  CAS  PubMed  Google Scholar 

  79. Lucas, M. et al. Relaxase DNA binding and cleavage are two distinguishable steps in conjugative DNA processing that involve different sequence elements of the nic site. J. Biol. Chem. 285, 8918–8926 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Kim, Y. J., Lin, L. S. & Meyer, R. J. Two domains at the origin are required for replication and maintenance of broad-host-range plasmid R1162. J. Bacteriol. 169, 5870–5872 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Pansegrau, W., Schroder, W. & Lanka, E. Concerted action of three distinct domains in the DNA cleaving-joining reaction catalyzed by relaxase (TraI) of conjugative plasmid RP4. J. Biol. Chem. 269, 2782–2789 (1994).

    Article  CAS  PubMed  Google Scholar 

  82. Meyer, R. Replication and conjugative mobilization of broad host-range IncQ plasmids. Plasmid 62, 57–70 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Geibel, S., Banchenko, S., Engel, M., Lanka, E. & Saenger, W. Structure and function of primase RepB′ encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode. Proc. Natl Acad. Sci. USA 106, 7810–7815 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Honda, Y., Sakai, H., Komano, T. & Bagdasarian, M. RepB′ is required in trans for the two single-strand DNA initiation signals in oriV of plasmid RSF1010. Gene 80, 155–159 (1989).

    Article  CAS  PubMed  Google Scholar 

  85. Mendiola, M. V., Bernales, I. & de la Cruz, F. Differential roles of the transposon termini in IS91 transposition. Proc. Natl Acad. Sci. USA 91, 1922–1926 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Lam, S. & Roth, J. R. IS200: a Salmonella-specific insertion sequence. Cell 34, 951–960 (1983).

    Article  CAS  PubMed  Google Scholar 

  87. Kersulyte, D. et al. Transposable element ISHp608 of Helicobacter pylori: nonrandom geographic distribution, functional organization, and insertion specificity. J. Bacteriol. 184, 992–1002 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Islam, S. M. et al. Characterization and distribution of IS8301 in the radioresistant bacterium Deinococcus radiodurans. Genes Genet. Syst. 78, 319–327 (2003).

    Article  CAS  PubMed  Google Scholar 

  89. Ton-Hoang, B. et al. Single-stranded DNA transposition is coupled to host replication. Cell 142, 398–408 (2010).

    Article  CAS  PubMed  Google Scholar 

  90. Pasternak, C. et al. Irradiation-induced Deinococcus radiodurans genome fragmentation triggers transposition of a single resident insertion sequence. PLoS Genet. 6, e1000799 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  91. Zahradka, K. et al. Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 443, 569–573 (2006).

    Article  CAS  PubMed  Google Scholar 

  92. He, S. et al. Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing. Nucleic Acids Res. 39, 8503–8512 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Guynet, C. et al. Resetting the site: redirecting integration of an insertion sequence in a predictable way. Mol. Cell 34, 612–619 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Garcillan-Barcia, M. P. & de la Cruz, F. Distribution of IS91 family insertion sequences in bacterial genomes: evolutionary implications. FEMS Microbiol. Ecol. 42, 303–313 (2002).

    Article  CAS  PubMed  Google Scholar 

  95. Pilar Garcillan-Barcia, M., Bernales, I., Mendiola, M. V. & de la Cruz, C. F. Single-stranded DNA intermediates in IS91 rolling-circle transposition. Mol. Microbiol. 39, 494–502 (2001).

    Article  PubMed  Google Scholar 

  96. Sinzelle, L., Izsvak, Z. & Ivics, Z. Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell. Mol. Life Sci. 66, 1073–1093 (2009).

    Article  CAS  PubMed  Google Scholar 

  97. Vega-Rocha, S., Gronenborn, A. M., Gronenborn, B. & Campos-Olivas, R. 1H, 13C, and 15N NMR assignment of the master Rep protein nuclease domain from the nanovirus FBNYV. J. Biomol. NMR 38, 169 (2007).

    Article  CAS  PubMed  Google Scholar 

  98. Varsaki, A., Lucas, M., Afendra, A. S., Drainas, C. & de la Cruz, F. Genetic and biochemical characterization of MbeA, the relaxase involved in plasmid ColE1 conjugative mobilization. Mol. Microbiol. 48, 481–493 (2003).

    Article  CAS  PubMed  Google Scholar 

  99. Burd, C. G. & Dreyfuss, G. Conserved structures and diversity of functions of RNA-binding proteins. Science 265, 615–621 (1994).

    Article  CAS  PubMed  Google Scholar 

  100. Scott, J. F., Eisenberg, S., Bertsch, L. L. & Kornberg, A. A mechanism of duplex DNA replication revealed by enzymatic studies of phage ϕX174: catalytic strand separation in advance of replication. Proc. Natl Acad. Sci. USA 74, 193–197 (1977).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Kotin, R. M. et al. Site-specific integration by adeno-associated virus. Proc. Natl Acad. Sci. USA 87, 2211–2215 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Smith, R. H., Spano, A. J. & Kotin, R. M. The Rep78 gene product of adeno-associated virus (AAV) self-associates to form a hexameric complex in the presence of AAV ori sequences. J. Virol. 71, 4461–4471 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Mansilla-Soto, J. et al. DNA structure modulates the oligomerization properties of the AAV initiator protein Rep68. PLoS Pathog. 5, e1000513 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  104. McCarty, D. M., Young, S. M. Jr & Samulski, R. J. Integration of adeno-associated virus (AAV) and recombinant AAV vectors. Annu. Rev. Genet. 38, 819–845 (2004).

    Article  CAS  PubMed  Google Scholar 

  105. Cesar, C. E., Machon, C., de la Cruz, F. & Llosa, M. A new domain of conjugative relaxase TrwC responsible for efficient oriT-specific recombination on minimal target sequences. Mol. Microbiol. 62, 984–996 (2006).

    Article  CAS  PubMed  Google Scholar 

  106. Cesar, C. E. & Llosa, M. TrwC-mediated site-specific recombination is controlled by host factors altering local DNA topology. J. Bacteriol. 189, 9037–9043 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Agundez, L., Gonzalez-Prieto, C., Machon, C. & Llosa, M. Site-specific integration of foreign DNA into minimal bacterial and human target sequences mediated by a conjugative relaxase. PLoS ONE 7, e31047 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Agundez, L. et al. Nuclear targeting of a bacterial integrase that mediates site-specific recombination between bacterial and human target sequences. Appl. Environ. Microbiol. 77, 201–210 (2011).

    Article  CAS  PubMed  Google Scholar 

  109. Schröder, G., Schuelein, R., Quebatte, M. & Dehio, C. Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae. Proc. Natl Acad. Sci. USA 108, 14643–14648 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  110. Fernandez-Gonzalez, E. et al. Transfer of R388 derivatives by a pathogenesis-associated type IV secretion system into both bacteria and human cells. J. Bacteriol. 193, 6257–6265 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. González-Prieto, C., Agúndez, L., Linden, R. M. & Llosa, M. HUH site-specific recombinases for targeted modification of the human genome. Trends Biotechnol. 31, 305–312 (2013).

    Article  PubMed  CAS  Google Scholar 

  112. Pritham, E. J. & Feschotte, C. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc. Natl Acad. Sci. USA 104, 1895–1900 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Kapitonov, V. V. & Jurka, J. Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet. 23, 521–529 (2007).

    Article  CAS  PubMed  Google Scholar 

  114. Feschotte, C. & Wessler, S. R. Treasures in the attic: rolling circle transposons discovered in eukaryotic genomes. Proc. Natl Acad. Sci. USA 98, 8923–8924 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Higgins, C. F., Ames, G. F., Barnes, W. M., Clement, J. M. & Hofnung, M. A novel intercistronic regulatory element of prokaryotic operons. Nature 298, 760–762 (1982).

    Article  CAS  PubMed  Google Scholar 

  116. Bachellier, S., Clément, J.-M. & Hofnung, M. Short palindromic repetitive DNA elements in enterobacteria: a survey. Res. Microbiol. 150, 627–639 (1999).

    Article  CAS  PubMed  Google Scholar 

  117. Nunvar, J., Huckova, T. & Licha, I. Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes. BMC Genomics 11, 44 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  118. Bertels, F. & Rainey, P. B. Within-genome evolution of REPINs: a new family of miniature mobile DNA in bacteria. PLoS Genet. 7, e1002132 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Braun, V. et al. A chimeric ribozyme in Clostridium difficile combines features of group I introns and insertion elements. Mol. Microbiol. 36, 1447–1459 (2000).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors thank C. Guynet, S. Messing and I. Molineau for discussions. This work was supported by intramural funding from the French Centre National de la Recherche Scientifique (to M.C. and B.T.H.) and the Intramural Program of the US National Institute of Diabetes and Digestive and Kidney Diseases (to A.B.H. and F.D.), and by grants from the French Agence National de Recherche (ANR-12-BSV8-0009-01; to B.T.H.), the Spanish Ministry of Science and Innovation (BIO2010-14809; to G.M.), the Spanish Ministry of Education (BFU2011-26608; to F.d.l.C.) and the European Seventh Framework Program (248919/FP7-ICT-2009-4 and 282004/FP7-HEALTH.2011.2.3.1-2; to F.d.l.C.).

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Authors and Affiliations

  1. Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5100, 118 Route de Narbonne, F31062, Toulouse Cedex, France

    Michael Chandler & Bao Ton-Hoang

  2. Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas–SODERCAN, 22 Calle Albert Einstein, 39011, Santander, Spain

    Fernando de la Cruz & Gabriel Moncalian

  3. Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, 5 Center Drive, Bethesda, 20892, Maryland, USA

    Fred Dyda & Alison B. Hickman

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Correspondence to Michael Chandler.

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FURTHER INFORMATION

ISfinder

PowerPoint slides

Supplementary information

Supplementary information S1 (table)

Major features of HUH enzymes (PDF 292 kb)

Glossary

Repetitive extragenic palindromic sequences

Abundant non-coding repeats that are found in bacterial genomes and form DNA hairpin structures that can have regulatory functions.

Rolling-circle replication

Unidirectional replication of circular DNA molecules (such as plasmids and phage genomes) in which a single-stranded product is 'peeled' from a circular DNA template.

Insertion sequences with a common region

Insertion sequences that contain a common ORF which has similarity to the transposase ORF encoded in insertion sequence IS91. These elements seem to be able to sequester additional neighbouring genes during their transposition.

Insertion sequences

Short transposable DNA segments that include one or more genes involved in their own mobility.

Helitron

A type of eukaryotic transposon that is thought to transpose using a rolling-circle replication mechanism similar to that of insertion sequence IS91.

Helicase

An enzyme that unwinds and separates double-stranded DNA. Helicases are classified into six major superfamilies (SF1–SF6) on the basis of the motifs and consensus sequences shared by the molecules and their activities (for example, 5′–3′ or 3′–5′ directionality).

Type IV secretion system

A multiprotein apparatus that is used by bacteria to transport both DNA and proteins across the bacterial cell envelope.

Integrative and conjugative element

A mobile genetic element that has the transfer properties of a conjugative plasmid but that is generally unable to replicate autonomously and possesses dedicated integration systems to allow the element to be maintained by integration into the host chromosome.

DDE family transposase

A transposase that contains a characteristic DDE amino acid motif.

R-loops

Regions of DNA in which the two strands are separated by a short RNA segment that forms a complementary RNA–DNA hybrid with one of the DNA strands.

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Chandler, M., de la Cruz, F., Dyda, F. et al. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol 11, 525–538 (2013). https://doi.org/10.1038/nrmicro3067

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