DNA recombination in somatic plant cells: Mechanisms and evolutionary consequences

Chromosome Research

Volumn 22, Issue 2, 2014, Pages 191-201

  Knoll, Alexander ^a   Fauser, Friedrich ^a   Puchta, Holger ^a  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

DSB repair; genome evolution; homologous recombination; non homologous end joining; plants; replication fork

Indexed keywords

PLANT DNA;

ARABIDOPSIS; CYTOLOGY; DNA REPAIR; GENE REARRANGEMENT; GENETICS; HOMOLOGOUS RECOMBINATION; MOLECULAR EVOLUTION; PLANT GENOME;

ARABIDOPSIS; DNA REPAIR; DNA, PLANT; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; GENOME, PLANT; HOMOLOGOUS RECOMBINATION;

EID: 84905123594     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-014-9415-y     Document Type: Review

References (33)

1. Bennetzen JL, Kellogg EA (1997)Do plants have a one-way ticket to genomic obesity? Plant Cell 9(9):1509-1514. doi:10.1105/tpc.9.9.1509
2. Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95(1):127-132. doi:10.1093/aob/mci008 (Pubitemid 41214455)
3. Charbonnel C, Allain E, Gallego ME, White CI (2011) Kinetic analysis of DNA double-strand break repair pathways in Arabidopsis. DNA Repair (Amst) 10(6):611-619. doi:10.1016/j.dnarep.2011.04.002
4. Da Ines O, Degroote F, Amiard S, Goubely C, Gallego ME, White CI (2013) Effects of XRCC2 and RAD51B mutations on somatic and meiotic recombination in Arabidopsis thaliana. Plant J 74(6):959-970. doi:10.1111/tpj.12182
5. Devos KM, Brown JK, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12(7):1075-1079. doi:10.1101/gr.132102 (Pubitemid 34785200)
6. Drouaud J, Camilleri C, Bourguignon P, Canaguier A, Bérard A, Vezon D, Giancola S, Brunel D, Colot V, Prum B, Quesneville H, Mézard C (2006) Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots". Genome Res 16(1):106-114. doi:10.1101/gr.4319006 (Pubitemid 43048939)
7. Dubest S, Gallego ME, White CI (2002) Role of the AtRad1p endonuclease in homologous recombination in plants. EMBO Rep 3(11):1049-1054. doi:10.1093/embo-reports/kvf211 (Pubitemid 35469896)
8. Fawcett JA, Rouze P, Van de Peer Y (2012) Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol Biol Evol 29(2):849-859. doi:10.1093/molbev/msr254
9. Fransz PF, Armstrong S, de Jong JH, Parnell LD, van Drunen C, Dean C, Zabel P, Bisseling T, Jones GH (2000) Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100(3):367-376 (Pubitemid 30353092)
10. Gisler B, Salomon S, Puchta H (2002) The role of double-strand break-induced allelic homologous recombination in somatic plant cells. Plant J 32(3):277-284 (Pubitemid 35307263)
11. Hartung F, Suer S, Knoll A, Wurz-Wildersinn R, Puchta H (2008) Topoisomerase 3alpha and RMI1 suppress somatic crossovers and are essential for resolution of meiotic recombination intermediates in Arabidopsis thaliana. PLoS Genet 4(12):e1000285. doi:10.1371/journal.pgen.1000285
12. Jia Q, den Dulk-Ras A, Shen H, Hooykaas PJ, de Pater S (2013) Poly(ADP-ribose)polymerases are involved in microhomology mediated back-up non-homologous end joining in Arabidopsis thaliana. Plant Mol Biol 82(4-5):339-351. doi:10.1007/s11103-013-0065-9
13. Kirik A, Salomon S, Puchta H (2000) Species-specific double-strand break repair and genome evolution in plants. EMBO J 19(20):5562-5566. doi:10.1093/emboj/19.20.5562
14. Knoll A, Higgins JD, Seeliger K, Reha SJ, Dangel NJ, Bauknecht M, Schropfer S, Franklin FC, Puchta H (2012) The Fanconi anemia ortholog FANCM ensures ordered homologous recombination in both somatic and meiotic cells in Arabidopsis. Plant Cell 24(4):1448-1464. doi:10.1105/tpc.112.096644
15. Lieberman-Lazarovich M, Levy AA (2011) Homologous recombination in plants: an antireview. Methods Mol Biol 701:51-65. doi:10.1007/978-1-61737-957- 4-3
16. Lloyd AH, Wang D, Timmis JN (2012) Single molecule PCR reveals similar patterns of non-homologous DSB repair in tobacco and Arabidopsis. PLoS One 7(2):e32255. doi:10.1371/journal.pone.0032255
17. Mannuss A, Dukowic-Schulze S, Suer S, Hartung F, Pacher M, Puchta H (2010) RAD5A, RECQ4A, and MUS81 have specific functions in homologous recombination and define different pathways of DNA repair in Arabidopsis thaliana. Plant Cell 22(10):3318-3330. doi:10.1105/tpc.110.078568
18. Mladenov E, Iliakis G (2011) Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways. Mutat Res 711(1-2):61-72. doi:10.1016/j.mrfmmm.2011.02.005
19. Osakabe K, OsakabeY, Toki S (2010) Site-directedmutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc Natl Acad Sci U S A 107(26):12034-12039. doi:10.1073/pnas.1000234107
20. Pacher M, Schmidt-Puchta W, Puchta H (2007) Two unlinked double-strand breaks can induce reciprocal exchanges in plant genomes via homologous recombination and nonhomologous end joining. Genetics 175(1):21-29. doi:10.1534/genetics.106.065185
21. Puchta H (1998) Repair of genomic double-strand breaks in somatic plant cells by one-sided invasion of homologous sequences. Plant J 13(3):331-339. doi:10.1046/j.1365-313X.1998.00035.x
22. Puchta H (1999) Double-strand break-induced recombination between ectopic homologous sequences in somatic plant cells. Genetics 152(3):1173-1181
23. Puchta H (2005) The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. J Exp Bot 56(409):1-14. doi:10.1093/jxb/eri025
24. Puchta H, Fauser F (2013) Synthetic nucleases for genome engineering in plants: prospects for a bright future. Plant J. doi:10.1111/tpj.12338
25. Puchta H, Hohn B (2012) In planta somatic homologous recombination assay revisited: a successful and versatile, but delicate tool. Plant Cell 24(11):4324-4331. doi:10.1105/tpc.112.101824
26. Roth N, Klimesch J, Dukowic-Schulze S, Pacher M, Mannuss A, Puchta H (2012) The requirement for recombination factors differs considerably between different pathways of homologous double-strand break repair in somatic plant cells. Plant J 72(5):781-790. doi:10.1111/j.1365-313X.2012.05119.x
27. Salomon S, Puchta H (1998) Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells. EMBO J 17(20):6086-6095. doi:10.1093/emboj/17.20.6086 (Pubitemid 28474802)
28. Shalev G, Levy AA (1997) The maize transposable element Ac induces recombination between the donor site and an homologous ectopic sequence. Genetics 146(3):1143-1151 (Pubitemid 27290995)
29. Shrivastav M, De Haro LP, Nickoloff JA (2008) Regulation of DNA double-strand break repair pathway choice. Cell Res 18(1):134-147
30. Siebert R, Puchta H (2002) Efficient repair of genomic double-strand breaks by homologous recombination between directly repeated sequences in the plant genome. Plant Cell 14(5):1121-1131 (Pubitemid 34609220)
31. Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW (1983) The double-strand-break repair model for recombination. Cell 33(1):25-35 (Pubitemid 13096431)
32. Voytas DF (2013) Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol 64:327-350. doi:10.1146/annurev-arplant-042811- 105552
33. Waterworth WM, Drury GE, Bray CM, West CE (2011) Repairing breaks in the plant genome: the importance of keeping it together. New Phytol 192(4):805-822. doi:10.1111/j.1469-8137.2011.03926.x