title: Single-nucleotide and long-patch base excision repair of DNA damage in plants.
abstract: Base excision repair (BER) is a critical pathway in cellular defense against endogenous or exogenous DNA damage. This elaborate multistep process is initiated by DNA glycosylases that excise the damaged base, and continues through the concerted action of additional proteins that finally restore DNA to the unmodified state. BER has been subject to detailed biochemical analysis in bacteria, yeast and animals, mainly through in vitro reproduction of the entire repair reaction in cell-free extracts. However, an understanding of this repair pathway in plants has consistently lagged behind. We report the extension of BER biochemical analysis to plants, using Arabidopsis cell extracts to monitor repair of DNA base damage in vitro. We have used this system to demonstrate that Arabidopsis cell extracts contain the enzymatic machinery required to completely repair ubiquitous DNA lesions, such as uracil and abasic (AP) sites. Our results reveal that AP sites generated after uracil excision are processed both by AP endonucleases and AP lyases, generating either 5'- or 3'-blocked ends, respectively. We have also found that gap filling and ligation may proceed either through insertion of just one nucleotide (short-patch BER) or several nucleotides (long-patch BER). This experimental system should prove useful in the biochemical and genetic dissection of BER in plants, and contribute to provide a broader picture of the evolution and biological relevance of DNA repair pathways.
authors.affiliation: Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
authors.forename: Dolores
authors.initials: D
authors.lastname: Córdoba-Cañero
authors.forename: Teresa
authors.initials: T
authors.lastname: Morales-Ruiz
authors.forename: Teresa
authors.initials: T
authors.lastname: Roldán-Arjona
authors.forename: Rafael R
authors.initials: RR
authors.lastname: Ariza
mesh_terms: D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics*; D004249:DNA Damage; D045647:DNA Glycosylases / Q000235:genetics / Q000378:metabolism; D004260:DNA Repair; D018744:DNA, Plant / Q000096:biosynthesis*; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000235:genetics / Q000378:metabolism; D014498:Uracil / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D014498:Uracil; D045647:DNA Glycosylases; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase
references.citation: Plant Cell. 2002 Jan;14(1):263-73
references.pmid: 11826311
references.citation: DNA Repair (Amst). 2004 Jul 2;3(7):703-10
references.pmid: 15177179
references.citation: DNA Repair (Amst). 2008 Nov 1;7(11):1869-81
references.pmid: 18721906
references.citation: DNA Repair (Amst). 2005 Jul 12;4(7):760-72
references.pmid: 15964249
references.citation: Nucleic Acids Res. 1996 Sep 1;24(17):3307-12
references.pmid: 8811082
references.citation: J Biol Chem. 2002 Jun 28;277(26):23675-83
references.pmid: 11948185
references.citation: Proc Natl Acad Sci U S A. 2006 May 2;103(18):6853-8
references.pmid: 16624880
references.citation: Environ Mol Mutagen. 2005 Mar-Apr;45(2-3):115-27
references.pmid: 15645454
references.citation: Nucleic Acids Res. 2004 Sep 27;32(17):5119-25
references.pmid: 15452279
references.citation: Mol Genet Genomics. 2001 Aug;265(6):954-63
references.pmid: 11523787
references.citation: Mol Cell. 2004 Jul 23;15(2):209-20
references.pmid: 15260972
references.citation: Biochemistry. 2000 Feb 1;39(4):763-72
references.pmid: 10651642
references.citation: DNA Repair (Amst). 2007 Apr 1;6(4):398-409
references.pmid: 17129767
references.citation: J Biol Chem. 1991 Jun 5;266(16):10420-8
references.pmid: 1674744
references.citation: Plant Mol Biol. 2001 Dec;47(6):795-804
references.pmid: 11785940
references.citation: Chem Rev. 2003 Jul;103(7):2729-59
references.pmid: 12848584
references.citation: Biochimie. 2009 Feb;91(2):165-70
references.pmid: 18706967
references.citation: DNA Repair (Amst). 2002 Aug 6;1(8):579-600
references.pmid: 12509283
references.citation: Mutat Res. 2003 Oct 29;531(1-2):141-56
references.pmid: 14637251
references.citation: Biochemistry. 1997 Jun 17;36(24):7557-66
references.pmid: 9200707
references.citation: Mol Cell Biol. 1993 Feb;13(2):1051-8
references.pmid: 8423775
references.citation: J Biol Chem. 1998 Aug 14;273(33):21203-9
references.pmid: 9694877
references.citation: Nucleic Acids Res. 1990 Sep 11;18(17):5069-75
references.pmid: 1698278
references.citation: Mol Cell Biol. 1992 Apr;12(4):1605-12
references.pmid: 1549115
references.citation: DNA Repair (Amst). 2004 Jan 5;3(1):23-31
references.pmid: 14697756
references.citation: J Mol Biol. 2000 Aug 25;301(4):851-67
references.pmid: 10966791
references.citation: Plant Mol Biol. 2000 Sep;44(1):43-52
references.pmid: 11094978
references.citation: Nucleic Acids Res. 1999 Sep 15;27(18):3712-9
references.pmid: 10471741
references.citation: J Biol Chem. 2000 Feb 11;275(6):4460-6
references.pmid: 10660619
references.citation: J Biol Chem. 1999 Nov 19;274(47):33696-702
references.pmid: 10559260
references.citation: Mutat Res. 2009 Mar-Jun;681(2-3):169-179
references.pmid: 18707020
references.citation: Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):8016-20
references.pmid: 9223306
references.citation: Oncogene. 2002 Aug 8;21(34):5204-12
references.pmid: 12149642
references.citation: J Biol Chem. 2002 Apr 12;277(15):13184-91
references.pmid: 11821417
references.citation: Cell. 2006 Feb 10;124(3):495-506
references.pmid: 16469697
references.citation: Toxicology. 2003 Nov 15;193(1-2):35-41
references.pmid: 14599766
references.citation: New Phytol. 2005 Dec;168(3):511-28
references.pmid: 16313635
references.citation: DNA Repair (Amst). 2008 Apr 2;7(4):605-16
references.pmid: 18295553
references.citation: J Biol Chem. 2001 Nov 9;276(45):42588-600
references.pmid: 11551933
references.citation: Mol Cell. 2005 Aug 5;19(3):421-8
references.pmid: 16061187
references.citation: Eur J Biochem. 2004 Jul;271(13):2799-807
references.pmid: 15206945
references.citation: Plant J. 1998 Sep;15(5):635-45
references.pmid: 9778846
references.citation: J Biol Chem. 2005 May 6;280(18):18469-75
references.pmid: 15749700
references.citation: EMBO J. 1997 Jun 2;16(11):3341-8
references.pmid: 9214649
references.citation: J Biol Chem. 2009 Jun 19;284(25):17006-17012
references.pmid: 19372224
references.citation: Chem Rev. 2006 Feb;106(2):753-66
references.pmid: 16464023
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11796-801
references.pmid: 16864782
references.citation: Mol Gen Genet. 1998 Oct;259(6):577-90
references.pmid: 9819050
references.citation: Acta Biochim Pol. 2003;50(1):169-79
references.pmid: 12673357
references.citation: J Biol Chem. 1995 Jan 13;270(2):949-57
references.pmid: 7822335
references.citation: DNA Repair (Amst). 2007 Apr 1;6(4):505-16
references.pmid: 17116429
references.citation: Cancer Res. 2003 Feb 1;63(3):549-54
references.pmid: 12566294
references.citation: Genes Cells. 2002 Jul;7(7):639-51
references.pmid: 12081642
references.citation: J Biol Chem. 1999 May 21;274(21):15230-6
references.pmid: 10329732
references.citation: Trends Biochem Sci. 1995 Oct;20(10):405-11
references.pmid: 8533153
references.citation: Mol Cell Biol. 1989 Sep;9(9):3750-7
references.pmid: 2779565
references.citation: Biochem Biophys Res Commun. 2004 Jul 16;320(1):145-55
references.pmid: 15207714
references.citation: Mutat Res. 2005 Sep 4;577(1-2):24-54
references.pmid: 15939442
references.citation: Mol Cell Biol. 1991 Sep;11(9):4441-7
references.pmid: 1875931
references.citation: EMBO J. 1996 Dec 2;15(23):6662-70
references.pmid: 8978692
references.citation: J Biol Chem. 1998 Dec 11;273(50):33811-6
references.pmid: 9837971
references.citation: Biochem J. 2002 Jul 15;365(Pt 2):547-53
references.pmid: 11966472
references.citation: Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3299-303
references.pmid: 7512729
references.citation: DNA Repair (Amst). 2004 Jan 5;3(1):1-12
references.pmid: 14697754
references.citation: Plant J. 2002 Apr;30(2):203-12
references.pmid: 12000456
references.citation: Curr Biol. 1994 Dec 1;4(12):1069-76
references.pmid: 7535646
references.citation: Plant Mol Biol. 2008 Aug;67(6):671-81
references.pmid: 18493721
references.citation: Nature. 1993 Apr 22;362(6422):709-15
references.pmid: 8469282