title: A novel single-stranded DNA-specific 3'-5' exonuclease, Thermus thermophilus exonuclease I, is involved in several DNA repair pathways.
abstract: Single-stranded DNA (ssDNA)-specific exonucleases (ssExos) are expected to be involved in a variety of DNA repair pathways corresponding to their cleavage polarities; however, the relationship between the cleavage polarity and the respective DNA repair pathways is only partially understood. To understand the cellular function of ssExos in DNA repair better, genes encoding ssExos were disrupted in Thermus thermophilus HB8 that seems to have only a single set of 5'-3' and 3'-5' ssExos unlike other model organisms. Disruption of the tthb178 gene, which was expected to encode a 3'-5' ssExo, resulted in significant increase in the sensitivity to H(2)O(2) and frequency of the spontaneous mutation rate, but scarcely affected the sensitivity to ultraviolet (UV) irradiation. In contrast, disruption of the recJ gene, which encodes a 5'-3' ssExo, showed little effect on the sensitivity to H(2)O(2), but caused increased sensitivity to UV irradiation. In vitro characterization revealed that TTHB178 possessed 3'-5' ssExo activity that degraded ssDNAs containing deaminated and methylated bases, but not those containing oxidized bases or abasic sites. Consequently, we concluded that TTHB178 is a novel 3'-5' ssExo that functions in various DNA repair systems in cooperation with or independently of RecJ. We named TTHB178 as T. thermophilus exonuclease I.
authors.affiliation: Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043 and RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
authors.forename: Atsuhiro
authors.initials: A
authors.lastname: Shimada
authors.forename: Ryoji
authors.initials: R
authors.lastname: Masui
authors.forename: Noriko
authors.initials: N
authors.lastname: Nakagawa
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Takahata
authors.forename: Kwang
authors.initials: K
authors.lastname: Kim
authors.forename: Seiki
authors.initials: S
authors.lastname: Kuramitsu
authors.forename: Kenji
authors.initials: K
authors.lastname: Fukui
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004260:DNA Repair; D004277:DNA, Single-Stranded / Q000378:metabolism*; D005090:Exodeoxyribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D009154:Mutation; D010641:Phenotype; D017386:Sequence Homology, Amino Acid; D016963:Thermus thermophilus / Q000201:enzymology*
chemical_list: D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D004247:DNA; D005090:Exodeoxyribonucleases; C070765:recJ protein, Bacteria; C028450:exodeoxyribonuclease I
references.citation: Nucleic Acids Res. 2009 Apr;37(7):2411-7
references.pmid: 19321497
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):5110-8
references.pmid: 9396823
references.citation: J Bacteriol. 2005 Feb;187(4):1350-6
references.pmid: 15687199
references.citation: Mutat Res. 1986 Jan;165(1):1-7
references.pmid: 3001515
references.citation: Nature. 2003 Jun 19;423(6942):893-7
references.pmid: 12815438
references.citation: Trends Biochem Sci. 1995 Oct;20(10):391-7
references.pmid: 8533150
references.citation: Nat Struct Mol Biol. 2009 Feb;16(2):138-43
references.pmid: 19136958
references.citation: Nucleic Acids Res. 1988 Oct 25;16(20):9631-9
references.pmid: 3054810
references.citation: J Bacteriol. 1998 May;180(10):2779-81
references.pmid: 9573169
references.citation: J Biol Chem. 2006 Oct 13;281(41):30305-9
references.pmid: 16905530
references.citation: J Bacteriol. 2007 May;189(10):3891-901
references.pmid: 17369302
references.citation: Extremophiles. 2008 Mar;12(2):217-23
references.pmid: 17989916
references.citation: Nucleic Acids Res. 2003 Jul 15;31(14):3893-900
references.pmid: 12853604
references.citation: Methods Enzymol. 2008;440:3-15
references.pmid: 18423208
references.citation: J Mol Biol. 2009 Feb 6;385(5):1375-96
references.pmid: 19094995
references.citation: Cell. 2006 Jul 28;126(2):297-308
references.pmid: 16873062
references.citation: J Biol Chem. 2008 Aug 1;283(31):21441-52
references.pmid: 18534978
references.citation: Cell. 2009 Feb 20;136(4):615-28
references.pmid: 19239884
references.citation: J Bacteriol. 1975 Feb;121(2):511-7
references.pmid: 1089633
references.citation: Cancer Res. 2001 Jan 1;61(1):23-6
references.pmid: 11196167
references.citation: Photochem Photobiol. 1983 Jul;38(1):51-5
references.pmid: 6622552
references.citation: Nat Struct Biol. 2000 Dec;7(12):1125-8
references.pmid: 11101894
references.citation: DNA Repair (Amst). 2006 Aug 13;5(8):894-903
references.pmid: 16781198
references.citation: J Biol Chem. 2009 Jun 5;284(23):15549-56
references.pmid: 19346251
references.citation: Annu Rev Biochem. 2005;74:681-710
references.pmid: 15952900
references.citation: J Biol Chem. 1999 Oct 15;274(42):30094-100
references.pmid: 10514496
references.citation: Mol Microbiol. 2005 Feb;55(3):853-61
references.pmid: 15661009
references.citation: Mutat Res. 2000 Feb 16;459(1):43-53
references.pmid: 10677682
references.citation: J Biol Chem. 2007 Dec 21;282(51):37181-90
references.pmid: 17951253
references.citation: Nucleic Acids Res. 2006 Feb 18;34(4):1084-91
references.pmid: 16488881
references.citation: Nat Genet. 2007 Sep;39(9):1065-7
references.pmid: 17660818
references.citation: Nat Genet. 2006 Aug;38(8):917-20
references.pmid: 16845398
references.citation: J Biol Chem. 1960 May;235:1479-87
references.pmid: 14415352
references.citation: Nat Rev Microbiol. 2008 Mar;6(3):181-6
references.pmid: 18157154
references.citation: Nucleic Acids Res. 2001 Nov 15;29(22):4617-24
references.pmid: 11713311
references.citation: Genetics. 1943 Nov;28(6):491-511
references.pmid: 17247100
references.citation: J Supramol Struct Cell Biochem. 1981;16(4):337-43
references.pmid: 6273595
references.citation: J Virol. 1989 Nov;63(11):4520-4
references.pmid: 2552137
references.citation: Nature. 2000 Oct 12;407(6805):703-10
references.pmid: 11048710
references.citation: Nucleic Acids Res. 1992 Sep 25;20(18):4699-703
references.pmid: 1329027
references.citation: Radiat Res. 1996 May;145(5):619-23
references.pmid: 8619028
references.citation: Cell. 1989 Oct 6;59(1):219-28
references.pmid: 2790959
references.citation: DNA Repair (Amst). 2003 Nov 21;2(11):1175-83
references.pmid: 14599740
references.citation: Nucleic Acids Res. 1998 Sep 15;26(18):4153-9
references.pmid: 9722634
references.citation: J Biol Chem. 2001 Aug 17;276(33):31053-8
references.pmid: 11418610
references.citation: J Biol Chem. 1989 Apr 15;264(11):6364-70
references.pmid: 2539380
references.citation: J Biol Chem. 2005 Apr 15;280(15):15212-8
references.pmid: 15661738
references.citation: Free Radic Res. 2002 Jan;36(1):13-21
references.pmid: 11999699
references.citation: Nucleic Acids Res. 1994 Jan 25;22(2):247-50
references.pmid: 8121810
references.citation: Nucleic Acids Res. 2007;35(15):e100
references.pmid: 17686785
references.citation: Nature. 1987 Jun 4-10;327(6121):389-94
references.pmid: 2953976
references.citation: J Am Soc Mass Spectrom. 1992 Jan;3(1):60-70
references.pmid: 24242838
references.citation: J Biochem. 2008 Aug;144(2):267-77
references.pmid: 18483064
references.citation: J Biochem. 1999 Nov;126(5):951-6
references.pmid: 10544290
references.citation: Acta Crystallogr D Biol Crystallogr. 2008 Feb;64(Pt 2):206-10
references.pmid: 18219121
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8196-202
references.pmid: 11459953
references.citation: J Mol Biol. 2010 Jan 15;395(2):270-81
references.pmid: 19891975
references.citation: Mol Cell. 2001 Dec;8(6):1163-74
references.pmid: 11779493
references.citation: Chem Rev. 2006 Feb;106(2):233-52
references.pmid: 16464004
references.citation: Nat Struct Biol. 2000 Nov;7 Suppl:943-5
references.pmid: 11103994
references.citation: J Biochem. 2004 Mar;135(3):375-84
references.pmid: 15113836
references.citation: J Biol Chem. 2007 Apr 6;282(14):10537-43
references.pmid: 17293595
references.citation: J Biol Chem. 1964 Aug;239:2628-36
references.pmid: 14235546
references.citation: FEBS Lett. 2001 Oct 12;506(3):231-4
references.pmid: 11602251
references.citation: Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6765-70
references.pmid: 11381137
references.citation: Biochemistry. 1992 Nov 17;31(45):10964-8
references.pmid: 1445834
references.citation: Mutat Res. 2001 Jan 5;461(4):301-9
references.pmid: 11104906
references.citation: J Biol Chem. 2008 May 2;283(18):12136-45
references.pmid: 18310077
references.citation: J Bacteriol. 2006 Feb;188(3):829-33
references.pmid: 16428385
references.citation: Anal Biochem. 2007 Mar 15;362(2):201-12
references.pmid: 17257573