title: Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli.
abstract: The rate of cytosine deamination is much higher in single-stranded DNA (ssDNA) than in double-stranded DNA, and copying the resulting uracils causes C to T mutations. To study this phenomenon, the catalytic domain of APOBEC3G (A3G-CTD), an ssDNA-specific cytosine deaminase, was expressed in an Escherichia coli strain defective in uracil repair (ung mutant), and the mutations that accumulated over thousands of generations were determined by whole-genome sequencing. C:G to T:A transitions dominated, with significantly more cytosines mutated to thymine in the lagging-strand template (LGST) than in the leading-strand template (LDST). This strand bias was present in both repair-defective and repair-proficient cells and was strongest and highly significant in cells expressing A3G-CTD. These results show that the LGST is accessible to cellular cytosine deaminating agents, explains the well-known GC skew in microbial genomes, and suggests the APOBEC3 family of mutators may target the LGST in the human genome.
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, MI 48202; Department of Immunology and Microbiology, Wayne State University School of Medicine, Detroit, MI 48201; axb@chem.wayne.edu.
authors.forename: Ashok S
authors.initials: AS
authors.lastname: Bhagwat
authors.affiliation: Department of Biological Sciences, Wayne State University, Detroit, MI 48202;
authors.forename: Weilong
authors.initials: W
authors.lastname: Hao
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405;
authors.forename: Jesse P
authors.initials: JP
authors.lastname: Townes
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47405.
authors.forename: Heewook
authors.initials: H
authors.lastname: Lee
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47405.
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405;
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Foster
mesh_terms: D000071480:APOBEC-3G Deaminase; D001483:Base Sequence; D003564:Cytidine Deaminase / Q000235:genetics / Q000378:metabolism; D003596:Cytosine / Q000378:metabolism; D004247:DNA / Q000235:genetics / Q000378:metabolism; D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000235:genetics / Q000378:metabolism; D003641:Deamination; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial; D006801:Humans; D009154:Mutation; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D013941:Thymine / Q000378:metabolism; D014498:Uracil / Q000378:metabolism; D051981:Uracil-DNA Glycosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D029968:Escherichia coli Proteins; D011994:Recombinant Proteins; D014498:Uracil; D003596:Cytosine; D004247:DNA; D051981:Uracil-DNA Glycosidase; D000071480:APOBEC-3G Deaminase; C464924:APOBEC3G protein, human; D003564:Cytidine Deaminase; D013941:Thymine
keywords: APOBEC3A; APOBEC3B; cancer genome mutations; kataegis; uracil-DNA glycosylase
references.citation: Microbiology. 2004 Jun;150(Pt 6):1609-27
references.pmid: 15184548
references.citation: PLoS Genet. 2013;9(9):e1003736
references.pmid: 24039593
references.citation: J Mol Biol. 1975 Nov 15;98(4):811-25
references.pmid: 172646
references.citation: Nat Rev Cancer. 2014 Dec;14(12):786-800
references.pmid: 25568919
references.citation: PLoS Genet. 2015 May;11(5):e1005217
references.pmid: 25941824
references.citation: Cancer Discov. 2015 Jul;5(7):704-12
references.pmid: 26091828
references.citation: Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5990-9
references.pmid: 26460006
references.citation: Cell. 2016 Jan 28;164(3):538-49
references.pmid: 26806129
references.citation: Cell Rep. 2016 Feb 16;14(6):1273-82
references.pmid: 26832400
references.citation: Prog Nucleic Acid Res Mol Biol. 1976;16:75-124
references.pmid: 2948
references.citation: J Bacteriol. 1978 Jun;134(3):1039-45
references.pmid: 350837
references.citation: J Bacteriol. 1982 Aug;151(2):750-5
references.pmid: 7047496
references.citation: Annu Rev Biochem. 1982;51:61-87
references.pmid: 6287922
references.citation: Proc Natl Acad Sci U S A. 1989 Apr;86(7):2172-5
references.pmid: 2648393
references.citation: Biochemistry. 1990 Mar 13;29(10):2532-7
references.pmid: 2185829
references.citation: Nucleic Acids Res. 1990 Apr 25;18(8):2153-7
references.pmid: 2186377
references.citation: Proc Natl Acad Sci U S A. 1990 Jun;87(12):4645-9
references.pmid: 2162051
references.citation: Nature. 2002 Jul 4;418(6893):99-103
references.pmid: 12097915
references.citation: Mol Cell. 2002 Nov;10(5):1247-53
references.pmid: 12453430
references.citation: Science. 2003 May 16;300(5622):1112
references.pmid: 12750511
references.citation: Cell. 2003 Jun 13;113(6):803-9
references.pmid: 12809610
references.citation: J Bacteriol. 1990 Aug;172(8):4719-20
references.pmid: 2115878
references.citation: Genetica. 1992;85(2):173-9
references.pmid: 1624139
references.citation: J Mol Biol. 1992 Sep 5;227(1):54-71
references.pmid: 1522601
references.citation: Nucleic Acids Res. 1994 Mar 25;22(6):972-6
references.pmid: 8152929
references.citation: Mol Biol Evol. 1996 May;13(5):660-5
references.pmid: 8676740
references.citation: Cancer Surv. 1996;28:21-31
references.pmid: 8977026
references.citation: Trends Genet. 1997 Jun;13(6):240-5
references.pmid: 9196330
references.citation: Mutat Res. 1999 Jul;437(1):11-20
references.pmid: 10425387
references.citation: Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):8919-24
references.pmid: 10430871
references.citation: Trends Microbiol. 1999 Aug;7(8):305-8
references.pmid: 10431198
references.citation: Annu Rev Biochem. 2005;74:317-53
references.pmid: 15952890
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W389-92
references.pmid: 15980495
references.citation: BMC Immunol. 2005;6:10
references.pmid: 15949042
references.citation: Mol Immunol. 2006 Mar;43(9):1481-4
references.pmid: 16219354
references.citation: Mol Syst Biol. 2006;2:2006.0008
references.pmid: 16738554
references.citation: Methods Enzymol. 2006;409:195-213
references.pmid: 16793403
references.citation: Mol Cell. 2006 Jul 21;23(2):155-60
references.pmid: 16857582
references.citation: Adv Immunol. 2007;94:37-73
references.pmid: 17560271
references.citation: Annu Rev Immunol. 2008;26:317-53
references.pmid: 18304004
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10197-202
references.pmid: 18621712
references.citation: Bioinformatics. 2009 Jun 15;25(12):1564-5
references.pmid: 19369502
references.citation: DNA Repair (Amst). 2010 May 4;9(5):579-87
references.pmid: 20338830
references.citation: J Biol Chem. 1999 Nov 5;274(45):31763-6
references.pmid: 10542196
references.citation: Gene. 1999 Sep 30;238(1):65-77
references.pmid: 10570985
references.citation: Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6640-5
references.pmid: 10829079
references.citation: EMBO J. 2000 Jun 15;19(12):3100-9
references.pmid: 10856253
references.citation: Nat Struct Biol. 2000 Aug;7(8):648-52
references.pmid: 10932248
references.citation: EMBO J. 2002 Apr 2;21(7):1855-63
references.pmid: 11927569
references.citation: Nature. 2003 Jul 3;424(6944):94-8
references.pmid: 12808465
references.citation: J Mol Biol. 2004 Mar 26;337(3):585-96
references.pmid: 15019779
references.citation: Cell. 2012 May 25;149(5):979-93
references.pmid: 22608084
references.citation: Mol Cell. 2012 May 25;46(4):424-35
references.pmid: 22607975
references.citation: Chem Rev. 2012 Jun 13;112(6):3427-81
references.pmid: 22372839
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):E2774-83
references.pmid: 22991466
references.citation: PLoS Genet. 2012;8(12):e1003149
references.pmid: 23271983
references.citation: G3 (Bethesda). 2013 Mar;3(3):399-407
references.pmid: 23450823
references.citation: Elife. 2013;2:e00534
references.pmid: 23599896
references.citation: Nature. 2013 Aug 22;500(7463):415-21
references.pmid: 23945592
references.citation: Biochemistry. 1974 Jul 30;13(16):3405-10
references.pmid: 4601435