title: Human polymerase kappa uses a template-slippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions.
abstract: Polymerases belonging to the DinB class of the Y-family translesion synthesis DNA polymerases have a preference for accurately and efficiently bypassing damaged guanosines. These DinB polymerases also generate single-base (-1) deletions at high frequencies with most occurring on repetitive 'deletion hotspot' sequences. Human DNA polymerase kappa (hPolκ), the eukaryotic DinB homologue, displays an unusual efficiency for to extend from mispaired primer termini, either by extending directly from the mispair or by primer-template misalignment. This latter property explains how hPolκ creates single-base deletions in non-repetitive sequences, but does not address how deletions occur in repetitive deletion hotspots. Here, we show that hPolκ uses a classical Streisinger template-slippage mechanism to generate -1 deletions in repetitive sequences, as do the bacterial and archaeal homologues. After the first nucleotide is added by template slippage, however, hPolκ can efficiently realign the primer-template duplex before continuing DNA synthesis. Strand realignment results in a base-substitution mutation, minimizing generation of more deleterious frameshift mutations. On non-repetitive sequences, we find that nucleotide misincorporation is slower if the incoming nucleotide can correctly basepair with the nucleotide immediately 5' to the templating base, thereby competing against the mispairing with the templating base.
authors.affiliation: Wadsworth Center, New York State Department of Health, University at Albany, School of Public Health, Albany, NY 12201-0509, USA.
authors.forename: Purba
authors.initials: P
authors.lastname: Mukherjee
authors.forename: Indrajit
authors.initials: I
authors.lastname: Lahiri
authors.forename: Janice D
authors.initials: JD
authors.lastname: Pata
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000096:biosynthesis* / Q000737:chemistry; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D003845:Deoxycytosine Nucleotides / Q000378:metabolism; D006801:Humans; D009154:Mutation; D009711:Nucleotides / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D013698:Templates, Genetic; D000099270:Y-Family DNA Polymerases
chemical_list: D004247:DNA; D004259:DNA-Directed DNA Polymerase; D003845:Deoxycytosine Nucleotides; D009711:Nucleotides; C024107:2'-deoxycytidine 5'-triphosphate; C404302:POLK protein, human; D000099270:Y-Family DNA Polymerases
references.citation: J Biol Chem. 2010 Jul 23;285(30):23086-95
references.pmid: 20467052
references.citation: J Biol Chem. 2002 Aug 2;277(31):28157-66
references.pmid: 12023283
references.citation: Nat Rev Mol Cell Biol. 2012 Feb 23;13(3):141-52
references.pmid: 22358330
references.citation: Mol Cell. 2007 Feb 23;25(4):601-14
references.pmid: 17317631
references.citation: J Biol Chem. 1997 Jan 24;272(4):2559-69
references.pmid: 8999973
references.citation: Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1910-4
references.pmid: 11842189
references.citation: J Biol Chem. 2000 Dec 15;275(50):39678-84
references.pmid: 11006276
references.citation: Biochemistry. 2004 Feb 24;43(7):2106-15
references.pmid: 14967050
references.citation: Nature. 2006 Jan 12;439(7073):225-8
references.pmid: 16407906
references.citation: Structure. 2013 Jan 8;21(1):20-31
references.pmid: 23245850
references.citation: J Bacteriol. 2011 May;193(10):2630-6
references.pmid: 21421759
references.citation: Genes Dev. 2003 Sep 1;17(17):2191-9
references.pmid: 12952891
references.citation: Chem Res Toxicol. 2008 Oct;21(10):1983-90
references.pmid: 18788757
references.citation: Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13792-7
references.pmid: 9391106
references.citation: J Biol Chem. 2008 Oct 10;283(41):27433-27437
references.pmid: 18697749
references.citation: Cold Spring Harb Symp Quant Biol. 1966;31:77-84
references.pmid: 5237214
references.citation: PLoS One. 2009 Jun 02;4(6):e5766
references.pmid: 19492058
references.citation: J Biol Chem. 2002 Feb 15;277(7):5265-74
references.pmid: 11734560
references.citation: Mol Cell. 2008 Mar 28;29(6):767-79
references.pmid: 18374650
references.citation: Cell. 2001 Oct 5;107(1):91-102
references.pmid: 11595188
references.citation: Proc Natl Acad Sci U S A. 1990 Jul;87(13):4946-50
references.pmid: 2195542
references.citation: J Biol Chem. 1988 Oct 15;263(29):14784-9
references.pmid: 3049589
references.citation: J Biol Chem. 2004 Jul 30;279(31):32932-40
references.pmid: 15155753
references.citation: Trends Biochem Sci. 2006 Apr;31(4):206-14
references.pmid: 16545956
references.citation: J Biol Chem. 1997 Oct 31;272(44):27919-30
references.pmid: 9346941
references.citation: Mol Cell. 2001 Jul;8(1):7-8
references.pmid: 11515498
references.citation: J Bacteriol. 2011 May;193(10):2637-41
references.pmid: 21421753
references.citation: J Biol Chem. 2002 May 31;277(22):19633-8
references.pmid: 11919199
references.citation: Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3838-43
references.pmid: 10760255
references.citation: DNA Repair (Amst). 2006 Apr 8;5(4):515-22
references.pmid: 16483853
references.citation: J Biol Chem. 1986 Oct 15;261(29):13581-7
references.pmid: 3759982
references.citation: Structure. 2004 Aug;12(8):1395-404
references.pmid: 15296733
references.citation: Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15776-81
references.pmid: 17043239
references.citation: Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15548-53
references.pmid: 12432099
references.citation: Biochemistry. 2007 Sep 25;46(38):10790-803
references.pmid: 17725324