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Comment on "A commensal strain of Staphylococcus epidermidis protects against skin neoplasia" by Nakatsuji et al.

Kozmin SG, Rogozin IB, Moore EA, Abney M, Schaaper RM, Pavlov YI.

Sci Adv. 2019 Sep 11;5(9):eaaw3915. doi: 10.1126/sciadv.aaw3915. eCollection 2019 Sep.


Replication fidelity in E. coli: Differential leading and lagging strand effects for dnaE antimutator alleles.

Makiela-Dzbenska K, Maslowska KH, Kuban W, Gawel D, Jonczyk P, Schaaper RM, Fijalkowska IJ.

DNA Repair (Amst). 2019 Nov;83:102643. doi: 10.1016/j.dnarep.2019.102643. Epub 2019 Jul 4.


High-accuracy lagging-strand DNA replication mediated by DNA polymerase dissociation.

Maslowska KH, Makiela-Dzbenska K, Mo JY, Fijalkowska IJ, Schaaper RM.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4212-4217. doi: 10.1073/pnas.1720353115. Epub 2018 Apr 2.


Suppressors of dGTP Starvation in Escherichia coli.

Itsko M, Schaaper RM.

J Bacteriol. 2017 May 25;199(12). pii: e00142-17. doi: 10.1128/JB.00142-17. Print 2017 Jun 15.


Insufficient levels of the nrdAB-encoded ribonucleotide reductase underlie the severe growth defect of the Δhda E. coli strain.

Babu VMP, Itsko M, Baxter JC, Schaaper RM, Sutton MD.

Mol Microbiol. 2017 May;104(3):377-399. doi: 10.1111/mmi.13632. Epub 2017 Mar 13.


Transcriptome Analysis of Escherichia coli during dGTP Starvation.

Itsko M, Schaaper RM.

J Bacteriol. 2016 May 13;198(11):1631-44. doi: 10.1128/JB.00218-16. Print 2016 Jun 1.


Extreme dNTP pool changes and hypermutability in dcd ndk strains.

Tse L, Kang TM, Yuan J, Mihora D, Becket E, Maslowska KH, Schaaper RM, Miller JH.

Mutat Res. 2016 Feb-Mar;784-785:16-24. doi: 10.1016/j.mrfmmm.2015.12.004. Epub 2015 Dec 29.


A continuous spectrophotometric enzyme-coupled assay for deoxynucleoside triphosphate triphosphohydrolases.

Singh D, Schaaper RM, Hochkoeppler A.

Anal Biochem. 2016 Mar 1;496:43-9. doi: 10.1016/j.ab.2015.11.027. Epub 2015 Dec 23.


Suppression of the E. coli SOS response by dNTP pool changes.

Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ, Schaaper RM.

Nucleic Acids Res. 2015 Apr 30;43(8):4109-20. doi: 10.1093/nar/gkv217. Epub 2015 Mar 30.


Mutagenesis in the lacI gene target of E. coli: improved analysis for lacI(d) and lacO mutants.

Swerdlow SJ, Schaaper RM.

Mutat Res. 2014 Dec;770:79-84. doi: 10.1016/j.mrfmmm.2014.09.004. Epub 2014 Sep 27.


Structure of Escherichia coli dGTP triphosphohydrolase: a hexameric enzyme with DNA effector molecules.

Singh D, Gawel D, Itsko M, Hochkoeppler A, Krahn JM, London RE, Schaaper RM.

J Biol Chem. 2015 Apr 17;290(16):10418-29. doi: 10.1074/jbc.M115.636936. Epub 2015 Feb 18.


dGTP starvation in Escherichia coli provides new insights into the thymineless-death phenomenon.

Itsko M, Schaaper RM.

PLoS Genet. 2014 May 8;10(5):e1004310. doi: 10.1371/journal.pgen.1004310. eCollection 2014 May.


Effect of dNTP pool alterations on fidelity of leading and lagging strand DNA replication in E. coli.

Gawel D, Fijalkowska IJ, Jonczyk P, Schaaper RM.

Mutat Res. 2014 Jan;759:22-8. doi: 10.1016/j.mrfmmm.2013.11.003. Epub 2013 Nov 22.


A critical role for the putative NCS2 nucleobase permease YjcD in the sensitivity of Escherichia coli to cytotoxic and mutagenic purine analogs.

Kozmin SG, Stepchenkova EI, Chow SC, Schaaper RM.

MBio. 2013 Oct 29;4(6):e00661-13. doi: 10.1128/mBio.00661-13.


Hypermutability and error catastrophe due to defects in ribonucleotide reductase.

Ahluwalia D, Schaaper RM.

Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18596-601. doi: 10.1073/pnas.1310849110. Epub 2013 Oct 28.


TusA (YhhP) and IscS are required for molybdenum cofactor-dependent base-analog detoxification.

Kozmin SG, Stepchenkova EI, Schaaper RM.

Microbiologyopen. 2013 Oct;2(5):743-55. doi: 10.1002/mbo3.108. Epub 2013 Jul 29.


Genetic characterization of moaB mutants of Escherichia coli.

Kozmin SG, Schaaper RM.

Res Microbiol. 2013 Sep;164(7):689-94. doi: 10.1016/j.resmic.2013.05.001. Epub 2013 May 13.


Distinct pathways for repairing mutagenic lesions induced by methylating and ethylating agents.

Taira K, Kaneto S, Nakano K, Watanabe S, Takahashi E, Arimoto S, Okamoto K, Schaaper RM, Negishi K, Negishi T.

Mutagenesis. 2013 May;28(3):341-50. doi: 10.1093/mutage/get010. Epub 2013 Feb 27.


Mutational consequences of dNTP pool imbalances in E. coli.

Schaaper RM, Mathews CK.

DNA Repair (Amst). 2013 Jan 1;12(1):73-9. doi: 10.1016/j.dnarep.2012.10.011. Epub 2012 Dec 6.


Stabilization of the Escherichia coli DNA polymerase III ε subunit by the θ subunit favors in vivo assembly of the Pol III catalytic core.

Conte E, Vincelli G, Schaaper RM, Bressanin D, Stefan A, Dal Piaz F, Hochkoeppler A.

Arch Biochem Biophys. 2012 Jul 15;523(2):135-43. doi: 10.1016/ Epub 2012 Apr 22.


Novel mutator mutants of E. coli nrdAB ribonucleotide reductase: insight into allosteric regulation and control of mutation rates.

Ahluwalia D, Bienstock RJ, Schaaper RM.

DNA Repair (Amst). 2012 May 1;11(5):480-7. doi: 10.1016/j.dnarep.2012.02.001. Epub 2012 Mar 13.


DNA replication fidelity in Escherichia coli: a multi-DNA polymerase affair.

Fijalkowska IJ, Schaaper RM, Jonczyk P.

FEMS Microbiol Rev. 2012 Nov;36(6):1105-21. doi: 10.1111/j.1574-6976.2012.00338.x. Epub 2012 Apr 5. Review.


The dgt gene of Escherichia coli facilitates thymine utilization in thymine-requiring strains.

Itsko M, Schaaper RM.

Mol Microbiol. 2011 Sep;81(5):1221-32. doi: 10.1111/j.1365-2958.2011.07756.x. Epub 2011 Jul 12.


Proofreading deficiency of Pol I increases the levels of spontaneous rpoB mutations in E. coli.

Makiela-Dzbenska K, Jonczyk P, Schaaper RM, Fijalkowska IJ.

Mutat Res. 2011 Jul 1;712(1-2):28-32. doi: 10.1016/j.mrfmmm.2011.03.011. Epub 2011 Apr 1.


dnaX36 Mutator of Escherichia coli: effects of the {tau} subunit of the DNA polymerase III holoenzyme on chromosomal DNA replication fidelity.

Gawel D, Jonczyk P, Fijalkowska IJ, Schaaper RM.

J Bacteriol. 2011 Jan;193(1):296-300. doi: 10.1128/JB.01191-10. Epub 2010 Oct 29.


Role for CysJ flavin reductase in molybdenum cofactor-dependent resistance of Escherichia coli to 6-N-hydroxylaminopurine.

Kozmin SG, Wang J, Schaaper RM.

J Bacteriol. 2010 Apr;192(8):2026-33. doi: 10.1128/JB.01438-09. Epub 2010 Jan 29.


Role of Escherichia coli DNA polymerase I in chromosomal DNA replication fidelity.

Makiela-Dzbenska K, Jaszczur M, Banach-Orlowska M, Jonczyk P, Schaaper RM, Fijalkowska IJ.

Mol Microbiol. 2009 Dec;74(5):1114-27. doi: 10.1111/j.1365-2958.2009.06921.x. Epub 2009 Oct 19.


Iminohydantoin lesion induced in DNA by peracids and other epoxidizing oxidants.

Ye W, Sangaiah R, Degen DE, Gold A, Jayaraj K, Koshlap KM, Boysen G, Williams J, Tomer KB, Mocanu V, Dicheva N, Parker CE, Schaaper RM, Ball LM.

J Am Chem Soc. 2009 May 6;131(17):6114-23. doi: 10.1021/ja8090752.


Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues.

Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA.

J Am Chem Soc. 2009 Feb 4;131(4):1550-6. doi: 10.1021/ja8082818.


A novel mutator of Escherichia coli carrying a defect in the dgt gene, encoding a dGTP triphosphohydrolase.

Gawel D, Hamilton MD, Schaaper RM.

J Bacteriol. 2008 Nov;190(21):6931-9. doi: 10.1128/JB.00935-08. Epub 2008 Sep 5.


YcbX and yiiM, two novel determinants for resistance of Escherichia coli to N-hydroxylated base analogues.

Kozmin SG, Leroy P, Pavlov YI, Schaaper RM.

Mol Microbiol. 2008 Apr;68(1):51-65. doi: 10.1111/j.1365-2958.2008.06128.x. Epub 2008 Feb 26.


Binding of MutS protein to oligonucleotides containing a methylated or an ethylated guanine residue, and correlation with mutation frequency.

Taira K, Nakamura S, Nakano K, Maehara D, Okamoto K, Arimoto S, Loakes D, Worth L Jr, Schaaper RM, Seio K, Sekine M, Negishi K, Negishi T.

Mutat Res. 2008 Apr 2;640(1-2):107-12. doi: 10.1016/j.mrfmmm.2007.12.009. Epub 2007 Dec 28.


Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant.

Gawel D, Pham PT, Fijalkowska IJ, Jonczyk P, Schaaper RM.

J Bacteriol. 2008 Mar;190(5):1730-42. Epub 2007 Dec 21.


Enhanced mutagenesis of Salmonella tester strains due to deletion of genes other than uvrB.

Swartz CD, Parks N, Umbach DM, Ward WO, Schaaper RM, DeMarini DM.

Environ Mol Mutagen. 2007 Oct;48(8):694-705.


Specialized mismatch repair function of Glu339 in the Phe-X-Glu motif of yeast Msh6.

Holmes SF, Scarpinato KD, McCulloch SD, Schaaper RM, Kunkel TA.

DNA Repair (Amst). 2007 Mar 1;6(3):293-303. Epub 2006 Dec 1.


Inhibition of spontaneous mutagenesis by vanillin and cinnamaldehyde in Escherichia coli: Dependence on recombinational repair.

Shaughnessy DT, Schaaper RM, Umbach DM, DeMarini DM.

Mutat Res. 2006 Dec 1;602(1-2):54-64. Epub 2006 Sep 26.


Role of DNA polymerase IV in Escherichia coli SOS mutator activity.

Kuban W, Banach-Orlowska M, Schaaper RM, Jonczyk P, Fijalkowska IJ.

J Bacteriol. 2006 Nov;188(22):7977-80. Epub 2006 Sep 15.


Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex.

Kirby TW, Harvey S, DeRose EF, Chalov S, Chikova AK, Perrino FW, Schaaper RM, London RE, Pedersen LC.

J Biol Chem. 2006 Dec 15;281(50):38466-71. Epub 2006 Sep 13.


Mutator and antimutator effects of the bacteriophage P1 hot gene product.

Chikova AK, Schaaper RM.

J Bacteriol. 2006 Aug;188(16):5831-8.


Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III tau subunit.

Pham PT, Zhao W, Schaaper RM.

Mol Microbiol. 2006 Feb;59(4):1149-61.


Nuclear magnetic resonance solution structure of the Escherichia coli DNA polymerase III theta subunit.

Mueller GA, Kirby TW, DeRose EF, Li D, Schaaper RM, London RE.

J Bacteriol. 2005 Oct;187(20):7081-9.


Mutator phenotype resulting from DNA polymerase IV overproduction in Escherichia coli: preferential mutagenesis on the lagging strand.

Kuban W, Banach-Orlowska M, Bialoskorska M, Lipowska A, Schaaper RM, Jonczyk P, Fijalkowska IJ.

J Bacteriol. 2005 Oct;187(19):6862-6.


DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli.

Banach-Orlowska M, Fijalkowska IJ, Schaaper RM, Jonczyk P.

Mol Microbiol. 2005 Oct;58(1):61-70.


Phage like it HOT: solution structure of the bacteriophage P1-encoded HOT protein, a homolog of the theta subunit of E. coli DNA polymerase III.

Derose EF, Kirby TW, Mueller GA, Chikova AK, Schaaper RM, London RE.

Structure. 2004 Dec;12(12):2221-31.


Role of Escherichia coli DNA polymerase IV in in vivo replication fidelity.

Kuban W, Jonczyk P, Gawel D, Malanowska K, Schaaper RM, Fijalkowska IJ.

J Bacteriol. 2004 Jul;186(14):4802-7.


Binding specificities of the mismatch binding protein, MutS, to oligonucleotides containing modified bases.

Negishi K, Maehara D, Nakamura S, Loakes D, Worth L Jr, Schaaper RM, Seio K, Sekine M, Negishi T.

Nucleic Acids Res Suppl. 2001;(1):221-2.


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