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Mechanisms of Mutation Group
Klemm BP, Singh D, Smith CE, Hsu AL, Dillard LB, Krahn JM, London RE, Mueller GA, Borgnia MJ, Schaaper RM. Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase. Proc Natl Acad Sci U S A . 2022;119(37):e2123092119. doi:10.1073/pnas.2123092119 [ Abstract Klemm BP, Singh D, Smith CE, Hsu AL, Dillard LB, Krahn JM, London RE, Mueller GA, Borgnia MJ, Schaaper RM. Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase. Proc Natl Acad Sci U S A. 2022;119(37):e2123092119. doi:10.1073/pnas.2123092119 ] Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM. High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP. J Biol Chem . 2022;298(7):102073. doi:10.1016/j.jbc.2022.102073 [ Abstract Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM. High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP. J Biol Chem. 2022;298(7):102073. doi:10.1016/j.jbc.2022.102073 ] Bhawsinghka N, Glenn KF, Schaaper RM. 2020. Complete Genome Sequence of Escherichia coli BL21-AI. Microbiol Resour Announc ; doi: 10.1128/MRA.00009-20 [Online 5 March 2020]. [ Abstract Bhawsinghka N, Glenn KF, Schaaper RM. 2020. Complete Genome Sequence of Escherichia coli BL21-AI. Microbiol Resour Announc; doi: 10.1128/MRA.00009-20 [Online 5 March 2020]. ] Kozmin SG, Rogozin IB, Moore EA, Abney M, Schaaper RM, Pavlov YI. Comment on "A commensal strain of Staphylococcus epidermidis protects against skin neoplasia" by Nakatsuji et al . Science Advances 2019 5(9):eaaw3915. [ Abstract Kozmin SG, Rogozin IB, Moore EA, Abney M, Schaaper RM, Pavlov YI. Comment on "A commensal strain of Staphylococcus epidermidis protects against skin neoplasia" by Nakatsuji et al. Science Advances 2019 5(9):eaaw3915. ] Makiela-Dzbenska K, Maslowska KH, Kuban W, Gawel D, Joncyzk P, Schaaper RM, Fijalkowska IJ. Replication fidelity in E. coli: Differential leading and lagging strand effects for dnaE antimutator alleles. DNA Repair 2019 ():-. [ Abstract Makiela-Dzbenska K, Maslowska KH, Kuban W, Gawel D, Joncyzk P, Schaaper RM, Fijalkowska IJ. Replication fidelity in E. coli: Differential leading and lagging strand effects for dnaE antimutator alleles. DNA Repair 2019 ():-. ] Babu VMP, Itsko I, Baxter JC , Schaaper RM, Sutton MD. Insufficient levels of the nrdAB-encoded ribonucleotide reductase underlie the severe growth defect of the Δhda E. coli strain. Molecular microbiology 2017 ():-. [ Abstract Babu VMP, Itsko I, Baxter JC , Schaaper RM, Sutton MD. Insufficient levels of the nrdAB-encoded ribonucleotide reductase underlie the severe growth defect of the Δhda E. coli strain. Molecular microbiology 2017 ():-. ] Itsko M, Schaaper RM. Transcriptome Analysis of Escherichia coli during dGTP Starvation. Journal of Bacteriology 2016 198(11):1631-1644. [ Abstract Itsko M, Schaaper RM. Transcriptome Analysis of Escherichia coli during dGTP Starvation. Journal of Bacteriology 2016 198(11):1631-1644. ] Singh D, Schaaper RM, Hochkoeppler A. A continuous spectrophotometric enzyme-coupled assay for deoxynucleoside triphosphate triphosphohydrolases. Analytical biochemistry 2016 496():43-49. [ Abstract Singh D, Schaaper RM, Hochkoeppler A. A continuous spectrophotometric enzyme-coupled assay for deoxynucleoside triphosphate triphosphohydrolases. Analytical biochemistry 2016 496():43-49. ] Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ, Schaaper RM. Suppression of the E. coli SOS response by dNTP pool changes. Nucleic acids research 2015 43(8):4109-4120. [ Abstract Maslowska KH, Makiela-Dzbenska K, Fijalkowska IJ, Schaaper RM. Suppression of the E. coli SOS response by dNTP pool changes. Nucleic acids research 2015 43(8):4109-4120. ] Singh D, Gawel D, Itsko M, Hochkoeppler A, Krahn JM, London RE, Schaaper RM. Structure of Escherichia coli dGTP triphosphohydrolase: a hexameric enzyme with DNA effector molecules. The Journal of biological chemistry 2015 290(60):10418-10429. [ Abstract Singh D, Gawel D, Itsko M, Hochkoeppler A, Krahn JM, London RE, Schaaper RM. Structure of Escherichia coli dGTP triphosphohydrolase: a hexameric enzyme with DNA effector molecules. The Journal of biological chemistry 2015 290(60):10418-10429. ] Tse L, Kang TM, Yuan J, Mihora D, Becket E, Maslowska KH, Schaaper RM, Miller JH. Extreme dNTP pool changes and hypermutability in dcd ndk strains. Mutation research. Fundamental and molecular mechanisms of mutagenesis 2015 784-785():16-24. [ Abstract Tse L, Kang TM, Yuan J, Mihora D, Becket E, Maslowska KH, Schaaper RM, Miller JH. Extreme dNTP pool changes and hypermutability in dcd ndk strains. Mutation research. Fundamental and molecular mechanisms of mutagenesis 2015 784-785():16-24. ] Swerdlow SJ, Schaaper RM. Mutagenesis in the lacI gene target of E. coli: improved analysis for lacI d and lacO mutants. Mutation research. Fundamental and molecular mechanisms of mutagenesis 2014 77():79-84. [ Abstract Swerdlow SJ, Schaaper RM. Mutagenesis in the lacI gene target of E. coli: improved analysis for lacI d and lacO mutants. Mutation research. Fundamental and molecular mechanisms of mutagenesis 2014 77():79-84. ] Itsko M, Schaaper RM. dGTP starvation in Escherichia coli provides new insights into the thymineless-death phenomenon. PLoS genetics 2014 10(5):e1004310- [ Abstract Itsko M, Schaaper RM. dGTP starvation in Escherichia coli provides new insights into the thymineless-death phenomenon. PLoS genetics 2014 10(5):e1004310- ] Gawel D, Fijalkowska IJ, Jonczyk P, Schaaper RM. Effect of dNTP pool alterations on fidelity of leading and lagging strand DNA replication in E. coli. Mutation research 2014 759(January):22-28. [ Abstract Gawel D, Fijalkowska IJ, Jonczyk P, Schaaper RM. Effect of dNTP pool alterations on fidelity of leading and lagging strand DNA replication in E. coli. Mutation research 2014 759(January):22-28. ] Kozmin SG, Stepchenkova EI, Schaaper RM. TusA(YhhP) and IscS are required for molybdenum-cofactor-dependent base-analog detoxification. MicrobiologyOpen 2013 2(5):743-755. [ Abstract Kozmin SG, Stepchenkova EI, Schaaper RM. TusA(YhhP) and IscS are required for molybdenum-cofactor-dependent base-analog detoxification. MicrobiologyOpen 2013 2(5):743-755. ] Ahluwalia D, Schaaper RM. Hypermutability and error catastrophe due to defects in ribonucleotide reductase. Proceedings of the National Academy of Sciences of the United States of America 2013 110(46):18596-18601. [ Abstract Ahluwalia D, Schaaper RM. Hypermutability and error catastrophe due to defects in ribonucleotide reductase. Proceedings of the National Academy of Sciences of the United States of America 2013 110(46):18596-18601. ] Kozmin SG, Stepchenkova EI, Chow SC, Schaaper RM. A Critical Role for the Putative NCS2 Nucleobase Permease YjcD in the Sensitivity of Escherichia coli to Cytotoxic and Mutagenic Purine Analogs. mBio 2013 4(6):e00661--13. [ Abstract Kozmin SG, Stepchenkova EI, Chow SC, Schaaper RM. A Critical Role for the Putative NCS2 Nucleobase Permease YjcD in the Sensitivity of Escherichia coli to Cytotoxic and Mutagenic Purine Analogs. mBio 2013 4(6):e00661--13. ] Kozmin SG, Schaaper RM. Genetic characterization of moaB mutants of Escherichia coli. Research in Microbiology 2013 164(7):689-694. [ Abstract Kozmin SG, Schaaper RM. Genetic characterization of moaB mutants of Escherichia coli. Research in Microbiology 2013 164(7):689-694. ] Taira K, Kaneto S, Nakano K, Watanabe S, Takahashi E, Arimoto S, Okamoto K, Schaaper RM, Negishi K, Negishi T. Distinct pathways for repairing mutagenic lesions induced by methylating and ethylating agents. Mutagenesis 2013 28(3):341-350. [ Abstract Taira K, Kaneto S, Nakano K, Watanabe S, Takahashi E, Arimoto S, Okamoto K, Schaaper RM, Negishi K, Negishi T. Distinct pathways for repairing mutagenic lesions induced by methylating and ethylating agents. Mutagenesis 2013 28(3):341-350. ] Schaaper RM, Mathews CK. Mutational consequences of dNTP pool imbalances in E. coli. DNA repair 2013 12(1):73-9. [ Abstract Schaaper RM, Mathews CK. Mutational consequences of dNTP pool imbalances in E. coli. DNA repair 2013 12(1):73-9. ] Conte E, Vincelli G, Schaaper RM, Bressanin D, Stefan A, Dal Piaz F, Hochkoeppler A. Stabilization of the E. coli DNA polymerase III ε subunit by the θ subunit favors in vivo assembly of the Pol III catalytic core. Archives of biochemistry and biophysics 2012 523(2):135-43. [ Abstract Conte E, Vincelli G, Schaaper RM, Bressanin D, Stefan A, Dal Piaz F, Hochkoeppler A. Stabilization of the E. coli DNA polymerase III ε subunit by the θ subunit favors in vivo assembly of the Pol III catalytic core. Archives of biochemistry and biophysics 2012 523(2):135-43. ] Ahluwalia D, Bienstock RJ, Schaaper RM. Novel mutator mutants of E. coli nrdAB ribonucleotide reductase: insight into allosteric regulation and control of mutation rates. DNA repair 2012 11(5):480-7. [ Abstract Ahluwalia D, Bienstock RJ, Schaaper RM. Novel mutator mutants of E. coli nrdAB ribonucleotide reductase: insight into allosteric regulation and control of mutation rates. DNA repair 2012 11(5):480-7. ] Fijalkowska IJ, Schaaper RM, Jonczyk P. DNA Replication fidelity in Escherichia coli: a multi-DNA polymerase affair. FEMS microbiology reviews 2012 36(6):1105-21. [ Abstract Fijalkowska IJ, Schaaper RM, Jonczyk P. DNA Replication fidelity in Escherichia coli: a multi-DNA polymerase affair. FEMS microbiology reviews 2012 36(6):1105-21. ] Itsko, M., Schaaper, R.M. (2011) The dgt gene of Escherichia coli facilitates thymine utilization in thymine-requiring strains. Molecular Microbiology 81(5):1221-1232. [ Abstract Itsko, M., Schaaper, R.M. (2011) The dgt gene of Escherichia coli facilitates thymine utilization in thymine-requiring strains. Molecular Microbiology 81(5):1221-1232. ] Makiela-Dzbenska, K., Jonczyk, P., Schaaper, R.M., Fijalkowska, I.J. (2011) Proofreading deficiency of Pol I increases the levels of spontaneous rpoB mutations in E. coli. Mutation Res. 712(1-2):28-32. [ Abstract Makiela-Dzbenska, K., Jonczyk, P., Schaaper, R.M., Fijalkowska, I.J. (2011) Proofreading deficiency of Pol I increases the levels of spontaneous rpoB mutations in E. coli. Mutation Res. 712(1-2):28-32. ] Gawel, D., Jonczyk, P., Fijalkowska, I.J., Schaaper, R.M. (2011) The dnaX36 mutator of Escherichia coli: effects of the DNA Polymerase III holoenzyme {tau} subunit on chromosomal DNA replication fidelity. Journal of Bacteriology. 193(1):296-300. [ Abstract Gawel, D., Jonczyk, P., Fijalkowska, I.J., Schaaper, R.M. (2011) The dnaX36 mutator of Escherichia coli: effects of the DNA Polymerase III holoenzyme {tau} subunit on chromosomal DNA replication fidelity. Journal of Bacteriology. 193(1):296-300. ] Lozmin, S.G., Wang, J., Schaaper, R.M. (2010) A role for CysJ flavin reductase in molybdenum cofactor-dependent resistance of Escherichia coli to 6-N-hydroxylaminopurine. Journal of Bacteriology. 192(8):2026-2033. [ Abstract Lozmin, S.G., Wang, J., Schaaper, R.M. (2010) A role for CysJ flavin reductase in molybdenum cofactor-dependent resistance of Escherichia coli to 6-N-hydroxylaminopurine. Journal of Bacteriology. 192(8):2026-2033. ] Makiela, K., Jaszczur, M., Banach-Orlowska, M., Jonczyk, P., Schaaper, R.M., Fijalkowska, I.J. (2009) Role of escherichia coli DNA polymerase I in chromosomal DNA replication fidelity. Molecular Microbiology. 74(5):1114-1127. [ Abstract Makiela, K., Jaszczur, M., Banach-Orlowska, M., Jonczyk, P., Schaaper, R.M., Fijalkowska, I.J. (2009) Role of escherichia coli DNA polymerase I in chromosomal DNA replication fidelity. Molecular Microbiology. 74(5):1114-1127. ] Ye, W., Sangaiah, R., Degen, D.E., Gold, A., Jayaraj, K., Koshlap, K.M., Boysen, B., Williams, J., Tomer, K.B., Mocanu, V., Dicheva, N., Parker, C., Schaaper, R.M., Ball, L.M. (2009) Iminohydantoin lesion induced in DNA by peracids and other epoxidizing oxidants. Journal of the American Chemical Society. 131(17):6114-6123. [ Abstract Ye, W., Sangaiah, R., Degen, D.E., Gold, A., Jayaraj, K., Koshlap, K.M., Boysen, B., Williams, J., Tomer, K.B., Mocanu, V., Dicheva, N., Parker, C., Schaaper, R.M., Ball, L.M. (2009) Iminohydantoin lesion induced in DNA by peracids and other epoxidizing oxidants. Journal of the American Chemical Society. 131(17):6114-6123. ] Gawel, D., Hamilton, M.D., Schaaper, R.M. (2008) A novel mutator of Escherichia coli carrying a defect in the dgt gene, encoding a dGTP triphosphohydrolase. Journal of Bacteriology. 190(21):6931-6939. [ Abstract Gawel, D., Hamilton, M.D., Schaaper, R.M. (2008) A novel mutator of Escherichia coli carrying a defect in the dgt gene, encoding a dGTP triphosphohydrolase. Journal of Bacteriology. 190(21):6931-6939. ] Gawel, D., Pham, P.T., Fijalkowska, I.J., Jonczyk, P., Schaaper, R.M. (2008) Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant. Journal of Bacteriology. 190(5):1730-1742. [ Abstract Gawel, D., Pham, P.T., Fijalkowska, I.J., Jonczyk, P., Schaaper, R.M. (2008) Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant. Journal of Bacteriology. 190(5):1730-1742. ] Kozmin, S.G., Leroy P., Pavlov Y.I., Schaaper R.M. (2008) YcbX and YiiM, two novel determinants for resistance of E. coli to N-hydroxylated base analogs. Molecular Microbiology. 68(1):51-65. [ Abstract Kozmin, S.G., Leroy P., Pavlov Y.I., Schaaper R.M. (2008) YcbX and YiiM, two novel determinants for resistance of E. coli to N-hydroxylated base analogs. Molecular Microbiology. 68(1):51-65. ] Taira, K., Nakamura, S., Maehara, D., Okamoto, K., Arimoto, S., Loakes, D., Worth, L., Schaaper, R.M., Seio, K., Sekine, M., Negishi, K., and Negishi, T. (2008) Binding of MutS protein to oligonucleotides containing a methylated or an ethylated guanine residue, and correlation with mutation frequency. Mutation Res. 640(1-2): 107-112. [ Abstract Taira, K., Nakamura, S., Maehara, D., Okamoto, K., Arimoto, S., Loakes, D., Worth, L., Schaaper, R.M., Seio, K., Sekine, M., Negishi, K., and Negishi, T. (2008) Binding of MutS protein to oligonucleotides containing a methylated or an ethylated guanine residue, and correlation with mutation frequency. Mutation Res. 640(1-2): 107-112. ] Swartz, C.D., Parks, N., Umbach, D.M., Ward, W.O., Schaaper, R.M., DeMarini, D.M. (2007) Enhanced mutagenesis of Salmonella tester strains due to deletion of genes other than uvrB. Environmental and Molecular Mutagenesis. 48(8):694-705. [ Abstract Swartz, C.D., Parks, N., Umbach, D.M., Ward, W.O., Schaaper, R.M., DeMarini, D.M. (2007) Enhanced mutagenesis of Salmonella tester strains due to deletion of genes other than uvrB. Environmental and Molecular Mutagenesis. 48(8):694-705. ] Chikova, A.C., and Schaaper, R.M. (2007) The bacteriophage P1 hot gene, encoding a homolog of the E. coli DNA polymerase theta subunit, is expressed during both lysogenic and lytic growth stages. Mutation Res. 1-2: 1-8. [ Abstract Chikova, A.C., and Schaaper, R.M. (2007) The bacteriophage P1 hot gene, encoding a homolog of the E. coli DNA polymerase theta subunit, is expressed during both lysogenic and lytic growth stages. Mutation Res. 1-2: 1-8. ] Kozmin, S.G., and R.M. Schaaper, R.M. (2007) Molybdenum cofactor-dependent resistance to N-hydroxylated base analogs in E. coli is independent of MobA function. Mutation Res. Jun 1;619(1-2): 9-15. Epub 2007 Feb 2. [ Abstract Kozmin, S.G., and R.M. Schaaper, R.M. (2007) Molybdenum cofactor-dependent resistance to N-hydroxylated base analogs in E. coli is independent of MobA function. Mutation Res. Jun 1;619(1-2): 9-15. Epub 2007 Feb 2. ] Pham, P.T., Zhao, W., and Schaaper, R.M. (2006) Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III τ subunit. Mol. Microbiol. 59: 1149-1161. [ Abstract Pham, P.T., Zhao, W., and Schaaper, R.M. (2006) Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III τ subunit. Mol. Microbiol. 59: 1149-1161. ] Chikova, A.K., and Schaaper, R.M. (2006) Mutator and antimutator effects of the bacteriophage P1 hot gene product. J. Bacteriol. 188: 5831-5838. [ Abstract Chikova, A.K., and Schaaper, R.M. (2006) Mutator and antimutator effects of the bacteriophage P1 hot gene product. J. Bacteriol. 188: 5831-5838. ] Kuban, W., Banach-Orlowska, M., Schaaper, R.M., Jonczyk, P., and Fijalkowska, I.J. (2006) Role of DNA Polymerase IV in the E. coli SOS mutator activity. J. Bacteriol. 188: 7977-7980. [ Abstract Kuban, W., Banach-Orlowska, M., Schaaper, R.M., Jonczyk, P., and Fijalkowska, I.J. (2006) Role of DNA Polymerase IV in the E. coli SOS mutator activity. J. Bacteriol. 188: 7977-7980. ] Kirby, T.W., Harvey, S., DeRose, E.F., Chalov, S., Chikova, A.K., Perrino, F.W., Schaaper, R.M., London, R.E., and Pedersen, L.C. (2006) Structure of the E. coli DNA Polymerase III ε-Hot Proofreading Complex. J. Biol. Chem. 281: 38466-38471. [ Abstract Kirby, T.W., Harvey, S., DeRose, E.F., Chalov, S., Chikova, A.K., Perrino, F.W., Schaaper, R.M., London, R.E., and Pedersen, L.C. (2006) Structure of the E. coli DNA Polymerase III ε-Hot Proofreading Complex. J. Biol. Chem. 281: 38466-38471. ] Chikova, A.K., and Schaaper, R.M. (2005) Bacteriophage P1 hot gene product can substitute for the θ subunit of E. coli DNA Polymerase III. J. Bacteriol. 187: 5528-5536. [ Abstract Chikova, A.K., and Schaaper, R.M. (2005) Bacteriophage P1 hot gene product can substitute for the θ subunit of E. coli DNA Polymerase III. J. Bacteriol. 187: 5528-5536. ] Banach-Orlowska, M., Fijalkowska, I.J., Schaaper, R.M., and Jonczyk, P. (2005) DNA Polymerase II as a fidelity factor in chromosomal DNA synthesis in E. coli. Mol. Microbiol. 58: 61-70. [ Abstract Banach-Orlowska, M., Fijalkowska, I.J., Schaaper, R.M., and Jonczyk, P. (2005) DNA Polymerase II as a fidelity factor in chromosomal DNA synthesis in E. coli. Mol. Microbiol. 58: 61-70. ] Kuban, W., Banach-Orlowska, M., Bialoskorska, M., Lipowska, A., Schaaper, R.M., Jonczyk, P., and Fijalkowska, I.J. (2005) Mutator phenotype resulting from Pol IV overproduction in E. coli: preferential mutagenesis on the lagging strand. J. Bacteriol. 187: 6862-6866. [ Abstract Kuban, W., Banach-Orlowska, M., Bialoskorska, M., Lipowska, A., Schaaper, R.M., Jonczyk, P., and Fijalkowska, I.J. (2005) Mutator phenotype resulting from Pol IV overproduction in E. coli: preferential mutagenesis on the lagging strand. J. Bacteriol. 187: 6862-6866. ] Mueller, G.A., Kirby, T.W., DeRose, E.F., Li, D., Schaaper, R.M., and London, R.E. (2005) Nuclear magnetic resonance solution structure of the E. coli DNA Polymerase III θ subunit. J. Bacteriol. 187: 7081-7089. [ Abstract Mueller, G.A., Kirby, T.W., DeRose, E.F., Li, D., Schaaper, R.M., and London, R.E. (2005) Nuclear magnetic resonance solution structure of the E. coli DNA Polymerase III θ subunit. J. Bacteriol. 187: 7081-7089. ] Fijalkowska, I.J., Jonczyk, P., Tkaczyk, M.M., Bialoskorska, M., and Schaaper, R.M. (1998) Unequal fidelity of leading- and lagging-strand DNA replication on the E. coli chromosome. Proc. Natl. Acad. Sci. USA 95: 10020-10025. [ Abstract Fijalkowska, I.J., Jonczyk, P., Tkaczyk, M.M., Bialoskorska, M., and Schaaper, R.M. (1998) Unequal fidelity of leading- and lagging-strand DNA replication on the E. coli chromosome. Proc. Natl. Acad. Sci. USA 95: 10020-10025. ]
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Last Reviewed: June 25, 2024
