M F Goodman

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. ncbi request reprint Lessons from 50 years of SOS DNA-damage-induced mutagenesis
    Katharina Schlacher
    University of Southern California, 1050 Childs Way, RIH 201B, Los Angeles, California 90089 2910, USA
    Nat Rev Mol Cell Biol 8:587-94. 2007
  2. pmc DNA polymerase fidelity: from genetics toward a biochemical understanding
    M F Goodman
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles 90089 1340, USA
    Genetics 148:1475-82. 1998
  3. ncbi request reprint Coping with replication 'train wrecks' in Escherichia coli using Pol V, Pol II and RecA proteins
    M F Goodman
    Dept of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles, CA 90089 1340, USA
    Trends Biochem Sci 25:189-95. 2000
  4. ncbi request reprint Error-prone repair DNA polymerases in prokaryotes and eukaryotes
    Myron F Goodman
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratory, University of Southern California, Los Angeles, California 90089 1340, USA
    Annu Rev Biochem 71:17-50. 2002
  5. ncbi request reprint Pre-steady state analysis of the assembly of wild type and mutant circular clamps of Escherichia coli DNA polymerase III onto DNA
    J G Bertram
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 273:24564-74. 1998
  6. pmc Biochemical basis of SOS-induced mutagenesis in Escherichia coli: reconstitution of in vitro lesion bypass dependent on the UmuD'2C mutagenic complex and RecA protein
    M Tang
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 95:9755-60. 1998
  7. ncbi request reprint Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis
    M Tang
    Department of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles 90089 1340, USA
    Nature 404:1014-8. 2000
  8. pmc A phenotype for enigmatic DNA polymerase II: a pivotal role for pol II in replication restart in UV-irradiated Escherichia coli
    S Rangarajan
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 96:9224-9. 1999
  9. pmc UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V
    M Tang
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 96:8919-24. 1999
  10. pmc Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli
    P Pham
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089-1340, USA
    Proc Natl Acad Sci U S A 98:8350-4. 2001

Collaborators

Detail Information

Publications98

  1. ncbi request reprint Lessons from 50 years of SOS DNA-damage-induced mutagenesis
    Katharina Schlacher
    University of Southern California, 1050 Childs Way, RIH 201B, Los Angeles, California 90089 2910, USA
    Nat Rev Mol Cell Biol 8:587-94. 2007
    ....
  2. pmc DNA polymerase fidelity: from genetics toward a biochemical understanding
    M F Goodman
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles 90089 1340, USA
    Genetics 148:1475-82. 1998
    ..The relative contributions of hydrogen bonding and base stacking to the accuracy of DNA synthesis are beginning to be deciphered. For the future, the main challenges lie in understanding the origins of mutational hot and cold spots...
  3. ncbi request reprint Coping with replication 'train wrecks' in Escherichia coli using Pol V, Pol II and RecA proteins
    M F Goodman
    Dept of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles, CA 90089 1340, USA
    Trends Biochem Sci 25:189-95. 2000
    ....
  4. ncbi request reprint Error-prone repair DNA polymerases in prokaryotes and eukaryotes
    Myron F Goodman
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratory, University of Southern California, Los Angeles, California 90089 1340, USA
    Annu Rev Biochem 71:17-50. 2002
    ..Macromolecular assemblies of replication-repair "factories" could enable a cell to handle the complex logistics governing the rapid migration and exchange of polymerases...
  5. ncbi request reprint Pre-steady state analysis of the assembly of wild type and mutant circular clamps of Escherichia coli DNA polymerase III onto DNA
    J G Bertram
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 273:24564-74. 1998
    ..Thus, the assembly of beta around DNA is coupled tightly to the ATPase activity of the gamma complex, and completion of the assembly process requires ATP hydrolysis for turnover of the catalytic clamp loader...
  6. pmc Biochemical basis of SOS-induced mutagenesis in Escherichia coli: reconstitution of in vitro lesion bypass dependent on the UmuD'2C mutagenic complex and RecA protein
    M Tang
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 95:9755-60. 1998
    ..These observations provide a biochemical basis for the role of the Umu complex in SOS-targeted and SOS-untargeted mutagenesis...
  7. ncbi request reprint Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis
    M Tang
    Department of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles 90089 1340, USA
    Nature 404:1014-8. 2000
    ..Lesion bypass by pol V does not require beta,gamma-complex in the presence of non-hydrolysable ATPgammaS, indicating that an intact RecA filament may be required for translesion synthesis...
  8. pmc A phenotype for enigmatic DNA polymerase II: a pivotal role for pol II in replication restart in UV-irradiated Escherichia coli
    S Rangarajan
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 96:9224-9. 1999
    ..Our data demonstrate that pol II and UmuD'(2)C act in independent pathways of replication restart, thereby providing a phenotype for pol II in the repair of UV-damaged DNA...
  9. pmc UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V
    M Tang
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 96:8919-24. 1999
    ..We show, however, that despite competition for primer-3'-ends, pol V and pol III HE can nevertheless interact synergistically to stimulate synthesis downstream from a template lesion...
  10. pmc Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli
    P Pham
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089-1340, USA
    Proc Natl Acad Sci U S A 98:8350-4. 2001
    ..Although the precise molecular mechanism of pol II-dependent replication-restart remains to be elucidated, it has recently been shown to operate in conjunction with RecFOR and PriA proteins...
  11. ncbi request reprint Molecular mechanism and energetics of clamp assembly in Escherichia coli. The role of ATP hydrolysis when gamma complex loads beta on DNA
    J G Bertram
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 275:28413-20. 2000
    ..The anisotropy data showed that these mutants decrease the steady-state rates of ATP hydrolysis by causing a buildup of "stuck" binary-ternary complexes on the primer/template DNA...
  12. ncbi request reprint A model for SOS-lesion-targeted mutations in Escherichia coli
    P Pham
    Department of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles 90089-1340, USA
    Nature 409:366-70. 2001
    ..The bidirectional collapse of the RecA filament restricts DNA synthesis by pol V to template sites that are proximal to the lesion, thereby minimizing the occurrence of untargeted mutations at undamaged template sites...
  13. ncbi request reprint Base mispair extension kinetics. Binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini
    S Creighton
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 267:2633-9. 1992
    ..Therefore, it appears that inefficient mismatch extension is caused primarily by a kinetic block inhibiting elongation from mispaired primer 3'-termini rather than to a difference in binding...
  14. pmc Escherichia coli DNA polymerase II catalyzes chromosomal and episomal DNA synthesis in vivo
    S Rangarajan
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340, USA
    Proc Natl Acad Sci U S A 94:946-51. 1997
    ..Pol II exo- caused a significant increase in the frequency of base substitution and frameshift mutations on F' episomes, even in dnaE+ cells, suggesting that Pol II is able to compete with Pol III for DNA synthesis on F episomes...
  15. ncbi request reprint Nearest neighbor influences on DNA polymerase insertion fidelity
    L V Mendelman
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 264:14415-23. 1989
    ..When Vmax and Km discrimination components have similar magnitudes, nearest neighbor effects tend to cancel thereby reducing the effects of base stacking on insertion error rates...
  16. ncbi request reprint Dynamics of loading the beta sliding clamp of DNA polymerase III onto DNA
    L B Bloom
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 271:30699-708. 1996
    ..The association rate appears to be limited by an intramolecular step occurring prior to the clamp-loading reaction, possibly the opening of the toroidal beta dimer...
  17. ncbi request reprint A biochemically defined system for mammalian nonhomologous DNA end joining
    Yunmei Ma
    University of Southern California Norris Comprehensive Cancer Center, Room 5428, Department of Pathology, University of Southern California Keck School, of Medicine, 1441 Eastlake Avenue, MC9176, Los Angeles, California 90033, USA
    Mol Cell 16:701-13. 2004
    ..The XRCC4:DNA ligase IV complex is able to ligate one strand that has only minimal base pairing with the antiparallel strand. This important aspect of the ligation leads to an iterative strand-processing model for the steps of NHEJ...
  18. ncbi request reprint Base mispair extension kinetics. Comparison of DNA polymerase alpha and reverse transcriptase
    L V Mendelman
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 265:2338-46. 1990
    ..The extension velocities depart from Michaelis-Menten kinetics by exhibiting positive cooperativity with respect to substrate concentration...
  19. ncbi request reprint Sloppier copier DNA polymerases involved in genome repair
    M F Goodman
    Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, 90089 1340, USA usc edu
    Curr Opin Genet Dev 10:162-8. 2000
    ..Ongoing studies of these low fidelity polymerases could provide new insights into the mechanism of somatic hypermutation, a key element in the immune response...
  20. ncbi request reprint Purification of a soluble UmuD'C complex from Escherichia coli. Cooperative binding of UmuD'C to single-stranded DNA
    I Bruck
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles 90089 1340, USA
    J Biol Chem 271:10767-74. 1996
    ..The UmuD'C complex associates with RecA-coated DNA, and the UmuD'C complex remains bound to DNA in the presence of RecA...
  21. ncbi request reprint Escherichia coli DNA polymerase V subunit exchange: a post-SOS mechanism to curtail error-prone DNA synthesis
    Xuan Shen
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 278:52546-50. 2003
    ..The subunit exchange between UmuD'2C and UmuD offers a biological means to inactivate error-prone polymerase V following translesion synthesis, thus preventing mutations from occurring on undamaged DNA...
  22. ncbi request reprint Comparison of HIV-1 and avian myeloblastosis virus reverse transcriptase fidelity on RNA and DNA templates
    H Yu
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 267:10888-96. 1992
    ....
  23. ncbi request reprint The expanding polymerase universe
    M F Goodman
    University of Southern California, Department of Biological Sciences and Chemistry, Stauffer Hall of Science 172, Los Angeles, California 90089 1340, USA
    Nat Rev Mol Cell Biol 1:101-9. 2000
    ....
  24. pmc DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli
    C A Bonner
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    Proc Natl Acad Sci U S A 87:7663-7. 1990
    ..The demonstration that DNA polymerase II is a component of the SOS response in E. coli suggests that it plays an important role in DNA repair and/or mutagenesis...
  25. ncbi request reprint Kinetic analysis of base substitution mutagenesis by transient misalignment of DNA and by miscoding
    M S Boosalis
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 264:11360-6. 1989
    ..Here nucleotide insertion fidelity results from substantial differences in both Km and Vmax for correct versus incorrect substrates and is influenced strongly by local base sequence...
  26. pmc Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation
    M Escarceller
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340, USA
    J Bacteriol 176:6221-8. 1994
    ..cerevisiae. Induction of Pol II by nalidixic acid was observed in E. coli K-12, B, and C, in Shigella flexneri, and in Salmonella typhimurium...
  27. ncbi request reprint The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol II purified from a polB mutant
    Z Qiu
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 272:8611-7. 1997
    ..We suggest that the normal level of exonucleolytic proofreading associated with the mutant Pol B100 enzyme may explain the repeated failures, over the past two decades, to detect phenotypes in polB mutant strains...
  28. ncbi request reprint Increased dNTP binding affinity reveals a nonprocessive role for Escherichia coli beta clamp with DNA polymerase IV
    Jeffrey G Bertram
    Departments of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, University Park, Los Angeles, California 90089 1340, USA
    J Biol Chem 279:33047-50. 2004
    ..We show that the increased DNA polymerase IV-dNTP binding affinity is an intrinsic property of the DNA polymerase IV-beta clamp interaction and not an indirect consequence of an increased binding of DNA polymerase IV to DNA...
  29. ncbi request reprint RecA acts in trans to allow replication of damaged DNA by DNA polymerase V
    Katharina Schlacher
    Department of Biological Sciences and Chemistry, University of Southern California, University Park, Los Angeles, California 90089 2910, USA
    Nature 442:883-7. 2006
    ....
  30. ncbi request reprint Lyase activities intrinsic to Escherichia coli polymerases IV and V
    Xuan Shen
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, University Park, Los Angeles, 90089 1340, USA
    DNA Repair (Amst) 4:1368-73. 2005
    ..The concomitant loss of both activities is strong evidence that pol V contains a bona fide lyase activity...
  31. ncbi request reprint Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta
    Christopher A Sucato
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Biochemistry 46:461-71. 2007
    ..The results are addressed theoretically in terms of the energetics of successive primer 3'-O addition (bond forming) and pyrophosphate analogue elimination (bond breaking) reaction energy barriers...
  32. ncbi request reprint Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins
    Savithri Rangarajan
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, CA 90089 1340, USA
    Mol Microbiol 43:617-28. 2002
    ..In con-trast, only RecF is required for the activation of RecA that leads to the formation of pol V (UmuD'2C) and facilitates replication readthrough...
  33. pmc DNA mismatch repair catalyzed by extracts of mitotic, postmitotic, and senescent Drosophila tissues and involvement of mei-9 gene function for full activity
    A Bhui-Kaur
    Department of Biological Sciences and Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles 90089 1340, USA
    Mol Cell Biol 18:1436-43. 1998
    ..mei-9 has been shown to be required in vivo for certain types of DNA mismatch repair, nucleotide excision repair (NER), and meiotic crossing over and is the Drosophila homolog of the yeast NER gene rad1...
  34. ncbi request reprint Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase
    H Cai
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 268:23567-72. 1993
    ..A striking result was that while primers were extended past an abasic lesion by HIV-1 RT in both direct and misalignment modes, avian myeloblastosis virus RT failed to catalyze significant extension by either mode...
  35. ncbi request reprint To slip or skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases
    Brigette Tippin
    Departments of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 279:45360-8. 2004
    ..Thus, two polymerases can use two different frameshift mechanisms on identical sequences, whereas one polymerase can alternate between frameshift mechanisms to process different sequences...
  36. ncbi request reprint DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state
    Christopher A Sucato
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Biochemistry 47:870-9. 2008
    ..Solvent pH and deuterium isotope-effect data are also used to evaluate mechanistic differences between correct and mispaired incorporation...
  37. ncbi request reprint DNA polymerase V and RecA protein, a minimal mutasome
    Katharina Schlacher
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Mol Cell 17:561-72. 2005
    ..Pol V activity is strongly enhanced with RecA mutants constitutive for mutagenesis in vivo, suggesting that RecA is an obligate accessory factor that activates pol V for SOS mutagenesis...
  38. ncbi request reprint Purification and characterization of Escherichia coli DNA polymerase V
    Katharina Schlacher
    Department of Biological Sciences, University of Southern California, Los Angeles, USA
    Methods Enzymol 408:378-90. 2006
    ..This chapter describes the preparation of highly purified native pol V that is suitable for a wide range of biochemical studies of protein-protein, protein-DNA interactions and translesion-synthesis (TLS) mechanisms...
  39. pmc SOS-induced DNA polymerases enhance long-term survival and evolutionary fitness
    Bethany Yeiser
    Program in Molecular and Computational Biology, Department of Biological Sciences, SHS 172, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 99:8737-41. 2002
    ..These polymerases contribute to survival by providing essential functions to ensure replication of the chromosome and by generating genetic diversity...
  40. pmc Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis
    Phuong Pham
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 99:11061-6. 2002
    ..However, it is only a RecA molecule located at the 3' filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis...
  41. ncbi request reprint Computer simulation studies of the fidelity of DNA polymerases
    Jan Florian
    Department of Chemistry, University of Southern California, Los Angeles, CA 90089 1062, USA
    Biopolymers 68:286-99. 2003
    ....
  42. pmc The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP
    Qingfei Jiang
    Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California 90089 2910, USA
    Nature 460:359-63. 2009
    ..Reactivation of pol V Mut is triggered by replacement of RecA-ATP from RecA*. Thus, the principal role of RecA* in SOS mutagenesis is to transfer RecA-ATP to pol V, and thus generate active mutasomal complex for translesion synthesis...
  43. pmc (R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta
    Charles E McKenna
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    J Am Chem Soc 129:15412-3. 2007
  44. pmc Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid
    G K Surya Prakash
    Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, Los Angeles, 90089 1661, USA
    Proc Natl Acad Sci U S A 107:15693-8. 2010
    ..5 A resolution crystal structure of a ternary complex with the enzyme. Unexpected dominating effect of triphosphate/Mg(2+) interaction over Watson-Crick hydrogen bonding was found and discussed...
  45. pmc Exploring the role of large conformational changes in the fidelity of DNA polymerase beta
    Yun Xiang
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Proteins 70:231-47. 2008
    ..The generation of free energy surfaces for R and W also allow us to analyze proposals about the relationship between induced fit and fidelity...
  46. doi request reprint Modifications to the dNTP triphosphate moiety: from mechanistic probes for DNA polymerases to antiviral and anti-cancer drug design
    Charles E McKenna
    Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
    Biochim Biophys Acta 1804:1223-30. 2010
    ....
  47. pmc Identifying protein-protein interactions in somatic hypermutation
    Myron F Goodman
    University of Southern California, Los Angeles, CA 90089, USA
    J Exp Med 201:493-6. 2005
    ..Here we comment on how, when, and why biochemistry is likely to emerge from the shadows and into the spotlight to elucidate how the somatic mutation of antibody variable (V) regions is generated...
  48. ncbi request reprint Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase
    Jan Florian
    Department of Chemistry, Loyola University Chicago, Chicago, Illinois 60626, USA
    J Am Chem Soc 125:8163-77. 2003
    ..The relative height of these barriers comparing right and wrong dNTP substrates should therefore be a primary focus of future computational studies of the fidelity of DNA polymerases...
  49. ncbi request reprint Processive DNA synthesis by DNA polymerase II mediated by DNA polymerase III accessory proteins
    C A Bonner
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 1340
    J Biol Chem 267:11431-8. 1992
    ..pol II also shows limited bypass of the abasic site, dependent on the presence of beta,gamma complex and SSB. pol III shows no significant bypass of the abasic site with or without beta,gamma complex...
  50. pmc A new class of errant DNA polymerases provides candidates for somatic hypermutation
    B Tippin
    Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles 90089-1340, USA
    Philos Trans R Soc Lond B Biol Sci 356:47-51. 2001
    ..In particular we discuss evidence for the in vitro biochemical misincorporation properties of human Rad30B/Pol iota and how it compares to the in vivo somatic hypermutation spectra...
  51. ncbi request reprint Weak strand displacement activity enables human DNA polymerase beta to expand CAG/CTG triplet repeats at strand breaks
    Michael J Hartenstine
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles 90089 1340, USA
    J Biol Chem 277:41379-89. 2002
    ..Such weak strand displacement activity in DNA repair at strand breaks may enable short tracts of repeats to be converted into longer, increasingly mutable ones associated with neurological diseases...
  52. pmc Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications
    Lauren G Holden
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 456:121-4. 2008
    ..These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family...
  53. pmc Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function
    Thomas G Upton
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Org Lett 11:1883-6. 2009
    ....
  54. ncbi request reprint Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta
    Yun Xiang
    Department of Chemistry, University of Southern California, Seeley G Mudd 418, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Biochemistry 45:7036-48. 2006
    ..We discuss the potential of direct calculations of binding energy of the TS in a rational design of TS analogues and in drug design...
  55. ncbi request reprint Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation
    Katharina Schlacher
    Department of Biological Sciences, University of Southern California, Los Angeles, 90089 1340, USA
    Chem Rev 106:406-19. 2006
  56. pmc DNA polymerase fidelity: comparing direct competition of right and wrong dNTP substrates with steady state and pre-steady state kinetics
    Jeffrey G Bertram
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    Biochemistry 49:20-8. 2010
    ..All the data are in quantitative agreement...
  57. ncbi request reprint Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment
    Sawami Kobayashi
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratories, University of Southern California, University Park, Los Angeles, CA 90089 1340, USA
    J Biol Chem 277:34198-207. 2002
    ..A crystal structure depicting dNTP-stabilized misalignment was reported recently for Sulfolubus solfataricus Dpo4, a Y family homolog of Escherichia coli pol IV...
  58. ncbi request reprint Analysis of mutational changes at the HLA locus in single human sperm
    M M Huang
    Molecular Biology Program, University of Southern California, Los Angeles 90089 1340, USA
    Hum Mutat 6:303-10. 1995
    ..The data may help explain allelic diversity in the MHC and suggest that a possible source of human mosaicism may be incomplete DNA mismatch repair during gametogenesis...
  59. ncbi request reprint Resolving a fidelity paradox: why Escherichia coli DNA polymerase II makes more base substitution errors in AT- compared with GC-rich DNA
    Zhijie Wang
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 277:4446-54. 2002
    ..The more efficient polymerization suppresses proofreading thereby causing a significant increase in base substitution error rates in AT-rich regions...
  60. ncbi request reprint Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo[a]pyrene-7,8-diol 9,10-epoxide A and G adducts
    Xuan Shen
    Department of Biological Sciences and Chemistry, Hedco Molecular Biology Laboratory, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 277:5265-74. 2002
    ..SOS polymerases are adept at copying a variety of lesions, but the relative contribution of each SOS polymerase to copying damaged DNA appears to be determined by the lesion's identity...
  61. pmc A model for oligomeric regulation of APOBEC3G cytosine deaminase-dependent restriction of HIV
    Linda Chelico
    Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California 90089 2910, USA
    J Biol Chem 283:13780-91. 2008
    ..We suggest that diverse A3G oligomerization modes contribute to the human immunodeficiency virus, type 1, proviral DNA mutational bias...
  62. ncbi request reprint APOBEC3G DNA deaminase acts processively 3' --> 5' on single-stranded DNA
    Linda Chelico
    Department of Biological Sciences Molecular and Computational Section, University of Southern California, Los Angeles, California 90089 2910, USA
    Nat Struct Mol Biol 13:392-9. 2006
    ..Our data suggest that the G --> A mutational gradient generated in viral genomic DNA in vivo could result from an intrinsic processive directional attack by APOBEC3G on single-stranded cDNA...
  63. pmc XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps
    Jiafeng Gu
    Department of Pathology, Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
    EMBO J 26:1010-23. 2007
    ..These observations provide an explanation for several in vivo observations that were difficult to understand previously...
  64. ncbi request reprint Error-prone replication for better or worse
    Brigette Tippin
    Hedco Molecular Biology Laboratories, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 1340, USA
    Trends Microbiol 12:288-95. 2004
    ..Here we focus on low-fidelity polymerases from bacteria, comparing Escherichia coli, archeabacteria and those most recently discovered in Gram-positive Bacilli, Streptococcus, pathogenic Mycobacterium and intein-containing cyanobacteria...
  65. pmc A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases
    Shina C L Kamerlin
    Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA
    Biochemistry 48:5963-71. 2009
    ..An understanding of the mechanism of this reaction in solution could thereby provide a steppingstone for understanding the factors governing the fidelity of DNA polymerases...
  66. pmc A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V
    Meghna Patel
    Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA, USA
    Crit Rev Biochem Mol Biol 45:171-84. 2010
    ..Based on unforeseen properties of RecA*, we describe a new model for pol V-catalyzed SOS-induced mutagenesis...
  67. pmc Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G
    Linda Chelico
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 2910, USA
    J Biol Chem 285:16195-205. 2010
    ..The CD1 domain is essential for both processivity and polarity. We propose a structure-based model to explain the scanning and catalytic behavior of Apo3G...
  68. pmc Oncogene homologue Sch9 promotes age-dependent mutations by a superoxide and Rev1/Polzeta-dependent mechanism
    Federica Madia
    Andrus Gerontology Center and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    J Cell Biol 186:509-23. 2009
    ....
  69. ncbi request reprint Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase
    Ronda Bransteitter
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089 1340, USA
    J Biol Chem 279:51612-21. 2004
    ....
  70. pmc Biochemical basis of immunological and retroviral responses to DNA-targeted cytosine deamination by activation-induced cytidine deaminase and APOBEC3G
    Linda Chelico
    Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089 2910, USA
    J Biol Chem 284:27761-5. 2009
    ....
  71. pmc Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G
    Linda Chelico
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    Philos Trans R Soc Lond B Biol Sci 364:583-93. 2009
    ..The potential for S43P to catalyse large numbers of aberrant deaminations in switch region sequences suggests a possible relationship between non-canonical AID deamination specificity and a loss of antibody diversification...
  72. ncbi request reprint AID-initiated purposeful mutations in immunoglobulin genes
    Myron F Goodman
    Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
    Adv Immunol 94:127-55. 2007
    ..The emerging experimental techniques help to address long-standing conundrums concerning evolution-imposed constraints on antibody structure and function...
  73. pmc Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase
    Phuong Pham
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 2910, USA
    J Biol Chem 283:17428-39. 2008
    ..Both motifs occur with exceptionally high frequency in human switch regions, suggesting a possible relationship between AID deamination specificity and a loss of antibody diversification...
  74. ncbi request reprint Somatic hypermutation: a mutational panacea
    Brigette Tippin
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Adv Protein Chem 69:307-35. 2004
  75. ncbi request reprint First AID (activation-induced cytidine deaminase) is needed to produce high affinity isotype-switched antibodies
    Ronda Bransteitter
    Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089 2910, USA
    J Biol Chem 281:16833-6. 2006
  76. ncbi request reprint Reward versus risk: DNA cytidine deaminases triggering immunity and disease
    Phuong Pham
    Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California 90089 1340, USA
    Biochemistry 44:2703-15. 2005
    ....
  77. ncbi request reprint Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation
    Phuong Pham
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, University Park, Los Angeles, California 90089 1340, USA
    Nature 424:103-7. 2003
    ....
  78. pmc Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase
    Ronda Bransteitter
    Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, University Park, Los Angeles, CA 90089 1340, USA
    Proc Natl Acad Sci U S A 100:4102-7. 2003
    ....
  79. pmc Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair
    Francisco J López de Saro
    Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    EMBO J 22:6408-18. 2003
    ..Given the limited amounts of clamps in the cell, these results suggest that clamp binding may be competitive and regulated, and that the different polymerases may use the same clamp sequentially during replication and repair...
  80. ncbi request reprint Effects of the C4'-oxidized abasic site on replication in Escherichia coli. An unusually large deletion is induced by a small lesion
    Kelly M Kroeger
    Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    Biochemistry 43:13621-7. 2004
    ..Formation of the C4-AP lesion may also be responsible for the formation of mutant proteins containing single-amino acid deletions that exhibit altered phenotypes...
  81. pmc A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli
    Kelly M Kroeger
    Department of Chemistry, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA
    Nucleic Acids Res 32:5480-5. 2004
    ..Our studies reveal that in uninduced E.coli the effects of individual polymerases in the replication of plasmids containing F or AP are distinct. However, when cells are SOS-induced, the biological effects of F and AP are similar...
  82. pmc Replication bypass of interstrand cross-link intermediates by Escherichia coli DNA polymerase IV
    Anuradha Kumari
    Center for Research on Occupational and Environmental Toxicology and the Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239 3098, USA
    J Biol Chem 283:27433-7. 2008
    ..However, the ability to replicate the modified vector DNA was nearly abolished in a pol IV-deficient strain. These data strongly suggest that pol IV is responsible for TLS past N(2)-N(2)-guanine ICLs...
  83. ncbi request reprint In vitro effects of a C4'-oxidized abasic site on DNA polymerases
    Marc M Greenberg
    Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    Biochemistry 43:2656-63. 2004
    ..The interaction between bypass polymerases and a C4-AP lesion could explain the high levels of G:C --> T:A transversions in cells treated with bleomycin...
  84. ncbi request reprint Mutagenic effects of 2-deoxyribonolactone in Escherichia coli. An abasic lesion that disobeys the A-rule
    Kelly M Kroeger
    Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    Biochemistry 43:6723-33. 2004
    ..Experiments carried out side by side using otherwise identical plasmids containing an AP site illustrate the distinct properties of these two abasic lesions and that neither should be thought of as noninstructive...
  85. pmc Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases
    Jan Florian
    Department of Chemistry, Loyola University, Chicago, IL 60626, USA
    Proc Natl Acad Sci U S A 102:6819-24. 2005
    ..The calculations demonstrate the potential for further integration of theoretical and experimental studies to analyze high- and low-fidelity DNA polymerases...
  86. ncbi request reprint A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously
    Chiara Indiani
    Laboratory of DNA Replication, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Mol Cell 19:805-15. 2005
    ..These polymerase dynamics within the beta toolbelt complex restrict the action of the error-prone Pol IV to only the area on DNA where it is required...
  87. pmc Replication of an oxidized abasic site in Escherichia coli by a dNTP-stabilized misalignment mechanism that reads upstream and downstream nucleotides
    Kelly M Kroeger
    Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, USA
    Biochemistry 45:5048-56. 2006
    ..The results raise further questions as to whether abasic lesions are noninstructive lesions. We suggest that abasic site bypass is affected by the local biopolymer structure in addition to the structure of the lesion...
  88. pmc A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on the sliding clamp
    Asako Furukohri
    Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630 0192, Japan
    J Biol Chem 283:11260-9. 2008
    ..Our study suggests a model in which the interaction between pol III* and the beta clamp is mediated by pol IV to ensure that DNA replication proceeds with minimal interruption...
  89. pmc DNA polymerase beta catalytic efficiency mirrors the Asn279-dCTP H-bonding strength
    Vaclav Martinek
    Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
    FEBS Lett 581:775-80. 2007
    ..This finding is consistent with the view that enzyme preorganization plays a major role in controlling DNA polymerase specific activity...
  90. ncbi request reprint Mechanism of loading the Escherichia coli DNA polymerase III beta sliding clamp on DNA. Bona fide primer/templates preferentially trigger the gamma complex to hydrolyze ATP and load the clamp
    Brandon Ason
    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville 32610 0245, USA
    J Biol Chem 278:10033-40. 2003
    ....
  91. doi request reprint The biochemistry of somatic hypermutation
    Jonathan U Peled
    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Annu Rev Immunol 26:481-511. 2008
    ..Both AID and these components of an emerging error-prone mutasome are regulated on many levels by complex mechanisms that are only beginning to be elucidated...
  92. ncbi request reprint The APOBEC-2 crystal structure and functional implications for the deaminase AID
    Courtney Prochnow
    Molecular and Computational Biology, University of Southern California Los Angeles, California 90089, USA
    Nature 445:447-51. 2007
    ..The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation...
  93. ncbi request reprint AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation
    Michelle L Duquette
    Department of Biochemistry, University of Washington Medical School, Seattle, 98195 7650, USA
    Oncogene 24:5791-8. 2005
    ..Aberrant targeting of AID to DNA structures formed upon c-MYC transcription may therefore contribute to the genetic instability of c-MYC in B-cell malignancies...
  94. ncbi request reprint Chelation of vanadium(V) by difluoromethylene bisphosphonate, a structural analogue of pyrophosphate
    Debbie C Crans
    Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
    Inorg Chem 46:6723-32. 2007
    ..Given the larger size of this anion compared to PPi, the chelation affinity upon CF2 substitution was found to be 4-5-fold reduced at neutral pH...
  95. pmc Steric and electrostatic effects in DNA synthesis by the SOS-induced DNA polymerases II and IV of Escherichia coli
    Adam P Silverman
    Department of Chemistry, Stanford University, Stanford, California 94305 5080, USA
    Biochemistry 46:13874-81. 2007
    ..Comparisons are made to recent data for DNA pol I (Klenow fragment), the archaeal polymerase Dpo4, and human pol kappa...
  96. ncbi request reprint Methylation protects cytidines from AID-mediated deamination
    Mani Larijani
    Department of Immunology, University of Toronto, Medical Sciences Bldg 5265, Toronto, Canada, M5S 1A8
    Mol Immunol 42:599-604. 2005
    ..These data also suggest that AID, and possibly other related cytidine deaminases, might represent a more rapid alternative to bisulfite sequencing for identifying methylated-CpG motifs...
  97. ncbi request reprint The essential C family DnaE polymerase is error-prone and efficient at lesion bypass
    Irina Bruck
    The Rockefeller University, New York, New York 10021, USA
    J Biol Chem 278:44361-8. 2003
    ..Thus, DnaE may function in an error-prone capacity that may be essential in Gram-positive cells but not Gram-negative cells, suggesting a fundamental difference in DNA metabolism between these two classes of bacteria...
  98. ncbi request reprint DNA deaminases AID and APOBEC3G act processively on single-stranded DNA
    Phuong Pham
    DNA Repair (Amst) 6:689-92; author reply 693-4. 2007