J W Drake

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Chaos and order in spontaneous mutation
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Genetics 173:1-8. 2006
  2. pmc The three faces of riboviral spontaneous mutation: spectrum, mode of genome replication, and mutation rate
    Libertad García-Villada
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    PLoS Genet 8:e1002832. 2012
  3. pmc Avoiding dangerous missense: thermophiles display especially low mutation rates
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
    PLoS Genet 5:e1000520. 2009
  4. pmc Too many mutants with multiple mutations
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Crit Rev Biochem Mol Biol 42:247-58. 2007
  5. pmc Mutations in clusters and showers
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 104:8203-4. 2007
  6. pmc Clusters of mutations from transient hypermutability
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 102:12849-54. 2005
  7. pmc Rates of spontaneous mutation
    J W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Genetics 148:1667-86. 1998
  8. ncbi request reprint The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes
    J W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Ann N Y Acad Sci 870:100-7. 1999
  9. pmc Mutation rates among RNA viruses
    J W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 2233, USA
    Proc Natl Acad Sci U S A 96:13910-3. 1999
  10. ncbi request reprint Conditional coupling of leading-strand and lagging-strand DNA synthesis at bacteriophage T4 replication forks
    F A Kadyrov
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 2233, USA
    J Biol Chem 276:29559-66. 2001

Collaborators

Detail Information

Publications27

  1. pmc Chaos and order in spontaneous mutation
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Genetics 173:1-8. 2006
  2. pmc The three faces of riboviral spontaneous mutation: spectrum, mode of genome replication, and mutation rate
    Libertad García-Villada
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    PLoS Genet 8:e1002832. 2012
    ..These results are contrasted with those previously reported for other riboviruses to depict the current state of the art in riboviral mutagenesis...
  3. pmc Avoiding dangerous missense: thermophiles display especially low mutation rates
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
    PLoS Genet 5:e1000520. 2009
    ..This result provides the first experimental support for the concept of an evolved balance between the total genomic impact of mutations and the cost of further reducing the basal mutation rate...
  4. pmc Too many mutants with multiple mutations
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Crit Rev Biochem Mol Biol 42:247-58. 2007
    ..Examples that impinge on human health may include carcinogenesis and the adaptation of microbial pathogens as they move between individual hosts...
  5. pmc Mutations in clusters and showers
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 104:8203-4. 2007
  6. pmc Clusters of mutations from transient hypermutability
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 102:12849-54. 2005
    ..In the case of the rapidly mutating riboviruses, the viral population appears to be composed of a majority with a mutation frequency substantially lower than the average and a minority with a huge mutational load...
  7. pmc Rates of spontaneous mutation
    J W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Genetics 148:1667-86. 1998
    ..It is now possible to specify some of the evolutionary forces that shape these diverse mutation rates...
  8. ncbi request reprint The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes
    J W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 2233, USA
    Ann N Y Acad Sci 870:100-7. 1999
    ..01. The reasons for different characteristic mutation rates among different organism groups remain mysterious and pose a substantial challenge to students of evolution...
  9. pmc Mutation rates among RNA viruses
    J W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 2233, USA
    Proc Natl Acad Sci U S A 96:13910-3. 1999
    ..76. (The rate per round of cell infection is twice this value or about 1.5.) This value is so large, and ribovirus genomes are so informationally dense, that even a modest increase extinguishes the population...
  10. ncbi request reprint Conditional coupling of leading-strand and lagging-strand DNA synthesis at bacteriophage T4 replication forks
    F A Kadyrov
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 2233, USA
    J Biol Chem 276:29559-66. 2001
    ..Instead, template DNA is required for the assembly of the T4 replication complex, which then catalyzes coordinated synthesis of leading and lagging strands in a conditionally coupled manner...
  11. ncbi request reprint Interacting fidelity defects in the replicative DNA polymerase of bacteriophage RB69
    A Bebenek
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
    J Biol Chem 276:10387-97. 2001
    ..Other replicative DNA polymerases may control fidelity by strategies similar to those used by RB69 gp43...
  12. pmc Mutational clusters generated by non-processive polymerases: A case study using DNA polymerase betain vitro
    Libertad García-Villada
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    DNA Repair (Amst) 9:871-8. 2010
    ..The reported excess of Pol beta-generated multiples in the HSV-tk system may reflect a reduced efficiency of detection of base substitutions that cause weak phenotypes, which in turn may artifactually increase the frequency of multiples...
  13. pmc On the mutation rate of herpes simplex virus type 1
    John W Drake
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709 2233, USA
    Genetics 170:969-70. 2005
    ..003 per chromosome replication. The pathogenic mammalian DNA virus herpes simplex type 1 has an estimated genomic mutation rate compatible with that value...
  14. pmc Characterization of DNA synthesis catalyzed by bacteriophage T4 replication complexes reconstituted on synthetic circular substrates
    Farid A Kadyrov
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 2233, USA
    Nucleic Acids Res 30:4387-97. 2002
    ..However, blocking lagging-strand synthesis by lowering the dCTP concentration, by omitting dCTP altogether, by adding ddCTP, or with a single abasic site had no immediate effect on the rate of extension of leading strands...
  15. ncbi request reprint UvsX recombinase and Dda helicase rescue stalled bacteriophage T4 DNA replication forks in vitro
    Farid A Kadyrov
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709 2233, USA
    J Biol Chem 279:35735-40. 2004
    ..This rescue is based on two sequential template-switching reactions that allow DNA replication to bypass a non-coding DNA lesion in a non-mutagenic manner...
  16. pmc Templated mutagenesis in bacteriophage T4 involving imperfect direct or indirect sequence repeats
    Gary E Schultz
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Genetics 178:661-73. 2008
    ..We also record an instance in which the mutation rates at two particular sites change concordantly with a distant sequence change, but in a manner that appears unrelated to templated mutagenesis...
  17. pmc Dissecting the fidelity of bacteriophage RB69 DNA polymerase: site-specific modulation of fidelity by polymerase accessory proteins
    Anna Bebenek
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709 2233, USA
    Genetics 162:1003-18. 2002
    ..Although the RB69 gp43 accessory proteins exerted little or no effect on total mutation rates in vitro, they strongly affected mutation rates at many specific sites, increasing some rates and decreasing others...
  18. ncbi request reprint A role for replication repair in the genesis of templated mutations
    Gary E Schultz
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, PO Box 12233, Research Triangle Park, NC 27709, USA
    J Mol Biol 358:963-73. 2006
    ....
  19. ncbi request reprint Properties of bacteriophage T4 proteins deficient in replication repair
    Farid A Kadyrov
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health Department of Health and Human Services, Research Triangle Park, North Carolina 27709 2233, USA
    J Biol Chem 278:25247-55. 2003
    ..In striking contrast, the mutant proteins are strongly impaired in promoting template switching, thus supporting the hypothesis of survival by template switching...
  20. pmc Anecdotal, historical and critical commentaries on genetics. Gisela Mosig
    Nancy G Nossal
    Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0830, USA
    Genetics 168:1097-104. 2004
  21. pmc The bacteriophage T4 rapid-lysis genes and their mutational proclivities
    Lauranell H Burch
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    J Bacteriol 193:3537-45. 2011
    ..We did not identify any mutations that might correspond to a putative rVI gene, and we did not focus on the famous rII genes because they appear to affect lysis only indirectly...
  22. pmc Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles
    Robert Friedman
    Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
    Genetics 167:1507-12. 2004
    ....
  23. pmc The roles of Tyr391 and Tyr619 in RB69 DNA polymerase replication fidelity
    Agata Jacewicz
    Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02 114 Warsaw, Pawinskiego 5A, Poland
    J Mol Biol 368:18-29. 2007
    ..The Y619F substitution would disrupt the hydrogen bond network at the primer terminus and may affect the alignment of the 3' primer terminus at the polymerase active site, slowing chemistry and overall DNA synthesis...
  24. pmc Processivity clamp gp45 and ssDNA-binding-protein gp32 modulate the fidelity of bacteriophage RB69 DNA polymerase in a sequence-specific manner, sometimes enhancing and sometimes compromising accuracy
    Anna Bebenek
    Institute of Biochemistry and Biophysics, Polish Academy of Science, Warsaw
    Genetics 169:1815-24. 2005
    ..Thus, accessory proteins contribute to the site-specific variability in mutation rates characteristically seen in mutational spectra...
  25. pmc The rate and character of spontaneous mutation in an RNA virus
    José M Malpica
    Departamento de Proteccion Vegetal, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, Carretera de la Coruña Km 7 5, 28040 Madrid, Spain
    Genetics 162:1505-11. 2002
    ..Therefore, the mutation process in populations of TMV and perhaps of riboviruses generally differs profoundly from that in populations of DNA-based microbes and may be strongly influenced by a subpopulation of mutator polymerases...
  26. pmc The rate and character of spontaneous mutation in Thermus thermophilus
    Reena R Mackwan
    Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45221 0006, USA
    Genetics 180:17-25. 2008
    ..thermophilus resembled those of the thermoacidophilic archaeon Sulfolobus acidocaldarius, despite important molecular differences between these two thermophiles and their genomes...
  27. pmc The L561A substitution in the nascent base-pair binding pocket of RB69 DNA polymerase reduces base discrimination
    Hong Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, Connecticut 06520, USA
    Biochemistry 45:2211-20. 2006
    ..This dominant-lethal phenotype was attributed to error catastrophe caused by the high rate of mutation expected from combining the pol L561A and exo(-) mutator activities...