John Roth

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Origin of mutations under selection: the adaptive mutation controversy
    John R Roth
    Microbiology Section, Division of Biological Sciences, University of California, Davis, California 95616, USA
    Annu Rev Microbiol 60:477-501. 2006
  2. ncbi request reprint Effect of chromosome location on bacterial mutation rates
    Richard Ellis Hudson
    Department of Ecology and Evolutionary Biology, 310 Biosciences West, University of Arizona, Tucson, AZ 85721, USA
    Mol Biol Evol 19:85-92. 2002
  3. pmc Accumulation of mutants in "aging" bacterial colonies is due to growth under selection, not stress-induced mutagenesis
    Marie Wrande
    Department of Cell and Molecular Biology, Box 596, The Biomedical Center, Uppsala University, S 75124 Uppsala, Sweden
    Proc Natl Acad Sci U S A 105:11863-8. 2008
  4. pmc The joys and terrors of fast adaptation: new findings elucidate antibiotic resistance and natural selection
    John R Roth
    Department of Microbiology, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
    Mol Microbiol 79:279-82. 2011
  5. ncbi request reprint Poxvirus use a "gene accordion" to tune out host defenses
    John R Roth
    Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
    Cell 150:671-2. 2012
  6. doi request reprint Genetic adaptation: a new piece for a very old puzzle
    John R Roth
    Department of Microbiology, University of California, Davis, Davis, CA 95616, USA
    Curr Biol 20:R15-7. 2010
  7. pmc Adaptive mutation: how growth under selection stimulates Lac(+) reversion by increasing target copy number
    John R Roth
    University of California Davis, Microbiology Section, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 186:4855-60. 2004
  8. pmc Rebuttal: adaptive mutation in Escherichia coli (Foster)
    John R Roth
    University of California, Davis, Microbiology Section, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 186:4854. 2004
  9. pmc Rebuttal: adaptive point mutation (Rosenberg and Hastings)
    John R Roth
    University of California Davis, Microbiology Section, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 186:4844. 2004
  10. ncbi request reprint Amplification-mutagenesis--how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation
    John R Roth
    Section of Microbiology, University of California Davis, Davis, CA 95616, USA
    Res Microbiol 155:342-51. 2004

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Origin of mutations under selection: the adaptive mutation controversy
    John R Roth
    Microbiology Section, Division of Biological Sciences, University of California, Davis, California 95616, USA
    Annu Rev Microbiol 60:477-501. 2006
    ..We suggest that the adaptive mutation controversy has persisted because the distinction between these two uses of selection has not been appreciated...
  2. ncbi request reprint Effect of chromosome location on bacterial mutation rates
    Richard Ellis Hudson
    Department of Ecology and Evolutionary Biology, 310 Biosciences West, University of Arizona, Tucson, AZ 85721, USA
    Mol Biol Evol 19:85-92. 2002
    ..At all loci, regardless of chromosome location, T.A --> G.C transversions were more frequent than A.T --> G.C transitions during the exponential phase...
  3. pmc Accumulation of mutants in "aging" bacterial colonies is due to growth under selection, not stress-induced mutagenesis
    Marie Wrande
    Department of Cell and Molecular Biology, Box 596, The Biomedical Center, Uppsala University, S 75124 Uppsala, Sweden
    Proc Natl Acad Sci U S A 105:11863-8. 2008
    ..Evidence is presented that these Rif(R) mutants accumulate because they grow faster than parent cells during the aging period. Direct tests revealed no increase in the frequency of other mutant types during the aging period...
  4. pmc The joys and terrors of fast adaptation: new findings elucidate antibiotic resistance and natural selection
    John R Roth
    Department of Microbiology, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
    Mol Microbiol 79:279-82. 2011
    ..The results strongly support the amplification-reversion model for fast adaptation and argue against the alternative idea of 'stress-induced mutagenesis'...
  5. ncbi request reprint Poxvirus use a "gene accordion" to tune out host defenses
    John R Roth
    Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
    Cell 150:671-2. 2012
    ..A multistep process of gene amplification, mutation, and reduction allows poxvirus to overcome host antiviral defenses. The mechanism speeds genetic adaptation and promises to be broadly applicable in many biological settings...
  6. doi request reprint Genetic adaptation: a new piece for a very old puzzle
    John R Roth
    Department of Microbiology, University of California, Davis, Davis, CA 95616, USA
    Curr Biol 20:R15-7. 2010
    ..Does stress create mutations or only serve as an agent of natural selection? New experiments reveal effects of transcription and temperature on the response to growth limitation and could help resolve a 150-year-old debate...
  7. pmc Adaptive mutation: how growth under selection stimulates Lac(+) reversion by increasing target copy number
    John R Roth
    University of California Davis, Microbiology Section, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 186:4855-60. 2004
  8. pmc Rebuttal: adaptive mutation in Escherichia coli (Foster)
    John R Roth
    University of California, Davis, Microbiology Section, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 186:4854. 2004
  9. pmc Rebuttal: adaptive point mutation (Rosenberg and Hastings)
    John R Roth
    University of California Davis, Microbiology Section, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 186:4844. 2004
  10. ncbi request reprint Amplification-mutagenesis--how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation
    John R Roth
    Section of Microbiology, University of California Davis, Davis, CA 95616, USA
    Res Microbiol 155:342-51. 2004
    ..Idiosyncrasies of the particular system described here accelerate this process, allowing an evolutionary series of events to be completed in only a few days...
  11. pmc Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation
    John R Roth
    Department of Biology, University of Utah, Salt Lake City, Utah 84122, USA
    Genetics 163:1483-96. 2003
    ..We conclude that temporary general mutagenesis during stress is unlikely to provide a long-term selective advantage in this or any similar genetic system...
  12. ncbi request reprint The effect of genomic position on reversion of a lac frameshift mutation (lacIZ33) during non-lethal selection (adaptive mutation)
    E Susan Slechta
    Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
    Mol Microbiol 44:1017-32. 2002
    ..These events are central to growth and reversion under selection because they increase the number of replicating lac alleles within each developing revertant clone...
  13. pmc Multiple pathways of selected gene amplification during adaptive mutation
    Elisabeth Kugelberg
    Section of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 103:17319-24. 2006
    ..These findings are relevant to genetic adaptation in any biological systems in which fitness can be increased by adding gene copies (e.g., cancer and bacterial drug resistance)...
  14. pmc The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types
    Elisabeth Kugelberg
    Department of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616, USA
    Genetics 185:65-80. 2010
    ..Growth improves with each step in formation of an SJ or aTID amplification, allowing selection to favor completion of the mutation process...
  15. pmc Formation of an F' plasmid by recombination between imperfectly repeated chromosomal Rep sequences: a closer look at an old friend (F'(128) pro lac)
    Eric Kofoid
    Department of Biology, University of Utah, Salt Lake City 84122, USA
    J Bacteriol 185:660-3. 2003
    ..The structure of F'(128) supports the idea that amplification is initiated by Rep-Rep recombination and that general mutagenesis requires coamplification of dinB (error-prone polymerase) with lac...
  16. pmc Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac
    E Susan Slechta
    Microbiology Section, Division of Biological Sciences, University of California, Davis, CA 95616, USA
    Proc Natl Acad Sci U S A 100:12847-52. 2003
    ..Thus mutagenesis is not a programmed response to stress but a side effect of amplification in a few clones; it is not central to the effect of selection on reversion...
  17. pmc Evidence that selected amplification of a bacterial lac frameshift allele stimulates Lac(+) reversion (adaptive mutation) with or without general hypermutability
    E Susan Slechta
    Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
    Genetics 161:945-56. 2002
    ..Reversion in the absence of mutagenesis is still dependent on RecA function, as expected if it depends on lac amplification (a recombination-dependent process). These observations support the amplification mutagenesis model...
  18. pmc Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination
    Andrew B Reams
    Department of Microbiology, College of Biological Sciences, University of California, Davis, California 95616, USA
    Genetics 184:1077-94. 2010
    ..While the reported results were obtained with the bacterium Salmonella enterica, the genetic implications seem likely to be of broader biological relevance...
  19. pmc Ohno's dilemma: evolution of new genes under continuous selection
    Ulfar Bergthorsson
    Department of Biology, University of New Mexico, Albuquerque, NM 87131 0001, USA
    Proc Natl Acad Sci U S A 104:17004-9. 2007
    ..Improvement of some copies relaxes selection on others and allows their loss by mutation (becoming pseudogenes). Ultimately one of the extra copies is able to provide all of the new activity...
  20. pmc Polyphosphate kinase protects Salmonella enterica from weak organic acid stress
    Marian Price-Carter
    Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
    J Bacteriol 187:3088-99. 2005
    ..The instability of MetA protein may provide a metabolic fuse that blocks growth under conditions that denature proteins; the sensitivity of this fuse is modulated by polyphosphate...
  21. pmc Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification
    Heather Hendrickson
    Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
    Proc Natl Acad Sci U S A 99:2164-9. 2002
    ..The sequence of events--amplification, mutation, segregation--may help to explain both the origins of some cancers and the evolution of new genes under selection...
  22. pmc One pathway can incorporate either adenine or dimethylbenzimidazole as an alpha-axial ligand of B12 cofactors in Salmonella enterica
    Peter J Anderson
    Section of Microbiology, University of California, Davis, California 95616, USA
    J Bacteriol 190:1160-71. 2008
    ..Synthesis of coenzyme pseudo-B12 cofactors requires the same enzymes (CobT, CobU, CobS, and CobC) that install DMB in the formation of coenzyme B12. Models are described for the mechanism and control of alpha-axial ligand installation...
  23. pmc Phenotypes of lexA mutations in Salmonella enterica: evidence for a lethal lexA null phenotype due to the Fels-2 prophage
    Kim Bunny
    Department of Biology, University of Utah, Salt Lake City 84112, USA
    J Bacteriol 184:6235-49. 2002
    ..In S. enterica, lexA(Ind(-)) mutants have the same phenotypes as their E. coli counterparts. Although lexA null mutants express their error-prone DinB polymerase constitutively, they are not mutators in either S. enterica or E. coli...
  24. pmc Assimilation of nicotinamide mononucleotide requires periplasmic AphA phosphatase in Salmonella enterica
    Julianne H Grose
    Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA
    J Bacteriol 187:4521-30. 2005
    ..Internal NMN produced by either route 2 or route 3 is deamidated to nicotinic acid mononucleotide and converted to NAD by the biosynthetic enzymes NadD and NadE...
  25. pmc Regulation of NAD synthesis by the trifunctional NadR protein of Salmonella enterica
    Julianne H Grose
    Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
    J Bacteriol 187:2774-82. 2005
    ..It is proposed that NAD and the superrepressor mutation exert their effects by preventing ATP from binding to the central domain...
  26. pmc A pH-sensitive function and phenotype: evidence that EutH facilitates diffusion of uncharged ethanolamine in Salmonella enterica
    Joseph T Penrod
    Section of Microbiology, University of California, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 186:6885-90. 2004
    ..As predicted for a transporter, EutH contributed to the toxicity of ethanolamine seen under some conditions; furthermore, fusion of EutH to fluorescent Yfp protein provided evidence that EutH is a membrane protein...
  27. pmc Lethal mutations in the isoprenoid pathway of Salmonella enterica
    Rita M Cornish
    Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
    J Bacteriol 188:1444-50. 2006
    ..The results complement the biochemical and bioinformatic approaches to the elucidation of the genes involved in the MEP pathway and also identify key residues for activity in the enzymes of the pathway...
  28. pmc Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica
    Joseph T Penrod
    Microbiology Section, Division of Biological Sciences, University of California Davis, Davis, CA, USA
    J Bacteriol 188:2865-74. 2006
    ..The EutG enzyme converts acetaldehyde to ethanol, which may improve carbon retention by forming acetals; alternatively, EutG may recycle NADH within the carboxysome...
  29. pmc Natural isolates of Salmonella enterica serovar Dublin carry a single nadA missense mutation
    Ulfar Bergthorsson
    Department of Biology, University of Utah, Salt Lake City, Utah, USA
    J Bacteriol 187:400-3. 2005
    ..A single nadA missense mutation causes the nutritional requirement of all serovar Dublin isolates tested. Models for persistence of this allele are tested and discussed...
  30. pmc Sinorhizobium meliloti bluB is necessary for production of 5,6-dimethylbenzimidazole, the lower ligand of B12
    Gordon R O Campbell
    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 103:4634-9. 2006
    ..Sequence comparison suggests that BluB is a member of the NADH/flavin mononucleotide (FMN)-dependent nitroreductase family, and we propose that it is involved in the conversion of FMN to DMB...
  31. pmc Evidence that feedback inhibition of NAD kinase controls responses to oxidative stress
    Julianne H Grose
    Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
    Proc Natl Acad Sci U S A 103:7601-6. 2006
    ..Activation of NadK may constitute a defensive response that resists loss of protective NADPH...
  32. pmc The amplification model for adaptive mutation: simulations and analysis
    Mats E Pettersson
    Department of Molecular Evolution, Uppsala University EBC, SE 75236 Uppsala, Sweden
    Genetics 169:1105-15. 2005
    ..The results imply that the amplification model can account for the behavior of the system using biologically reasonable parameter values and thus can, in principle, explain Cairnsian adaptive mutation...
  33. ncbi request reprint Genomic buffering mitigates the effects of deleterious mutations in bacteria
    Sophie Maisnier-Patin
    Department of Bacteriology, Swedish Institute for Infectious Disease Control and Microbiology and Tumor Center, Karolinska Institute, S 171 82 Stockholm, Sweden
    Nat Genet 37:1376-9. 2005
    ..These findings suggest that overexpression of chaperones contributes to antagonistic epistasis...
  34. pmc Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica
    David E Sheppard
    Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
    J Bacteriol 186:7635-44. 2004
    ..Another protein encoded in the operon (EutA) protects EA-lyase from inhibition by CN-B12 but does so without adenosylation of this corrinoid...

Research Grants52

  1. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 2009
    ..We've developed an assay for duplication segregation rate that avoids growth rate problems and shows that palindromic sequence stimulate duplication formation. ..
  2. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 1980
    ..The mechanism of chromosome rearrangement by Tn5 will be studied including identification of genes required for Tn5-mediated exchanges and determination of whether these functions are regulated...
  3. BIOSYNTHESIS OF VITAMIN B12 & ANAEROBIC METABOLISM
    John Roth; Fiscal Year: 1993
    ..coli, anaerobic behavior has received rather little attention. We have to contribute to a better understanding of anaerobic metabolism and its regulation, with special attention to the role of B-12...
  4. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 2002
    ..Finally, the proposal includes studying the behavior of the unusual transposable element IS200, which is found in virtually all Salmonella strains, but transposes very rarely. ..
  5. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John R Roth; Fiscal Year: 2010
    ..We've developed an assay for duplication segregation rate that avoids growth rate problems and shows that palindromic sequence stimulate duplication formation. ..
  6. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 2007
    ..We've developed an assay for duplication segregation rate that avoids growth rate problems and shows that palindromic sequence stimulates duplication formation. ..
  7. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 2006
    ..Thus they can be used to identify endogenous metabolic sources of DNA damage and the role of long-range replication in completion of a recombination event. ..
  8. BIOSYNTHESIS OF VITAMIN B12 AND ANAEROBIC METABOLISM
    John Roth; Fiscal Year: 2004
    ..coli. Understanding this metabolism may contribute to understanding the natural lifestyle of Salmonellae. ..
  9. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 2003
    ..Thus they can be used to identify endogenous metabolic sources of DNA damage and the role of long-range replication in completion of a recombination event. ..
  10. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 1993
    ..This work will be done in conjunction with other work on the recombination mechanisms and pathways involved in chromosomal rearrangement...
  11. GENETIC ANALYSIS OF BACTERIAL CHROMOSOME STRUCTURE
    John Roth; Fiscal Year: 1990
    ..We suspect that the structure of the bacterial chromosome includes sequences located appropriately for generation of advantageous duplications...