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John R Roth

TitlePROF-AY
InstitutionUniversity of California Davis
DepartmentMICROBIOLOGY & MOLEC GENETICS
Address314 Briggs Hall
CA 95616
Phone530-752-6679
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    Collapse Research 
    Collapse Research Activities and Funding
    POPULATION BIOLOGY AND EVOLUTION OF MICROORGANISMS
    NIH/NIAID R13AI034518Jun 25, 1993 - Jun 24, 1994
    Role: Principal Investigator
    BIOSYNTHESIS OF VITAMIN B12 AND ANAEROBIC METABOLISM
    NIH/NIGMS R01GM034804Jul 1, 1985 - Aug 31, 2005
    Role: Principal Investigator
    Duplications, amplifications and the response of bacterial populations to selection
    NIH/NIGMS R01GM027068Dec 1, 1979 - Jun 30, 2019
    Role: Principal Investigator
    Training Program in Genetics
    NIH/NIGMS T32GM007464Jul 1, 1977 - Jun 30, 2021
    Role: Co-Principal Investigator
    GENE REGULATION IN BACTERIA
    NIH/NIGMS R01GM023408Jan 1, 1977 - Dec 31, 1999
    Role: Principal Investigator
    GENE REGULATION IN BACTERIA
    NIH/NIGMS R37GM023408Jan 1, 1977 - Dec 31, 1994
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Yamayoshi I, Maisnier-Patin S, Roth J. Selection-Enhanced Mutagenesis of lac Genes Is Due to Their Coamplification with dinB Encoding an Error-Prone DNA Polymerase. Genetics. 2018 Mar; 208(3):1009-1021. PMID: 29301907.
      View in: PubMed
    2. Cole AE, Hani FM, Altman R, Meservy M, Roth J, Altman E. The Promiscuous sumA Missense Suppressor from Salmonella enterica Has an Intriguing Mechanism of Action. Genetics. 2017 02; 205(2):577-588. PMID: 27974497.
      View in: PubMed
    3. Roth J, Maisnier-Patin S. Reinterpreting Long-Term Evolution Experiments: Is Delayed Adaptation an Example of Historical Contingency or a Consequence of Intermittent Selection? J Bacteriol. 2016 Feb 16; 198(7):1009-12. PMID: 26883821; PMCID: PMC4800865 [Available on 10/01/16].
    4. Maisnier-Patin S, Roth J. The Origin of Mutants Under Selection: How Natural Selection Mimics Mutagenesis (Adaptive Mutation). Cold Spring Harb Perspect Biol. 2015 Jul 01; 7(7):a018176. PMID: 26134316.
      View in: PubMed
    5. Reams AB, Roth J. Mechanisms of gene duplication and amplification. Cold Spring Harb Perspect Biol. 2015 Feb 02; 7(2):a016592. PMID: 25646380.
      View in: PubMed
    6. Sano E, Maisnier-Patin S, Aboubechara JP, Quiñones-Soto S, Roth J. Plasmid copy number underlies adaptive mutability in bacteria. Genetics. 2014 Nov; 198(3):919-33. PMID: 25173846; PMCID: PMC4224180.
    7. Reams AB, Kofoid E, Duleba N, Roth J. Recombination and annealing pathways compete for substrates in making rrn duplications in Salmonella enterica. Genetics. 2014 Jan; 196(1):119-35. PMID: 24214339; PMCID: PMC3872179.
    8. Huseby DL, Roth J. Evidence that a metabolic microcompartment contains and recycles private cofactor pools. J Bacteriol. 2013 Jun; 195(12):2864-79. PMID: 23585538; PMCID: PMC3697265.
    9. Näsvall J, Sun L, Roth J, Andersson DI. Real-time evolution of new genes by innovation, amplification, and divergence. Science. 2012 Oct 19; 338(6105):384-7. PMID: 23087246; PMCID: PMC4392837.
    10. Roth J, Andersson DI. Poxvirus use a "gene accordion" to tune out host defenses. Cell. 2012 Aug 17; 150(4):671-2. PMID: 22901801.
      View in: PubMed
    11. Quiñones-Soto S, Reams AB, Roth J. Pathways of genetic adaptation: multistep origin of mutants under selection without induced mutagenesis in Salmonella enterica. Genetics. 2012 Nov; 192(3):987-99. PMID: 22887815; PMCID: PMC3522171.
    12. Reams AB, Kofoid E, Kugelberg E, Roth J. Multiple pathways of duplication formation with and without recombination (RecA) in Salmonella enterica. Genetics. 2012 Oct; 192(2):397-415. PMID: 22865732; PMCID: PMC3454872.
    13. Andersson DI, Hughes D, Roth J. The Origin of Mutants under Selection: Interactions of Mutation, Growth, and Selection. EcoSal Plus. 2011 Dec; 4(2). PMID: 26442510.
      View in: PubMed
    14. Thiennimitr P, Winter SE, Winter MG, Xavier MN, Tolstikov V, Huseby DL, Sterzenbach T, Tsolis RM, Roth J, Bäumler AJ. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc Natl Acad Sci U S A. 2011 Oct 18; 108(42):17480-5. PMID: 21969563; PMCID: PMC3198331.
    15. Quiñones-Soto S, Roth J. Effect of growth under selection on appearance of chromosomal mutations in Salmonella enterica. Genetics. 2011 Sep; 189(1):37-53. PMID: 21705757; PMCID: PMC3176110.
    16. Roth J. The joys and terrors of fast adaptation: new findings elucidate antibiotic resistance and natural selection. Mol Microbiol. 2011 Jan; 79(2):279-82. PMID: 21219449; PMCID: PMC3064428.
    17. Winter SE, Thiennimitr P, Winter MG, Butler BP, Huseby DL, Crawford RW, Russell JM, Bevins CL, Adams LG, Tsolis RM, Roth J, Bäumler AJ. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature. 2010 Sep 23; 467(7314):426-9. PMID: 20864996; PMCID: PMC2946174.
    18. Kugelberg E, Kofoid E, Andersson DI, Lu Y, Mellor J, Roth FP, Roth J. The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types. Genetics. 2010 May; 185(1):65-80. PMID: 20215473; PMCID: PMC2870977.
    19. Reams AB, Kofoid E, Savageau M, Roth J. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics. 2010 Apr; 184(4):1077-94. PMID: 20083614; PMCID: PMC2865909.
    20. Roth J. Genetic adaptation: a new piece for a very old puzzle. Curr Biol. 2010 Jan 12; 20(1):R15-7. PMID: 20152136.
      View in: PubMed
    21. Sun S, Berg OG, Roth J, Andersson DI. Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium. Genetics. 2009 Aug; 182(4):1183-95. PMID: 19474201; PMCID: PMC2728858.
    22. Wrande M, Roth J, Hughes D. Accumulation of mutants in "aging" bacterial colonies is due to growth under selection, not stress-induced mutagenesis. Proc Natl Acad Sci U S A. 2008 Aug 19; 105(33):11863-8. PMID: 18701713; PMCID: PMC2515621.
    23. Anderson PJ, Lango J, Carkeet C, Britten A, Kräutler B, Hammock BD, Roth J. One pathway can incorporate either adenine or dimethylbenzimidazole as an alpha-axial ligand of B12 cofactors in Salmonella enterica. J Bacteriol. 2008 Feb; 190(4):1160-71. PMID: 17981976; PMCID: PMC2238215.
    24. Bergthorsson U, Andersson DI, Roth J. Ohno's dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A. 2007 Oct 23; 104(43):17004-9. PMID: 17942681; PMCID: PMC2040452.
    25. Kugelberg E, Kofoid E, Reams AB, Andersson DI, Roth J. Multiple pathways of selected gene amplification during adaptive mutation. Proc Natl Acad Sci U S A. 2006 Nov 14; 103(46):17319-24. PMID: 17082307; PMCID: PMC1633709.
    26. Grose JH, Joss L, Velick SF, Roth J. Evidence that feedback inhibition of NAD kinase controls responses to oxidative stress. Proc Natl Acad Sci U S A. 2006 May 16; 103(20):7601-6. PMID: 16682646; PMCID: PMC1472491.
    27. Penrod JT, Roth J. Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol. 2006 Apr; 188(8):2865-74. PMID: 16585748; PMCID: PMC1447003.
    28. Cornish RM, Roth J, Poulter CD. Lethal mutations in the isoprenoid pathway of Salmonella enterica. J Bacteriol. 2006 Feb; 188(4):1444-50. PMID: 16452427; PMCID: PMC1367239.
    29. Roth J, Kugelberg E, Reams AB, Kofoid E, Andersson DI. Origin of mutations under selection: the adaptive mutation controversy. Annu Rev Microbiol. 2006; 60:477-501. PMID: 16761951.
      View in: PubMed
    30. Maisnier-Patin S, Roth J, Fredriksson A, Nyström T, Berg OG, Andersson DI. Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat Genet. 2005 Dec; 37(12):1376-9. PMID: 16273106.
      View in: PubMed
    31. Grose JH, Bergthorsson U, Xu Y, Sterneckert J, Khodaverdian B, Roth J. Assimilation of nicotinamide mononucleotide requires periplasmic AphA phosphatase in Salmonella enterica. J Bacteriol. 2005 Jul; 187(13):4521-30. PMID: 15968063; PMCID: PMC1151756.
    32. Price-Carter M, Fazzio TG, Vallbona EI, Roth J. Polyphosphate kinase protects Salmonella enterica from weak organic acid stress. J Bacteriol. 2005 May; 187(9):3088-99. PMID: 15838036; PMCID: PMC1082818.
    33. Grose JH, Bergthorsson U, Roth J. Regulation of NAD synthesis by the trifunctional NadR protein of Salmonella enterica. J Bacteriol. 2005 Apr; 187(8):2774-82. PMID: 15805524; PMCID: PMC1070365.
    34. Bergthorsson U, Roth J. Natural isolates of Salmonella enterica serovar Dublin carry a single nadA missense mutation. J Bacteriol. 2005 Jan; 187(1):400-3. PMID: 15601727; PMCID: PMC538839.
    35. Sheppard DE, Penrod JT, Bobik T, Kofoid E, Roth J. Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica. J Bacteriol. 2004 Nov; 186(22):7635-44. PMID: 15516577; PMCID: PMC524904.
    36. Pettersson ME, Andersson DI, Roth J, Berg OG. The amplification model for adaptive mutation: simulations and analysis. Genetics. 2005 Feb; 169(2):1105-15. PMID: 15489536; PMCID: PMC1449099.
    37. Penrod JT, Mace CC, Roth J. A pH-sensitive function and phenotype: evidence that EutH facilitates diffusion of uncharged ethanolamine in Salmonella enterica. J Bacteriol. 2004 Oct; 186(20):6885-90. PMID: 15466042; PMCID: PMC522209.
    38. Roth J, Andersson DI. Adaptive mutation: how growth under selection stimulates Lac(+) reversion by increasing target copy number. J Bacteriol. 2004 Aug; 186(15):4855-60. PMID: 15262920; PMCID: PMC451646.
    39. Roth J, Andersson DI. Rebuttal: adaptive point mutation (Rosenberg and Hastings). J Bacteriol. 2004 Aug; 186(15):4844. PMID: 15262915; PMCID: PMC451647.
    40. Roth J, Andersson DI. Rebuttal: adaptive mutation in Escherichia coli (Foster). J Bacteriol. 2004 Aug; 186(15):4854. PMID: 15262919; PMCID: PMC451648.
    41. Roth J, Andersson DI. Amplification-mutagenesis--how growth under selection contributes to the origin of genetic diversity and explains the phenomenon of adaptive mutation. Res Microbiol. 2004 Jun; 155(5):342-51. PMID: 15207866.
      View in: PubMed
    42. Slechta ES, Bunny KL, Kugelberg E, Kofoid E, Andersson DI, Roth J. Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12847-52. PMID: 14559967; PMCID: PMC240707.
    43. Roth J, Kofoid E, Roth FP, Berg OG, Seger J, Andersson DI. Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation. Genetics. 2003 Apr; 163(4):1483-96. PMID: 12702691; PMCID: PMC1462528.
    44. Kofoid E, Bergthorsson U, Slechta ES, Roth J. Formation of an F' plasmid by recombination between imperfectly repeated chromosomal Rep sequences: a closer look at an old friend (F'(128) pro lac). J Bacteriol. 2003 Jan; 185(2):660-3. PMID: 12511513; PMCID: PMC145332.
    45. Slechta ES, Liu J, Andersson DI, Roth J. Evidence that selected amplification of a bacterial lac frameshift allele stimulates Lac(+) reversion (adaptive mutation) with or without general hypermutability. Genetics. 2002 Jul; 161(3):945-56. PMID: 12136002; PMCID: PMC1462195.
    46. Slechta ES, Harold J, Andersson DI, Roth J. The effect of genomic position on reversion of a lac frameshift mutation (lacIZ33) during non-lethal selection (adaptive mutation). Mol Microbiol. 2002 May; 44(4):1017-32. PMID: 12010495.
      View in: PubMed
    47. Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth J. Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification. Proc Natl Acad Sci U S A. 2002 Feb 19; 99(4):2164-9. PMID: 11830643; PMCID: PMC122336.
    48. Hudson RE, Bergthorsson U, Roth J, Ochman H. Effect of chromosome location on bacterial mutation rates. Mol Biol Evol. 2002 Jan; 19(1):85-92. PMID: 11752193.
      View in: PubMed
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