John R Roth

Title(s)Professor Emeritus, Microbiology and Molecular Genetics
SchoolUniversity of California, Davis
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. to make corrections and additions.
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    1. Integration of the pSLT Plasmid into the Salmonella Chromosome Results in a Temperature-Sensitive Growth Defect Due to Aberrant DNA Replication. J Bacteriol. 2020 09 23; 202(20). Wozniak CE, Hendriksen JJ, Olivera BM, Roth JR, Hughes KT. PMID: 32747428; PMCID: PMC7515242.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    2. Selective Inbreeding: Genetic Crosses Drive Apparent Adaptive Mutation in the Cairns-Foster System of Escherichia coli. Genetics. 2020 02; 214(2):333-354. Nguyen A, Maisnier-Patin S, Yamayoshi I, Kofoid E, Roth JR. PMID: 31810989; PMCID: PMC7017022.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    3. Selection and Plasmid Transfer Underlie Adaptive Mutation in Escherichia coli. Genetics. 2018 11; 210(3):821-841. Maisnier-Patin S, Roth JR. PMID: 30194073; PMCID: PMC6218229.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    4. Selection-Enhanced Mutagenesis of lac Genes Is Due to Their Coamplification with dinB Encoding an Error-Prone DNA Polymerase. Genetics. 2018 03; 208(3):1009-1021. Yamayoshi I, Maisnier-Patin S, Roth JR. PMID: 29301907; PMCID: PMC5844319.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    5. The Promiscuous sumA Missense Suppressor from Salmonella enterica Has an Intriguing Mechanism of Action. Genetics. 2017 02; 205(2):577-588. Cole AE, Hani FM, Altman R, Meservy M, Roth JR, Altman E. PMID: 27974497; PMCID: PMC5289838.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    6. 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. Roth JR, Maisnier-Patin S. PMID: 26883821; PMCID: PMC4800865.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    7. The Origin of Mutants Under Selection: How Natural Selection Mimics Mutagenesis (Adaptive Mutation). Cold Spring Harb Perspect Biol. 2015 Jul 01; 7(7):a018176. Maisnier-Patin S, Roth JR. PMID: 26134316; PMCID: PMC4484973.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    8. Mechanisms of gene duplication and amplification. Cold Spring Harb Perspect Biol. 2015 Feb 02; 7(2):a016592. Reams AB, Roth JR. PMID: 25646380; PMCID: PMC4315931.
      View in: PubMed   Mentions: 54     Fields:    Translation:Cells
    9. Plasmid copy number underlies adaptive mutability in bacteria. Genetics. 2014 Nov; 198(3):919-33. Sano E, Maisnier-Patin S, Aboubechara JP, Quiñones-Soto S, Roth JR. PMID: 25173846; PMCID: PMC4224180.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    10. Recombination and annealing pathways compete for substrates in making rrn duplications in Salmonella enterica. Genetics. 2014 Jan; 196(1):119-35. Reams AB, Kofoid E, Duleba N, Roth JR. PMID: 24214339; PMCID: PMC3872179.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    11. Evidence that a metabolic microcompartment contains and recycles private cofactor pools. J Bacteriol. 2013 Jun; 195(12):2864-79. Huseby DL, Roth JR. PMID: 23585538; PMCID: PMC3697265.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    12. Real-time evolution of new genes by innovation, amplification, and divergence. Science. 2012 Oct 19; 338(6105):384-7. Näsvall J, Sun L, Roth JR, Andersson DI. PMID: 23087246; PMCID: PMC4392837.
      View in: PubMed   Mentions: 89     Fields:    Translation:Cells
    13. Poxvirus use a "gene accordion" to tune out host defenses. Cell. 2012 Aug 17; 150(4):671-2. Roth JR, Andersson DI. PMID: 22901801.
      View in: PubMed   Mentions: 2     Fields:    
    14. Pathways of genetic adaptation: multistep origin of mutants under selection without induced mutagenesis in Salmonella enterica. Genetics. 2012 Nov; 192(3):987-99. Quiñones-Soto S, Reams AB, Roth JR. PMID: 22887815; PMCID: PMC3522171.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    15. Multiple pathways of duplication formation with and without recombination (RecA) in Salmonella enterica. Genetics. 2012 Oct; 192(2):397-415. Reams AB, Kofoid E, Kugelberg E, Roth JR. PMID: 22865732; PMCID: PMC3454872.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    16. The Origin of Mutants under Selection: Interactions of Mutation, Growth, and Selection. EcoSal Plus. 2011 Dec; 4(2). Andersson DI, Hughes D, Roth JR. PMID: 26442510.
      View in: PubMed   Mentions: 9     Fields:    
    17. 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. Thiennimitr P, Winter SE, Winter MG, Xavier MN, Tolstikov V, Huseby DL, Sterzenbach T, Tsolis RM, Roth JR, Bäumler AJ. PMID: 21969563; PMCID: PMC3198331.
      View in: PubMed   Mentions: 271     Fields:    Translation:AnimalsCells
    18. Effect of growth under selection on appearance of chromosomal mutations in Salmonella enterica. Genetics. 2011 Sep; 189(1):37-53. Quiñones-Soto S, Roth JR. PMID: 21705757; PMCID: PMC3176110.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    19. The joys and terrors of fast adaptation: new findings elucidate antibiotic resistance and natural selection. Mol Microbiol. 2011 Jan; 79(2):279-82. Roth JR. PMID: 21219449; PMCID: PMC3064428.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    20. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature. 2010 Sep 23; 467(7314):426-9. Winter SE, Thiennimitr P, Winter MG, Butler BP, Huseby DL, Crawford RW, Russell JM, Bevins CL, Adams LG, Tsolis RM, Roth JR, Bäumler AJ. PMID: 20864996; PMCID: PMC2946174.
      View in: PubMed   Mentions: 503     Fields:    Translation:AnimalsCells
    21. The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types. Genetics. 2010 May; 185(1):65-80. Kugelberg E, Kofoid E, Andersson DI, Lu Y, Mellor J, Roth FP, Roth JR. PMID: 20215473; PMCID: PMC2870977.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    22. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics. 2010 Apr; 184(4):1077-94. Reams AB, Kofoid E, Savageau M, Roth JR. PMID: 20083614; PMCID: PMC2865909.
      View in: PubMed   Mentions: 60     Fields:    Translation:Cells
    23. Genetic adaptation: a new piece for a very old puzzle. Curr Biol. 2010 Jan 12; 20(1):R15-7. Roth JR. PMID: 20152136.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    24. Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium. Genetics. 2009 Aug; 182(4):1183-95. Sun S, Berg OG, Roth JR, Andersson DI. PMID: 19474201; PMCID: PMC2728858.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    25. 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. Wrande M, Roth JR, Hughes D. PMID: 18701713; PMCID: PMC2515621.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    26. 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. Anderson PJ, Lango J, Carkeet C, Britten A, Kräutler B, Hammock BD, Roth JR. PMID: 17981976; PMCID: PMC2238215.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    27. Ohno's dilemma: evolution of new genes under continuous selection. Proc Natl Acad Sci U S A. 2007 Oct 23; 104(43):17004-9. Bergthorsson U, Andersson DI, Roth JR. PMID: 17942681; PMCID: PMC2040452.
      View in: PubMed   Mentions: 154     Fields:    
    28. Multiple pathways of selected gene amplification during adaptive mutation. Proc Natl Acad Sci U S A. 2006 Nov 14; 103(46):17319-24. Kugelberg E, Kofoid E, Reams AB, Andersson DI, Roth JR. PMID: 17082307; PMCID: PMC1633709.
      View in: PubMed   Mentions: 50     Fields:    Translation:Cells
    29. 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. Grose JH, Joss L, Velick SF, Roth JR. PMID: 16682646; PMCID: PMC1472491.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    30. Human vitamin B12 absorption measurement by accelerator mass spectrometry using specifically labeled (14)C-cobalamin. Proc Natl Acad Sci U S A. 2006 Apr 11; 103(15):5694-9. Carkeet C, Dueker SR, Lango J, Buchholz BA, Miller JW, Green R, Hammock BD, Roth JR, Anderson PJ. PMID: 16585531; PMCID: PMC1458635.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    31. Conserving a volatile metabolite: a role for carboxysome-like organelles in Salmonella enterica. J Bacteriol. 2006 Apr; 188(8):2865-74. Penrod JT, Roth JR. PMID: 16585748; PMCID: PMC1447003.
      View in: PubMed   Mentions: 84     Fields:    Translation:Cells
    32. Sinorhizobium meliloti bluB is necessary for production of 5,6-dimethylbenzimidazole, the lower ligand of B12. Proc Natl Acad Sci U S A. 2006 Mar 21; 103(12):4634-9. Campbell GR, Taga ME, Mistry K, Lloret J, Anderson PJ, Roth JR, Walker GC. PMID: 16537439; PMCID: PMC1450223.
      View in: PubMed   Mentions: 39     Fields:    Translation:AnimalsCells
    33. Lethal mutations in the isoprenoid pathway of Salmonella enterica. J Bacteriol. 2006 Feb; 188(4):1444-50. Cornish RM, Roth JR, Poulter CD. PMID: 16452427; PMCID: PMC1367239.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    34. Origin of mutations under selection: the adaptive mutation controversy. Annu Rev Microbiol. 2006; 60:477-501. Roth JR, Kugelberg E, Reams AB, Kofoid E, Andersson DI. PMID: 16761951.
      View in: PubMed   Mentions: 69     Fields:    
    35. Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat Genet. 2005 Dec; 37(12):1376-9. Maisnier-Patin S, Roth JR, Fredriksson A, Nyström T, Berg OG, Andersson DI. PMID: 16273106.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    36. Assimilation of nicotinamide mononucleotide requires periplasmic AphA phosphatase in Salmonella enterica. J Bacteriol. 2005 Jul; 187(13):4521-30. Grose JH, Bergthorsson U, Xu Y, Sterneckert J, Khodaverdian B, Roth JR. PMID: 15968063; PMCID: PMC1151756.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    37. Polyphosphate kinase protects Salmonella enterica from weak organic acid stress. J Bacteriol. 2005 May; 187(9):3088-99. Price-Carter M, Fazzio TG, Vallbona EI, Roth JR. PMID: 15838036; PMCID: PMC1082818.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    38. Regulation of NAD synthesis by the trifunctional NadR protein of Salmonella enterica. J Bacteriol. 2005 Apr; 187(8):2774-82. Grose JH, Bergthorsson U, Roth JR. PMID: 15805524; PMCID: PMC1070365.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    39. Natural isolates of Salmonella enterica serovar Dublin carry a single nadA missense mutation. J Bacteriol. 2005 Jan; 187(1):400-3. Bergthorsson U, Roth JR. PMID: 15601727; PMCID: PMC538839.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    40. Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica. J Bacteriol. 2004 Nov; 186(22):7635-44. Sheppard DE, Penrod JT, Bobik T, Kofoid E, Roth JR. PMID: 15516577; PMCID: PMC524904.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    41. The amplification model for adaptive mutation: simulations and analysis. Genetics. 2005 Feb; 169(2):1105-15. Pettersson ME, Andersson DI, Roth JR, Berg OG. PMID: 15489536; PMCID: PMC1449099.
      View in: PubMed   Mentions: 11     Fields:    
    42. 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. Penrod JT, Mace CC, Roth JR. PMID: 15466042; PMCID: PMC522209.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    43. Adaptive mutation: how growth under selection stimulates Lac(+) reversion by increasing target copy number. J Bacteriol. 2004 Aug; 186(15):4855-60. Roth JR, Andersson DI. PMID: 15262920; PMCID: PMC451646.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    44. Rebuttal: adaptive mutation in Escherichia coli (Foster). J Bacteriol. 2004 Aug; 186(15):4854. Roth JR, Andersson DI. PMID: 15262919; PMCID: PMC451648.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    45. Rebuttal: adaptive point mutation (Rosenberg and Hastings). J Bacteriol. 2004 Aug; 186(15):4844. Roth JR, Andersson DI. PMID: 15262915; PMCID: PMC451647.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    46. 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. Roth JR, Andersson DI. PMID: 15207866.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    47. 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. Slechta ES, Bunny KL, Kugelberg E, Kofoid E, Andersson DI, Roth JR. PMID: 14559967; PMCID: PMC240707.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    48. Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation. Genetics. 2003 Apr; 163(4):1483-96. Roth JR, Kofoid E, Roth FP, Berg OG, Seger J, Andersson DI. PMID: 12702691; PMCID: PMC1462528.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    49. 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. Kofoid E, Bergthorsson U, Slechta ES, Roth JR. PMID: 12511513; PMCID: PMC145332.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    50. 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. Slechta ES, Liu J, Andersson DI, Roth JR. PMID: 12136002; PMCID: PMC1462195.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    51. 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. Slechta ES, Harold J, Andersson DI, Roth JR. PMID: 12010495.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    52. 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. Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth JR. PMID: 11830643; PMCID: PMC122336.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansCells
    53. Effect of chromosome location on bacterial mutation rates. Mol Biol Evol. 2002 Jan; 19(1):85-92. Hudson RE, Bergthorsson U, Roth JR, Ochman H. PMID: 11752193.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells