John R Roth

Title(s)Professor Emeritus, Microbiology and Molecular Genetics
SchoolCollege of Biological Sciences
Address314 Briggs Hall
CA 95616
Phone530-752-6679
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    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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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    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: 3     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: 20     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: 114     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: 13     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: 10     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: 38     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: 110     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: 6     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: 3     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: 20     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: 15     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: 351     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: 7     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: 5     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: 646     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: 33     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: 72     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: 7     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: 59     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: 52     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: 28     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: 187     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: 54     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: 49     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: 18     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: 99     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: 48     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: 74     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: 74     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: 20     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: 26     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: 38     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: 5     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: 36     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: 21     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 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
    45. 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
    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: 16     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: 40     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: 23     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: 24     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: 18     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: 70     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: 21     Fields:    Translation:Cells
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