John R. Roth
Distinguished Professor
jrroth@ucdavis.edu

Microbiology

Office
314 Briggs Hall
530 752-6679


Picture of John Roth
 
Degrees:
1997 PhD (Honoris Causa) Umeå University, Umeå, Sweden
1965 PhD Johns Hopkins University Biology (Genetics)
1961 BA Harvard College Biochemical Sciences
Research Interests:

While natural selection is simple to define, it is difficult to follow in natural settings since common small-effect mutations dictate the sequence of events. This process seems to underlie the enhanced frequency with which favored variants appear during growth under selection. We are trying to dissect in detail one system that is often cited as evidence for stress-induced mutagenesis (adaptive mutation). We think we can convince you that it's all about growth under selection and has nothing to do with mutagenesis.
All Salmonellae dedicate 1% of their genome in synthesis of cobalamin (vitamin B12), which must contribute heavily to their fitness in a natural setting. Yet, in the laboratory, it is difficult to demonstrate an important role of B12 in wild type bacteria. The main uses of B12 are in supporting degradation of ethanolamine and propanediol for use as a source of carbon and energy. Enzymes for catabolizing these compounds are found in a carboxysome-like micro-compartment. We are trying to determine how this compartment works and how it benefits Salmonella in the wild. We think that understanding this compartment in Salmonella, may help us understand why similar compartments contain enzymes of CO2 fixation in bacteria that perform 30% of the global carbon fixation.
While genetic recombination is generally studied using genetic crosses, the process is used internally in bacteria, primarily for DNA repair and replication fork restarting. We study formation of chromosome rearrangments in Salmonella to learn about recombination mechanisms. Most recently we've found (to our surprise) that gene duplications arise by a mechanism that does not require recombination. Many duplications are not simple tandem repeats but have repeats that flank a central fragment positioned in inverse order (inversion duplications). We're testing a model by which inversion duplications form by a series of events initiated by short palindromes in the parent sequence. These are then converted by remodeling deletions into the several types of duplications that are commonly studied.
Awards:
1974-5 Guggenheim Fellow, Cold Spring Harbor Laboratory
1986 University of Utah Distinguished Research Award
1987 First Governor's Medal for Science and Technology for the State of Utah
1988 Member, National Academy of Sciences
1990 Rosenblatt Prize, University of Utah
1990-2002 Distinguished Professor, University of Utah
1996 Recipient of the James E. Talmage Presidential Endowed Chair in Biology, U. of Utah
1997 Fellow, American Academy of Microbiology
1998 Sackler Fellow at Tel Aviv University, Tel Aviv, Israel
2000-1 Leverhulme Fellow, Oxford University, Oxford, England
2009 Thomas Hunt Morgan Medal, Genetics Society of America
Department and Center Affiliations:
Department of Microbiology
Professional Societies:
American Society for Microbiology
Genetics Society of America
Society for General Microbiology
CBS Graduate Group Affiliations:
Genetics  
Graduate Groups not Housed in CBS:
Microbiology  
Publications: Last updated 9/22/2009
  • One pathway can incorporate either adenine or dimethylbenzimidazole as alpha-axial ligand of B12 cofactors in Salmonella enterica (2008) Anderson, P. J., Lango, J., Carkeet, C., Britten, A., Krautler, B., Hammock, B.D., and John R. Roth. J. Bacteriol.190:1160-1171
  • Ohno's Dilemma: Evolution of new genes under continuous selection. (2007) Bergthorsson, U., Andersson, D. I. and John. R. Roth Proc Natl Acad Sci (US) 104:17004-9
  • Multiple pathways of selected gene amplification during adaptive mutation. (2006) Kugelberg, E., Kofoid. E., Reams, A.B., Andersson, D.I. and J.R. Roth Proc. Natl Acad. Sci 103:17319-24.
  • Origins of Mutations Under Selection: The Adaptive Mutation Controversy Roth, J.R. (2006) Kugelberg, E., Reams, A.B., Kofoid, E. and D.I. Andersson. Ann Rev Microbiol 60:477-501.
  • Conserving a volatile metabolite: a role for carboxysomes in Salmonella enterica. (2006) Penrod, J. T. and J.R. Roth J. Bacteriol. 188: 2865-74
  • Evidence that feedback inhibition of NAD kinase controls responses to oxidative stress. (2006) Grose, J. H., Joss, L., Velick, S. and J.R. Roth Proc Natl Acad. Sci (US) 103:7601-7606
  • Wrande, M, Roth, J. R., Hughes, D. (2008) Accumulation of mutants in aging bacterial colonies is due to growth under selection, not stress-induced mutagensis. Proc Natl Acad Sci (US) 105:11863-11868
  • Sun, S., Berg, O. G., Roth, J. R., Andersson, D. I. (2009) Contribution of gene amplification to evolution of encreased antibiotic resistance in Salmonella typhimurium. Genetics 182:1183-1195
Laboratory Personnel:
Briggs 316, 318
http://rothlab.ucdavis.edu/
Associates: Eric Kofoid, Sophie Maisnier-Patin Post-docs: Andrew Reams, Cristina Tun-Garrido Grad Students: Semarhy Quinones-Soto, Emiko Sano, Douglas Huseby Support staff: Shery Roth, Natalie Duleba

Teaching Interests:
Origins of Life
Genetics of Bacteria
Analytical Genetics
Courses:
Biology Bis2A Origins and Essentials of Life Winter
Genetics GGG201A Analytical Genetics Fall
Key Words:
genetics, bacterial genetics, natural selection, origin of mutations, cobalamin, NAD