Roth -1JOHN R. ROTH
CURRICULUM VITAE
Education:
1957-1961
1961-1965
B. A.
Ph.D.
Harvard College, Cambridge, Massachusetts
The Johns Hopkins University, Baltimore, Maryland
(Philip Hartman - Advisor)
Postdoctoral Training:
1965-1967
National Institutes of Health, Bethesda, Maryland (Bruce Ames - Advisor)
University Positions Held:
1967
1971
1975
1976-1990
1989-1993
1990-2002
2002-present
2003-
Assistant Professor, University of California, Berkeley
Associate Professor, University of California, Berkeley
Professor, University of California, Berkeley
Professor, University of Utah, Department of Biology
Chairman, Department of Biology, University of Utah
Distinguished Professor, University of Utah
Distinguished Professor, Microbiology Section of Biological Sciences,
University of California, Davis
Chair, Microbiology Section , College of Biological Sciences, UC Davis
Other Experience:
1974-1975
1972-1976
1977-1980
1983-1987
1985-1988
1998
1999
2000-1
Guggenheim Fellow at Cold Spring Harbor Laboratory
Member of Genetics Study Section, NIH
Taught Bacterial Genetics course at Cold Spring Harbor Laboratory with David
Botstein and Ron Davis
Member of Microbial Physiology and Genetics Study Section
Coordinator of Program in Molecular Biology; Campus-wide graduate program
at University of Utah
Consultant to Merck Sharp & Doehm
Consultant to Synergen, Inc.
Consultant to Rhône Poulenc Sante, Paris, France
Sackler Fellow at Tel Aviv University, Tel Aviv, Israel
Sabbatical visitor in Toulouse, France
Leverhulme Fellow at Oxford University, Oxford, England
Honors and Awards:
1984
1986
1986, 1987
Co-Chairman of Gordon Research Conference (Biological Regulatory
Mechanisms)
University of Utah Distinguished Research Award
Co-Chairman of Cold Spring Harbor Phage and Bacterial Genetics Meeting
Roth -21987
1988
1990
1993
1995-present
1996
1997
First Annual Governor's Medal for Science and Technology for the State of
Utah
Member, National Academy of Sciences
Rosenblatt Prize, University of Utah
Chairman of Gordon Research Conference (Microbial Population Biology &
Evolution)
Co-Chairman of Keystone Conference (Bacterial Chromosomes)
Recipient of the James E. Talmage Presidential Endowed Chair in Biology
Honorary Doctorate, Umeå University, Umeå, Sweden
Areas of Interest and Current Research Projects:
All of the projects outlined below involve genetic analysis of the bacterium, Salmonella
typhimurium. While the projects have distinct goals, they are related in the methods and general
approaches used.
1) Recombination and chromosome rearrangements - This project was initiated in an attempt to
better understand the structure of the folded bacterial chromosome and the selective forces that have
conserved the genetic map over the past 108 years (since the divergence of Salmonella and E. coli).
We have found that duplications are frequent, well-tolerated and can be selectively valuable while
inversions are rare and sometimes deleterious. This has suggested that the recombination system of
bacteria may be structured to minimize exchanges between inverse-order repeats.
In the course of this work, we have realized that rearrangements provide a very useful system
for studying the process of recombination. Repeated chromosomal sequences provide substrates that
lack the double stranded ends provided by sexual assays and thus may more accurately reflect the
normal role of recombination. Using duplication segregation as an assay, we have found that the
RecBC and RecF pathways seem to operate on distinct types of initiating damage. We have also
found evidence that reactive oxygen species generated by oxitative metabolism are the major source
of DNA damage for initiating sister strand recombination. Recombination between separated directorder repeats allows one to observe reciprocality of recombination; a reciprocal exchange generates
two cells, one with a deletion and the other with a duplication of the intervening region. Thus far we
estimate that about 25% of sister strand exchanges are reciprocal. Reciprocal recombination
between inverse-order sequences seems to be prohibited when the intervening region includes a
replication terminatioin (TER) site. This suggests that intrachromosomal recombination may initiate
extensive chromosomal replication.
We have also been using P22-mediated transduction to develop new recombination assays. It
is our general belief that there is still a role for genetic analysis in the study of recombination, and in
assessing the biological role of known recombination proteins.
2) Synthesis and significance of cobalamin (B12) - This cofactor is unevenly distributed among
living things, suggesting that it might be associated with particular lifestyles or growth conditions.
We discovered that Salmonella dedicates about 1% of its genome to B12 production and import,
suggesting frequent use of the cofactor under natural conditions. Under standard laboratory
conditions, there is no growth phenotype associated with B12 deficiency. Recently we have found
that during anaerobic growth using tetrationate as electron acceptor, Salmonella uses endogenous
B12 to support respiration of propanediol and ethanolamine. We are using genetics to approach the
Roth -3synthetic pathway of B12 and it's regulation. We are also studying the structure and control of the
two operon that encode degradative enzymes for ethanolamine (eut) and propanediol (pdu).
3) Recycling of NAD - While NAD is well known as an electron carrier, it also energizes DNA
ligation and supports the potentially dangerous Fenton reaction which generates OH radicals from
H2O2. We are trying to understand the synthesis and recycling of NAD and how it relates to energy
metabolism, DNA repair and oxidative stress. The large NAD pool is subject to breakdown to NMN
which is recycled to NAD through two pathways. The ligase-dependent NAD breakdown is only
about 20% of the NMN production under aerobic conditions. The rest of the cycle is eliminated
during anaerobic growth by unknown reactions. In pursuit of this major metabolic cycle we have
isolated mutants for almost every known step of NAD synthesis and metabolism. We have
discovered two NAD kinases (producing NADP) and we have found that a deficit in NAD kinase
leads to oxygen-sensitivity and inability to grow on glucose. We have recently discovered a
recycling activity (NMN deamidase) that depends on DNA ligase and acts only in the presence of
oxygen. Thus oxygen appears to be a major player in control and significance of the recycling
pathway.
4) Adaptive mutation - We got involved in this controversial but very interesting area because of a
model we developed in which gene amplification is an intermediate in the reversion process. In
testing the model, we first found that the system used to demonstrate "adaptive mutation" requires
that the gene under selection be located on an F' plasmid and subject to transfer replication. We later
found that reversion of the plasmid-borne gene (both in Salmonella and E. coli) involves
intermediate amplification. We found evidence for adaptive mutation of chromosomal genes and
demonstrated that the delayed appearance of clones formed by pre-existing mutants could be
explained by competition between revertants and parental cells. Our working hypothesis is that all
the rare systems that appear to show stimulation of mutation by stress will prove to be explainable
by standard bacterial physiology and genetics and will not reflect evolved mechanisms to
deliberately mutagenize the genome.
Publications:
Roth, John R. and Philip E. Hartman (1965). Heterogeneity in P22 transducing particles. Virology
27:297-307.
Roth, John R. and Kenneth E. Sanderson (1966). Orientation of the isoleucine-valine genes in the
Salmonella typhimurium linkage map. Genetics 53:971-976.
Roth, John R., Dora N. Anton and Philip E. Hartman (1966). Histidine regulatory mutants in
Salmonella typhimurium. I: Isolation and general properties. J. Mol. Biol. 22:305-323.
Roth, John R. and Bruce N. Ames (1966). Histidine regulatory mutants in Salmonella typhimurium.
II: Histidine regulatory mutants having altered histidyl-tRNA synthetase. J. Mol. Biol.
22:325-334.
Roth -4Roth, John R., David F. Silbert, Gerald R. Fink, Mary Jane Voll, Dora Anton, Philip E. Hartman and
Bruce N. Ames (1966). Transfer RNA and the control of the histidine operon. Cold Spring
Harbor Symp. on Quant. Biol. 31:383-392.
Ames, B. N., Goldberger, R. F., Hartman, P. E., Martin R. G. and Roth, J. R. (1967) The histidine
operon. In: Regulation of Nucleic Acid and Protein Biosynthesis. V. V. Koningsberger and L.
Bosch (Eds.), Elsevier Publishing Co., Amsterdam. pp. 273-287.
Ames, G. F. and Roth, J. R. (1968) Histidine and aromatic permeases of Salmonella typhimurim. J.
Bacteriol. 96: 1742-1749.
Berkowitz, D., Hushon, J. M., Whitfield, H. J., Roth, J. R. and Ames, B. N. (1968) Procedure for
identifying nonsense mutations. J. Bacteriol. 96: 215-220.
Fink, G.R. and John R. Roth (1968). Histidine regulatory mutants in Salmonella typhimurium. VI.
Dominance studies. J. Mol. Biol. 33: 547-557.
Martin, R. G., Bagdasarian, M. and Roth, J. R. (1969) Regulation of the histidine operon.
Federation of European Biochemical Societies Symposium. 19: 1-4.
Roth, John R. (1970). Genetic techniques in studies of bacterial metabolism. In: Methods in
Enzmology, pages 3-35. Academic Press.
Roth, John R. (1970). UGA nonsense mutations in Salmonella typhimurium. J. Bacteriol. 102:467475.
Yourno, Joseph, Tadahiko Kohno and John R. Roth (1970). Enzyme evolution: Generation of a
bifunctional enzyme by fusion of adjacent genes. Nature 228:820-824.
Riddle, Donald L. and John R. Roth (1970). Suppressors of frameshift mutations in Salmonella
typhimurium. J. Mol. Biol. 54:131-144
Chang, George W., John R. Roth and Bruce N. Ames (1971). Histidine regulation in Salmonella
typhimurium. VIII. Mutations of the hisT gene. J. Bacteriol. 108:410-414.
Miller, Charles G. and John R. Roth (1971). Recessive-lethal nonsense suppressors in Salmonella
typhimurium. J. Mol. Biol. 59:63-75.
Reeves, Robert H. and John R. Roth (1971). A recessive UGA suppressor. J. Mol. Biol. 56:523533.
Riddle, Donald L. and John R. Roth (1972). Frameshift suppressors. II. Genetic mapping and
dominance studies. J. Mol. Biol. 66:483-493.
Lew, Kenneth K. and John R. Roth (1972). Genetic approaches to determination of enzyme
quaternary structure. Biochemistry 10:204-207.
Roth -5Syvanen, J. Michael and John R. Roth (1972). The structural genes for ornithine transcarbamylase
in Salmonella typhimurium and Escherichia coli K12. J. Bacteriol. 110:66-70.
Riddle, Donald L. and John R. Roth (1972). Frameshift suppressors. III. Effects of suppressor
mutations on transfer RNA. J. Mol. Biol. 66:495-506.
Syvanen, J. Michael and John R. Roth (1973). Structural genes of catalytic and regulatory subunits
of aspartate transcarbamylase. J. Mol. Biol. 767:363-378.
Hartman, P.E. and John R. Roth (1973). Mechanisms of suppression. Adv. in Genetics 17:1-105.
Uomini, Joanne and John R. Roth (1974).
Suppressor-dependent frameshift mutants of
bacteriophage P22. Molec. Gen. Genet. 134:237-241.
Lew, Kenneth K. and John R. Roth (1974). Isolation of UGA and UAG nonsense mutants of
bacteriophage P22. Virology 40:1059-1062.
Roth, John R. (1974). Frameshift mutations. Ann. Rev. Genetics 8:319-346.
Kohno, Tadahiko and John R. Roth (1974). Proflavin mutagenesis of bacteria. J. Mol. Biol. 89:1725.
Hoppe, Ingrid and John R. Roth (1974). Specialized transducing phages derived from Salmonella
phage P22. Genetics 76:633-654.
Kaye, Robert, John Barraveccio and John R. Roth (1974). Isolation of P22 specialized transducing
phage following F'episome fusion. Genetics 76:655-670.
Reeves, Robert H. and John R. Roth (1975). Transfer ribonucleic acid methylase deficiency found
in UGA suppressor strains. J. Bacteriol. 124:332-335.
Scott, John F., John R. Roth and S. Artz (1975). Regulation of the histidine operon is normal in
hisG deletion mutants of Salmonella typhimurium. Proc. Natl. Acad. Sci. USA 72:5021-5025.
Anderson, R.P., Charles G.M. and J.R. Roth (1976). Tandem duplications of the histidine operon
observed following generalized transduction in Salmonella typhimurium. J. Mol. Biol.
105:201-218.
Anderson, R.P. and J.R. Roth (1977). Tandem genetic duplications in phage and bacteria. Ann.
Rev. Microbiol. 31:473-505.
Kleckner, N., J.R. Roth and D. Botstein (1977). Genetic engineering in vivo using translocatable
drug-resistance elements. J. Mol. Biol. 116:125-159.
Anderson R.P. and J.R. Roth (1978).
Tandem chromosomal duplications in
Salmonellatyphimurium: Fusion of histidine genes to novel promoters. J. Mol. Biol. 119:137166.
Roth -6-
Anderson, R.P. and J.R. Roth (1978). Tandem genetic duplications in Salmonella typhimurium:
Amplification of the histidine operon. J. Mol. Biol. 126:561-575.
Kohno, Tadahiko and John R. Roth (1978). A Salmonella frameshift suppressor that acts at runs of
A residues in the messenger RNA. J. Mol. Biol. 126:37-52.
Ratzkin, B. and John R. Roth (1978). Regulation of the major proline permease gene of Salmonella
typhimurium. J. Bacteriol. 133:737-743.
Ratzkin, B. and John R. Roth (1978). Cluster of genes controlling proline degradation in Salmonella
typhimurium. J. Bacteriol. 133:744-754.
Chumley, F., R. Menzel and J.R. Roth (1979). Hfr formation directed by Tn10. Genetics 91:639655.
Anderson, R. Philip and John R. Roth (1979). Gene duplication in bacteria: Alteration of gene
dosage by sister-chromosome exchanges. Cold Spring Harbor Symp. in Quant. Biol. 43:10831087.
Johnston, H. Mark and John R. Roth (1979). Histidine mutants requiring adenine: Selection of
mutants with reduced hisG expression in Salmonella typhimurium. Genetics 92:17-26.
Hoppe, I., H.M. Johnston, D. Biek, J.R. Roth (1979). A refined map of the hisG gene of Salmonella
typhimurium. Genetics 92:17-26.
Kohno, Tadahiko and John R. Roth (1979). Electrolyte effects on the activity of mutant enzymes in
vivo and in vitro. Biochemistry 18:1386-1392.
Kohno, Tadahiko, Molly B. Schmid and John R. Roth (1980). Effect of electrolytes of growth of
mutant bacteria. In: Genetic Engineering of Osmoregulation, D. W. Rains, R. C. Valentine and
Alexander Hollaender (eds.), Plenum Publishing Corp.
Davis, R.W., D. Botstein, and J. Roth (1980). Advanced Bacterial Genetics Laboratory Manual.
Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
Johnston, H. Mark, W. Barnes, F.G. Chumley, L. Bossi and John R. Roth (1980). A model for
regulation of the histidine operon of Salmonella typhimurium. Proc. Natl. Acad. Sci. USA
77:508-512.
Biek, D. and J.R. Roth (1980). Regulation of Tn5 transposition. Proc. Natl. Acad. Sci. USA
77:6047-6051.
Bossi, Lionello and John R. Roth (1980).
translation. Nature 286:123-127.
The influence of codon context on genetic code
Roth -7Johnston, H. Mark and John R. Roth (1980). UGA suppressor that maps within a cluster of
ribosomal protein genes. J. Bacteriol. 144:300-305.
Chumley F. and J.R. Roth (1980). Rearrangement of the bacterial chromosome using Tn10 as a
region of homology. Genetics 94:1-14.
Menzel, Rolf and John R. Roth (1980). Identification and mapping of a second proline permease in
Salmonella typhimurium. J. Bacteriol. 141:1064-1070.
Schmid, Molly B. and J.R. Roth (1980). Circularization of transduced fragments: A mechanism for
adding segments on the bacterial chromosome. Genetics 94:15-29.
Biek, D. and J.R. Roth (1981). Regulation of Tn5 transposition. Cold Spring Harbor Symp. Quant.
Biol. 45:189-191.
Roth, J.R. (1981). New genetic techniques using transposable drug resistance elements.
Microbiology 1980, D. Schlessinger (ed.), American Society for Microbiology Press.
In:
Anderson, R. Philip and John R. Roth (1981). Spontaneous tandem genetic duplications in
Salmonella typhimurium arise by unequal recombination between ribosomal RNA (rrn)
cistrons. Proc. Natl. Acad. Sci. USA 78:3113-3117.
Roth, J.R. and M.B. Schmid (1981). Arrangement and rearrangement of the bacterial chromosome.
Stadler Symposium Vol. 13:53-70.
Bossi, Lionello and John R. Roth (1981). Four-base codons ACCA, ACCU and ACCC are
recognized by the frameshift suppressor sufJ. Cell 24:489-496.
Menzel, Rolf and John R. Roth (1981). Regulation of the genes for proline utilization in S.
typhimurium: Autogenous repression by the putA gene product. J. Mol. Biol. 148:21-44.
Menzel, Rolf and John R. Roth (1981). Purification of the putA gene product: A bifunctional
membrane-bound protein from S. typhimurium responsible for the two step oxidation of
proline to glutamate. J. Biol. Chem. 256:9755-9761.
Menzel, Rolf and John R. Roth (1981). Enzymatic properties of the purified putA protein from
Salmonella typhimurium. J. Biol. Chem. 256:9762-9766.
Roth, John R. (1981). Frameshift suppression. Cell 24:601-602.
Chumley, Forrest G. and John R. Roth (1981). Genetic fusions that place the lactose genes under
histidine operon control. J. Mol. Biol. 145:697-712.
Johnston, H. Mark and John R. Roth (1981). Genetic analysis of the histidine operon control region
of Salmonella typhimurium. J. Mol. Biol. 145:713-734.
Roth -8Johnston, H. Mark and John R. Roth (1981). DNA sequence changes of mutations altering
attenuation control of the histidine operon of Salmonella typhimurium. J. Mol. Biol. 145:735756.
Ciampi, M.S., M.B. Schmid and J.R. Roth (1982). The transposon Tn10 provides a promoter for
transcription of adjacent sequences. Proc. Natl. Acad. Sci. USA 79:5016-5020.
Kohno, Tadahiko, Lionello Bossi and John R. Roth (1982). New suppressors of frameshift
mutations in Salmonella typhimurium. Genetics 103:23-29.
Bossi, Lionello, Tadahiko Kohno and John R. Roth (1982). Genetic characteristics of the sufJ
suppressor in Salmonella typhimurium. Genetics 103:31-42.
Maloy, Stanley and John R. Roth (1983).
typhimurium. J. Bacteriol. 154:561-568
Regulation of proline utilization in Salmonella
Sanderson, K.E. and John R. Roth (1983).
Microbiological Reviews 47:410-453.
The linkage map of Salmonella typhimurium.
Lam, S. and J.R. Roth (1983). IS200: A Salmonella-specific insertion sequence element. Cell
34:931-939.
Lam, S. and J.R. Roth (1983). Genetic mapping of all IS200 copies in Salmonella typhimurium
strain LT2. Genetics 105:801-811.
Schmid, M. and J.R. Roth (1983). Genetic methods for analysis and manipulation of inversion
mutations in bacteria. Genetics 105:517-535.
Schmid, M. and J.R. Roth (1983). Selection and endpoint distribution of bacterial inversion
mutations. Genetics 105:539-557.
Hughes, Kelly T., Brad T. Cookson, Dubravka Ladika, Baldomero M. Olivera and John R. Roth
(1983). 6-Aminonicotinamide resistant mutants of Salmonella typhimurium. J. Bacteriol.
154:1126-1136.
Hughes, Kelly T., Dubravka Ladika, John R. Roth and Baldomero M. Olivera (1983).
indispensable gene involved in NAD biosynthesis, nadD. J. Bacteriol. 155:213-221.
An
Schmid, Molly and John R. Roth (1983). Internal promoters of the his operon of Salmonella
typhimurium. J. Bacteriol. 153:1114-1119.
Jeter, R. and J.R. Roth (1984). Salmonella typhimurium synthesizes cobalamin (vitamin B12) de
novo under anaerobic growth conditions. J. Bacteriol. 159:206-213.
Hughes, K.T. and J.R. Roth (1984). Conditionally transposition-defective derivative of Mu dl(Amp
Lac). J. Bacteriol. 159:130-137.
Roth -9Rudd, Kenneth, Barry Bochner, Michael Cashel and John R. Roth (1985). Mutation in the spoT gene
of Salmonella typhimurium: Effects on his operon expression. J. Bacteriol. 163:534-542.
Hughes, K.T. and J.R. Roth (1985). Directed formation of deletions and duplications using Mud
(Ap, lac). Genetics 109:263-282.
Hartman, P. E., Ames, B. N., Roth, J. R., Barnes, W. M. and Levin, D. E. (1986) Target sequences
for mutagenesis in Salmonella histidine-requiring mutants. Environmental Mutagenesis 8:
631-641.
Lam, S. and J.R. Roth (1986). Structural and functional studies of IS200. J. Mol. Biol. 187:157167.
Downs, Diana, Lloyd Waxman, Alfred Goldberg and John R. Roth (1986). Isolation and
characterization of lon mutants of Salmonella typhimurium. J. Bacteriol. 165:193-197.
Downs, Diana and J.R. Roth (1987). A novel P22 prophage in Salmonella typhimurium. Genetics
117:367-380.
Hughes, K.T., B.M. Olivera and J.R. Roth (1987). Rec dependence of Mu transposition from P22transduced fragments. J. Bacteriol. 169:403-409.
Escalante, J. and J.R. Roth (1987). Regulation of cobalamin biosynthetic operons in Salmonella
typhimurium. J. Bacteriol. 169:2251-2258.
Schmid, M.B. and J.R. Roth (1987). Gene location affects expression level in S. typhimurium. J.
Bacteriol. 169:2872-2875.
Jeter, R., J. Escalante-Semerena, D. Roof, B. Olivera, and J.R. Roth (1987). Synthesis and use of
vitamin B12. In: Escherichia coli and Salmonella typhimurium: Cellular and Molecular
Biology, F. Neidhardt, J. Ingraham, K. Low, B. Magasanik, M. Schaechter and H. Umbarger
(eds.), American Society for Microbiology, Washington, D.C., pp. 551-556.
Jeter, Randall and J.R. Roth (1987). Cobalamin (Vitamin B12) biosynthetic genes of Salmonella
typhimurium. J. Bacteriol. 169:3189-3198.
Cookson, B.T., B. Olivera, and J.R. Roth (1987). Genetic characterization of the nadB locus of S.
typhimurium and its regulation. J. Bacteriol. 169: 4285-4293.
Sanderson, K.E. and John R. Roth (1988). The linkage map of Salmonella typhimurium. Edition
VII. Microbiological Reviews. 52:485-532.
Ciampi, Sofia and John R. Roth (1988). Polarity effects in the hisG gene of Salmonella require a
site within the coding sequence. Genetics 118:193-202.
Hughes, Kelly T. and John R. Roth (1988). Transitory cis complementation: a general method for
providing transposase to defective transposons. Genetics 119:9-12.
Roth -10-
Elliot, Thomas and John R. Roth (1988). Characterization of Tn10dCAM: A transposition-defective
Tn10 specifying chloramphenicol resistance. Mol. Gen. Genet. 213: 332-338.
Wang, Aoquan and John R. Roth (1988). Activation of silent genes in insertion of transposable
elements Tn10 and Tn5. Genetics 120:875-885.
Mahan, M. and J.R. Roth (1988). Reciprocality of recombination that rearrange the chromosome.
Genetics 120:23-35.
Segall, A., M. Mahan and J.R. Roth (1988). Rearrangement of the bacterial chromosome: Forbidden
inversion. Science 241:1314-1318.
Zhu, Ning, B. Olivera, and J.R. Roth (1988). Identification of a repressor gene involved in
regulation of NAD synthesis in Salmonella typhimurium. J. Bacteriol. 170:117-125.
Hughes, K., B. Olivera and J.R. Roth (1988). Structural gene for NAD-synthetase in Salmonella
typhimurium. J. Bacteriol. 120:2113-2120.
Park, U.E., J. R. Roth and B. Olivera (1988). Salmonella typhimurium mutants lacking NAD
pyrophosphatase. J. Bacteriol. 170:3725-3730.
Roof, David M. and J.R. Roth (1988). Ethanolamine utilization in Salmonella typhimurium. J.
Bacteriol. 170:3855-3863.
Zhu, Ning, Baldomero M. Olivera and John R. Roth (1989). Genetic characterization of the pnuC
gene which encodes a component of the nicotinamide mononucleotide transport system in
Salmonella typhimurium. J. Bacteriol. 171:4402-4409.
Park, Uhnmee E., Baldomero M. Olivera, Kelly T. Hughes, John R. Roth, and David R. Hillyard
(1989). DNA ligase and the pyridine nucleotide cycle in Salmonella typhimurium. J.
Bacteriol. 171:2173-2180.
Olivera, B.M., K.T. Hughes, P. Cordray and J.R. Roth (1989). Aspects of NAD metabolism in
prokaryotes and eukaryotes. In: Niacin Nutrition, ADP-Ribosylation and Cancer, M. Jacobson
and E. Jacobson (Eds.).
Roof, David M. and J.R. Roth (1989). Functions required for Vitamin B12-dependent ethanolamine
utilization in Salmonella typhimurium. J. Bacteriol. 171:3316-3323.
Elliot, Thomas and J.R. Roth (1989). Heme-deficient mutants of Salmonella typhimurium: Two
genes required for ALA synthesis. Mol. Gen. Genet. 216:303-314.
Andersson, Dan I. and John R. Roth (1989). Mutations affecting regulation of the cobinamide
biosynthetic genes in Salmonella typhimurium. J. Bacteriol. 171:6726-6733.
Roth -11Andersson, Dan I. and John R. Roth (1989). Redox regulation of the genes for cobinamide
biosynthesis in Salmonella typhimurium. J. Bacteriol. 171:6734-6739.
Mahan, M.J. and J.R. Roth (1988). recB and recC genes of Salmonella typhimurium. J. Bacteriol.
171:612-615.
Sonti, R. and J.R. Roth (1988). Role of gene duplications in the adaptation of Salmonella
typhimurium to growth limiting carbon sources. Genetics 123:19-28.
Mahan, M. and J.R. Roth (1989). Role of recBC in intrachromosomal recombination. Genetics
121:433-443.
Segall, A. and J.R. Roth (1989). Recombination events between homologous sequences flanking
chromosomal segments that are non-permissive for inversions. Genetics 122:737-747.
Casadesus, Josep and J.R. Roth (1989). Transcriptional occlusion of transposon targets. Mol. Gen.
Genet. 216:204-209.
Casadesus, Josep and J.R. Roth (1989). Absence of insertions among spontaneous mutants of
Salmonella typhimurium. Mol. Gen. Genet. 216:210-216.
Escalante-Semerena, Jorge C., Sang-Jin Suh, and John R. Roth (1990). cobA Function is required
for both de novo cobalamin biosynthesis and assimilation of exogenous corrinoids in
Salmonella typhimurium. J. Bacteriol. 172:273-280.
Thaler, D.S., Roth, J.R. and Hirschbein, L. (1990) Imprinting as a mechanism for the control of
gene expression. In: The Bacterial Chromosome, Drlica, K. and Riley, M. (eds.), ASM.
Zhu, Ning, and Roth, J.R. (1991). The nadI region of Salmonella typhimurium encodes a
bifunctional regulatory protein. J. Bacteriol. 173:1302-1310.
Zhu, N., Olivera, B.M., and Roth, J.R. (1991). Activity of the NMN transport system is regulated in
Salmonella typhimurium. J. Bacteriol. 173:1311-1320.
Hughes, R. T., Roth, J. R. and Olivera, B. M. (1991) A genetic characterization of the nadC gene of
Salmonella typhimurium. Genetics 127: 657-6.
Roth, J. R., Grabau, C. and Doak, T. G. (1991) Genetic approaches to the synthesis and
physiological significance of B12 in Salmonella typhimurium. In: Chemical Aspects of
Enzyme Biotechnology, Baldwin, T. O., et al (eds).
Downs, D. M. and Roth, J. R. (1991) Synthesis of thiamine in Salmonella typhimurium independent
of the purF Function. J. Bacteriol. 173: 6597-6604.
Mahan, M.J. and Roth, J.R. (1991) Ability of a bacterial chromosome segment to invert is dictated
by included material rather than flanking sequence. Genetics 129: 1021-1032.
Roth -12Escalante-Semerena, J. C., M. Johnson and Roth, J. R. (1992). The CobII and CobIII regions of the
cobalamin (Vitamin B12) operon of Salmonella typhimurium. J. Bacteriol. 174: 24-29.
Grabau, C. and Roth, J. R. (1992). A Salmonella typhimurium cobalamin-deficient mutant blocked
in 1-amino-2-propanol synthesis. J. Bacteriol. 174: 2138-2144.
Bobik, T. A., Ailion, M. and Roth, J. R. (1992). A single regulatory gene integrates control of
Vitamin B12 synthesis and propanediol degradation. J. Bacteriol. 174: 2253-2266.
Mahan, M.J., Casadesus, J. and J.R. Roth (1992) The Salmonella typhimurium Rec J. function
permits growth of P22 abc phage on recBCD+ hosts. Mol. Gen. Genet. 232: 470-478.
Roof, David M. and J.R. Roth (1992). Autogenous regulation of ethanolamine utilization by a
transcriptional activator of the eut operon in Salmonella typhimurium. J. Bacteriol. 174: 66346643.
Sonti, Ramesh V., David H. Keating and John R. Roth. (1993). Lethal transposition of Mud phages
in Rec- straubs if Salmonella typhimurium. (Genetics 133:17-28.)
Goldman, B. S. and Roth, J. R. (1993) Genetic structure and regulation of the cysG gene in
Salmonella typhimurium. J. Bacteriol. 175: 1457-1466.
Roth, J.R., Lawrence, J.G., Rubenfield, M., Kieffer-Higgins, S. and Church, G.M. (1993)
Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella
typhimurium. J. Bacteriol. 175:3303-3316.
Ailion, M., Bobik, T.A. and Roth, J.R. (1993) Two global regulatory systems (Crp and Arc) control
the cobalamin/propanediol regulon of Salmonella typhimurium. J. Bacteriol. 175:7200-7208
Segall, A.M. and J.R. Roth. (1994) Approaches to half-tetrad analysis in bacteria: Recombination
between repeated, inverse-order chromosomal sequences. Genetics 136: 27-39.
Sheppard, D.E., and Roth, J.R. (1994) A rationale for autoinduction of a transcriptional activator:
ethanolamine ammonia-lyase (EutBC) and the operon activator (EutR) compete for adenosylcobalamin in Salmonella typhimurium. J. Bacteriol. 176:1287-1296.
Miesel, L. and J.R. Roth (1994) Salmonella recD mutations increase recombination in a "short
sequence" transduction assay. J. Bacteriol. 176:4092-4103.
Cheng, W. and J.R. Roth (1994) Evidence for two NAD kinases in Salmonella typhimurium. J.
Bacteriol. 176:4260-4268.
Miesel, L., Segall, A. and J.R. Roth (1994) Construction of chromosomal rearrangements in
Salmonella by transduction: inversions of non-permissive segments are not lethal. Genetics
137:919-932.
Roth -13Benson, N.R. and J.R. Roth (1994) Suppressors of recB mutations in Salmonella typhimurium.
Genetics 138:11-29.
Chen, P., Andersson, D. and J.R. Roth (1994) The control region of the Salmonella pdu/cob
regulon. J. Bacteriol. 176: 5474-5482.
Chen, P., Ailion, M., Weyand, N. and J. R. Roth (1994) The end of the cob operon: Evidence that
the last gene (cobT) catalyzes the synthesis of the lower ligand of vitamin B12,
Dimethylbenzimidazole. J. Bacteriol. 177:1461-1469.
Galitski, T. and J.R. Roth (1995) Evidence that F plasmid transfer replication underlies apparent
adaptive mutation. Science 268:421-423.
Chen, P., Ailion, M., Bobik, T., Stormo, G., and Roth, J.R. (1995) Five promotors integrate control
of the cob/pdu regulon in Salmonella typhimurium. J. Bacteriol.177:5401-5410.
Lawrence, J.G., and J.R. Roth. (1995) The cobalamin (coenzyme B12) biosynthetic genes of
Escherichia coli. J. Bacteriol.:6371-6380.
Cheng, W. and J.R. Roth (1995) Isolation of NAD cycle mutants defective in nicotinamide
mononucleotide deamidase in Salmonella typhimurium. J. Bacteriol. 177:6711-6717.
Haack, Kenneth R. and John R. Roth (1995) Recombination between chromosomal IS200 elements
supports frequent duplication formation in Salmonella typhimurium. Genetics 141:1245-1252.
Roth, J.R., Benson, N., Galitski, T., Haack, K., Lawrence, J., and L. Miesel. (1996) Rearrangements
of the bacterial chromosome: Formation and applications. In: Escherichia coli and Salmonella
typhimurium: Cellular and Molecular Biology, F. Neidhardt, J. Ingraham, K. Low, B.
Magasanik, M. Schaechter and H. Umbarger (eds.), American Society for Microbiology,
Washington, D.C. Chap. 120, pp. 2256-2276.
Altman, E., Roth, J.R., Hessel, A., and K.E. Sanderson (1996) Transposons currently in use in
genetic analysis of Salmonella typhimurium.
In: Escherichia coli and Salmonella
typhimurium: Cellular and Molecular Biology, F. Neidhardt, J. Ingraham, K. Low, B.
Magasanik, M. Schaechter and H. Umbarger (eds.), American Society for Microbiology,
Washington, D.C. Chap. 141, pp. 2613-2626.
Roth, J.R., Lawrence, J.G. and T.A. Bobik (1996) Cobalamin (coenzyme B12): Synthesis and
biological significance. Annu. Rev. Microbiol. 50:137-81
Lupski, J.R., J.R. Roth and G.M. Weinstock (1996) Chromosomal duplications in bacteria, fruit
flies, and humans. Am. J. Hum. Genet. 58:21-27.
Lawrence, J.G., and J.R. Roth (1996) Evolution of coenzyme B12 among enteric bacteria: evidence
for loss and reacquisition of a multigene complex. Genetics 142:11-24.
Roth -14Higgins, N.P., Yang, X., Fu, Q. and Roth, J.R. (1996) Surveying a supercoil domain by using the 
resolution system in Salmonella typhimurium. J. Bacteriol. 178:2825-2835.
Galitski, T. and J.R. Roth (1996) A search for a general phenomenon of adaptive mutability.
Genetics 143:645-659.
Miesel, L. and J.R. Roth (1996) Evidence that SbcB and "RecF" pathway functions contribute to
RecBC-dependent transductional recombination. J. Bacteriol. 178:3146-3155.
Lawrence, J.G. and J.R.Roth (1996) Selfish operons: Horizontal transfer may drive the evolution of
gene clusters. Genetics 143:1843-1860.
Fazzio, T.G. and J.R. Roth (1996) Evidence that the CysG protein catalyzes the first reaction
specific to B12 synthesis in Salmonella typhimurium, insertion of cobalt. J. Bacteriol.
178:6952-6959.
Benson, N. and J.R. Roth (1997) A Salmonella phase P22 mutant defective in abortive transduction.
Genetics 145:17-27.
Walter, D., Ailion, M. and J. R. Roth (1997) Genetic characterization of the pdu operon: Use of 1,2
propanediol in Salmonella typhimurium. J. Bacteriol.179:1013-1022.
Rappleye, C.A. and J.R. Roth (1997) Transposition without transposase: A spontaneous mutation in
bacteria. J. Bacteriol.179:2047-2052.
Galitski, T. and Roth, J.R (1997) Pathways for homologous recombination between chromosomal
direct repeats in Salmonella typhimurium. Genetics 146:751-767.
Rappleye, C. A. and J.R. Roth (1997) A Tn10 derivative ("T-POP") for isolation of insertions with
conditional (tetracycline-dependent) phenotypes J. Bacteriol. 179:5827-5834.
Ailion, M. and J.R. Roth (1996) Repression of the cob operon of Salmonella typhimurium by
adenosylcobalamin is influenced by mutations in the pdu operon. J. Bacteriol. 179:6084-6091.
Bobik, T.A., Xu, Yaping, Jeter, R.M. Otto, K.E. and J.R. Roth (1997) Propanediol utilization genes
(pdu) of Salmonella typhimurium: Three genes for the propanediol dehydratase. J. Bacteriol.
179:6633-6639.
Lawrence, J.G. and J.R. Roth (1998) Roles of horizontal transfer in bacterial evolution. In:
Horizontal Gene Transfer, M. Syvanen and C. Kado, (eds.), Chapman and Hall, London, pp.
208-225.
Andersson, D.I., Slechta, E.S. and J.R. Roth (1998) Evidence that gene amplification underlies
adaptive mutability of the bacterial lac operon. Science 282: 1133-1135.
Lawrence, J.G. and J.R. Roth (1999) Genomic Flux: Genome Evolutaion by Gene Loss and
Acquisition. In: Analysis of Small Genomes, R. Charlebois (ed.) ASM Press, pp. 263-289.
Roth -15-
Van Bibber, M., Bradbeer, C., Clark, N. and J.R. Roth (1999) A new class of Cobalamin transport
mutants (btuF) provides genetic evidence for a periplasmic binding protein in Salmonella
typhimurium. J. Bacteriol. 181:5539-5541.
Kofoid, E., Rappleye, C., Stojiljkovic, I. and J.R. Roth (1999) The seventeen-gene ethanolamine
(eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell
proteins. J. Bacteriol. 181:5317-5329.
Warren, J. W., Walker, J.R., Roth, J.R., and E. Altman (2000) Construction and characterization of
a highly regulable expression vector, pLAC22, and its multipurpose derivatives, pLAC22 and
pLAC33. Plasmid 44:138-151.
Price-Carter, M., Tingey, J., Bobik, T.A. and J.R. Roth (2001) The alternative electron acceptor
tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar
typhimurium on ethanolamine or 1,2-propanediol. J. Bacteriol. 183:2463-2475.
Roth, J. (2001) Salmonella. In: The Encyclopedia of Genetics. Academic Press, London, pp.
1766-1767.
Walker, J.R., Roth, J.R. and E. Altman (2001) An in vivo study of novel bioactive peptides that
inhibit the growth of Escherichia coli. J. Peptide Res. 58:380-388.
Hudson, R. L., Bergthorsson, U., ,Roth, J. R. and H. Ochman. (2002) Effect of Chromosome
location on bacterial mutation rates. Mol. Biol. Evol. 19(1):85-92.
Hendrickson, H., Slechta, E. S., Bergthorsson, U., Anderson, D.I., and J. R. Roth (2002)
Amplification Mutagenesis: Evidence that growth with a selected gene amplification causes
adaptive mutation and hyper-mutability. PNAS 99:2164-2169.
Slechta, E.S., Harold, J., Andersson, D.I. and J.R. Roth (2002) The effect of genomic position on
reverion of a lac frameshift mutation (lacIZ33) during non-lethal selection (adaptive mutation).
Molecular Microbiology 44:1017-1032.
Slechta, E.S., Liu, J., Andersson, D.I., and J.R. Roth (2002) Evidence that selected amplification of
a bacterial lac frameshift allele stimulates Lac+ reversion (adaptive mutation) with or without
general hyper-mutability. Genetics 161:945-956.
Bunny, K.L., Liu, J. and J.R. Roth (2002) Phenotypes of lexA mutations in Salmonella enterica:
Evidence for a lethal lexA null phenotype due to induction of the Fels2 prophage. J. Bacteriol
184:6235-6249.
Kofoid, E., Bergthorsson, U., Slechta, E. S., and John R. Roth (2002) Formation of an F' plasmid by
recombination between imperfectly repeated chromosomal Rep(BIME) sequence: A closer
look at an old friend (F'128 pro lac). J. Bacteriol. 185:660-663.
Roth -16Roth, J.R., Kofoid, E., Roth, F.P., Berg, O.G., Seger, J., and D.I Andersson. (2003) Regulating
general mutation rates: Examination of the Hypermutable State model for Cairnsian adaptive
mutation. Genetics 163:1483-1496
Slechta, E.S, Bunny, K.L., Kugelberg, E., Kofoid, E., Andersson, D.I. and J.R. Roth (2003)
Adaptive mutation: General mutagenesis is not a programmed response to stress but results
from rare coamplification of dinB with lac. PNAS 100:12847-12852.
Roth, J.R., Kofoid, E., Roth, F.P., Berg, O.G., Seger, J., and D. I. Andersson. (2003) Adaptive
mutation requires no mutagenesis - Only growth under selection: A response. Genetics 165:
2319-2321.
Roth, J.R. and D.I. Andersson (2004) Amplification-mutagenesis: How growth under selection
contributes to the origin of genetic diversity and explains the phenomenon of adaptive
mutation. Res. Microbiol. 155:342-351
Roth, J.R. and D.I. Andersson (2004) Adaptive Mutation: How growth under selection stimulates
Lac+ reversion by increasing target copy number. J. Bacteriol. 186:4855-4860.
Roth, J.R. and D.I. Andersson (2004) Rebuttal: Adaptive mutation in Escherichia coli (Foster) J.
Bacteriol. 186: 4854.
Roth, J.R. and D.I. Andersson (2004) Rebuttal: Adaptive point mutation (Rosenberg and Hastings)
J. Bacteriol. 186: 4844..
Penrod, J., Mace, C., J. R. Roth (2004) A pH-sensitive function and phenotype: Evidence that
EutH facilitates diffusion of uncharged ethanolamine in Salmonella enterica. J. Bacteriol.
186:6885-6890
Sheppard, D.E., Penrod, J. Kofoid, E., Bobik, T. and J.R. Roth (2004) Evidence that a B12-adenosyl
transferase is encoded within the ethanolamine operon of Salmonella enterica J Bacteriol.
186:7635-7644
Roth, J.R. (2005) Where’s the Beef? Looking for information about bacterial chromosomes. In:
The Bacterial Chromosome. N. Patrick Higgins (ed.). American Society for Microbiology
Press, Washington, D.C., pp 3-18,
Bergthorsson, U. and J. R. Roth (2004) Natural isolates of Salmonella enterica serovar Dublin
carry a nadA missense mutation. J Bacteriol. 187:400-403.
Pettersson, M. E., D. I. Andersson, J. R. Roth and Otto G. Berg (2005) The amplification model
for adaptive mutation – simulations and analysis. Genetics 169(2):1105-15.
Grose, Julianne H., Bergthorsson, U. and J.R. Roth. (2005) Regulation of NAD synthesis by the
trifunctional NadR protein of Salmonella enterica. J. Bacteriol. 187:2774-2782.
Roth -17Price-Carter, M., Fazzio, T.G., Vallbona, E.I. and J. R. Roth (2005) Polyphosphate kinase
protects Salmonella enterica from weak organic acid stress. J. Bacteriol. 187:3088-3099.
Grose, J.H., Bergthorsson, U., Xu, Y., Sterneckert, J., Khodaverdian, B. and J. R. Roth (2005)
Assimilation of nicotinamide mononucleotide requires periplasmic AphA phosphatase in
Salmonella enterica. J. Bateriol. 187:4521-4530.
Maisnier-Patin, S., Roth, J.R., Fredriksson, A., Nystrom, T., Berg, O.G., & D.I. Andersson.
(2005) Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat
Genet. 37(12):1376-9.
Cornish, R.M., Roth, J. R., and C. D. Poulter. (2006) Lethal mutations in the isoprenoid pathway
of Salmonella enterica. J. Bacteriol. 188:1444-1450.
In press
Colleen Carkeet, Stephen R. Dueker, Jozsef Lango, Bruce A. Buchholz, Joshua W. Miller,
Ralph Green, Bruce Hammock, John R. Roth, Peter J. Anderson (2006) Human vitamin
B12 absorption measured by accelerator mass spectrometry using specifically labeled 14Ccobalamin. (2006). PNAS (in press)
Campbell, G. R. O, M. Taga, K. Mistry, J. Lloret, P. Anderson, J. R. Roth and G. C. Walker.
(2006) Identification of a novel gene in Sinorhizobium meliloti necessary for production of
5,6-dimethylbenzimidazole, the lower ligand of B12. PNAS (in press)
Grose, J. H., L. Joss, S. Velick, J. R. Roth (2006) Feedback inhibition of the essential NAD
kinase of Salmonella enterica: Mechanism and Biological Role. PNAS (submitted)
Penrod, J. T. and J. R. Roth (2006) Conserving a volatile metabolite: A role for carboxysomelike organelles in Salmonella enterica. J. Bacteriol. (in press)
John R. Roth, E. Kugelberg, A B. Reams D. I. Andersson (2006) Origins of mutations under
selection - the adaptive mutation controversy Ann Rev. Microbiol. (in press)