0. Recent Publications
John R. Roth. Teaching the Questions. Unpublished essay. PDF
Maisnier-Patin, S. & Roth, J. R. (2018) Selection and Plasmid
Transfer Underlie Adaptive Mutation in Escherichia coli.
Genetics 210: 821-841 PDF
Yamayoshi, I., Maisnier-Patin, S. & Roth, J.R. (2018) Selection-
enhanced mutagenesis of lac genes is due to their coamplification
with dinB encoding an error-prone DNA polymerase. Genetics 208:
1009-1021 PDF
Cole, A.E., Hani, F.M., Altman, R, Meservy, M., Roth, J.R. &
Altman, E (2017) The Promiscuous sumA Missense Suppressor from
Salmonella enterica Has an Intriguing Mechanism of Action.
Genetics 205: 577-588 PDF
Roth, J.R. & Sophie Maisnier-Patin (2016) Reinterpreting Long-
Term Evolution Experiments: Is Delayed Adaptation an Example of
Historical Contingency or a Consequence of Intermittent Selection?
J. Bact. 198: 1009-1012 PDF
Maisnier-Patin, S. & Roth, J.R. (2016) Adaptive Mutation Controversy.
in Encyclopedia of Evolutionary Biology (ed. Kliman, R. M.) 1, 26-36
(Academic Press, 2016). PDF
Maisnier-Patin, S. and John R. Roth (2015) The Origin of Mutants
Under Selection: How Natural Selection Mimics Mutagenesis
(Adaptive Mutation). Cold Spring Harb. Perspect. Biol. 7, a018176.
PDF
Reams, A. B. and J. R. Roth (2015) Mechanisms of Gene Duplication
and Amplification, In: Recombination Mechanisms,
Editors: Stephen Kowalczykowski, Neil Hunter and Wolf Heyer,
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY PDF
Reams, A.B., Kofoid, E. Duleba, N. and J. R. Roth (2014)
Recombination and annealing pathways compete for substrates
in making rrn duplications in Salmonella enterica Genetics
196: 1-17. PDF
Sano, E., S. Maisnier-Patin, J. P. Aboubechara, S. Quinones-Soto,
John R. Roth (2014) Plasmid copy number underlies adaptiave
mutability in bacteria. Genetics 198: 919-933 PDF
I. Informational Suppression
Berkowitz, D., Hushon, J. M., Whitfield, H. J., Roth, J. R.
and Ames, B.N. (1968) Procedure for identifying nonsense
mutations. Bacteriol. 96:215-220.
Roth, John R. (1970). UGA nonsense mutations in Salmonella
typhimurium. J. Bacteriol. 102:467-475.
Riddle, Donald L. and John R. Roth (1970). Suppressors of
frameshift mutations in Salmonella typhimurium. J. Mol. Biol.
54:131-144.
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. 56:523-533.
Riddle, Donald L. and John R. Roth (1972). Frameshift
suppressors. II. Genetic mapping and dominance studies. J.
Mol. Biol. 66:483-493.
Riddle, Donald L. and John R. Roth (1972). Frameshift
suppressors. III. Effects of suppressor mutations on transfer
RNA. J. Mol. Biol. 66:495-506.
Hartman, P.E. and John R. Roth (1973). Mechanisms of
suppression. Adv. in Genetics 17:1-105.PDF
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.
Reeves, Robert H. and John R. Roth (1975). Transfer
ribonucleic acid methylase deficiency found in UGA suppressor
strains. J. Bacteriol. 124:332-335.
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.
Bossi, Lionello and John R. Roth (1980). The influence of
codon context on genetic code translation. Nature 286:123-127.
Johnston, H. Mark and John R. Roth (1980). UGA suppressor that
maps within a cluster of ribosomal protein genes. J.
Bacteriol. 144:300-305.
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.
Roth, John R. (1981). Frameshift suppression. Cell 24:601-602.
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.
Cole, A.E., Hani, F.M., Altman, R, Meservy, M., Roth, J.R. &
Altman, E (2017) The Promiscuous sumA Missense Suppressor from
Salmonella enterica Has an Intriguing Mechanism of Action.
Genetics 205: 577-588 PDF
II. Regulation of Histidine Biosynthesis
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.
PDF
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.PDF
Roth, 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.PDF
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.
PDF
Fink, G.R. and John R. Roth (1968). Histidine regulatory
mutants in Salmonella typhimurium. VI. Dominance studies. J.
Mol. Biol. 33: 547-557.PDF
Martin, R. G., Bagdasarian, M. and Roth, J. R. (1969)
Regulation of the histidine operon. Federation of European
Biochemical Societies Symposium. 19: 1-4.
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.
PDF
Scott, John F., John R. Roth and S. Artz (1975). Regulation of
histidine operon does not require hisG enzyme. Proc. Natl.
Acad. Sci. USA 72:5021-5025.
PDF
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. PDF
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. PDF
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.PDF
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.PDF
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.PDF
Johnston, 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.
145:735-756.PDF
Schmid, Molly and John R. Roth (1983). Internal promoters of
the his operon of Salmonella typhimurium. J. Bacteriol.
153:1114-1119.PDF
Rudd, 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.
PDF
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.
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.PDF
III. Regulation of Proline Degradation
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.
Menzel, Rolf and John R. Roth (1980). Identification and
mapping of a second proline permease in Salmonella
typhimurium. J. Bacteriol. 141:1064-1070.
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. Biol.
Chem. 256:9762-9766.
Maloy, Stanley and John R. Roth (1983). Regulation of proline
utilization in Salmonella typhimurium. J. Bacteriol.
154:561-568.
IV. Biosynthesis of NAD
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). An indispensable gene involved in NAD
biosynthesis, nadD. J. Bacteriol. 155:213-221.
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.
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.
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.).
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.
Cheng, W. and J.R. Roth (1994) Evidence for two NAD kinases in
Salmonella typhimurium. J. Bacteriol. 176:4260-4268.
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.
Bergthorsson, U. and J. R. Roth (2004) Natural isolates of
Salmonella enterica serovar Dublin carry a nadA missense
mutation. J Bacteriol. 187:400-403. PDF
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. PDF
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. Bacteriol.
187:4521-4530. PDF
Grose, J.H., L.Joss, S.Velick, J.R.Roth (2006) Evidence that
feedback inhibition of NAD kinase controls responses to
oxidative stress. PNAS 103:7601-7606. PDF
V. Vitamin B12 Synthesis and Use in Salmonella Biosynthesis
Jeter, Randall and J.R. Roth (1984). Salmonella typhimurium
synthesizes cobalamin (vitamin B12) de novo under anaerobic
growth conditions. J. Bacteriol. 159:206-213.
Escalante, J. and J.R. Roth (1987). Regulation of cobalamin
biosynthetic operons in Salmonella typhimurium. J. Bacteriol.
169:2251-2258.
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.
Roof, David M. and J.R. Roth (1988). Ethanolamine utilization
in Salmonella typhimurium. J. Bacteriol. 170:3855-3863. PDF
Roof, David M. and J.R. Roth (1989). Functions required for
Vitamin B12-dependent ethanolamine utilization in Salmonella
typhimurium. J. Bacteriol. 171:3316-3323. PDF
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. PDF
Andersson, Dan I. and John R. Roth (1989). Redox regulation of
the genes for cobinamide biosynthesis in Salmonella
typhimurium. J. Bacteriol. 171:6734-6739.
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.
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).
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.
Escalante-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.
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:
6634-6643.PDF
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. PDF
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.
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 adenosyl-cobalamin in Salmonella typhimurium. J.
Bacteriol. 176:1287-1296. PDF
Chen, P., Andersson, D. and J.R. Roth (1994) The control
region of the Salmonella pdu/cob regulon. J. Bacteriol. 176:
5474-5482. PDF
Chen, P., Ailion, M., Weyand, N. and J. R. Roth (1995) 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. PDF
Chen, P., Ailion, M., Bobik, T., Stormo, G., and Roth, J.R.
(1995) Five promoters integrate control of the cob/pdu regulon
in Salmonella typhimurium. J. Bacteriol.177:5401-5410. PDF
Lawrence, J.G., and J.R. Roth. (1995) The cobalamin (coenzyme
B12) biosynthetic genes of Escherichia coli. J.
Bacteriol.:6371-6380.
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, J.R., Lawrence, J.G. and T.A. Bobik (1996) Cobalamin
(coenzyme B12): Synthesis and biological significance. Annu.
Rev. Microbiol. 50:137-81. PDF
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. PDF
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.
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.
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. PDF
Kofoid, E., Rappleye, C., Stojiljkovic, I. and J.R. Roth
(1999) The 17-gene ethanolamine (eut) operon of Salmonella
typhimurium encodes five homologues of carboxysome shell
proteins. J. Bacteriol. 181:5317-5329. PDF
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. PDF
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. PDF
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. PDF
Colleen Carkeet, Stephen R. Dueker, Jozsef Lango, Bruce A.
Buchholz, Joshua W. Miller, Ralph Green, Bruce D. Hammock,
John R. Roth, and Peter J. Anderson. (2006) Human vitamin B12
absorption measurement by accelerator mass spectrometry using
specifically labeled 14C-cobalamin. PNAS 103:5694-5699. PDF
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
103:4634-4639. PDF
Penrod, J. T. and J. R. Roth (2006) Conserving a volatile
metabolite: A role for carboxysome-like organelles in
Salmonella enterica. J. Bacteriol. 188:2865-2874. PDF
Winter, S.E., Thiennimitr, P., Winter, M.G., Butler, B.P.,
Huseby, D.L., Crawford, R.W., Russell, J.M., Bevins, C.L.,
Adams, L.G., Tsolis, R.M., Roth, J.R. & A.J. Baumler
(2010) Gut inflammation provides a respiratory electron acceptor
for Salmonella. Nature 467:426-429. PDF
Thiennimitr, P., Winter, S.E., Winter, M.G., Xavier, M.N.,
Tolstikov, V., Huseby, D.L., Sterzenbach, T., Tsolis, R.M.,
Roth, J.R. & A.J. Baumler (2011) Intestinal inflammation allows
Salmonella to use ethanolamine to compete with the microbiota.
PNAS [Epub ahead of print]. PDF
VI. Chromosomal Rearrangements & Recombination Mechanisms
Anderson, R.P. and J.R. Roth (1976). Tendem Genetic Duplications
in Phage and Bacteria. Ann. Rev. Microbiol. 31:471-505. PDF
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. PDF
Anderson R.P. and J.R. Roth (1978). Tandem chromosomal
duplications in Salmonella typhimurium: Fusion of histidine
genes to novel promoters. J. Mol. Biol. 119:137-166. PDF
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. PDF
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.
43:1083-1087. PDF
Chumley F. and J.R. Roth (1980). Rearrangement of the
bacterial chromosome using Tn10 as a region of homology.
Genetics 94:1-14.
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.
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. PDF
Roth, J.R. and M.B. Schmid (1981). Arrangement and
rearrangement of the bacterial chromosome. Stadler Symposium
Vol. 13:53-70.
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, K.T. and J.R. Roth (1985). Directed formation of
deletions and duplications using Mud (Ap, lac). Genetics
109:263-282.
Schmid, M.B. and J.R. Roth (1987). Gene location affects
expression level in S. typhimurium. J. Bacteriol.
169:2872-2875.
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.
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.
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.
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.
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.
Miesel, L. and J.R. Roth (1994) Salmonella recD mutations
increase recombination in a "short sequence" transduction
assay. J. Bacteriol. 176:4092-4103.
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.
Benson, N.R. and J.R. Roth (1994) Suppressors of recB
mutations in Salmonella typhimurium. Genetics 138:11-29.
Lupski, J.R., J.R. Roth and G.M. Weinstock (1996) Chromosomal
dduplications in bacteria, fruit flies, and humans. Am. J.
Hum. Genet. 58:21-27.
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.
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.
Higgins, N.P., Yang, X., Fu, Q. and Roth, J.R. (1996)
Surveying a supercoil domain by using the gamma delta resolution
system in Salmonella typhimurium. J. Bacteriol. 178:2825-2835.
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. PDF
Galitski, T. and Roth, J.R (1997) Pathways for homologous
recombination between chromosomal direct repeats in Salmonella
typhimurium. Genetics 146:751-767.
VII. Transposons and Their Applications
Kleckner, N., J.R. Roth and D. Botstein (1977). Genetic
engineering in vivo using translocatable drug-resistance
elements. J. Mol. Biol. 116:125-159. PDF
Chumley, F., R. Menzel and J.R. Roth (1979). Hfr formation
directed by Tn10. Genetics 91:639-655.
Biek, D. and J.R. Roth (1980). Regulation of Tn5
transposition. Proc. Natl. Acad. Sci. USA 77:6047-6051.
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. In: Microbiology 1980, D.
Schlessinger (ed.), American Society for Microbiology Press.
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.
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.
Hughes, K.T. and J.R. Roth (1984). Conditionally
transposition-defective derivative of Mu dl(Amp Lac). J.
Bacteriol. 159:130-137. PDF
Lam, S. and J.R. Roth (1986). Structural and functional
studies of IS200. J. Mol. Biol. 187:157-167. PDF
Hughes, K.T., B.M. Olivera and J.R. Roth (1987). Rec
dependence of Mu transposition from P22-transduced fragments.
J. Bacteriol. 169:403-409.
Hughes, Kelly T. and John R. Roth (1988). Transitory cis
complementation: a general method for providing transposase to
defective transposons. Genetics 119:9-12. PDF
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. PDF
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.
SSonti, Ramesh V., David H. Keating and John R. Roth. (1993).
Lethal transposition of Mud phages in Rec- strains of
Salmonella typhimurium. Genetics 133:17-28.
Haack, Kenneth R. and John R. Roth (1995) Recombination
between chromosomal IS200 elements supports frequent
duplication formation in Salmonella typhimurium. Genetics
141:1245-1252.PDF
Rappleye, C.A. and J.R. Roth (1997) Transposition without
transposase: A spontaneous mutation in bacteria. J.
Bacteriol.179:2047-2052.
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. PDF
VIII. Genetic Approaches to Protein Structure
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.
Lew, Kenneth K. and John R. Roth (1972). Genetic approaches to
determination of enzyme quaternary structure. Biochemistry
10:204-207. Syvanen, 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.
Syvanen, J. Michael and John R. Roth (1973). Structural genes
of catalytic and regulatory subunits of aspartate
transcarbamylase. J. Mol. Biol. 767:363-378.
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,æR. C.
Valentine and Alexander Hollaender (eds.), Plenum Publishing
Corp.
IX. General Genetics of Bacteria
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. (1970). Genetic techniques in studies of
bacterial metabolism. In: Methods in Enzmology, pages 3-35.
Academic Press.
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. 89:17-25.
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.
Anderson, R.P. and J.R. Roth (1977). Tandem genetic
duplications in phage and bacteria. Ann. Rev. Microbiol.
31:473-505.
Davis, R.W., D. Botstein, and J. Roth (1980). Advanced
Bacterial Genetics Laboratory Manual. Cold Spring Harbor
Laboratory, Cold Spring Harbor, N.Y.
Sanderson, K.E. and John R. Roth (1983). The linkage map of
Salmonella typhimurium. Microbiological Reviews 47:410-453.
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.
Sanderson, K.E. and John R. Roth (1988). The linkage map of
Salmonella typhimurium. Edition VII. Microbiological Reviews.
52:485-532. PDF
Sanderson, K.E. and John R. Roth (1983). The linkage map of
Salmonella typhimurium. Edition VI. Microbiological Reviews.
47:410-453. PDF
Downs, D. M. and Roth, J. R. (1991) Synthesis of thiamine in
Salmonella typhimurium independent of the purF Function. J.
Bacteriol. 173: 6597-6604.
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.
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. PDF
Benson, N. and J.R. Roth (1997) A Salmonella phase P22 mutant
defective in abortive transduction. Genetics 145:17-27.
Warren, J. W., Walker, J.R., Roth, J.R., and E. Altman (2000)
Construction and characterization of a highly regulable
expression vector, pLAC11, and its multipurpose derivatives,
pLAC22 and pLAC33. Plasmid 44:138-151. PDF
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. PDF
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. PDF
Price-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. PDF
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. PDF
X. Genome Evolution & Adaptive Mutagenesis
Galitski, T. and J.R. Roth (1995) Evidence that F plasmid
transfer replication underlies apparent adaptive mutatio.
Science 268:421-423. PDF
Galitski, T. and J.R. Roth (1996) A search for a general
phenomenon of adaptive mutability. Genetics 143:645-659.
Lawrence, J.G. and J.R.Roth (1996) Selfish operons: Horizontal
transfer may drive the evolution of gene clusters. Genetics
143:1843-1860.
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. PDF
Lawrence, J.G. and J.R. Roth (1999) Genomic Flux: Genome
Evolution by Gene Loss and Acquisition. In: Analysis of Small
Genomes, R. Charlebois (ed.) ASM Press, pp. 263-289. PDF
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. PDF
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. PDF
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. PDF
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. PDF
Kofoid, E., Bergthorsson, U., Slechta, E. S., and John R. Roth
(2003) 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. PDF
Roth, 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. PDF
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. PDF
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. PDF
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. PDF
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. PDF
Roth, J.R. and D.I. Andersson (2004) Rebuttal: Adaptive
mutation in Escherichia coli (Foster) J. Bacteriol. 186: 4854. PDF
Roth, J.R. and D.I. Andersson (2004) Rebuttal: Adaptive point
mutation (Rosenberg and Hastings) J. Bacteriol. 186: 4844. PDF
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. PDF
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. PDF
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.
Nature Genet. 37(12): 1376-9. PDF
John R. Roth, E. Kugelberg, A.B. Reams, E.C. Kofoid, & D. I.
Andersson (2006) Origins of mutations under selection - the
adaptive mutation controversy. Ann.Rev. Microbiol. 60:477-501. PDF
Kugelberg, E., Kofoid. E., Reams, A.B., Andersson, D.I. and
J.R. Roth (2006) Multiple pathways of selected gene amplification
during adaptive mutation. Proc Natl Acad Sci 103:17319-24 PDF
U. Bergthorsson, D.I. Andersson & John R. Roth (2007) Ohno's
dilemma: evolution of new genes under continuous selection.
Proc.Natl.Acad.Sci.USA 104:17004-17009. PDF
P.J. Anderson, J. Lango, C. Carkeet, A. Britten, B. Krautler,
B.D. Hammock & John R. Roth (2008) One pathway can incorporate
either adenine or dimethylbenzimidazole as an alpha-axial
ligand of B12 cofactors in Salmonella enterica. J.Bacteriol.
190:1160-1171. PDF
M. Wrande, John R. Roth & D. Hughes (2008) Accumulation of
mutants in 'aging' bacterial colonies is due to growth under
selection, not stress- induced mutagenesis.
Proc.Natl.Acad.Sci.USA 105:11863-11868. PDF
S. Sun, O.G. Berg, John R. Roth & D.I. Andersson (2009)
Contribution of gene amplification to evolution of increased
antibiotic resistance in Salmonella typhimurium. Genetics
182:1183-1195. PDF
John R. Roth (2010) Genetic Adaptation: A New Piece for a Very
Old Puzzle. Curr.Biol. 20:R15-R17. PDF
A.B. Reams, E. Kofoid, M. Savageau & John R. Roth (2010)
Duplication Frequency in a Population of Salmonella enterica
Rapidly Approaches Steady State With or Without Recombination.
Genetics 184:1077-1094. PDF
E. Kugelberg, E. Kofoid, D.I. Andersson, Y. Lu, J. Mellor,
F.P. Roth & John R. Roth (2010) The tandem
inversion duplication in Salmonella enterica: Selection
drives unstable precursors to final mutation types. Genetics
185:65-80. PDF
John R. Roth (2010) The joys and terrors of fast adaptation:
new findings elucidate antibiotic resistance and natural
selection. Mol.Microbiol. 79:279-282. PDF
D.I. Andersson, D. Hughes & John R. Roth (2011) The Origin of
Mutants under Selection: Interactions of Mutation, Growth, and
Selection, EcoSal Plus 2013; doi:10.1128/ecosalplus.5.6.6,
Ed. James M. Slauch, http://www.ecosal.org/, ASM Press,
Washington, DC.PDF
Reams, A.B., Kofoid E., Kugelberg E., Roth J.R. (2012) Multiple
pathways of duplication formation with and without recombination
(RecA) in Salmonella enterica. Genetics 192:397-415 PDF
Quinones-Soto, S. & J.R. Roth (2011) Effect of growth under
selection on appearance of chromosomal mutations in Salmonella
enterica. Genetics 189:37-53 PDF
Quinones-Soto, S., A.B. Reams and J.R.Roth, (2012) Pathways of
genetic adaptation: Multistep origin of mutants under selection
without induced mutagenesis in Salmonella enterica. Genetics
192:987-999. PDF
Reams, A.B., Kofoid, E. Duleba, N. and J. R. Roth (2014)
Recombination and annealing pathways compete for substrates
in making rrn duplications in Salmonella enterica Genetics
196: 1-17. PDF
Sano, E., Maisnier-Patin, S., Aboubechara, J. P., Quinones-Soto,
S. & Roth, J. R. (2014) Plasmid copy number underlies adaptive
mutability in bacteria. Genetics 198, 919-933 PDF
Reams, A. B. and J. R. Roth (2014) Mechanisms of Gene Duplication
and Amplification. (2015) Mechanisms of Gene Duplication and
Amplificatioation. Cold Spring Harb. Perspect. Biol. 7, a016592 PDF
Maisnier-Patin, S. and John R. Roth (2015) The Origin of Mutants
Under Selection: How Natural Selection Mimics Mutagenesis
(Adaptive Mutation). Cold Spring Harb. Perspect. Biol. 7, a018176.
PDF
Maisnier-Patin, S. & Roth, J.R. (2016) Adaptive Mutation Controversy.
in Encyclopedia of Evolutionary Biology (ed. Kliman, R. M.) 1, 26-36
(Academic Press, 2016). PDF
Roth, J.R. & Sophie Maisnier-Patin (2016) Reinterpreting Long-
Term Evolution Experiments: Is Delayed Adaptation an Example of
Historical Contingency or a Consequence of Intermittent Selection?
J. Bact. 198: 1009-1012 PDF
Yamayoshi, I., Maisnier-Patin, S. & Roth, J.R. (2018) Selection-
enhanced mutagenesis of lac genes is due to their coamplification
with dinB encoding an error-prone DNA polymerase. Genetics 208:
1009-1021 PDF
Maisnier-Patin, S. & Roth, J. R. (2018) Selection and Plasmid
Transfer Underlie Adaptive Mutation in Escherichia coli.
Genetics 210: 821-841 PDF
X. Miscellaneous
John R. Roth (2011) Giving a Seminar: Suggestions for Graduate
Students, Ch. 2, The Lure of Bacterial Genetics: a Tribute to
John Roth, eds. S. Maloy, K.T.Hughes & J.Casadesus, ASM Press,
Washington, DC, 9-22. PDF
John R. Roth (2011) Predicting the Future: A Fish Story, Ch. 33,
The Lure of Bacterial Genetics: a Tribute to John Roth, eds.
S. Maloy, K.T.Hughes & J.Casadesus, ASM Press, Washington, DC,
343-348. PDF
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