RothLab - Publications
I. Informational Suppression
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.
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.
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.
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.
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, John R., David F. Silbert, Gerald R. Fink, Mary Jane Voll,æDora
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. PDF
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.
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.
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.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.
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.
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.
Schmid, Molly and John R. Roth (1983). Internal promoters of the his
operon of Salmonella typhimurium. J. Bacteriol. 153:1114-1119.
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.
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.
CCiampi, 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.
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. J. 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.
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.
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.
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.
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.
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.
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
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.
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
VI. Chromosomal Rearrangements & Recombination Mechanisms
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 (1978). Tandem chromosomal duplications in
Salmonella typhimurium: Fusion of histidine genes to novel promoters. J.
Mol. Biol. 119:137-166.
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.
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.
CChumley 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.
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.
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
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 (( resolution system in Salmonella
typhimurium. J. Bacteriol. 178:2825-2835.
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.
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.
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.
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.
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
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
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.
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.
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. PDF
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. PDF
Roth, J.R. and D.I. Andersson (2004) Adaptive Mutation: 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) 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. Nat
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. (2006) Ann
Rev. Microbiol. 60:477-501. PDF
Last Update: 5 April 2006
Eric Kofoid
eckofoid@ucdavis.edu