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.
        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. 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.
        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
        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.
        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.
        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
        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-duplications in Salmonella enterica (TID): Selection
        drives unstable precursors to final mutation types. Genetics
        185:65-80. PDF
        D.I. Andersson, D. Hughes & John R. Roth (2011) The Origin of
        Mutants under Selection: Interactions of Mutation, Growth, and
        Selection, Chapter 5.6.6, EcoSal -- Escherichia coli and
        Salmonella: Cellular and Molecular Biology 10.1128, Section Ed. 
	Steven Finkel, http://www.ecosal.org/, ASM Press, Washington, DC. 
	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
        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

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
        John R. Roth (2013) Teaching the Questions. Unpublished essay.
        PDF

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