Publications

Journal

Seesandra V Rajagopala,S.V.,Yamamoto,N., Zweifel,A.E., Nakamichi,T., Huang,H.-K., Mendez-Rios,J.D., Jonathan Franca-Koh,J., Boorgula,M.P., Fujita,K., Suzuki,K.-I., Hu,J.C., Wanner,B.L., Mori,H., and Uetz,P. 2010. The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology. BMC Genomics 2010 in press.

Hsieh, Y.-J., and Wanner, B. L. 2010. Global Regulation by the Seven-component P_i Signaling System. Curr. Opin. Microbiol. 13 (2):198-203. PM:20171928.

Kierzek, A.M., Zhou, L., and Wanner, B. L. 2010. Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses. Mol.Biosyst. 6 (3):531-542. PM:20174681.

Sharma, O., K. A. Datsenko, S. C. Ess, M. V. Zhalnina, B. L. Wanner, and W. A. Cramer. 2009. Genome-wide screens: novel mechanisms in colicin import and cytotoxicity. Molecular Microbiology. 73: 571-585. PM:19650773.

Yamamoto, N. ,  K. Nakahigashi, T. Nakamichi, M. Yoshino, Y. Takai, Y. Touda, A. Furubayashi, S. Kinjyo, H. Dose, M. Hasegawa, K. A. Datsenko, T. Nakayashiki, M. Tomita, B. L. Wanner^*, and H. Mori*. 2009. Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol.Syst.Biol. 5:335. ^*Co-corresponding authors. PM:20029369.

Liu, X., G. R. Pena Sandoval, B. L. Wanner, W. S. Jung, D. Georgellis, and O. Kwon. 2009. Evidence against the physiological role of acetyl phosphate in the phosphorylation of the ArcA response regulator in Escherichia coli. J. Microbiol. 47 (5):657-662. PM:19851741.

Kazakov, T., Vondenhoff, G. H., Datsenko, K. A., Novikova, M., Metlitskaya, A., Wanner, B. L., Severinov, K. 2008. Escherichia coli peptidase A, B, or N can process translation inhibitor microcin C. J Bacteriol. 190: 2607-2610.

Lamarche, M. G., Wanner, B. L., Crepin, S., Harel, J. 2008. The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis. FEMS Microbiol Rev. 32: 461-473.

Hu, J. C., Aramayo, R., Bolser, D., Conway, T., Elsik, C. G., Gribskov, M., Kelder, T., Kihara, D., Knight, T. F., Pico, A. R., Siegele, D. A., Wanner, B. L., Welch, R. D. 2008. The emerging world of wikis. Science. 320: 1289-1290.

Arribas-Bosacoma, R., Kim, S. K., Ferrer-Orta, C., Blanco, A. G., Pereira, P. J., Gomis-Ruth, F. X., Wanner, B. L., Coll, M., Sola, M. 2007. The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation. J Mol Biol. 366: 626-641.

Baba, T., Huan, H. C., Datsenko, K., Wanner, B. L., Mori, H. 2007. The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. Methods Mol Biol. 416: 183-194.

Cui, T. L., Moro-oka, N., Ohsumi, K., Kodama, K., Ohshima, T., Ogasawara, N., Mori, H., Wanner, B., Niki, H., Horiuchi, T. 2007. Escherichia coli with a linear genome. Embo Reports. 8: 181-187.

Novikova, M., Metlitskaya, A., Datsenko, K., Kazakov, T., Kazakov, A., Wanner, B., Severinov, K. 2007. The E. coli Yej Transporter is Required for the Uptake of Translation Inhibitor Microcin C. J Bacteriol. 189: 8361-8365.

Novikova, M., Metlitskaya, A., Datsenko, K., Kazakov, T., Kazakov, A., Wanner, B., Severinov, K. 2007. The Escherichia coli Yej transporter is required for the uptake of translation inhibitor microcin C. Journal of Bacteriology. 189: 8361-8365.

Oh, D., Yu, Y., Wanner, B., Ritchie, K. 2007. Imaging the motion of individual protein molecules in the inner membrane of Escherichia coli. Biophysical Journal. 528A-528A.

Sharma, O., Yamashita, E., Zhalnina, M. V., Zakharov, S. D., Datsenko, K. A., Wanner, B. L., Cramer, W. A. 2007. Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon. J Biol Chem. 282: 23163-23170.

Stepanova, E., Lee, J., Ozerova, M., Semenova, E., Datsenko, K., Wanner, B. L., Severinov, K., Borukhov, S. 2007. Analysis of promoter targets for E. coli transcription elongation factor GreA in vivo and in vitro. J Bacteriol. 189: 8772-8785.

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., Mori, H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2: 2006-2008.

Baba, T., Narifusa, Y. , Hasegawa, M., Takai, Y., M., Tomita, Wanner, B. 2006. Core genome structure and function of Escherichia coli K-12. Seikagaku. A12476.

Fischbach, M. A., Lin, H., Zhou, L., Yu, Y., Abergel, R. J., Liu, D. R., Raymond, K. N., Wanner, B. L., Strong, R. K., Walsh, C. T., Aderem, A., Smith, K. D. 2006. The pathogen-associated iroA gene cluster mediates bacterial evasion of lipocalin 2. Proc Natl Acad Sci U S A. 103: 16502-16507.

Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. 2006. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2: 2006 0007.

Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K. B., Blattner, F. R., Chaudhuri, R. R., Glasner, J. D., Horiuchi, T., Keseler, I. M., Kosuge, T., Mori, H., Perna, N. T., Plunkett, G., Rudd, K. E., Serres, M. H., Thomas, G. H., Thomson, N. R., Wishart, D., Wanner, B. L. 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot - 2005. Nucleic Acids Research. 34: 1-9.

Wanner, B. L., Grandi, G. 2006. Techniques. Curr Opin Microbiol. 9: 295-296.

Le Novere, N., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J. L., Spence, H. D., Wanner, B. L. 2005. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology. 23: 1509-1515.

Tong, X., Campbell, J. W., Balazsi, G., Kay, K. A., Wanner, B. L., Gerdes, S. Y., Oltvai, Z. N. 2004. Genome-scale identification of conditionally essential genes in E-coli by DNA microarrays. Biochem. Biophys. Res. Commun.. 322: 347-354.

Zhou, L., Zhang, K., Wanner, B. L. 2004. Chromosomal expression of foreign and native genes from regulatable promoters in Escherichia coli. Methods Mol Biol. 267: 123-134.

Hove-Jensen, B., Rosenkrantz, T. J., Haldimann, A., Wanner, B. L. 2003. Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): Dual role in phosphonate degradation and NAD biosynthesis pathways. Journal of Bacteriology. 185: 2793-2801.

Ismail, W., Mohamed, M. E., Wanner, B. L., Datsenko, K. A., Eisenreich, W., Rohdich, F., Bacher, A., Fuchs, G. 2003. Functional genomics by NMR spectroscopy - Phenylacetate catabolism in Escherichia coli. European Journal of Biochemistry. 270: 3047-3054.

Zhou, L., Lei, X. H., Bochner, B. R., Wanner, B. L. 2003. Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems. J Bacteriol. 185: 4956-4972.

Kim, A. D., Baker, A. S., Dunaway-Mariano, D., Metcalf, W. W., Wanner, B. L., Martin, B. M. 2002. The 2-aminoethylphosphonate-specific transaminase of the 2-aminoethylphosphonate degradation pathway. Journal of Bacteriology. 184: 4134-4140.

Oshima, T., Aiba, H., Masuda, Y., Kanaya, S., Sugiura, M., Wanner, B. L., Mori, H., Mizuno, T. 2002. Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Molecular Microbiology. 46: 281-291.

Haldimann, A., Wanner, B. L. 2001. Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J Bacteriol. 183: 6384-6393.

Khlebnikov, A., Datsenko, K. A., Skaug, T., Wanner, B. L., Keasling, J. D. 2001. Homogeneous expression of the P-BAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology-Sgm. 147: 3241-3247.

Datsenko, K. A., Wanner, B. L. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A. 97: 6640-6645.

Kim, S. K., Kimura, S., Shinagawa, H., Nakata, A., Lee, K. S., Wanner, B. L., Makino, K. 2000. Dual transcriptional regulation of the Escherichia coli phosphate-starvation-inducible psiE gene of the phosphate regulon by PhoB and the cyclic AMP (cAMP)-cAMP receptor protein complex. J Bacteriol. 182: 5596-5599.

Lee, K. S., Song, S. B., Kim, K. E., Kim, Y. H., Kim, S. K., Kho, B. H., Ko, D. K., Choi, Y. K., Lee, Y. K., Kim, C. K., Kim, Y. C., Lim, J. Y., Kim, Y., Min, K. H., Wanner, B. L. 2000. Cloning and characterization of the UDP-sugar hydrolase gene (ushA) of Enterobacter aerogenes IFO 12010. Biochem Biophys Res Commun. 269: 526-531.

Lucas, R. L., Lostroh, C. P., DiRusso, C. C., Spector, M. P., Wanner, B. L., Lee, C. A. 2000. Multiple factors independently regulate hilA and invasion gene expression in Salmonella enterica serovar typhimurium. J Bacteriol. 182: 1872-1882.

Stern, R. J., Lee, T. Y., Lee, T. J., Yan, W., Scherman, M. S., Vissa, V. D., Kim, S. K., Wanner, B. L., McNeil, M. R. 1999. Conversion of dTDP-4-keto-6-deoxyglucose to free dTDP-4-keto-rhamnose by the rmIC gene products of Escherichia coli and Mycobacterium tuberculosis. Microbiology. 145 ( Pt 3): 663-671.

Baker, A. S., Ciocci, M. J., Metcalf, W. W., Kim, J., Babbitt, P. C., Wanner, B. L., Martin, B. M., Dunaway-Mariano, D. 1998. Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis. Biochemistry. 37: 9305-9315.

Haldimann, A., Daniels, L. L., Wanner, B. L. 1998. Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon. J Bacteriol. 180: 1277-1286.

Lessard, I. A., Pratt, S. D., McCafferty, D. G., Bussiere, D. E., Hutchins, C., Wanner, B. L., Katz, L., Walsh, C. T. 1998. Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function. Chem Biol. 5: 489-504.

Lu, F., Schumacher, M. A., Arvidson, D. N., Haldimann, A., Wanner, B. L., Zalkin, H., Brennan, R. G. 1998. Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190. Biochemistry. 37: 971-982.

Silva, J. C., Haldimann, A., Prahalad, M. K., Walsh, C. T., Wanner, B. L. 1998. In vivo characterization of the type A and B vancomycin-resistant enterococci (VRE) VanRS two-component systems in Escherichia coli: a nonpathogenic model for studying the VRE signal transduction pathways. Proc Natl Acad Sci U S A. 95: 11951-11956.

Yakovleva, G. M., Kim, S. K., Wanner, B. L. 1998. Phosphate-independent expression of the carbon-phosphorus lyase activity of Escherichia coli. Appl Microbiol Biotechnol. 49: 573-578.

Haldimann, A., Fisher, S. L., Daniels, L. L., Walsh, C. T., Wanner, B. L. 1997. Transcriptional regulation of the Enterococcus faecium BM4147 vancomycin resistance gene cluster by the VanS-VanR two-component regulatory system in Escherichia coli K-12. J Bacteriol. 179: 5903-5913.

Fisher, S. L., Kim, S. K., Wanner, B. L., Walsh, C. T. 1996. Kinetic comparison of the specificity of the vancomycin resistance VanSfor two response regulators, VanR and PhoB. Biochemistry. 35: 4732-4740.

Haldimann, A., Prahalad, M. K., Fisher, S. L., Kim, S. K., Walsh, C. T., Wanner, B. L. 1996. Altered recognition mutants of the response regulator PhoB: a new genetic strategy for studying protein-protein interactions. Proc Natl Acad Sci U S A. 93: 14361-14366.

Kim, S. K., Wilmes-Riesenberg, M. R., Wanner, B. L. 1996. Involvement of the sensor kinase EnvZ in the in vivo activation of the response-regulator PhoB by acetyl phosphate. Mol Microbiol. 22: 135-147.

Metcalf, W. W., Jiang, W., Daniels, L. L., Kim, S. K., Haldimann, A., Wanner, B. L. 1996. Conditionally replicative and conjugative plasmids carrying lacZ alpha for cloning, mutagenesis, and allele replacement in bacteria. Plasmid. 35: 1-13.

VanBogelen, R. A., Olson, E. R., Wanner, B. L., Neidhardt, F. C. 1996. Global analysis of proteins synthesized during phosphorus restriction in Escherichia coli. J Bacteriol. 178: 4344-4366.

Wanner, B. L. 1996. Signal transduction in the control of phosphate-regulated genes of Escherichia coli. Kidney Int. 49: 964-967.

Fisher, S. L., Jiang, W., Wanner, B. L., Walsh, C. T. 1995. Cross-talk between the histidine protein kinase VanS and the response regulator PhoB. Characterization and identification of a VanS domain that inhibits activation of PhoB. J Biol Chem. 270: 23143-23149.

Jiang, W., Metcalf, W. W., Lee, K. S., Wanner, B. L. 1995. Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2. J Bacteriol. 177: 6411-6421.

Holman, T. R., Wu, Z., Wanner, B. L., Walsh, C. T. 1994. Identification of the DNA-binding site for the phosphorylated VanR protein required for vancomycin resistance in Enterococcus faecium. Biochemistry. 33: 4625-4631.

Metcalf, W. W., Jiang, W., Wanner, B. L. 1994. Use of the rep technique for allele replacement to construct new Escherichia coli hosts for maintenance of R6K gamma origin plasmids at different copy numbers. Gene. 138: 1-7.

Wanner, B. L. 1994. Molecular genetics of carbon-phosphorus bond cleavage in bacteria. Biodegradation. 5: 175-184.

Metcalf, W. W., Wanner, B. L. 1993. Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli. Gene. 129: 27-32.

Metcalf, W. W., Wanner, B. L. 1993. Construction of new beta-glucuronidase cassettes for making transcriptional fusions and their use with new methods for allele replacement. Gene. 129: 17-25.

Metcalf, W. W., Wanner, B. L. 1993. Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements. J Bacteriol. 175: 3430-3442.

Steed, P. M., Wanner, B. L. 1993. Use of the rep technique for allele replacement to construct mutants with deletions of the pstSCAB-phoU operon: evidence of a new role for the PhoU protein in the phosphate regulon. J Bacteriol. 175: 6797-6809.

Wanner, B. L. 1993. Gene regulation by phosphate in enteric bacteria. J Cell Biochem. 51: 47-54.

Feng, J., Atkinson, M. R., McCleary, W., Stock, J. B., Wanner, B. L., Ninfa, A. J. 1992. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J Bacteriol. 174: 6061-6070.

Lee, K. S., Metcalf, W. W., Wanner, B. L. 1992. Evidence for two phosphonate degradative pathways in Enterobacter aerogenes. J Bacteriol. 174: 2501-2510.

Wanner, B. L. 1992. Is cross regulation by phosphorylation of two-component response regulator proteins important in bacteria?. J Bacteriol. 174: 2053-2058.

Wanner, B. L. 1992. Genes for phosphonate biodegradation in Escherichia coli. SAAS Bull Biochem Biotechnol. 5: 1-6.

Wanner, B. L., Metcalf, W. W. 1992. Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation. FEMS Microbiol Lett. 79: 133-139.

Wanner, B. L., Wilmes-Riesenberg, M. R. 1992. Involvement of phosphotransacetylase, acetate kinase, and acetyl phosphate synthesis in control of the phosphate regulon in Escherichia coli. J Bacteriol. 174: 2124-2130.

Wilmes-Riesenberg, M. R., Wanner, B. L. 1992. TnphoA and TnphoA' elements for making and switching fusions for study of transcription, translation, and cell surface localization. J Bacteriol. 174: 4558-4575.

Metcalf, W. W., Wanner, B. L. 1991. Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi. J Bacteriol. 173: 587-600.

Agrawal, D. K., Wanner, B. L. 1990. A phoA structural gene mutation that conditionally affects formation of the enzyme bacterial alkaline phosphatase. J Bacteriol. 172: 3180-3190.

Chen, C. M., Ye, Q. Z., Zhu, Z. M., Wanner, B. L., Walsh, C. T. 1990. Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B. J Biol Chem. 265: 4461-4471.

Metcalf, W. W., Steed, P. M., Wanner, B. L. 1990. Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions. J Bacteriol. 172: 3191-3200.

Wanner, B. L., Boline, J. A. 1990. Mapping and molecular cloning of the phn (psiD) locus for phosphonate utilization in Escherichia coli. J Bacteriol. 172: 1186-1196.

Wanner, B. L., Wilmes, M. R., Hunter, E. 1988. Molecular cloning of the wild-type phoM operon in Escherichia coli K-12. J Bacteriol. 170: 279-288.

Wanner, B. L., Wilmes, M. R., Young, D. C. 1988. Control of bacterial alkaline phosphatase synthesis and variation in an Escherichia coli K-12 phoR mutant by adenyl cyclase, the cyclic AMP receptor protein, and the phoM operon. J Bacteriol. 170: 1092-1102.

Wackett, L. P., Wanner, B. L., Venditti, C. P., Walsh, C. T. 1987. Involvement of the phosphate regulon and the psiD locus in carbon-phosphorus lyase activity of Escherichia coli K-12. J Bacteriol. 169: 1753-1756.

Wanner, B. L. 1987. Control of phoR-dependent bacterial alkaline phosphatase clonal variation by the phoM region. J Bacteriol. 169: 900-903.

Wanner, B. L. 1987. Molecular cloning of Mu d(bla lacZ) transcriptional and translational fusions. J Bacteriol. 169: 2026-2030.

Wanner, B. L., Chang, B. D. 1987. The phoBR operon in Escherichia coli K-12. J Bacteriol. 169: 5569-5574.

Wanner, B. L. 1986. Novel regulatory mutants of the phosphate regulon in Escherichia coli K-12. J Mol Biol. 191: 39-58.

Wanner, B. L. 1986. Bacterial alkaline phosphatase clonal variation in some Escherichia coli K-12 phoR mutant strains. J Bacteriol. 168: 1366-1371.

Wanner, B. L. 1983. Overlapping and separate controls on the phosphate regulon in Escherichia coli K12. J Mol Biol. 166: 283-308.

Wanner, B. L., Bernstein, J. 1982. Determining the phoM map location in Escherichia coli K-12 by using a nearby transposon Tn10 insertion. J Bacteriol. 150: 429-432.

Wanner, B. L., McSharry, R. 1982. Phosphate-controlled gene expression in Escherichia coli K12 using Mudl-directed lacZ fusions. J Mol Biol. 158: 347-363.

Wanner, B. L., Wieder, S., McSharry, R. 1981. Use of bacteriophage transposon Mu d1 to determine the orientation for three proC-linked phosphate-starvation-inducible (psi) genes in Escherichia coli K-12. J Bacteriol. 146: 93-101.

Wanner, B. L., Latterell, P. 1980. Mutants affected in alkaline phosphatase, expression: evidence for multiple positive regulators of the phosphate regulon in Escherichia coli. Genetics. 96: 353-366.

Wanner, B. L., Sarthy, A., Beckwith, J. 1979. Escherichia coli pleiotropic mutant that reduces amounts of several periplasmic and outer membrane proteins. J Bacteriol. 140: 229-239.

Wanner, B. L., Kodaira, R., Neidhardt, F. C. 1978. Regulation of lac operon expression: reappraisal of the theory of catabolite repression. J Bacteriol. 136: 947-954.

Wanner, B. L., Kodaira, R., Neidhart, F. C. 1977. Physiological regulation of a decontrolled lac operon. J Bacteriol. 130: 212-222.