Section on Environmental Gene Regulation

Selected Publications

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2012 | 2011 | 2010 | 2000's | 1990's

2012

Hobbs, E. C., Yin, X., Paul, B. L., Astarita, J. L. and Storz, G. (2012) Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance. Proc. Natl. Acad. Sci. USA 109, 16699-1670. PDF, Supplemental Material
Beisel C. L., Updegrove, T. B., Janson, B. J, and Storz G. (2012) Multiple factors dictate target selection by Hfq-binding small RNAs. EMBO J. 31, 961-974. PDF, Supplemental Material
Thomason MK, Fontaine F, De Lay N, Storz G. (2012) A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli. Mol Microbiol. 84, 17-35. PDF, Supplemental Material

2011

Waters, L. S., Sandoval, M. and Storz, G. (2011) The Escherichia coli MntR mini regulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. J. Bacteriol. 193, 5887-5897. PDF, Supplemental Material
Storz, G., Vogel, J. and Wassarman, K. M. (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol. Cell, 43, 880-891. PDF
Fontaine, F., Fuchs, R. J. and Storz, G. (2011) Membrane localization of small proteins in Escherichia coli. J. Biol. Chem. 286, 32464-32474. PDF, Supplemental Material
Hobbs, E. C., Fontaine, F., Yin, X. and Storz, G. (2011) An expanding universe of small proteins. Curr. Opin. Microbiol. 14, 167-173. PDF
Beisel, C. L. and Storz, G. (2011) The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli. Mol. Cell 41, 286-297. PDF, Supplemental Material 1 (PDF), Supplemental Material 2 (XLS)
Opdyke, J. A., Fozo, E. M., Hemm, M. R. and Storz, G. (2011) RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA. J. Mol. Biol. 406, 29-43. PDF, Supplemental Material

2010

Thomason, M. K. and Storz, G. (2010) Bacterial antisense RNAs: How many are there and what are they doing? Annu. Rev. Genet. 44, 167-188. PDF
Beisel C. L. and Storz G. (2010) Base pairing small RNAs and their roles in global regulatory networks. FEMS Microbiol. Rev. 34, 866-882. PDF
Fozo, E. M., Makarova, K. S., Shabalina, S. A., Yutin, N., Koonin, E. V. and Storz, G. (2010) Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res. 38, 3743-3759. PDF, Supplemental Material
Fozo, E. M., Makarova, K. S., Shabalina, S. A., Yutin, N., Koonin, E. V. and Storz, G. (2010) Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families. Nucleic Acids Res. 38, 3743-3759. PDF, Supplemental Material
Durand S. and Storz, G. (2010) Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol. Microbiol. 75, 1215-1231. PDF, Supplemental Material
Hemm, M. R., Paul, B. J., Miranda-Rios, J. Zhang, A., Soltanzad, N. and Storz, G. (2010) Small stress response proteins in Escherichia coli: proteins that were missed by classical proteomic studies. J. Bacteriol. 192, 46-58. PDF, Supplemental Material
Hobbs, E. C., Astarita, J. L. and Storz, G. (2010) Small RNAs and small proteins involved in resistance to cell envelope stress and acid shock in Escherichia coli: analysis of a bar-coded mutant collection. J. Bacteriol. 192, 59-67. PDF, Supplemental Material

2009

Waters, L. S. and Storz, G. (2009) Regulatory RNAs in bacteria. Cell 136, 615-628. PDF

2008

Fozo, E. M., Hemm, M. R., and Storz, G. (2008) Small toxic proteins and the antisense RNAs that repress them. Mol. Biol. Rev. 72, 579-589. PDF
Hemm, M. R., Paul, B. J., Schneider, T. D., Storz, G. and Rudd, K. E. (2008) Small membrane proteins found by comparative genomics and ribosome binding site models. Mol. Microbiol. 70, 1487-1501. PDF, Supplemental Material
Fozo, E. M., Kawano, M., Fontaine, F., Kaya, Y., Mendieta, K. S., Jones, K. L., Ocampo, A., Rudd, K. E., and Storz, G. (2008) Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol. Microbiol. 70, 1076-1093. PDF, Supplemental Material

2007

Chen, Z., Lewis, K. A., Shultzaberger, R. K., Lyakhov, I. G., Zheng, M., Doan, B., Storz, G., and Schneider, T. D. (2007) Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res. 35, 6762-6777 PDF, Supplemental Material
Bender, R, A,, Downs, D., Kiley, P., LaRossa, R. A., Sonenshein, A. L., and Storz G. (2007) Bridges and chasms: summary of the IMAGE 2 meeting in Montreal, Canada, 30 April to 3 May 2007. J. Bacteriol. 190, 792-797.
Kawano, M., Aravind, L., and Storz, G. (2007) An antisense RNA controls synthesis on an SOS-induced toxin evolved from an antitoxin. Mol. Microbiol. 64, 738-754. PDF Supplemental Material
Storz, G. and Haas, D. (2007) A guide to small RNAs in microorganisms. Curr. Opin. Microbiol. 10, 93-95. PDF
Storz, G., Opdyke, J. A., and Wassarman, K. M. (2007) Regulating bacterial transcription with small RNAs. Cold Spring Harb. Symp. Quant. Biol. 71, 269-273.

2006

Wang, X., Mukhopadhyay, P., Wood, M. J., Outten, F. W., Opdyke, J. A., and Storz, G. (2006) Mutational analysis to define an activating region on the redox-sensitive transcriptional regulator OxyR. J. Bacteriol. 188, 8335-8342. PDF
Guillier, M., Gottesman, S., and Storz, G. (2006) Modulating the outer membrane with small RNAs. Genes Dev. 20, 2338-2348. PDF
Tjaden, B., Goodwin, S. S., Opdyke, J. A., Guillier, M., Fu, D. X., Gottesman, S., and Storz, G. (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res. 34, 2791-2802. PDF, Supplemental Material
Hu, Z., Zhang, Z., Storz, G., Gottesman, S., and Leppla, S. H. (2006) An antibody-based microarray assay for small RNA detection. Nucleic Acids Res. 34, e52. PDF, Supplemental Material
Storz, G. and Gottesman, S. (2006) Versatile roles of small RNA regulators in bacteria. In The RNA World, 3rd edition. Gesteland, R. F., Cech, T. R., Atkins, J. F. (eds). Cold Spring Harbor: CSHL Press, pp. 567-594.

2005

Kawano, M., Storz, G., Rao, B. S., Rosner, J. L., and Martin, R. G. (2005) Detection of low-level promoter activity within open reading frame sequences of Escherichia coli. Nucleic Acids Res. 33, 6268-6276. PDF, Supplemental Material
Storz, G., Altuvia, S., and Wassarman K. M. (2005) An abundance of RNA regulators. Annu. Rev. Biochem. 74, 199-217. PDF
Kawano, M., Reynolds, A. A., Miranda-Rios, J., and Storz, G. (2005) Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res. 33, 1040-1050. PDF, Supplemental Material
Wood, M. J. and Storz, G. (2005) Oxygen, metabolism and gene expression: the T-Rex connection. Structure 13, 2-4. PDF

2004

Lee, C., Lee, S. M., Mukhopadhyay, P., Kim, S. J., Lee, S. C., Ahn, W.-S., Yu, M.-H., Storz, G., and Ryu, S. E. (2004) Redox regulation of OxyR requires specific disulfide bond formation involving a rapid kinetic reaction path. Nat. Struct. Mol. Biol. 11, 1179-1185. PDF, Supplemental Material
Kiley, P. J. and Storz, G. (2004) Exploiting thiol modifications. PLoS Biol. 2, 1714-1717. PDF
Chen, S., Zhang, A., Blyn, L. B., and Storz, G. (2004) MicC, a second small RNA regulator of Omp protein expression in Escherichia coli. J. Bacteriol. 186, 6689-6697. PDF, Supplemental Material
Opdyke, J. A., Kang, J.-G., and Storz, G. (2004) GadY, a small RNA regulator of acid response genes in Escherichia coli. J. Bacteriol. 186, 6698-6705. PDF, Supplemental Material
Wood, M. J., Storz, G., and Tjandra, N. (2004) Structural basis for redox regulation of Yap1 transcription factor localization. Nature 430, 917-921. PDF, Supplemental Material.
Outten, F. W., Djaman, O., and Storz, G. (2004) A suf operon requirement for Fe-S cluster assembly during iron starvation in E. coli. Mol. Microbiol. 52, 861-872. PDF, Supplemental Material
Storz, G., Opdyke, J. A., and Zhang, A. (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol. 7, 140-144. PDF
Mukhopadhyay, P., Zheng, M., LaRossa, R. A., and Storz, G. (2004) Prominent roles of the norR and fur regulators in the Escherichia coli transcriptional response to reactive nitrogen species. Proc. Natl. Acad. Sci. USA 101, 745-750. PDF, Supplemental Material

2003

Zhang, A., Wassarman, K. M., Rosenow, C., Tjaden, B. C., Storz, G., and Gottesman, S. (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50:1111-1124. PDF, Supplemental Material
Outten, F. W., Wood, M. J., Muñoz, F. M., and Storz, G. (2003) The SufE protein and the SufBCD complex enhance SufS cysteine desulfurase activity as part of a sulfur transfer pathway for Fe-S cluster assembly in E. coli. J. Biol. Chem. 278:45713-45719. PDF, Supplemental Material
Wood, M. J., Andrade, E. C., and Storz, G. (2003) The redox domain of the Yap1p transcription factor contains two disulfide bonds. Biochemistry 42:11982-11991. PDF

2002

Weisberg, R. A., and Storz, G. (2002) Take your vitamins with a pinch of RNA. Mol. Cell 10, 1266-1268. PDF
Storz, G. (2002) An expanding universe of non-coding RNAs. Science 296, 1260-1263. PDF
Zhang, A., Wassarman, K.M., Ortega, J., Steven, A.C., and Storz, G. (2002) The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell 9, 11-22. PDF, Supplemental Material.

2001

Zheng, M., Wang, X., Templeton, L. J., Smulski, D. R., LaRossa, R. A., and Storz, G. (2001) DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. J. Bacteriol. 183, 4562-4570. PDF
Zheng, M., Wang, X., Doan, B., Lewis, K. A., Schneider, T. D., and Storz, G. (2001) Computation-directed identification of OxyR DNA binding sites in Escherichia coli. J. Bacteriol. 183, 4571-4579. PDF, Supplemental Material
Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G., and Gottesman, S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15, 1637-1651. PDF, Supplemental Material
Choi, H.-J., Kim, S.-H., Mukhopadhyay, P., Cho, S., Woo, J.-R., Storz, G., and Ryu, S.-E. (2001) Structural basis of the redox switch in the OxyR transcription factor. Cell 105, 103-113. PDF

2000

Carmel-Harel, O., Stearman, R., Gasch, A. P., Botstein, D., Brown, P. O., and Storz, G. (2000) Role of Thioredoxin Reductase in the Yap1p-Dependent Response to Oxidative Stress in Saccharomyces cerevisiae. Mol. Microbiol., 39, 595-605. PDF, Supplemental Material
Gasch A. P., Spellman P. T., Kao C. M., Carmel-Harel O., Eisen M. B., Storz G., Botstein D., and Brown P. O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Cell Biol. 11, 4241-4257. PDF, Supplemental Material
Carmel-Harel O. and Storz G. (2000) Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and Saccharomyces cerevisiae response to oxidative stress. Annu. Rev. Microbiol. 54, 439-461. PDF
Wassarman K. M. and Storz G. (2000) 6S RNA regulates E. coli RNA polymerase activity. Cell 101, 613-623. PDF
Storz G. and Zheng M. (2000) Oxidative Stress. In Bacterial Stress Responses. Storz, G. and Hengge-Aronis, R. (eds). Washington DC: ASM Press. pp. 47-59.
Ritz D., Patel H., Doan B., Zheng M., Åslund F., Storz G., and Beckwith, J. (2000) Thioredoxin 2 is involved in the oxidative stress response in Escherichia coli. J. Biol. Chem. 275, 2505-2512. PDF

1990-1999

Zheng M., Doan B., Schneider T. D., and Storz G. (1999) OxyR and SoxRS regulation of fur. J. Bacteriol. 181, 4639-4643. PDF, Supplemental Material
Åslund F., Zheng M., Beckwith J., and Storz, G.(1999) Regulation of the OxyR transcription factor by hydrogen peroxide and the cellular thiol-disulfide status. Proc. Natl. Acad. Sci. USA 96, 6161-6165. PDF
Storz G. and Imlay J. A. (1999) Oxidative stress. Curr. Opin. Microbiol. 2, 188-194
Wassarman K. M., Zhang A., and Storz G. (1999) Small RNAs in Escherichia coli. Trends Microbiol. 7, 37-44. PDF
Zhang A., Altuvia S., Tiwari A., Argaman L., Hengge-Aronis R., and Storz G. (1998) The oxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J. 17, 6061-6068. PDF
Altuvia S., Zhang A., Argaman L., Tiwari A., and Storz G. (1998) The Escherichia coli oxyS regulatory RNA represses fhlA translation by blocking ribosome binding. EMBO J. 17, 6069-6075. PDF
Zheng M., Åslund F., and Storz G.(1998) Activation of the OxyR transcription factor by reversible disulfide bond formation. Science 279, 1718-1721. PDF
Altuvia S., Weinstein-Fischer D., Zhang A., Postow L., and Storz G. (1997) A small, stable RNA induced by oxidative stress: Role as a pleiotropic regulator and antimutator. Cell 90, 43-53. PDF
Kullik I., Toledano M. B., Tartaglia L. A., and Storz G. (1995) Mutational analysis of the redox-sensitive transcriptional regulator OxyR: Regions important for oxidation and transcriptional activation. J. Bacteriol. 177, 1275-1284.
Kullik I., Stevens J., Toledano M. B., and Storz G. (1995) Mutational analysis of the redox-sensitive transcriptional regulator OxyR: Regions important for DNA-binding and multimerization. J. Bacteriol. 177, 1285-1291.
Toledano M. B., Kullik I., Trinh F., Baird P. T., Schneider T. D., and Storz G. (1994) Redox-Dependent Shift of OxyR-DNA Contacts Along An Extended DNA Binding Site: A Mechanism for Differential Promoter Selection. Cell 78, 897-909.
Altuvia S., Almirón M., Huisman G., Kolter R., and Storz G. (1994) The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. Mol. Microbiol. 13, 265-272.
Chae H. Z., Robison K., Poole L. B., Church G., Storz G., and Rhee S. G. (1994) Purification, cloning, and sequencing of thiol-specific antioxidant from mammalian brain: Alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes. Proc. Natl. Acad. Sci. USA 91:7017-7021.