UW-Madison Dept of Bacteriology

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• Rutherford ST, Villers CL, Lee JH, Ross W, Gourse RL. 2009.
  Allosteric control of Escherichia coli rRNA promoter complexes by
  DksA. Genes Dev. 23:236-48..
  
• Ross W, Gourse RL. 2009. Analysis of RNA polymerase-promoter
  complex formation. Methods 47:13-24.
  
• Lamour V, Rutherford ST, Kuznedelov K, Ramagopal UA, Gourse RL, Severinov K, Darst SA. 2008. Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein. J Mol Biol. 383:367-79.
• Haugen SP, Ross W, Gourse RL. 2008. Advances in bacterial promoter
  recognition and its control by factors that do not bind DNA. Nat Rev
  Microbiol. 6:507-19.

Vrentas CE, Gaal T, Berkmen MB, Rutherford ST, Haugen SP, Ross W, Gourse RL. 2008. Still looking for the magic spot: the crystallographically-defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J. Mol. Biol., in press.

Haugen SP, Ross W, Manrique M, Gourse RL. 2008. Fine structure of the promoter - sigma region 1.2 interaction. Proc. Natl. Acad. Sci. USA, in press.

Costanzo A, Nicoloff H, Barchinger S, Banta A, Gourse RL, Ades SE. 2008. Mechanism of regulation of the extracytoplasmic stress factor sigmaE in Escherichia coli by DksA and the alarmone ppGpp. Mol. Microbiol. 67:619-632.

Gourse R.L. and Keck, J.L. 2007 Magic Spots Cast a Spell on DNA Primase. Cell 128:823-824.

Suthers P.F., Gourse R.L., Yin J. 2007 Rapid responses of ribosomal RNA synthesis to nutrient shifts. Biotechnol. Bioeng. 97:1230-45.

Rutherford S.T., Lemke J.J., Vrentas C.E., Gaal T., Ross W., Gourse R.L.2007 Effects of DksA, GreA, and GreB on Transcription Initiation: Insights into the Mechanisms of Factors that Bind in the Secondary Channel of RNA Polymerase. J. Mol. Biol. 366:1243-57.

Quinones M., Kimsey H.H., Ross W., Gourse R.L., Waldor M.K. 2006. LexA represses CTXphi transcription by blocking access of the alpha C-terminal domain of RNA polymerase to promoter DNA. J. Biol. Chem. 281:39407-12.

Gaal T., Mandel M.J., Silhavy T.J., Gourse R.L. 2006. Crl facilitates RNA polymerase holoenzyme formation. J. Bacteriol. 188:7966-70.

Mallik P., Paul B.J., Rutherford S.T., Gourse R.L., Osuna R. 2006. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J. Bacteriol. 188:5775-82.

Gourse R.L., Ross W., and Rutherford S.T. 2006. General Pathway for Turning On Promoters Transcribed by RNA Polymerases Containing Alternative sigma Factors J. Bacteriol. 188:4589-91. Review.

Haugen S.P., Berkmen M.B., Ross W., Gaal T., Ward C., and Gourse R.L. 2006. rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase Cell 125 in press.

Vrentas C.E., Gaal T., Ross W., Ebright R.H., and Gourse R.L. 2005. Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes Dev. 19 2378-2387.

Paul B.J., Berkmen M.B., and Gourse R.L. 2005. DksA potentiates direct activation of amino acid promoters by ppG promoters by ppGpp Proc Natl Acad Sci USA. 102 7823–7828.

Ross, W, and Gourse R.L. 2005. Sequence-independent upstream DNA-alpha-CTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association Proc Natl Acad Sci USA. 102 291-296.

Krásný L, and Gourse R.L. 2004. An alternative strategy for bacterial ribosome synthesis: B. subtilis rRNA transcription regulation. EMBO J., 23:4473-4483.

Paul B.J., Ross W, Gaal T, Gourse R.L. 2004. rRNA Transcription in Escherichia coli. Annu Rev Genet, 38:749-770. (Review)

Paul B.J., Barker M.M., Ross W, Schneider D.A, Webb C, Foster JW, Gourse RL. 2004. DksA: A critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118: 311-322.

Murray, H.D., and Gourse, R.L. 2004. Unique roles of the rrn P2 rRNA promoters in Escherichia coli. Mol. Microbiol. 52:1375-1387.

Schneider, D.A., and Gourse, R.L. 2004. Relationship between growth rate and ATP concentration in Escherichia coli: A bioassay for available cellular ATP. J. Biol. Chem. 279: 8262-68.

Schneider, D.A., H.D. Murray, and R.L. Gourse. 2003. Measuring control of transcription initiation by changing concentrations of nucleotides and their derivatives. Methods Enzymol. 370:606-617.

Barker, M.M., and R.L. Gourse. 2003. Control of stable RNA synthesis, in Translation Mechanisms, Lapointe, J. and Brakier-Gingras, L. (eds.) Landes Biosciences, Austin, TX, pp 370-387.

Stokes, N.R., Murray, H.D., Subramaniam, C., Gourse, R.L., Louis, P., Bartlett, W., Miller, S., and Booth, I.R. 2003. A role for mechanosensitive channels in survival of stationary phase: Regulation of channel expression by RpoS. Proc Natl Acad Sci USA. 100:15959-15964.

Schneider, D.A., Gourse, R.L. 2003. Changes in Escherichia coli rRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate (iNTP) and Guanosine 5'-diphosphate 3'-diphosphate (ppGpp) Concentrations after Induction of Feedback Control of Ribosome Synthesis. J. Bacteriol. 185:6185-6191.

Schneider, D.A., Gourse, R.L. 2003. Changes in the concentrations of guanosine 5’-diphosphate 3’- diphosphate (ppGpp) and the initiating nucleoside triphosphate (iNTP) account for inhibition of rRNA transcription in fructose 1,6 diphosphate aldolase (fda) mutants J. Bacteriol. 185:6192-6194.

Murray, H.D., Schneider, D.A., Gourse, R.L. 2003. Control of rRNA expression by small molecules is dynamic and non-redundant. Molecular Cell.12:125-134.

Ross, W., Schneider, D.A., Paul, B.J., Mertens, A., Gourse, R.L. 2003. An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev.15:1293-1307.

Schneider, D.A., Ross, W., Gourse, R.L. 2003. Control of rRNA expression in Escherichia coli. Curr. Opin. Microbiol. 6:151-156.

Murray, H.D., Appleman J.A., Gourse R.L. 2003. Regulation of the Escherichia coli rrnB P2 Promoter. J. Bacteriol. 185, 28-34

Schneider, D.A., Gaal, T., and Gourse, R.L. 2002. NTP-sensing by rRNA promoters in Escherichia coli is direct. Proc. Natl. Acad. Sci.USA.99,8602-8607

Peck, M.C., Gaal, T., Fisher, R.F., Gourse, R.L., Long, S.L. 2002. The RNA polymerase a subunit from Sinorhizobium meliloti can assemble with RNA polymerase subunits from Escherichia coli and function in basal and activated transcription both in vivo and in vitro. J. Bacteriol. 184, 3808-3814

Aiyar, S.E., T. Gaal, and R.L. Gourse. 2002. rRNA promoter activity in the fast growing bacterium Vibrio natriegens. J. Bacteriol.184, 1349-135

McLeod, S.M., Aiyar, S.E., Gourse, R.L. & Johnson, R.C. 2002. The C-terminal domains of the RNA polymerase alpha subunits: Contact site with Fis and localization during co-activation with CRP at the Escherichia coli proP P2 promoter. J. Mol. Biol. 316, 517-529

Aiyar, S.E., McLeod, S.M., Ross, W., Hirvonen, C.A., Thomas, M.S., Johnson, R.C., and Gourse, R. L. 2002. Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters. J. Mol. Biol. 316, 501-516

Savery, N.J., Lloyd, G., Busby, S.J.W., Thomas, M.S., Ebright, R.H. and Gourse, R.L. 2002. Interactions between CRP and the C-terminal domain of the RNA polymerase alpha subunit at Class I CRP-dependent promoters. J. Bacteriol. 184, 2273-2280

Gaal, T., Ross, W., Estrem, S.T., Nguyen, L.H., Burgess, R.R. and Gourse, R.L. 2001. Promoter recognition and discrimination by E-sigma-S RNA polymerase. Mol. Microbiol., 42, 939-954.

Meng, W., Belyaeva, T., Savery, N.J., Busby, S.W., Ross, W.E., Gaal, T., Gourse, R.L., Thomas, M.S. 2001. UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker. Nucl. Acids. Res. 29, 4166-4178.

Barker, M.M., and Gourse, R.L. 2001. Regulation of rRNA transcription correlates with NTP-sensing. J. Bacteriol. 183, 6315-6323.

Hirvonen, C.A., Ross, W., Wozniak, C.E., Marasco, E., Anthony, J.R., Aiyar, S.E., Newburn, V.H., and Gourse, R.L. 2001. Contributions of UP elements and and the transcription factor FIS to expression from the rrn P1 promoters in Escherichia coli. J. Bacteriol. 183, 6305-6314.

Ross, W., Ernst, A., and Gourse. R.L. 2001 Fine structure of E. coli RNA polymerase-promoter iteractions: a subunit binding to the UP element minor groove. Genes Dev. 15, 491-506.

Barker, M.M., Gaal, T., and Gourse, R.L. 2001. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP J. Mol. Biol. 305, 689-702

Barker, M.M., Gaal, T., Josaitis, C., and Gourse, R.L. 2001. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol. 305, 673-86

Gourse, R.L., Ross, W., and Gaal, T.. 2000. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37, 687-695.

Bartlett, M.S., Gaal, T., Ross, W., and Gourse, R.L.. 2000. Regulation of ribosomal RNA transcription is remarkably robust: FIS compensates for altered NTP-sensing by mutant RNA polymerases at Escherichia coli rrn P1 promoters. J. Bacteriol. 182, 1969-1977.

McLeod SM, Xu JM, Cramton SE, Gaal T, Gourse RL, Johnson RC. 1999. Localization of amino acids required for Fis to function as a class II transcriptional activator at the RpoS-dependent proP P2 promoter. J. Mol. Biol. 294, 333-346 (1999)

Estrem, S.T., Ross, W., Gaal, T., Chen, S., Niu, W., Ebright, R.H., and Gourse, R.L. 1999. Bacterial promoter architecture: subsite structure of UP elements and interactions with the C-terminal domain of the RNA polymerase alpha subunit. Genes Dev. 13, 2134-2147.

Voulgaris, J., French, S., Gourse, R.L., Squires, C., and Squires, C.L. 1999. Increased rrn gene dosage causes intermittent transcription of rRNA in E. coli. J. Bacteriol. 181, 4170-4175.

Ross, W., Salomon, J., Holmes, W.M., and Gourse, R.L.1999. Activation of Escherichia coli leuV transcription by FIS. J. Bacteriol. 181, 3864-3868.

He, Y., Gaal, T., Karls, R., Donohue, T.J., Gourse, R.L., and Roberts, G.P. 1999. Transcription activation by CooA, the CO-sensing factor from Rhodospirillum rubrum: the interaction between CooA and the C-terminal domain of the a subunit of RNA polymerase. J. Biol. Chem. 274, 10840-10845.

Gourse, R.L., Gaal, T., Aiyar, S.E., Barker, M.M., Estrem, S.T., Hirvonen, C.A., and Ross, W. 1998. Strength and regulation without transcription factors: Lessons from bacterial rRNA promoters. Cold Spring Harbor Symposium on Quantitative Biology 63, 131-139.

Aiyar, S.E., Gourse, R.L., Ross, W. 1998. Upstream A-tracts increase prokaryotic promoter activity through interactions with the RNA polymerase alpha subunit. Proc. Natl. Acad. Sci. USA 95, 14652-14657.

Kainz, M., Gourse, R.L..1998. The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription termination. J. Mol. Biol. 284, 1379-1390.

Ross, W., Aiyar, S.E., Salomon, J. and Gourse, R.L. 1998. E. coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J. Bacteriol. 180, 5375-5383.

Estrem, S.T., Gaal, T., Ross, W. and Gourse, R.L. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. USA. 95, 9761-9766.

Savery, N.J., Lloyd, G.S., Kainz, M., Gaal, T., Ebright, R.H., Gourse, R.L. and Busby, S.J.W. 1998. Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase alpha subunit. EMBO J. 17, 3439-3447.

Tan, M., Gaal, T., Gourse, R.L. and Engel, J.N. 1998. Mutational analysis of the Chlamydia trachomatis rRNA P1 promoter defines four regions important for transcription in vitro. J. Bacteriol. 180, 2359-2366.

Bartlett, M.S., Gaal, T., Ross, W., and Gourse, R.L. 1998. RNA polymerase mutants defective in the NTP-sensing mechanism for growth rate-dependent control of rRNA transcription. J. Mol. Biol. 279, 331-345.

Appleman, J.A., Ross, W., Salomon, J. and Gourse, R.L. 1998. Activation of Escherichia coli rRNA transcription by FIS during a growth cycle. J. Bacteriol. 180, 1525-1532.

Gaal, T., Bartlett, M.S., Ross, W., Turnbough, C.L., Jr., and Gourse, R.L. 1997. NTP concentration as a regulator of transcription initiation: control of rRNA synthesis in bacteria. Science 278, 2092-2097.

Bokal, A.J. IV, Ross, W., Gaal, T., Johnson, R.C., and Gourse, R.L. 1997. Molecular anatomy of a transcription activation patch: FIS-RNA polymerase interactions at the Escherichia coli rrnB P1 promoter. EMBO J. 16, 154-162.

Van Ulsen, P., Hillebrand, M., Kainz, M., Collard, R., Zulianello, L., van de Putte, P., Gourse, R.L., and Goosen,N. 1997. Function of the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase in basal expression and IHF-mediated activation of the early promoter of bacteriophage Mu. J. Bacteriol. 179, 530-537.

Landini, P., Gaal, T., Ross, W., and Volkert, M.R. 1997. Transcriptional activation of alkA involves activator-dependent promoter binding of the alpha subunit of RNA polymerase J. Biol. Chem. 272, 15914-15919.

Gourse, R.L., Gaal, T., Bartlett, M.S., Appleman, J.A., and Ross, W. 1996. rRNA transcription and growth rate dependent regulation of ribosome synthesis in Escherichia coli. Annu. Rev. Microbiol. 50, 645-677.

Gosink, K.K., Gaal, T., Bokal IV, A.J., and Gourse, R.L. 1996. A positive control mutant of the transcription activator protein FIS. J. Bacteriol. 178, 5182-5187.

Gaal, T., Ross, W., Blatter, E.E., Tang, H., Jia, X., Krishnan, V.V., Assa-Munt, N., Ebright, R.H., and Gourse, R.L. 1996. DNA Binding Determinants of the a Subunit of RNA Polymerase: Novel DNA Binding Domain Architecture. Genes Dev. 10, 16-26.

Josaitis, C.A., Gaal, T., and Gourse, R.L. 1995. Stringent control and growth rate dependent control have nonidentical promoter sequence determinants. Proc. Natl. Acad. Sci. USA 92, 1117-1121.

Bokal, A.J. IV, Ross, W., and Gourse, R.L. 1995. The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J. Mol. Biol. 245, 197-207.

Blatter, E.E., Ross, W., Tang, H., Gourse, R.L., and Ebright, R.H. 1994. Domain organization of RNA polymerase a subunit: C-terminal 85 amino acids constitute an independently folded domain capable of dimerization and DNA binding. Cell 78, 889-896.

Bartlett, M.S. and Gourse, R.L. 1994. Growth rate dependent control of the rrnB P1 core promoter in Escherichia coli. J. Bacteriol. 176, 5560-5564.

Gaal, T., Rao, L., Estrem, S.T., Yang, J., Wartell, R.M., and Gourse, R.L. 1994. Localization of the intrinsically bent DNA region upstream of the E. coli rrnB P1 promoter. Nucleic Acids Res. 22, 2344-2350.

Rao, L., Ross, W., Appleman, J.A., Gaal, T., Leirmo, S., Schlax, P.J., Record, M.T. Jr., and Gourse, R.L. 1994. Factor-independent activation of rrnB P1: An "extended" promoter with an upstream element that dramatically increases promoter strength. J. Mol. Biol. 235, 1421-1435.

Suh, W.-S., Ross, W. and Record, M.T. Jr. 1993. Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site. Science 259, 358-361.

Borukhov, S., Sagitov, V., Josaitis, C.A., Gourse, R.L., and Goldfarb, A. 1993. Two modes of transcription initiation at the rrnB P1 promoter of Escherichia coli. J. Biol. Chem. 268, 23477-23482.

Gosink, K.K., Ross, W., Leirmo, S., Osuna, R., Finkel, S.E., Johnson, R.C., and Gourse, R.L. 1993. DNA binding and bending are necessary but not sufficient for Fis-dependent activation of rrnB P1. J. Bacteriol. 175, 1580-1589.

Newlands, J.T., Gaal, T., Mecsas, J., and Gourse, R.L. 1993. Transcription of the E. coli rrnB P1 promoter by the heat shock RNA polymerase (Es32) in vitro. J. Bacteriol. 175, 661-668.

Ross, W., Gosink, K.K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K., and Gourse, R.L. 1993. A third recognition element in bacterial promoters: DNA binding by the a subunit of RNA polymerase. Science 262, 1407-1413.