Research Topics
Genomes and Genes | Richard GourseSummaryAffiliation: University of Wisconsin Country: USA Publications
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Publications
CoSMoS unravels mysteries of transcription initiationRichard L Gourse
Department of Bacteriology, University of Wisconsin Madison, Madison, WI 53706, USA
Cell 148:635-7. 2012..Ultimately, CoSMoS could greatly aid the study of the effects of DNA sequence and transcription factors on both prokaryotic and eukaryotic promoters...
Suppression of a dnaKJ deletion by multicopy dksA results from non-feedback-regulated transcripts that originate upstream of the major dksA promoterPete Chandrangsu
Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin, USA
J Bacteriol 194:1437-46. 2012....- General pathway for turning on promoters transcribed by RNA polymerases containing alternative sigma factorsRichard L Gourse
Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706, USA
J Bacteriol 188:4589-91. 2006 - rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coliR L Gourse
Department of Bacteriology, University of Wisconsin, Madison 53706, USA
Annu Rev Microbiol 50:645-77. 1996..The mechanisms contributing to rRNA transcription work together and compensate for one another when individual systems are rendered inoperative... - Magic spots cast a spell on DNA primaseRichard L Gourse
Department of Bacteriology, University of Wisconsin Madison, 420 Henry Mall, Madison, WI 53706, USA
Cell 128:823-4. 2007..2007) show that (p)ppGpp also inhibits DNA replication elongation by interfering with DNA primase activity. Halting replication may help cells to maintain genomic integrity during periods of transient nutrient limitation... - UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognitionR L Gourse
Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
Mol Microbiol 37:687-95. 2000..e. in the absence of proteins other than RNA polymerase) and activated transcription initiation (i.e. when stimulated by transcription factors)... - Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAPM M Barker
Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI, 53706, USA
J Mol Biol 305:689-702. 2001..Our data also place considerable constraints on models invoking hypothetical factors that might increase amino acid promoter activity in a ppGpp-dependent fashion... - Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitroM M Barker
Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI, 53706, USA
J Mol Biol 305:673-88. 2001..The accompanying paper evaluates potential models for positive control of amino acid promoters by ppGpp that might explain the requirement of ppGpp for amino acid prototrophy... - Both fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependentJ T Newlands
Department of Bacteriology, University of Wisconsin, Madison 53706
Nucleic Acids Res 20:719-26. 1992..We also demonstrate that RNAP interacts with the -53 region of the rrnB P1 UAR even when these sequences are displaced upstream of the RNAP binding site, and that these interactions correlate with factor-independent activation... - DNA binding and bending are necessary but not sufficient for Fis-dependent activation of rrnB P1K K Gosink
Department of Bacteriology, University of Wisconsin, Madison 53706
J Bacteriol 175:1580-9. 1993..Rather, the data are most easily interpreted in terms of transcription activation by direct interactions between Fis and RNA polymerase, requiring precise positioning of the two proteins facilitated by bending of the DNA binding site... - Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strengthL Rao
Department of Bacteriology, University of Wisconsin, Madison 53706
J Mol Biol 235:1421-35. 1994..A functional UP element is not absolutely essential for stimulation of rrnB P1 by the Fis protein... - Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor grooveW Ross
Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
Genes Dev 15:491-506. 2001..These studies greatly improve the resolution of our picture of the promoter-RNAP interaction... - E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivoW Ross
Department of Bacteriology, University of Wisconsin, Madison 53706
EMBO J 9:3733-42. 1990..On the basis of these results, we propose roles for Fis and the upstream activation system in rRNA synthesis... - Regulation of rRNA transcription correlates with nucleoside triphosphate sensingM M Barker
Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
J Bacteriol 183:6315-23. 2001.... - Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promotersW Ross
Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
J Bacteriol 180:5375-83. 1998.... - Sequences upstream of the-35 hexamer of rrnB P1 affect promoter strength and upstream activationC A Josaitis
Department of Bacteriology, University of Wisconsin, Madison 53706
Biochim Biophys Acta 1050:307-11. 1990..UAR function appears dependent on its position relative to the RNA polymerase binding site, suggesting that a particular spatial geometry may be necessary for Fis-dependent and/or factor-independent activation to occur... - The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription terminationM Kainz
Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI, 53706, USA
J Mol Biol 284:1379-90. 1998..We conclude that the alphaCTD is a target for interactions with NusA that influence both termination and pausing, but in addition it participates in rho-dependent transcription termination in a NusA-independent manner... - Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coliC A Hirvonen
Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
J Bacteriol 183:6305-14. 2001..These studies have implications for the control of gene expression of unlinked multigene families... - Promoter recognition and discrimination by EsigmaS RNA polymeraseT Gaal
Department of Bacteriology, University of Wisconsin, Madison WI 53706, USA
Mol Microbiol 42:939-54. 2001..DNA recognition by EsigmaS versus Esigma70 thus presents an alternative solution to the problem of promoter selectivity... - DksA potentiates direct activation of amino acid promoters by ppGppBrian J Paul
Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706, USA
Proc Natl Acad Sci U S A 102:7823-8. 2005.... - Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksACatherine E Vrentas
Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
Genes Dev 19:2378-87. 2005..Furthermore, these results suggest that either one or both of two short segments in the beta' subunit that physically link omega to the ppGpp-binding region of the enzyme may play crucial roles in ppGpp and DksA function... - rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymeraseShanil P Haugen
Department of Bacteriology, University of Wisconsin Madison, 420 Henry Mall, 53706, USA
Cell 125:1069-82. 2006..2-discriminator interaction, rRNA promoters create the short-lived complex required for specific responses to the RNAP binding factors ppGpp and DksA, ultimately accounting for regulation of ribosome synthesis... - DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coliPrabhat Mallik
Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
J Bacteriol 188:5775-82. 2006..This work extends our understanding of the multiple factors controlling fis expression and demonstrates the generality of the DksA requirement for regulation of kinetically similar promoters... - Crl facilitates RNA polymerase holoenzyme formationTamas Gaal
Department of Bacteriology, University of Wisconsin Madison, 420 Henry Mall, Madison, WI 53706, USA
J Bacteriol 188:7966-70. 2006..Our results suggest that Crl facilitates holoenzyme formation, the first positive regulator identified with this mechanism of action... - LexA represses CTXphi transcription by blocking access of the alpha C-terminal domain of RNA polymerase to promoter DNAMariam Quinones
Department of Molecular Microbiology, Tufts University School of Medicine and The Howard Hughes Medical Institute, Boston, Massachusetts 02111, USA
J Biol Chem 281:39407-12. 2006..To our knowledge, this is the first report of a repressor blocking transcription initiation by occluding a promoter UP element... - Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymeraseSteven T Rutherford
Department of Bacteriology, University of Wisconsin Madison, 420 Henry Mall, Madison, WI 53706, USA
J Mol Biol 366:1243-57. 2007..Our results provide important clues to the mechanisms of both negative and positive control of transcription initiation by DksA... - Rapid responses of ribosomal RNA synthesis to nutrient shiftsPatrick F Suthers
Department of Chemical and Biological Engineering, University of Wisconsin Madison, WI 53706 1607, USA
Biotechnol Bioeng 97:1230-45. 2007..Inclusion of DksA was essential in all three cases. Our work provides a foundation for using data-driven computational models to predict the kinetics of in vivo transcriptional responses... - Changes in Escherichia coli rRNA promoter activity correlate with changes in initiating nucleoside triphosphate and guanosine 5' diphosphate 3'-diphosphate concentrations after induction of feedback control of ribosome synthesisDavid A Schneider
Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
J Bacteriol 185:6185-91. 2003..In contrast, we observed no change in the level of DNA supercoiling under the feedback conditions examined... - ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanismsAlessandra Costanzo
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
Mol Microbiol 67:619-32. 2008..However, ppGpp and its cofactor DksA can also activate transcription by EsigmaEin vitro, suggesting that the effects of ppGpp on sigmaE activity are both direct and indirect... - Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulationCatherine E Vrentas
Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI 53706, USA
J Mol Biol 377:551-64. 2008..coli ribosomal RNA transcription initiation and highlight the importance of inclusion of omega in bacterial RNAP preparations... - Fine structure of the promoter-sigma region 1.2 interactionShanil P Haugen
Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA
Proc Natl Acad Sci U S A 105:3292-7. 2008..2. Our results refine models of RNAP-DNA interactions in the promoter complex that are crucial for regulation of transcription initiation... 
Advances in bacterial promoter recognition and its control by factors that do not bind DNAShanil P Haugen
Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, Wisconsin 53706, USA
Nat Rev Microbiol 6:507-19. 2008..These factors can target promoters by affecting specific kinetic steps on the pathway to open complex formation, thereby regulating RNA output from specific promoters...- Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter associationWilma Ross
Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706, USA
Proc Natl Acad Sci U S A 102:291-6. 2005.... - rRNA transcription in Escherichia coliBrian J Paul
Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
Annu Rev Genet 38:749-70. 2004..Together, these advances provide clues important for our molecular understanding not only of rRNA transcription, but also of transcription in general... - An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulationLibor Krásný
Department of Bacteriology, University of Wisconsin, Madison, WI, USA
EMBO J 23:4473-83. 2004..subtilis RNA polymerase directly. Rather, increases in the ppGpp concentration might reduce the available GTP pools, thereby modulating rRNA promoter activity indirectly... - Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promotersSarah E Aiyar
Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706 1567, USA
J Mol Biol 316:501-16. 2002..Thus, similar Fis-alphaCTD interactions are used for activation of transcription when the activator is bound at very different positions on the DNA... - 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 promoterSarah M McLeod
Department of Biological Chemistry, UCLA School of Medicine, Los Angeles, CA 90095 1737, USA
J Mol Biol 316:517-29. 2002..These experiments define the overall architecture of the proP P2 initiation complex where Fis and CRP each function through a different alphaCTD... - Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at class I cyclic AMP receptor protein-dependent promotersNigel J Savery
Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, United Kingdom
J Bacteriol 184:2273-80. 2002..We also conclude that the relative contributions of individual residues within the 265 determinant depend on promoter sequence, and we discuss explanations for effects of substitutions in the 261 determinant... - NTP-sensing by rRNA promoters in Escherichia coli is directDavid A Schneider
Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706-1567, USA
Proc Natl Acad Sci U S A 99:8602-7. 2002..We conclude that translation is a major consumer of purine NTPs, and that NTP-sensing by rrn P1 promoters serves as a direct regulatory link between translation and ribosome synthesis... - Regulation of the Escherichia coli rrnB P2 promoterHeath D Murray
Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA
J Bacteriol 185:28-34. 2003..The rrnB P2 core promoter sequence (-37 to +7) is sufficient to serve as the target for growth rate-dependent regulation... - Control of rRNA expression in Escherichia coliDavid A Schneider
Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA
Curr Opin Microbiol 6:151-6. 2003..Recent work has dissected many of the molecular mechanisms responsible for the strength and regulation of rRNA promoters... - An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4Wilma Ross
Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
Genes Dev 17:1293-307. 2003..Previous data from the literature suggest that this same sigma-alphaCTD interaction also plays a role in transcription factor-mediated activation... - Control of rRNA expression by small molecules is dynamic and nonredundantHeath D Murray
Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706, USA
Mol Cell 12:125-34. 2003..The results suggest a molecular logic for the use of two homeostatic regulatory mechanisms to monitor different aspects of ribosome activity and provide general insights into the nature of overlapping regulatory circuits... - Changes in the concentrations of guanosine 5'-diphosphate 3'-diphosphate and the initiating nucleoside triphosphate account for inhibition of rRNA transcription in fructose-1,6-diphosphate aldolase (fda) mutantsDavid A Schneider
Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
J Bacteriol 185:6192-4. 2003.... - A role for mechanosensitive channels in survival of stationary phase: regulation of channel expression by RpoSNeil R Stokes
Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, United Kingdom
Proc Natl Acad Sci U S A 100:15959-64. 2003..These data suggest that MscS and MscL are components of the RpoS regulon and play an important role in ensuring structural integrity in stationary phase bacteria... - Measuring control of transcription initiation by changing concentrations of nucleotides and their derivativesDavid A Schneider
Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, Wisconsin 53706-1567, USA
Methods Enzymol 370:606-17. 2003 - Unique roles of the rrn P2 rRNA promoters in Escherichia coliHeath D Murray
Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison, WI 53706, USA
Mol Microbiol 52:1375-87. 2004..Our work significantly extends previous information about the regulators responsible for control of the rrn P2 promoters and the relationship between the tandem rRNA promoters... - DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTPBrian J Paul
Department of Bacteriology, University of Wisconsin, 420 Henry Mall, Madison 53706, USA
Cell 118:311-22. 2004.... - rRNA promoter activity in the fast-growing bacterium Vibrio natriegensSarah E Aiyar
Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
J Bacteriol 184:1349-58. 2002..coli, i.e., high gene dose and strong activation by UP elements and Fis... - Relationship between growth rate and ATP concentration in Escherichia coli: a bioassay for available cellular ATPDavid A Schneider
Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
J Biol Chem 279:8262-8. 2004..More broadly, the luciferase bioassay described here provides a general method for evaluating the ATP concentration available for biochemical processes in E. coli and potentially in other organisms... - The RNA polymerase alpha 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 vitroMelicent C Peck
Department of Biological Sciences, Stanford University, California 94305, USA
J Bacteriol 184:3808-14. 2002..The ability to utilize E. coli as a heterologous system in which to study the regulation of S. meliloti genes could provide an important tool for our understanding and manipulation of these processes...
Research Grants
- MECHANISM, ACTIVATION AND CONTROL OF RRNA TRANSCRIPTIONRichard Gourse; Fiscal Year: 2002..We now propose to begin to determine the relationship(s) between the multiple mechanisms affecting regulation of the synthesis of the translation apparatus during steady state growth, upshifts, and in stationary phase. ..
- MECHANISM, ACTIVATION, AND CONTROL OF RRNA TRANSCRIPTIONRichard Gourse; Fiscal Year: 2006..In the fourth specific aim, we will use the tools of cell biology to determine the locations of rRNA operons in the bacterial nucleoid. ..
- MECHANISM, ACTIVATION, AND CONTROL OF RRNA TRANSCRIPTIONRichard Gourse; Fiscal Year: 2007....
- MECHANISM, ACTIVATION, & CONTROL OF RRNA TRANSCRIPTIONRichard Gourse; Fiscal Year: 1993....