About

Richard Gourse is a Wisconsin Alumni Research Foundation Professor, Emeritus at the Department of Bacteriology. His research focuses on bacteriology, and he is recognized for his contributions to the field as a professor and researcher. His work has significantly impacted the understanding of bacterial processes and microbiology, contributing to the broader scientific community through his academic and research activities at the University of Wisconsin-Madison.

Research topics

• Biology
• Cell biology
• Genetics
• Biochemistry
• Chemistry
• Biophysics
• Molecular biology

Selected publications

• Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA

  Nucleic Acids Research · 2023-01-09 · 5 citations

  articleOpen accessSenior authorCorresponding

  Ligand-binding RNAs (RNA aptamers) are widespread in the three domains of life, serving as sensors of metabolites and other small molecules. When aptamers are embedded within RNA transcripts as components of riboswitches, they can regulate gene expression upon binding their ligands. Previous methods for biochemical validation of computationally predicted aptamers are not well-suited for rapid screening of large numbers of RNA aptamers. Therefore, we utilized DRaCALA (Differential Radial Capillary Action of Ligand Assay), a technique designed originally to study protein-ligand interactions, to examine RNA-ligand binding, permitting rapid screening of dozens of RNA aptamer candidates concurrently. Using this method, which we call RNA-DRaCALA, we screened 30 ykkC family subtype 2a RNA aptamers that were computationally predicted to bind (p)ppGpp. Most of the aptamers bound both ppGpp and pppGpp, but some strongly favored only ppGpp or pppGpp, and some bound neither. Expansion of the number of biochemically verified sites allowed construction of more accurate secondary structure models and prediction of key features in the aptamers that distinguish a ppGpp from a pppGpp binding site. To demonstrate that the method works with other ligands, we also used RNA DRaCALA to analyze aptamer binding by thiamine pyrophosphate.

  PublisherOA PDFDOI

• Homologs of the Escherichia coli F Element Protein TraR, Including Phage Lambda Orf73, Directly Reprogram Host Transcription

  mBio · 2022-05-18 · 7 citations

  articleOpen accessSenior authorCorresponding

  TraR is a distant homolog of the transcription factor DksA and the founding member of a large family of small proteins encoded by proteobacterial phages and conjugative plasmids. Reprogramming transcription during the stringent response requires the interaction of DksA not only with RNA polymerase but also with the stress-induced regulatory nucleotide ppGpp. We show here that five phage TraR homologs by themselves, without ppGpp, regulate transcription of host promoters, mimicking the effects of DksA and ppGpp together. During a stringent response, ppGpp independently binds directly to, and inhibits the activities of, many proteins in addition to RNA polymerase, including translation factors, enzymes needed for ribonucleotide biosynthesis, and other metabolic enzymes. Here, we suggest a physiological role for TraR-like proteins: bacteriophages utilize TraR homologs to reprogram host transcription in the absence of ppGpp induction and thus without inhibiting host enzymes needed for phage development.

  PublisherDOI

• CHAPTER 6. Global Regulation of Transcription by Nucleotides and (p)ppGpp

  Chemical biology · 2021-01-01 · 2 citations

  book-chapterSenior author

  The activity of the RNA polymerase (RNAP) molecular machine is highly regulated in response to the external environment. In this chapter, we focus on regulation of transcription by ribonucleotides, the substrates of RNAP, and by nucleotide derivatives that act as signaling molecules to control transcription. We explain how the concentration of the ribonucleotides directly regulates RNAP activity during transcription initiation by affecting the rate limiting step of nucleotide addition, which depends on both the identity of the initiating nucleotide and the promoter sequence. We describe recent breakthroughs about how the stress signaling nucleotide alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) [collectively known as (p)ppGpp] regulate the synthesis or degradation of the substrates of the transcription machinery regulated transcription in an organism-specific manner, or they directly modify the activity of the core transcription machinery itself in conjunction with the transcription factor DnaK suppressor A (DksA). Finally, we describe emerging work characterizing how (p)ppGpp and DksA act beyond transcription initiation by coordinating transcription with other macromolecular machines involved in DNA replication and repair to promote genome stability.

  PublisherDOI

• Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter

  Journal of Bacteriology · 2021-06-21 · 12 citations

  articleOpen accessSenior authorCorresponding

  R. sphaeroides CarD activates many promoters by binding directly to RNAP and DNA just upstream of the -10 element. In contrast, we show here that CarD inhibits its own promoter using the same interactions with RNAP and DNA used for activation. Inhibition results from increasing abortive transcript formation, thereby decreasing promoter escape and full-length RNA synthesis. We propose that the combined interactions of RNAP with CarD, with the extended -10 element and with features in the adjacent -10/-35 spacer DNA, stabilize the promoter complex, reducing promoter clearance. These findings support previous predictions that the effects of CarD on transcription can be either positive or negative, depending on the kinetic properties of the specific promoter.

  PublisherOA PDFDOI

• Deciphering the RNA capping process in bacteria

  Proceedings of the National Academy of Sciences · 2020-02-05 · 3 citations

  letterOpen accessSenior author

  Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.

  PublisherOA PDFDOI

• Reverse engineering of fatty acid-tolerant Escherichia coli identifies design strategies for robust microbial cell factories

  Metabolic Engineering · 2020 · 41 citations

  • Biochemistry
  • Biology
  • Chemistry
  PublisherOA PDFDOI

• Guanosine Tetraphosphate Has a Similar Affinity for Each of Its Two Binding Sites on Escherichia coli RNA Polymerase

  Frontiers in Microbiology · 2020-11-05 · 14 citations

  articleOpen accessSenior authorCorresponding

  , ppGpp regulates transcription of as many as 750 genes within 5 min of induction by binding directly to RNA polymerase (RNAP) at two sites ~60 Å apart. One proposal for the presence of two sites is that they have different affinities for ppGpp, expanding the dynamic range over which ppGpp acts. We show here, primarily using the Differential Radial Capillary Action of Ligand Assay (DRaCALA), that ppGpp has a similar affinity for each site, contradicting the proposal. Because the ppGpp binding sites are formed by interactions of the β' subunit of RNAP with two small protein factors, the ω subunit of RNAP which contributes to Site 1 and the transcription factor DksA which contributes to Site 2, variation in the concentrations of ω or DksA potentially could differentially regulate ppGpp occupancy of the two sites. It was shown previously that DksA varies little at different growth rates or growth phases, but little is known about variation of the ω concentration. Therefore, we raised an anti-ω antibody and performed Western blots at different times in growth and during a stringent response. We show here that ω, like DksA, changes little with growth conditions. Together, our data suggest that the two ppGpp binding sites fill in parallel, and occupancy with changing nutritional conditions is determined by variation in the ppGpp concentration, not by variation in ω or DksA.

  PublisherDOI

• Stepwise Promoter Melting by Bacterial RNA Polymerase

  Molecular Cell · 2020 · 133 citations

  • Biology
  • Cell biology
  • Biophysics
  PublisherOA PDFDOI

• A majority of <i>Rhodobacter sphaeroides</i> promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation

  Proceedings of the National Academy of Sciences · 2020 · 25 citations

  Senior authorCorresponding
  • Biology
  • Genetics
  • Cell biology

  CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.

  PublisherOA PDFDOI

• E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation

  eLife · 2019-12-16 · 81 citations

  articleOpen access

  TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.

  PublisherDOI

Recent grants

• Mechanism, Activation, and Control of rRNA Transcription

  NIH · $8.9M · 1988–2023

• NIH Grant R37GM037048

  NIH · $6.6M · 2017

• NIH Grant K04AI000935

  NIH · $275k · 1993

Frequent coauthors

• Wilma Ross

  104 shared

• Tamás Gaál

  University of Wisconsin–Madison

  58 shared

• Michael J. R. Stark

  21 shared

• Albert E. Dahĺberg

  Providence College

  21 shared

• Susan A. Gerbi

  John Brown University

  19 shared

• Richard H. Ebright

  Rutgers, The State University of New Jersey

  18 shared

• Catherine E. Vrentas

  Pharmaceutical Product Development (United States)

  15 shared

• Michio Nomura

  Kyoto University

  14 shared

Labs

• Richard Gourse LabPI

Education

• Ph.D., Microbiology

  University of Wisconsin-Madison

  1980

• M.S., Microbiology

  University of Wisconsin-Madison

  1976

• B.S., Microbiology

  University of Wisconsin-Madison

  1974