W. Ross

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UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition

R. Gourse, W. Ross, T. Gaal, 2000, Molecular microbiology.

Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit.

R. Ebright, R. Gourse, Z. Chen, 1999, Genes & development.

Contributions of UP Elements and the Transcription Factor FIS to Expression from the Seven rrn P1 Promoters inEscherichia coli

S. Aiyar, R. Gourse, W. Ross, 2001, Journal of bacteriology.

Control of rRNA expression in Escherichia coli.

R. Gourse, W. Ross, D. Schneider, 2003, Current opinion in microbiology.

rRNA transcription in Escherichia coli.

R. Gourse, W. Ross, T. Gaal, 2004, Annual review of genetics.

E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo.

R. Gourse, J. F. Thompson, W. Ross, 1990, The EMBO journal.

A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase.

R. Gourse, A. Ishihama, K. Severinov, 1993, Science.

Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength.

R. Gourse, W. Ross, T. Gaal, 1994, Journal of molecular biology.

rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli.

R. Gourse, W. Ross, T. Gaal, 1996, Annual review of microbiology.

Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria.

C. Turnbough, R. Gourse, W. Ross, 1997, Science.

Identification of an UP element consensus sequence for bacterial promoters.

R. Gourse, W. Ross, T. Gaal, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Activation of Escherichia coli rRNA Transcription by FIS during a Growth Cycle

R. Gourse, W. Ross, Richard L. Gourse, 1998, Journal of bacteriology.

Escherichia coli Promoters with UP Elements of Different Strengths: Modular Structure of Bacterial Promoters

S. Aiyar, R. Gourse, W. Ross, 1998, Journal of bacteriology.

DksA A Critical Component of the Transcription Initiation Machinery that Potentiates the Regulation of rRNA Promoters by ppGpp and the Initiating NTP

John W. Foster, J. Foster, R. Gourse, 2004, Cell.

Strength and regulation without transcription factors: lessons from bacterial rRNA promoters.

S. Aiyar, R. Gourse, W. Ross, 1998, Cold Spring Harbor symposia on quantitative biology.

Structural organization of Escherichia coli tRNAtyr gene clusters in four different transducing bacteriophages.

D. Lipman, J. Rossi, W. Ross, 1979, Journal of molecular biology.

DNA binding and bending are necessary but not sufficient for Fis-dependent activation of rrnB P1

R. C. Johnson, R. Gourse, W. Ross, 1993, Journal of bacteriology.

Bacteriophage lambda int protein recognizes two classes of sequence in the phage att site: characterization of arm-type sites.

W. Ross, A. Landy, 1982, Proceedings of the National Academy of Sciences of the United States of America.

The RNA Polymerase α Subunit Carboxyl-terminal Domain Is Required for Both Basal and Activated Transcription from thealkA Promoter*

W. Ross, T. Gaal, M. Volkert, 1997, The Journal of Biological Chemistry.

Stepwise Promoter Melting by Bacterial RNA Polymerase.

Albert Y. Chen, B. Chait, R. Gourse, 2020, Molecular cell.

A Rhodobacter sphaeroides Protein Mechanistically Similar to Escherichia coli DksA Regulates Photosynthetic Growth

Kimberly C. Lemmer, T. Donohue, R. Gourse, 2014, mBio.

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

L. Jarboe, J. Dickerson, R. Gourse, 2020, Metabolic engineering.

Mutants of Escherichia coli Defective for Replicative Transposition

W. Ross, M. Howe, H. Scott, 2003 .

Mutants of Escherichia coli defective for replicative transposition of bacteriophage Mu

W. Ross, M. Howe, S. Shore, 1986, Journal of bacteriology.

Transcriptional Responses to ppGpp and DksA.

Albert Y. Chen, R. Gourse, W. Ross, 2018, Annual review of microbiology.

ppGpp Binding to a Site at the RNAP-DksA Interface Accounts for Its Dramatic Effects on Transcription Initiation during the Stringent Response.

Albert Y. Chen, R. Gourse, W. Ross, 2016, Molecular cell.

Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation.

S. Butcher, R. Gourse, W. Ross, 2012, Genes & development.

Super DksAs: substitutions in DksA enhancing its effects on transcription initiation

J. A. Halliday, R. Gourse, W. Ross, 2009, The EMBO journal.

Anomalous electrophoretic mobility of restriction fragments containing the att region.

W. Ross, A. Landy, 1982, Journal of molecular biology.

An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: interaction of the (cid:1) C-terminal domain and (cid:2) region 4

R. Gourse, W. Ross, B. Paul, 2003 .

Role of the coiled-coil tip of Escherichia coli DksA in promoter control.

R. Gourse, W. Ross, C. Lennon, 2012, Journal of molecular biology.

Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding

R. Ebright, R. Gourse, W. Ross, 1994, Cell.

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

D. Court, R. Gourse, W. Ross, 2022, mBio.

RNA polymerase mutants that destabilize RNA polymerase-promoter complexes alter NTP-sensing by rrn P1 promoters.

R. Gourse, W. Ross, T. Gaal, 1998, Journal of molecular biology.

Isolation of a functional lac regulatory region

W. Ross, A. Landy, G. Reiness, 2004, Molecular and General Genetics MGG.

DNA fragments carrying genes for tRNATyrI

W. Ross, A. Landy, C. Foeller, 1974, Nature.

Digestion of deoxyribonucleic acids from bacteriophage T7, lambda, and phi 80h with site-specific nucleases from Hemophilus influenzae strain Rc and strain Rd.

W. Ross, A. Landy, C. Foeller, 1974, Biochemistry.

The lambda phage att site: functional limits and interaction with Int protein.

W. Ross, P. Hsu, A. Landy, 1980, Nature.

Molecular anatomy of a transcription activation patch: FIS–RNA polymerase interactions at the Escherichia coli rrnB P1 promoter

R. Gourse, Reid C. Johnson, W. Ross, 1997, The EMBO journal.

Generation of DNA fragments by enzymatic cleavage at sites sensitive to denaturation.

W. Ross, A. Landy, C. Foeller, 1973, Biochimica et biophysica acta.

The magic spot: a ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation.

R. Gourse, W. Ross, Catherine E. Vrentas, 2013, Molecular cell.

Advances in bacterial promoter recognition and its control by factors that do not bind DNA

R. Gourse, W. Ross, Shanil P. Haugen, 2008, Nature Reviews Microbiology.

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.

Melanie B. Berkmen, R. Gourse, D. Vassylyev, 2008, Journal of molecular biology.

Allosteric control of Escherichia coli rRNA promoter complexes by DksA.

R. Gourse, W. Ross, S. Rutherford, 2009, Genes & development.

Analysis of RNA polymerase-promoter complex formation.

R. Gourse, W. Ross, 2009, Methods.

A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation

Kevin S. Myers, Kimberly C. Lemmer, T. Donohue, 2020, Proceedings of the National Academy of Sciences.

Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of E. coli ribosomal RNA promoters

R. Gourse, W. Ross, Jared T. Winkelman, 2016, Proceedings of the National Academy of Sciences.

Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes.

Albert Y. Chen, R. Gourse, W. Ross, 2015, Molecular cell.

Fine structure of the promoter–σ region 1.2 interaction

R. Gourse, W. Ross, Shanil P. Haugen, 2008, Proceedings of the National Academy of Sciences.

rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase

Melanie B. Berkmen, R. Gourse, W. Ross, 2006, Cell.

Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA.

R. Ebright, R. Gourse, W. Ross, 2005, Genes & development.

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

Albert Y. Chen, R. Gourse, S. Darst, 2019, eLife.

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

Albert Y. Chen, R. Gourse, S. Darst, 2019, bioRxiv.

UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker.

R. Gourse, S. Busby, N. Savery, 2001, Nucleic acids research.

Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove.

R. Gourse, W. Ross, A. Ernst, 2001, Genes & development.

Structural basis for transcription activation by Crl through tethering of σS and RNA polymerase

R. Gourse, S. Darst, W. Ross, 2019, Proceedings of the National Academy of Sciences.

Escherichia coli DksA Binds to Free RNA Polymerase with Higher Affinity than to RNA Polymerase in an Open Complex

R. Gourse, W. Ross, C. Lennon, 2009, Journal of bacteriology.

Sequence-dependent upstream DNA-RNA polymerase interactions in the open complex with lambdaPR and lambdaPRM promoters and implications for the mechanism of promoter interference.

C. Bustamante, W. Ross, C. Rivetti, 2009, Journal of molecular biology.

Sequence-dependent upstream DNA-RNA polymerase interactions in the open complex with λ P R λ P RM promoters and implications for the mechanism of promoter interference

C. Bustamante, W. Ross, C. Rivetti, 2009 .

An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4.

R. Gourse, W. Ross, B. Paul, 2003, Genes & development.

Promoter recognition and discrimination by EσS RNA polymerase

R. Burgess, R. Gourse, W. Ross, 2001, Molecular microbiology.

Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

R. Gourse, W. Ross, Justin J. Lemke, 2011, Proceedings of the National Academy of Sciences.

EPIGENETIC REGULATION OF CELLULAR MEMORY BY THE POLYCOMB AND TRITHORAX GROUP PROTEINS

Jo Handelsman, Julian Parkhill, David Haig, 2008 .

Viral integration and excision: structure of the lambda att sites.

W. Ross, A. Landy, 1977, Science.

Dissection of the molecular circuitry controlling virulence in Francisella tularensis

R. Gourse, M. Schumacher, R. Brennan, 2017, Genes & development.

Structure of the RNA Polymerase Assembly Factor Crl and Identification of Its Interaction Surface with Sigma S

A. Joachimiak, R. Gourse, W. Ross, 2014, Journal of Bacteriology.

Involvement of Fis protein in replication of the Escherichia coli chromosome

R. Gourse, W. Ross, M. Filutowicz, 1992, Journal of bacteriology.

Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters.

Mark S. Thomas, S. McLeod, S. Aiyar, 2002, Journal of molecular biology.

Transcription activation at Class II CRP‐dependent promoters: identification of determinants in the C‐terminal domain of the RNA polymerase α subunit

R. Ebright, R. Gourse, S. Busby, 1998, The EMBO journal.

Patterns of λ int recognition in the regions of strand exchange

W. Ross, A. Landy, 1983, Cell.

The λ phage att site: functional limits and interaction with Int protein

W. Ross, P. Hsu, A. Landy, 1980, Nature.

Interaction of int protein with specific sites on λ att DNA

W. Ross, H. Nash, A. Landy, 1979, Cell.

Involvement ofFisProtein inReplication ofthe Escherichia coli Chromosome

W. Ross, 1992 .

Biochemical analysis of att-defective mutants of the phage lambda site-specific recombination system.

W. Ross, M. Shulman, A. Landy, 1982, Journal of molecular biology.

Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site.

W. Ross, W. Suh, M. Record, 1993, Science.

SITE-SPECIFIC RECOMBINATION IN BACTERIOPHAGE λ: REQUIREMENTS FOR THE PHAGE att SITE AND ORGANIZATION OF THE RECOMBINATION FUNCTIONS

W. Ross, P. Hsu, R. Hoess, 1980 .

Activation of the σE-Dependent Stress Pathway by Conjugative TraR May Anticipate Conjugational Stress

R. Gourse, W. Ross, Matthew D. Blankschien, 2014, Journal of bacteriology.

Structure and function of the phage lambda att site: size, int-binding sites, and location of the crossover point.

L. Enquist, R. Weisberg, W. Ross, 1981, Cold Spring Harbor symposia on quantitative biology.

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

R. Gourse, W. Ross, Angela R. Myers, 2020, Frontiers in Microbiology.

Binding Modes of the Initiator and Inhibitor Forms of the Replication Protein π to the γ ori Iteron of Plasmid R6K*[boxs]

W. Ross, M. Filutowicz, S. A. Rakowski, 2004, Journal of Biological Chemistry.

Genetic analysis of transcriptional activation and repression in the Tn21 mer operon

S. Park, W. Ross, A. Summers, 1989, Journal of bacteriology.

Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

Colin N. Dewey, R. Gourse, W. Ross, 2019, Proceedings of the National Academy of Sciences.

DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture.

R. Ebright, R. Gourse, N. Assa‐Munt, 1996, Genes & development.

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

R. Gourse, W. Ross, Jonathan Jagodnik, 2022 .

Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter

R. Gourse, W. Ross, Kemardo K Henry, 2021, Journal of bacteriology.

TraR directly regulates transcription initiation by mimicking the combined effects of the global regulators DksA and ppGpp

Albert Y. Chen, R. Gourse, W. Ross, 2017, Proceedings of the National Academy of Sciences.

Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit.

S. Aiyar, R. Gourse, W. Ross, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Transcriptome Complexity in a Genome-Reduced Bacterium

Richard H. Ebright, R. Ebright, R. Gourse, 2009 .

Both fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependent.

R. Gourse, W. Ross, J. Newlands, 1992, Nucleic acids research.

Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase a subunit (A-tract DNAyDNA curvatureyUP element)

S. Aiyar, R. Gourse, W. Ross, 1998 .

Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase.

R. Gourse, W. Ross, S. Rutherford, 2007, Journal of molecular biology.

General Pathway for Turning on Promoters Transcribed by RNA Polymerases Containing Alternative σ Factors

R. Gourse, W. Ross, S. Rutherford, 2006, Journal of bacteriology.

GUEST COMMENTARY General Pathway for Turning on Promoters Transcribed by RNA Polymerases Containing Alternative (cid:2) Factors

R. Gourse, W. Ross, S. Rutherford, 2006 .

The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter.

R. Gourse, W. Ross, A. Bokal, 1995, Journal of molecular biology.

Factor-independent activation of Escherichia coli rRNA transcription. II. characterization of complexes of rrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase.

R. Gourse, W. Ross, K. Gosink, 1991, Journal of molecular biology.

Activation of Escherichia coli leuVTranscription by FIS

R. Gourse, W. Ross, J. Salomon, 1999, Journal of bacteriology.

Sequences upstream of the-35 hexamer of rrnB P1 affect promoter strength and upstream activation.

R. Gourse, W. Ross, C. A. Josaitis, 1990, Biochimica et biophysica acta.

LexA Represses CTXΦ Transcription by Blocking Access of the α C-terminal Domain of RNA Polymerase to Promoter DNA*

M. Waldor, R. Gourse, W. Ross, 2006, Journal of Biological Chemistry.

Control of rRNA and ribosome synthesis

R. Gourse, W. Ross, 1996 .

Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association.

R. Gourse, W. Ross, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Regulation of rRNA Transcription Is Remarkably Robust: FIS Compensates for Altered Nucleoside Triphosphate Sensing by Mutant RNA Polymerases at Escherichia coli rrn P1 Promoters

R. Gourse, W. Ross, M. Bartlett, 2000, Journal of bacteriology.

Transcriptional switching by the MerR protein: activation and repression mutants implicate distinct DNA and mercury(II) binding domains.

C. Walsh, S. Park, L. Shewchuk, 1989, Biochemistry.

Binding modes of the initiator and inhibitor forms of the replication protein pi to the gamma ori iteron of plasmid R6K.

W. Ross, M. Filutowicz, S. A. Rakowski, 2004, The Journal of biological chemistry.

Author response: E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation

Albert Y. Chen, R. Gourse, S. Darst, 2019 .

In vitro evidence that RNA Polymerase acetylation and acetyl phosphate-dependent CpxR phosphorylation affect cpxP transcription regulation.

R. Gourse, W. Ross, A. Wolfe, 2016, FEMS microbiology letters.

The magic spot: a ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation.

R. Gourse, W. Ross, Patricia Sanchez-Vazquez, 2013, Molecular cell.

Site-specific recombination in bacteriophage lambda: structural features of recombining sites.

W. Ross, R. Hoess, A. Landy, 1979, Cold Spring Harbor symposia on quantitative biology.

LexA represses CTXphi transcription by blocking access of the alpha C-terminal domain of RNA polymerase to promoter DNA.

M. Waldor, R. Gourse, W. Ross, 2006, The Journal of biological chemistry.