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Roberts, Jeffrey Warren
Robert J. Appel Professor of Molecular and Cell Biology
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Research
research overview
- My general research interest is biochemical mechanisms controlling gene expression, particularly those which determine the ability of RNA polymerase to transcribe particular genes. Our primary subject is the activity of transcription antiterminators, regulatory proteins that affect the ability of RNA polymerase to recognize transcription terminators. We also study the nature of promoter recognition by initiation factors, in particular the mechanism by which sigma factors recognize and mediate melting of promoter sequences.
research activities
principal investigator on
- GENE CONTROL IN INFECTION AND LYSOGENY BY PHAGE LAMBDA awarded by NATL INST OF HEALTH DHHS 2009 - 2013
area(s) of concentration/expertise
keywords
- Gene regulation
submitted impact statement
Publications
individual publications
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academic article
- Σ(70)-dependent transcription pausing in Escherichia coli.. Journal of Molecular Biology. 412:782-792. 2011
- A backtrack-inducing sequence is an essential component of Escherichia coli s70-dependent promoter-proximal pausing. Molecular Microbiology. 78:636-650. 2010
- Syntheses That Stay Together (A Perspective). Science. 328:436-437. 2010
- “Promoter-specific control of E. coli RNA polymerase by ppGpp and a general transcription factor” . Genes & Development. 23:143-146. 2009
- Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation. Molecular Microbiology. 68:17-28. 2008
- “RNA Polymerase Elongation Factors” . Annual Review of Plant Biology. 62:211-233. 2008
- A Transcription Antiterminator Constructs a NusA-Dependent Shield to the Emerging Transcript. Mol. Cell. 27:914-927. 2007
- "Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique". Applied and Environmental Microbiology. 72:4987-4994. 2006
- Kinetic Investigation of Escherichia coli RNA Polymerase Mutants that Influence Nucleotide Discrimination and Transcription Fidelity. Journal of Biological Chemistry. 281:186777-18683. 2006
- RNA Polymerase, A Scrunching Machine. Science. 314:1097-1098. 2006
- RNA-Mediated Destabilization of the σ70 Region 4/β Flap Interaction Facilitates Engagement of RNA Polymerase by the Q Antiterminator. Mol. Cell.. 24:457-468. 2006
- A single-molecule technique to study sequence-dependent transcription pausing. Biophysical Journal. 87:3945-3953. 2004
- DNA Binding Regions of Q Proteins of Phages λ and [var phi]80. Journal of Bacteriology. 186:3599-3608. 2004
- Forward Translocation Is the Natural Pathway of RNA Release at an Intrinsic Terminator. Mol. Cell. 14:117-126. 2004
- Interactions among CII protein, RNA polymerase and the lambda PRE promoter: contacts between RNA polymerase and the -35 region of PRE are identical in the presence and absence of CII protein. Nucleic Acids Research. 32:1083-90. 2004
- Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Current Opinion in Microbiology. 7:120-125. 2004
- Formation of long DNA templates containing site-specific alkane-disulfide DNA interstrand cross-links for use in transcription reactions. Methods in Enzymology. 371:120-32. 2003
- RNA Polymerase mutations that impair conversion to a termination resistant complex by Q antiterminator proteins. Genes & Development. 17:1281-1292. 2003
- Role of the Non-template Strand of the Elongation Bubble in Intrinsic Transcription Termination. J. Mol. Biol. 334:205-213. 2003
- E. coli Transcription Repair Coupling Factor (Mfd protein) Rescues Arrested Complexes by Promoting Forward Translocation. Cell. 109:757-767. 2002
- RfaH, A Bacterial Transcription Antiterminator. Mol. Cell. 9:698-700. 2002
- Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proceedings at the National Academy of Science USA. 99:13538-43. 2002
- The 70 subunit of RNA polymerase is contacted by the Q antiterminator during early elongation. Molecular Cell. 10:611-622. 2002
- Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins. Proceedings at the National Academy of Science USA. 98:8972-8978. 2001
- Function of Transcription Factors GreA and GreB at a Regulatory Pause Site. Molecular Cell. 6:1275-1285. 2000
- Mechanism of Intrinsic Transcription Termination and Antitermination. Science. 284:611-615. 1999
- The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. Genes & Development. 13:3015-3026. 1999
- A Surface of E. coli 70 required for Promoter Function and Antitermination by Phage Lambda Q Protein. Genes & Development. 12:3276-3285. 1998
- Control of the Supply Line. Science. 278:2073-2074. 1998
- Pribnow Box Recognition and Melting by Escherichia coli RNA Polymerase. Nucleic Acids & Mol. Biol.. 11:551-556. 1997
- Promoter Recognition As Measured by Binding of Polymerase to Nontemplate Strand Oligonucleotide. Science. 276:1258-1260. 1997
- Base Specific Recognition of the Nontemplate Strand of Promoter DNA by E. coli RNA Polymerase. Cell. 86:495-501. 1996
- Domain Organization of the Escherichia coli RNA Polymerase 70 subunit. J. Mol. Biol.. 263:637-647. 1996
- Function of E. coli RNA Polymerase Sigma Factor 70 in Promoter-Proximal Pausing. Cell. 86:485-493. 1996
- The Shrewd Grasp of RNA Polymerase. Science. 273:202-203. 1996
- Kinetics of RNA Polymerase Initiation and Pausing at the Lambda Late Gene Promoter In Vivo. J. Mol. Biol. 254:808-814. 1995
- Deletion Analysis of the Lambda tR1 Termination Region: Effect of Sequences near the Transcript Release Sites, and the Minimum Length of Rho-dependent Transcripts. J. Mol. Biol. 237:255-265. 1994
- Determination of Intrinsic Transcription Termination Efficiency by RNA Polymerase Elongation Rate. Science. 266:822-825. 1994
- Function of a Nontranscribed DNA Strand Site in Transcription Elongation. Cell. 78:317-324. 1994
- RNA and Protein Elements of E. coli and Transcription Antitermination Complexes. Cell. 72:653-656. 1993
- Structure of Transcription Elongation Complexes In Vivo. Science. 255:838-841. 1992
- The Phage Gene Q Transcription Antiterminator Binds DNA in the Late Gene Promoter as it Modifies RNA Polymerase. Cell. 69:1181-1189. 1992
- Characterization of the Late Gene Regulatory Region of Phage 21. Journal of Bacteriology. 173:1554-1560. 1991
- Constitutive and UV-Mediated Activation of RecA Protein: Combined Effect of RecA441 and RecF143 Mutations and of Addition of Nucleosides and Adenine. Journal of Bacteriology. 173:5869-5875. 1991
- Rho-dependent Transcription Termination: Characterization of the Requirement for Cytidine in the Nascent Transcript. Journal of Biological Chemistry. 266:24140-24148. 1991
- Heterogeneous Initiation Due to Slippage at the Bacteriophage 82 Late Gene Promoter In Vitro. Biochemistry. 29:10702-10709. 1990
- Nature of the SOS Inducing Signal in E. coli: The Involvement of DNA Replication. J. Mol. Biol.. 212:79-96. 1990
- Early Transcribed Sequences Affect Termination Efficiency of Escherichia coli RNA Polymerase. J. Mol. Biol.. 205:331-341. 1989
- Gene Q Antiterminator Proteins of E. coli Phages 82 and Suppress Pausing by RNA Polymerase at a -dependent Terminator, and at Other Sites. Proceedings at the National Academy of Science USA. 86:5301-5305. 1989
- Sequences Required for Antitermination by Phage 82 Q Protein. J. Mol. Biol.. 210:461-471. 1989
- Specificity and Mechanism of Antitermination by Q Proteins of Bacteriophages and 82. J. Mol. Biol.. 210:453-460. 1989
- Upstream Regulatory Sequences of the Yeast RNR2 Gene Include a Repression Sequence and an Activation Site that Binds the RAP1 Protein. Molecular and Cellular Biology. 9:5359-5372. 1989
- Activation of the Protease Constitutive RecA Proteins of Escherichia coli by All the Common Nucleoside Triphosphates. Journal of Bacteriology. 170:4816-4822. 1988
- Induction of the RecA Protein Analog and a Damage-Inducible Operon by DNA Damage in Rec+ and DNA Repair-Deficient Strains. Journal of Bacteriology. 170:1467-1474. 1988
- Phage Lambda and the Regulation of Transcription Termination. Cell. 52:5-6. 1988
- Bacteriophage 82 Gene Q and Q Protein: Sequence, Overproduction, and Activity as a Transcription Antiterminator In Vitro. Journal of Biological Chemistry. 262:11721-11725. 1987
- Identification of the Gene for Yeast Ribonucleotide Reductase Small Subunit, and Its Inducibility by Methyl Methanesulfonate. Molecular and Cellular Biology. 7:3673-3677. 1987
- Transcription Antitermination by Phage Lambda Gene Q Protein Requires a DNA Segment Spanning the RNA Start Site. Genes and Development. 1:217-226. 1987
- Phage Lambda Gene Q Antiterminator Recognizes RNA Polymerase Near the Promoter and Accelerates It Through a Pause Site. Cell. 42:259-269. 1985
- Purification of a RecA Protein Analogue From Bacillus subtilis. Journal of Biological Chemistry. 260:3305. 1985
- Rho-dependent Transcription Termination at Lambda tR1 Requires Upstream Sequences. Journal of Biological Chemistry. 260:574. 1985
- A Potential Stem-loop Structure and the Sequence CAAUCAA in the Transcript are Insufficient to Signal -dependent Transcription Termination at tR1. Nucleic Acids Research. 12:1287. 1984
- RecA Protein-Promoted Lambda Repressor Cleavage: Complementation Between RecA441 and RecA430 Proteins In Vitro. Molecular Genetics and Genomics. 198:25. 1984
- Purification of the Bacteriophage Lambda Late Gene Regulator Encoded by Gene Q. Journal of Biological Chemistry. 258:9192. 1983
- RNA Polymerase Pausing and Transcript Release at the Lambda tR1 Terminator In Vitro. Journal of Biological Chemistry. 258:9391. 1983
- A Brief Consideration of the SOS Inducing Signal. Biochimie. 64:805. 1982
- Comparison of the Polyoma Virus Early and Late Promoters by Transcription In Vitro. Nucleic Acids Research. 10:871-888. 1982
- The Phage Q Gene Product: Activity of a Transcription Anti–terminator In Vitro. Cell. 30:637. 1982
- Transcription Terminates at tR1 in Three Clusters. Proceedings at the National Academy of Science USA. 79:6171. 1982
- Function of Nucleoside Triphosphate and Polynucleotide in E. coli RecA Protein-Directed Cleavage of Phage Lambda Repressor. Journal of Biological Chemistry. 256:8039. 1981
- Induction of SOS Functions: Regulation of Proteolytic Activity of E. coli RecA Protein by Interaction with DNA and Nucleoside Triphosphate. Cell. 25:259. 1981
- Two Mutations That Alter the Regulatory Activity of E. coli RecA Protein. Nature. 290:422. 1981
- Assay and Characterization of Late Gene Regulators of Phages 82 and . J. Mol. Biol.. 142:269. 1980
- E. coli RecA Protein-Directed Cleavage of Phage Repressor Requires Polynucleotide. Nature. 283:26. 1980
- Genetics and Structure of the Late Gene Regulatory Region of Phage 82. Virology. 105:393. 1980
- Kinetics of RecA Protein-Directed Inactivation of Repressors of Phage and Phage P22. J. Mol. Biol.. 139:319. 1980
- The E. coli RecA Gene Product Inactivates Phage Repressor. Proceedings at the National Academy of Science USA. 75:4714. 1978
- Inactivation and Proteolytic Cleavage of Bacteriophage Lambda Repressor In Vitro in an ATP-dependent Reaction. Proceedings at the National Academy of Science USA. 74:2283. 1977
- Proteolytic Cleavage of Bacteriophage Lambda Repressor in Induction. Proceedings at the National Academy of Science USA. 72:147. 1975
- Transcription Termination and Late Control in Phage Lambda. Proceedings at the National Academy of Science USA. 72:3300. 1975
- Promoter Mutation In Vitro. Nature. 223:480. 1969
- Termination Factor for RNA Synthesis. Nature. 224:1168. 1969
- Polarity in an Amber Mutant of Bacteriophage R17. J. Mol. Biol.. 30:565. 1967
- The Reconstitution of Infective Bacteriophage R17. Proceedings at the National Academy of Science USA. 58:1416. 1967
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book
- Molecular Biology of the Gene. Vol. 4. 1987
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booksection
-
conference paper
- Role of DNA Bubble Rewinding in Enzymatic Transcription Termination. Proc. Nat. Acad. Sci. USA. 4870-4875. 2006
- Antitermination by phage Q protein. Cold Spring Harbor Symposium on Quantitative Biology. 319-325. 1998
- Activity of the E. coli RecA Gene Product. Cold Spring Harbor Symposium. 917. 1979
- The Rho Factor: Termination and Antitermination in Lambda. Cold Spring Harbor Symposium on Quantitative Biology. 121. 1970
selected publications listing
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- B.Z. Ring, W.S. Yarnell, and J.W. Roberts (1996). Function of E. coli RNA Polymerase Sigma Factor s70 in Promoter-Proximal Pausing. Cell, 86, 485-493.
- C.W. Roberts and J.W. Roberts (1996). Base Specific Recognition of the Nontemplate Strand of Promoter DNA by E. coli RNA Polymerase. Cell 86, 495-501 (1996)
- M.T. Marr and J.W. Roberts (1997). "Promoter Recognition As Measured by Binding of Polymerase to Nontemplate Strand Oligonucleotide." Science, 276, 1258-1260.
- Ko, D.C., Marr, M.T., Guo, J., and Roberts, J.W. (1998). A Surface of E. coli s70 Required for Promoter Function and Antitermination by Phage Lambda Q Protein. Genes and Development 12, 3276-3285.
- Roberts, J.W., Yarnell, W., Bartlett, E., Guo, J., Marr, M., Ko, D., Sun, H., and Roberts, C.W. (1999). Antitermination by Phage l Q Protein. Cold Spring Harbor Symposium on Quantitative Biology 63, 319-325.
- Yarnell, W.S., and Roberts, J.W. (1999). Mechanism of Intrinsic Transcription Termination and Antitermination. Science 284, 611-615.
- Marr, M.T., & J.W. Roberts (2000). "Function of Transcription Factors GreA and GreB at a Regulatory Pause Site", Molecular Cell, 6, 1275-1285.
- Marr, M.T., Saul A. Datwyler, Claude F. Meares, & Jeffrey W. Roberts (2001). "Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins" Proc. Nat. Acad. Sci. USA, 98, 8972-8978
- Park, J.-S., M.T. Marr, & J.W. Roberts (2002). "E. coli Transcription Repair Coupling Factor (Mfd protein) Rescues Arrested Complexes by Promoting Forward Translocation" Cell 109, 757-767
- Nickels, B.E., Roberts, C.W., Sun, H., Roberts, J.W., & Hochschild, A. (2002). "The s70 subunit of RNA polymerase is contacted by the lQ antiterminator during early elongation " Molecular Cell, 10, 611-622
- Adelman, K., La Porta, A., Santangelo, T.J., Lis, J.T., Roberts, J.W., & Wang, M.D. (2002) "Single Molecule Analysis of RNA Polymerase Elongation Reveals Uniform Kinetic Behavior" Proc. Nat. Acad. Sci. USA 99, 13538-13543
- Santangelo, T.J., Mooney, R.A., Landick, R., & Roberts, J.W., (2003). "RNA Polymerase mutations that impair conversion to a termination resistant complex by Q antiterminator proteins" Genes & Development, 17, 1281-1292
- Ryder, Andrew M. & Jeffrey W. Roberts (2003). “Role of the Non-template Strand of the Elongation Bubble in Intrinsic Transcription Termination”. J. Mol. Biol. 334, 205-213
- Guo, Jingshu and Roberts, Jeffrey W. (2004). “DNA Binding Regions of Q Proteins of Phages land f80” J. Bacteriology 186, 3599-3608
- Santangelo, T.J. and Roberts, J.W., (2004). “Forward Translocation Is the Natural Pathway of RNA Release at an Intrinsic Terminator”. Mol. Cell 14, 117-126.
- Park, J.-S. & J.W. Roberts (2006). “Role of DNA Bubble Rewinding in Enzymatic Transcription Termination” Proc. Nat. Acad. Sci. USA 103, 4870-4875
- Nickels, B.E., Roberts, C.W., Roberts, J.W., and Hochschild, A. (2006). “RNA-Mediated Destabilization of the s70 Region 4/b Flap Interaction Facilitates Engagement of RNA Polymerase by the Q Antiterminator” Mol. Cell. 24, 457-468
- Roberts, J.W. (2006). “RNA Polymerase, A Scrunching Machine” Science 314, 1097-1098. [A Perspective]
Teaching
Service
service to the profession
- American Academy of Microbiology
- American Association for the Advancement of Science
- Encyclopedia of Life Sciences
- National Institutes of Health Chairperson 2012 - 2014
- National Institues of Health Research Review Panel 2012
reviewer or editor for
Background
education and training
- Ph.D. in Biophysics, Harvard University 1970
- B.A. in Liberal Arts, Physics, University of Texas 1964
awards and honors
Other
college
- CALS
research keyword
- Gene regulation
name prefix
- Professor