Transcription in bacteria depends on a multi-subunit RNA polymerase (RNAP) that is conserved from bacteria to man. The study of prokaryotic systems has defined the basic transcription cycle, providing a mechanistic framework for the study of transcription in all organisms. Because RNAP is the primary target of gene regulation, an in depth understanding of its structure and function is essential for elucidating the variety of regulatory mechanisms that control gene expression. The principles that emerge from investigations of the transcription apparatus and its regulation in bacterial systems continue to drive both the development of new strategies to control microbial pathogens and the study of the many transcription-based processes that underlie human development and disease processes. For transcription to initiate in bacteria, the catalytically proficient core enzyme must combine with ? factor to form the holoenzyme. In addition to the roles of ? factors in transcription initiation, which have been intensively investigated over many years, accumulating evidence indicates that ? factors can participate in events downstream of initiation and, moreover, that regulators can target the RNAP holoenzyme during elongation. This has been established for the Q antiterminator protein of bacteriophage ?, which engages the RNAP holoenzyme at a ?-dependent early elongation pause.
The first aim of the proposed research is to investigate Q's interactions with the RNAP holoenzyme during early elongation to understand the nature of the specialized pathway by which Q gains access to and alters the behavior of the transcription complex.
The second aim of the proposed research is to investigate a ?/core interaction that influences the functional properties of RNAP in a stage-specific manner, modulating both promoter escape and early elongation pausing.
The third aim of the proposed research is to investigate an unexpected role for a ? factor as a transcription antiterminator and to investigate how the presence of ? in mature elongation complexes might be regulated. Together, the experiments proposed in Aims 2 and 3 will lead to a deeper understanding of the dynamic roles played by ? factors throughout the transcription cycle.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Tompkins, Laurie
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Harvard University
Schools of Medicine
United States
Zip Code
Wang Erickson, Anna F; Deighan, Padraig; Garcia, Cinthia P et al. (2017) An Amino Acid Substitution in RNA Polymerase That Inhibits the Utilization of an Alternative Sigma Factor. J Bacteriol 199:
Wang Erickson, Anna F; Deighan, Padraig; Chen, Shanshan et al. (2017) A novel RNA polymerase-binding protein that interacts with a sigma-factor docking site. Mol Microbiol 105:652-662
Wells, Christopher D; Deighan, Padraig; Brigham, MacKenzie et al. (2016) Nascent RNA length dictates opposing effects of NusA on antitermination. Nucleic Acids Res 44:5378-89
Harden, Timothy T; Wells, Christopher D; Friedman, Larry J et al. (2016) Bacterial RNA polymerase can retain ?70 throughout transcription. Proc Natl Acad Sci U S A 113:602-7
Goldman, Seth R; Nair, Nikhil U; Wells, Christopher D et al. (2015) The primary ? factor in Escherichia coli can access the transcription elongation complex from solution in vivo. Elife 4:
Hochschild, Ann (2015) Mastering Transcription: Multiplexed Analysis of Transcription Start Site Sequences. Mol Cell 60:829-31
Bikard, David; Jiang, Wenyan; Samai, Poulami et al. (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res 41:7429-37
Montero-Diez, Cristina; Deighan, Padraig; Osmundson, Joseph et al. (2013) Phage-encoded inhibitor of Staphylococcus aureus transcription exerts context-dependent effects on promoter function in a modified Escherichia coli-based transcription system. J Bacteriol 195:3621-8
Osmundson, Joseph; Montero-Diez, Cristina; Westblade, Lars F et al. (2012) Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein. Cell 151:1005-16
Twist, Kelly-Anne F; Campbell, Elizabeth A; Deighan, Padraig et al. (2011) Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the ?-subunit flap domain of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 108:19961-6

Showing the most recent 10 out of 25 publications