Heads of Laboratories
Jack Fishman Professor
Laboratory of Molecular Biophysics
RNA, the blueprint for proteins, is made by a complex molecular machine, the DNA-dependent RNA polymerase, present in all cells. Using bacteria as a model organism, Dr. Darst’s research explores the mechanism and regulation of transcription by determining three-dimensional structures of RNA polymerase and associated proteins. This work has implications for understanding how gene expression is controlled in many organisms.
In its simplest bacterial form, the RNA polymerase complex is made up of at least four proteins, whereas the eukaryotic complex comprises a dozen individual proteins or more. However, the catalytic core of RNA polymerase is evolutionarily conserved among all organisms, with a very high retention of the basic sequence. In all cells, the RNA polymerase core can synthesize RNA chains from a DNA template but is unable to recognize promoters, specific sites within DNA where transcription initiates. In bacteria, a separate protein — the σ factor — must bind to the RNA polymerase core to form the RNA holoenzyme, which can locate promoters and open the DNA for transcription.
The Darst laboratory is purifying, crystallizing, and determining the structures of proteins involved in transcription using a combination of approaches, including x-ray crystallography and electron microscopy. Solving these structures provides scientists with snapshots of different, kinetically stable states of the transcription complex, offering insight into the dynamic events that occur during transcription. As more structures are solved, they will shed light on the molecular mechanisms of the regulatory factors acting at different stages of transcription.
Members of the Darst lab have purified, crystallized, and determined the structure of the core RNA polymerase from the thermophilic eubacteria Thermus aquaticus. The results were the first high-resolution structure of a multisubunit cellular RNA polymerase. The lab then tracked the path of the transcript RNA and the template DNA through the polymerase structure using RNA-protein and DNA-protein cross-links, a method that gave the scientists a model of the elongation complex that makes RNA as the polymerase moves along the DNA.
The lab has also worked to understand how the introduction of specific molecules impacts RNA polymerase. To determine how the antibiotic rifampicin inhibits RNA polymerase function, Dr. Darst used a combination of x-ray crystallography and biochemical studies. Electron microscopy was used to reveal how a known regulatory factor modulates the transcript elongation process.
Research from the Darst lab has also described the structure of σ, the key transcription initiation factor in bacteria. Another structural study by members of the lab described the transcription-repair coupling factor, a protein cells use to remove RNA polymerase molecules stalled at sites of DNA damage and to recruit repair proteins to fix the damage.
Dr. Darst’s studies have furthered scientists’ knowledge of the transcription process in several ways. Structures of the RNA polymerase holoenzyme and holoenzyme with a promoter DNA fragment have provided insight into transcription initiation. In addition, high-resolution structures of σ factor domains in complex with promoter DNA or with inhibitory anti-σ factors have provided the basis for structural and functional analysis of the key regulatory factor in bacterial transcription.
Darst is a faculty member in the David Rockefeller Graduate Program, the Tri-Institutional M.D.-Ph.D. Program, and the Tri-Institutional Ph.D. Program in Chemical Biology.
B.S. in chemical engineering, 1982
University of Colorado, Boulder
M.S. in chemical engineering, 1984
Ph.D. in chemical engineering, 1987
Stanford University, 1987–1992
Assistant Professor, 1992–1997
Associate Professor, 1997–2000
The Rockefeller University
Irma T. Hirschl/Monique Weill-Caulier Trust Research Award, 1994
Pew Biomedical Scholar, 1995
National Academy of Sciences
Bae, B. et al. Phage T7 gp2 inhibits Escherichia coli RNA polymerase by misappropriation of σ70 domain 1.1. Proc. Natl. Acad. Sci. U.S.A. 110, 19772–19777 (2013).
Srivastava, D.B. et al. Structure and function of CarD, an essential mycobacterial transcription factor. Proc. Natl. Acad. Sci. U.S.A. 110, 12619–12624 (2013).
Weixlbaumer, A. et al. Structural basis of transcriptional pausing in bacteria, Cell 152, 431–441 (2013).
Osmundson, J. et al. Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein. Cell 151, 1005–1016 (2012).
Twist, K.A. et al. Crystal structure of the bacteriophage T4 late-transcription co-activator gp33 with the β-subunit flap domain of Escherichia coli RNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 108, 19961–19966 (2011).
Dr. Darst is a faculty member in the David Rockefeller Graduate Program, the Tri-Institutional M.D.-Ph.D. Program, and the Tri-Institutional Ph.D. Program in Chemical Biology.