Zachary F. Burton - US grants

Human RAP74 is the large subunit of Transcription Factor IIF (TFIIF), an initiation and elongation factor for transcription by RNA polymerase II. This protein is highly phosphorylated in vivo. RAP74 has a somewhat unusual domain structure, with basic N- and C-terminal domains separated by a highly charged and overall acidic central region. The N-terminal domain is involved in binding to RAP30, the small subunit of TFIIF. The C-terminal domain binds to DNA and RNA polymerase II and affects the catalytic potential of polymerase in in vitro transcription assays. The central portion includes sites of phosphorylation and appears to be a regulatory hinge for the N- and C-terminal domains. Using casein kinase II in vitro, RAP74 is phosphorylated within the central portion of the molecule. These phosphorylation sites are being precisely located by peptide mass mapping using specific enzymatic digestions and MALDI-MS analysis. In vivo phosphorylated material will be similarly analyzed to determine whether the casein kinase sites are of physiological importance. Assays are being developed to analyze the importance of phosphorylation of RAP74 in transcription.

RNA polymerase II-associating protein (RAP) 74 is the large subunit of human transcription factor (TF) IIF. This protein cooperates with TFIIA, TFIID, TFIIB, RNA polymerase II, RAP30, TFIIE, and TFIIH to accurately initiate transcription from a promoter. TFIIF (RAP30-RAP74) also stimulates the elongation rate of RNA polymerase II. RAP74 is phosphorylated in vivo on serine at unknown positions. Phosphorylation of RAP74 increases activity in accurate initiation and appears to strengthen the affinity of TFIIF for RNA polymerase II. We are interested in mapping the natural phosphorylation sites on RAP74 using mass spectrometry. Inspection of a serine-rich region within RAP74 revealed several potential casein kinase II sites. Casein kinase II phosphorylates RAP74 in vitro, and several of the sites that are modified have been identified using mass spectrometry. RAP74 also appears to be a substrate for phosphorylation by human transcription factors TAF II250 and TFIIH.

DESCRIPTION (adapted from applicant's abstract): The broad aim of this research is to determine the role of human transcription factor IIF (TFIIF) in initiation and elongation. TFIIF appears to have a key role in isomerization of RNA polymerase II initiation and elongation complexes, supporting an activated state of RNA polymerase II for transcription. Mutations in the L155 to M177 region of the RAP74 subunit of TFIIF have startlingly similar effects on initiation and elongation. In initiation, TFIIF appears to induce promoter DNA to wrap around RNA polymerase II. TFIIF may isomerize elongation complexes by enhancing DNA bending through the RNA polymerase II active site. Specific aims are directed toward testing conformational models for TFIIF function in initiation and elongation. Other aims are directed toward analysis of DNA wrapping and helix untwisting in transcriptional mechanisms. Highly sensitive assays for TFIIF functions have been developed to monitor transcription complex. Abortive initiation, productive initiation, and runoff transcription assays will be done to analyze the roles of TFIIF in initiation. Transcription complexes will be probed with chemical modification reagents that are specific for single-stranded DNA to correlate maintenance of an open complex with transcriptional function. During elongation, RNA polymerase II may extend an RNA chain according to a branched kinetic pathway in which the enzyme partitions between an activated conformation for elongation and an inactive form. Elongation experiments will test this hypothesis. DNA wrapping around RNA polymerase II and the general transcription factors will be analyzed by fluorescence energy transfer and photocrosslinking studies. The role of TFIIF in this process will be analyzed. TFIIF is also proposed to have a role in DNA bending through the RNA polymerase II active site and in DNA untwisting. Helix untwisting is thought to result from constraint of the DNA between a DNA bend formed at the TATA box by TBP and TFIIB and a second DNA bend through the RNA polymerase II active site formed in part by TFIIF and TFIIE. DNA topology assays and gel mobility shift assays will be used to determine roles for TFIIF and TFIIE in conformational isomerization of the pre-initiation complex.

DESCRIPTION (provided by applicant) This proposal is designed to determine the mechanism of elongation by human RNA polymerase II (RNAP II) and to elucidate combinatorial control by elongation factors. The Burton laboratory has pioneered and verified rapid chemical quench-flow kinetic methods to analyze RNAP II functional dynamics during elongation in real time (millisecond phase), using combinations of potent regulators. The Specific Aims are to: 1) characterize the RNAP II elongation control system, develop and refine a kinetic mechanism for elongation by human RNAP II, and challenge the NTP driven translocation model for RNAP II elongation; 2) determine the roles of viral hepatitis delta antigen (HDAg), human Transcription Factor IIF (TFIIF), and human TFIIS in regulation of RNAP II elongation, and use these factors as probes of the RNAP II mechanism; 3) identify mechanisms for fidelity and efficiency of RNAP II elongation; and 4) initiate rapid quench-flow studies of yeast RNAP II elongation to exploit the yeast RNAP II elongation control proteome. Kinetic analysis of human RNAP II gives novel insight into the mechanism and regulation of translocation, NTP loading, pyrophosphate release and the efficiency and fidelity of NMP incorporation.

Intellectual merit
Multi-subunit RNA polymerases, which synthesize an RNA polymer from a DNA template, are highly conserved in evolution and are highly dynamic. Because RNA polymerases move along a DNA template as RNA is synthesized, they are considered to be 'molecular motors', moving in single base increments. RNA polymerases utilize four nucleoside triphosphate substrates to incorporate bases into the growing RNA polymer. During each base addition, the substrate added is specified by the sequence of the DNA template. Supercomputer simulation is used to understand the atomic motions of RNA polymerase during RNA polymerization and during RNA polymerase translocation. In order to better simulate the polymerization reaction and RNA polymerase movement along template DNA, different stages of the reaction are simulated separately. To merge consecutive steps in the reaction, a method termed 'replica exchange' is used in which the likeliest trajectory between two reaction steps is simulated. Because simulations are done in a bath of water and ions, predictions are obtained for the likeliest water placements in the structure. During the polymerization reaction, RNA polymerases exclude water. A major effort is to learn the importance of water exclusion in polymerization and in maintaining the accuracy of polymerization. Many amino acid changes have been made in RNA polymerases resulting in altered protein function. To better understand these changes, altered proteins will be studied for their polymerization and translocation functions, and then analyzed by computer simulation to ensure that results from chemical tests are supported by predicted atomic motions.

Broader impacts
Multi-subunit RNA polymerases are necessary for accurate genetic information flow in biological systems. As such, the mechanism, dynamics and accuracy of RNA synthesis are fundamental to complex living systems. Sophisticated computer simulation is applied to one of the largest and most difficult problems in modern biology. Trainees will become expert in biochemical, genetic and computational methods, preparing them as flexible, interdisciplinary scientists. Computer simulation data will be incorporated into undergraduate teaching at Michigan State University. Every effort will be made to recruit talented undergraduates and underrepresented groups into this research program, for instance, through the MSU IDEAS research program (http://www.bmb.msu.edu/~ugrad/research/res-oppor-minority.htm ).