Research Interests
While the term "biochemistry" tends to invoke the image of enzymatic chemical reactions, whereby starting materials are broken down and used for biological processes, there are many nonenzymatic chemical reactions that are involved in mediating the location and regulation of enzymes. For example, protein-protein interactions are important for localization of proteins to a particular site, thus increasing the local concentration of that protein and promoting its activity. Conversely, by sequestering a protein away from the location of its substrate, the protein will be prevented from performing its function.
Transcription of messenger RNA (mRNA) in eukaryotic cells is mediated by RNA Polymerase II (PolII). PolII is unique among polymerases because it contains a C-terminal extention that is made up of tandem repeats of the consensus heptad sequence YSPTSPS. This C-terminal domain (CTD) is conserved among eukaryotic organisms and varies in length, which roughly correlates with species complexity, and is absolutely required for cell viability. The function of this domain is to provide a scaffold for proteins involved in various transcription related processes, including mRNA splicing and processing, chromatin remodeling, and mRNA packaging and export. To the left, you can see the primary amino acid sequence of the Saccharomyces cerevisiae CTD with the heptad repeat structure emphasized.
The CTD is a substrate for phosphorylation by a number of characterized kinases. The phosphorylation mainly occurs on serines 2 and 5 of the concensus heptad repeat in budding yeast. The phosphorylation pattern changes during the transcription cycle and the changes in phosphorylation correlate with the different stages of transcription, which include Initiation (ser5P), Elongation (ser2,5P), and Termination (ser2P).
My work focuses on the interactions between mRNA packaging and export factors and the CTD. While many proteins have been implicated in mRNA export, the exact functions of these factors are unknown. Yra1 is essential for cell viability and mRNA export in Saccharomyces cerevisiae. My preliminary data indicates that this protein is able to bind to the CTD in vitro. The implications of this interaction are yet to be determined using biochemical and genetic approaches.
Selected Lab Publications
- Phatnani, H.P. and Greenleaf, A.L. (2006). "Phosphorylation and functions of the RNA polymerase II CTD." Genes and Development 20: 2922-2936. (Abstract)
- Li, M., Phatnani, H. P., Guan, Z., Sage, H., Greenleaf, A., and Zhou, P. (2005). "Solution Structure of the SRI Domain of Human Set2 and Its Interaction with the PhosphoCTD." Proc Natl Acad Sci U S A 102: 17636-41. (Abstract)
- Jones, J. C., Phatnani, H. P., Haystead, T. A., MacDonald, J. A., Alam, S. M., and Greenleaf, A. L. (2004). " C-terminal Repeat Domain Kinase I Phosphorylates Ser2 and Ser5 of RNA Polymerase II C-terminal Domain Repeats." J Biol Chem 279: 24957-24964. (Abstract)
- Phatnani, H. P., Jones, J. C., and Greenleaf, A. L. (2004). " Expanding the Functional Repertoire of CTD Kinase I and RNA Polymerase II: Novel PhosphoCTD-Associating Proteins in the Yeast Proteome." BIOCHEMISTRY 43: 15702-15719. (Abstract)
