Our motivation
Since starting graduate school I have worked with RNA polymerases (initially in E. coli, then yeast, then mammalian cells). These amazing machines are responsible for finding the right places in the genome to start transcription (with the help of other factors), binding the DNA, opening the DNA helix, and then reading the DNA template to yield a complimentary RNA molecule. The RNA polymerases must be fast, accurate, and tightly controllable. All cells in your body have the same DNA genome, but the wide variety in cell types and activities is due in large part to controlling this process of transcription. The control of gene expression is amazing!
The majority of our current projects focus on defining the mechanisms by which eukaryotic cells control ribosomal RNA synthesis by RNA polymerase I. Ribosomes are the molecular machines that catalyze protein synthesis, which is the last step in the Central Dogma of Molecular Biology. Thus, understanding how cells control ribosome biosynthesis is fundamentally important for understanding cell biology.
Since protein makes up most of the cell mass (other than water) it stands to reason that the protein synthesis machinery is critical for cell growth. Indeed, ribosome biosynthesis is proportional to the rates of cell growth and proliferation. Consequently, ribosome biosynthesis is almost always elevated in pathologies like cancer where cell growth is more rapid. Therefore, understanding mechanisms by which cells control ribosome synthesis has direct translational value. We and others are creating ways to control ribosome synthesis for potential application in anticancer chemotherapy.
Defining mechanisms that govern RNA polymerase I activity
Ribosomal RNA forms the backbone of the ribosome, and eukaryotic cells devote an entire RNA polymerase (RNA polymerase I) to the synthesis of ribosomal RNA. RNA polymerase I activity is controlled via multiple robust regulatory networks. Since the start of my postdoctoral training with Dr. Masayasu Nomura in 2003, the majority of my research interests have been focused on defining RNA polymerase I function and the regulatory networks that control it. The methodologies that we deploy have evolved over the years, of course, but our commitment to aggressive but rigorous discovery is unwavering.
Here I highlight some of the key areas of ongoing study of RNA polymerase I:
- Define the kinetic mechanism of nucleotide addition by RNA polymerase (translation: How does this enzyme work?)
- Identify and characterize trans-acting factors that influence ribosomal RNA synthesis (translation: what other players touch the enzyme and change its activity?)
- Understand the relationship between transcription elongation rate and processing of the nascent ribosomal RNA (translation: what happens to folding of the new RNA when RNA polymerase I moves too fast or too slow?)
- Determine how ribosomal DNA sequence features govern transcription elongation properties (translation: how does the template DNA affect the enzyme?)
- Characterize cellular networks that monitor RNA polymerase I activity (translation: How do cells make cure the enzyme does its job correctly?)
Discovering new potential therapeutics
The nucleolus is the subnuclear compartment where ribosomes are built in eukaryotic cells. Large and more numerous nucleoli have been recognized as a hallmark of cancer since seminal discoveries by Guiseppe Pianese in 1896. Cancer cells demand robust ribosome biosynthesis, and we exploit that vulnerability by discovering new compounds that can inhibit ribosome synthesis, resulting in reduced or eliminated tumor cell growth. We work with collaborators in Birmingham and around to world on a mission to bring new cancer control strategies to the forefront of medicine.
Ongoing studies include:
- Discover new compounds that inhibit ribosome synthesis and characterize their mechanisms of action in malignant melanoma and triple negative breast cancer cells (collaboration with Southern Research, USA)
- Define the mechanism by which BMH-21 induces degradation of RNA polymerase I (collaboration with Dr. Marikki Laiho, Johns Hopkins University, USA)
- Define the mechanism by which naphthalene-diimides inhibit RNA polymerase I (in collaboration with Dr. Jose A. García Salcedo; Universidad de Granada, Spain)
Characterizing “other” RNA polymerases
Over the course of our studies, we have gained skills/expertise in characterizing RNA polymerase functions. In recent years, we have begun to leverage our expertise to answer key questions surrounding the activities of other RNA polymerases.
Some of these projects are highlighted here:
- Defining the divergent enzymatic properties of eukaryotic RNA polymerases I, II, and III. (translation: All eukaryotes have at least three nuclear RNA polymerases. Why?)
- Characterize nucleotide addition kinetics for SARS-CoV2 and influenza RNA-dependent RNA polymerases (translation: How do these viral enzymes work, and how can we kill them?)
- Understand fidelity mechanisms that control viral RNA synthesis in SARS-CoV2 and influenza (translation: Some viruses make almost no mistakes and others make a lot. How does that work?)