Interaction between protein and RNA is central to cellular and viral processes ranging from expressing genes to directing cell mortality, yet the principles that govern protein-RNA recognition are poorly understood. RNA can fold and as a consequence can create a great variety of distinctive molecular surfaces. How do these surfaces enable protein-RNA and RNA-RNA recognition? What role do these surfaces play in the structure, function and assembly of ribonucleoprotein (RNP) complexes? Which RNP proteins mediate RNA structural rearrangements and what mechanism do they use? We aim to address these questions by combining crystallographic, energetic and kinetic studies. Current projects focus on deciphering the molecular underpinnings of essential RNA–protein interactions in ribosome biogenesis--a vital cellular process that is emerging as an unexplored target for cancer treatment.
CURRENT RESEARCH PROJECTS IN THE CORRELL LAB
The U3 project (NIH R01 GM070491 funded until 03/31/12)
Studies in the Correll lab combine structural (crystallographic), functional (kinetic and energetic) and mutational studies to decipher the molecular basis of key RNA-protein interactions in ribosome biogenesis. This process is vital for cell growth, regulated and emerging as an unexplored target for cancer treatment. We investigate the molecular and structural basis of two key early steps in biogenesis of the small ribosomal subunit. One step involves dynamic RNA rearrangements another involves site-specific cleavage. How do several essential proteins and their assemblies chaperone proper docking of the U3 small nucleolar RNA (snoRNA) with its associated proteins onto the pre-rRNA? Once docked, what is the molecular basis of target site selection for the subsequent endonucleolytic cleavage events that liberate the small and large subunit rRNA precursors? We have developed three projects to address these fundamental questions.
One project builds on our discovery that two site-specific RNA chaperones lower barriers that impede rapid U3-pre-rRNA duplex formation and high duplex yield (PNAS '04 paper and JMB '09 paper). Our ongoing studies show that only when these two chaperones assemble with the U3 snoRNA does the measured hybridization rates and the duplex yield fall within the values expected for rapid cell growth. Future studies will exploit FRET assays that we have developed to probe the molecular mechanisms by which this assembly mediates U3-pre-rRNA duplex formation and stability to satisfy these in vivo requirements.
A second related project will determine the structural basis by which this chaperone assembly mediates U3-pre-rRNA interactions by solving crystal structures of relevant RNA-protein complexes by X-ray crystallography. This project will rely upon the lab’s crystallographic expertise (see example of RNA-protein structure see NSB '01 paper ).
A third project will develop in vitro assays to assess whether a putative endonuclease is the one required for the early cleavage steps in 18S rRNA maturation. What activities does this putative endonuclease possess? How specific are these activities? How do the site-specifc chaperones modulate these activities? This work will build on our experience with another site-specific endonuclease, restrictocin (see NSMB '06 paper ).