Ph.D.: Massachusetts Institute of Technology, 1997
Postdoctoral Fellow: Yale University, 1997 - 2001
RNA plays a central role in almost every facet of the maintenance, transmission and decoding of genetic information in the cell. The remarkable versatility of RNA is rooted in its ability to act both as a carrier of information like DNA and fold into complex functional three-dimensional structures like proteins. Understanding this dual nature of RNA from a structural perspective is the principal goal of our research group. Using a combination of techniques including X-ray crystallography, isothermal titration calorimetry, fluorescence methods, single molecule measurements and chemical probing, we seek to illuminate the mechanisms by which RNA can perform a diverse number of functions in the cell. Currently, our work is focused upon three areas:
Riboswitches are recently discovered genetic regulatory elements found in the 5’-untranslated regions of bacterial mRNAs that act through their ability to specifically bind small molecule metabolites. Binding of the ligand to the aptamer domain of the riboswitch is communicated to a second domain, the expression platform, which directs transcription or translation of the mRNA. Our laboratory has solved the three-dimensional structures of two classes, the purine and S-adenosylmethionine riboswitches, using X-ray crystallography. These structures reveal that the mRNA element adopts an intricate three-dimensional fold that encapsulates the cognate ligand. Binding of the ligand induces conformational changes in the RNA that allows the aptamer domain to communicate the binding event to the expression platform to achieve genetic control. Research in this area continues to focus upon investigating the three-dimensional structures of other classes of riboswitches as well as using biophysical and biochemical tools to probe their mechanism of action.
RNA modifying enzymes
Many RNAs are post-transcriptionally modified in order for them to achieve full biological function. Of the ~100 different types of chemical modifications found in RNA, we are focusing on enzymes that are involved in 2’-O-methylation of the ribose sugar. In bacteria, modification of tRNA and rRNA is achieved by a number of proteins that each specifically recognize a sugar in a specific structural context. We have recently solved the X-ray structure of one of these enzymes, TrmH, from A. aeolicus. In archaea and eukarya, methylation of the 2’-hydroxyl group is performed by the Box C/D ribonucleoprotein (RNP) particle. This enzyme uses an RNA component as a guide sequence for targeting the RNP to the appropriate site in tRNA or rRNA. A protein component, Fibrillarin, then performs the modification with the assistance of an S-adenosylmethionine cofactor. This division of labor is common to RNPs including the RISC complex in which the RNA is used for targeting and protein is used for catalysis. Our work seeks to understand from a structural and biophysical perspective the mechanism of this process.
The signal recognition particle
The signal recognition particle is an RNP that facilitates the targeting of proteins for secretion in eukarya or insertion into the inner plasma membrane in bacteria. The bacterial SRP, which is essential for cell viability, consists of a single protein, Ffh, bound to a small RNA, the 4.5S RNA. This RNP is divided into two functional domains: a ras-type GTPase domain that serves to regulate SRP function, and a ribonucleoprotein domain that recognizes a signal sequence contained within the targeted protein. Our goal is determine the structure of the intact bacterial SRP using X-ray crystallography, biochemical and structural characterization of signal sequence recognition by the RNP domain, and mechanistic understanding of the communication between the two functional domains.
R. K. Montange and R. T. Batey, "Riboswitches: emerging themes in RNA structure and function," Annu Rev Biophys 37, 117-133, (2008).
S. D. Gilbert, R. P. Rambo, D. Van Tyne, and R. T. Batey, "Structure of the SAM-II riboswitch bound to S-adenosylmethionine," Nat Struct Mol Biol. 15, 177-182, (2008).
A. Y. Keel, R. P. Rambo, R. T. Batey, and J. S. Kieft, "A general strategy to solve the phase problem in RNA crystallography," Structure 15: 761-772, (2007).
J. W. Hardin, and R. T. Batey, "A bipartite architecture of the sRNA in an archaeal box C/D complex is the primary determinant of specificity," Nucleic Acids Res. 34, 5039-5051, (2006).
R. K. Montange and R. T. Batey, “Structure of the S-adenosylmethionine riboswitch regulatory mRNA element,” Nature 441, 1172-5, (2006).
S. D. Gilbert, C. D Stoddard, S. J. Wise and R. T. Batey, “Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain,” J. Mol Biol 359, 754-768, (2006).
E. Pleshe, J. Truesdell, and R. T. Batey, “Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus,” Acta Crystall. F 61, 722-728, (2005).
R. T. Batey, S. D. Gilbert and R. K. Montange, “Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine,” Nature 432, 411-415, (2004).
J. S. Kieft, and R. T. Batey, “A general method for rapid and nondenaturing purification of RNAs,” RNA 10, 988-995, (2004).