RNA Processing Meeting (the RNA Society), May 24-29 1994, Madison, WI

A Phylogenetic Approach to Modeling Ribonuclease P RNA Tertiary Structure

James M. Nolan, Michael E. Harris, Bong-Kyeong Oh, Jiunn-Liang Chen, James W. Brown*, and Norman R. Pace.

Department of Biology, Indiana University, Bloomington, IN 47405
*Department of Microbiology, North Carolina State University, Raleigh, NC 27695

We have mapped the crosslinking sites of RNase P RNAs from three diverse bacterial species to four different nucleotides of its tRNA substrate. By mapping the many sites in RNase P to which tRNA crosslinks, we have obtained data with which to model the tertiary structure of RNase P RNA. We are using a phylogenetic perspective for this analysis. The RNase P RNAs chosen, from Escherichia coli ,Bacillus subtilis, and Thermotoga maritima, differ to some extent in secondary structure. They are, however, homologous and therefore must share a common core tertiary structure. Thus, any valid model of RNase P tertiary structure that satisfies the secondary structure and crosslinking constraints of one species should also be able to accommodate the constraints imposed upon the RNAs from other species.

This assumption is the basis of our strategy for modeling the three-dimensional structure of RNase P RNA, using the YAMMP RNA modeling package, in collaboration with Steve Harvey and Arun Malhotra at the University of Alabama-Birmingham. We have developed a procedure for the extrapolation of coordinates of YAMMP models generated for one species to those for another species. This allows the enforcement of constraints imposed by each species onto a particular YAMMP model. The results of the YAMMP modeling are being used as constraints for all-atom modeling, using MC-SYM, in collaboration with Francois Major at the National Center for Biotechnology Information, and Thomas Easterwood at the University of Alabama-Birmingham.

This approach is being used to further refine our model of RNase P RNA tertiary structure.