RNA Structure Symposium, June 25-29, 1997 Santa Cruz, CA

BROWN, J.W., HAAS, E.S., HARRIS, J.K. PANNUCCI, J.A., RUDD, L.E, AND VUCSON, B.M.

RNASE P RNA STRUCTURE AND FUNCTION IN ARCHAEA.

Department of Microbiology, North Carolina State University, Box 7615, Raleigh, NC 27695

Although the catalytic RNA subunit of RNase P has been well characterized in Bacteria, it is poorly understood in other organisms, such as the Archaea, in which the RNA subunit is not by itself catalytically proficient. RNase P RNA sequences from 25 species of Archaea have been used in a comparative analysis to construct a model for the secondary structure of the archaeal RNA. Surprizingly, all of the elements thought to be required for substrate recognition and catalysis are present in at least some of the archaeal RNAs. In addition, most (ca. 90%) of the nucleotides that are invariant in Bacteria are also present in the archaeal sequences. In a survey of the catalytic proficiency of RNase P enzymes, pre-tRNA^Asp from either Bacillus subtilis or Methanobacterium thermoautotrophicum were efficiently 5´-processed in cell extracts from a wide phylogenetic range of Archaea. However, the RNase P RNAs from these species, either synthesized in vitro or extracted from cells, were not capable of processing these pre-tRNAs in a variety of assay conditions. The archaeal RNase P RNAs are apparently defective in both binding and catalysis; they have a very low affinity for pre-tRNA (>10^-4 that of E. coli) and cannot self-cleave in the context of synthetic enzyme:substrate RNAs, in which pre-tRNA sequences are tethered by either their 5´ or 3´ ends to the appropriate sites of circularly-permuted archaeal RNase P RNAs. The structural basis for the deficiency seems to be the inability of the RNA to fold into the catalytic configuration. Pb++ cleavage sites in the archaeal RNase P RNAs are weak and non-specific, similar to structurally-defective mutant bacterial RNase P RNAs. The identity and contribution of the additional components of the catalytically-active holoenzyme are as yet unknown.