RNA 96 (the RNA Society), May 28 - June 2 1996, Madison, WI

RNase P RNA structure in Archaea

J. Brown1, E. Haas1, D. Armbruster2, B. Vucson1, and C. Daniels2

1Department of Microbiology, North Carolina State University, Raleigh, NC 27695 USA
2Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA

Although the structure of the catalytic RNA component of ribonuclease P has been well characterized in Bacteria, it has been little studied in other organisms such as the Archaea. We have determined the sequences encoding RNase P RNA in eight euryarchaeal species: Halococcus morrhuae, Natronobacterium gregoryi, Halobacterium cutirubrum, Halobacterium trapanicum, Methanobacterium thermoautotrophicum strains deltaH and Marburg, Methanothermus fervidus, and Thermococcus celer strain AL-1. On the basis of these and previously available sequences from Sulfolobus acidocaldarius, Haloferax volcanii and Methanosarcina barkeri, the secondary structure of RNase P RNA in Archaea has been analyzed by phylogenetic comparative analysis.

The archaeal RNAs are similar in both primary and secondary structure to bacterial RNase P RNAs, but unlike their bacterial counterparts these archaeal RNase P RNAs are not by themselves catalytically proficient in vitro. Of the 39 nucleotides that are invariant in bacterial RNase P RNA sequences, 32 (89%) are also present in the archaeal RNAs. The archaeal consensus secondary structure contains all but one helix present in the bacterial consensus structure, the 2bp helix P11. P18, present in nearly all bacterial RNase P RNAs and known to be involved in stabilizing the structure of the RNA, is also absent in all of the archaeal RNase P RNAs. The structure of the P15/P16 region, known to be important in substrate recognition and highly conserved in the bacterial RNAs, is quite variable in the archaeal RNAs, although in some instances it conforms to the bacterial consensus. The structural basis for the absolute dependence of the archaeal RNase P RNAs on (presumably) protein for function is not obvious from the primary or secondary structures of these RNAs.