Comparative analysis of ribonuclease P RNA structure in Archaea

Brown, J.W., Haas, E.S., Vucson, B.M., Department of Microbiology, North Carolina State University, Raleigh, NC 27695

Armbruster, D., and Daniels, C.J. Department of Microbiology, The Ohio State University, Columbus, OH 43210.

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. Secondary structure models of the archaeal RNase P RNAs presented so far have been unconvincing, representing little more than the archaeal sequences 'forced' into the model developed for bacterial RNase P RNA secondary structure. In order to develop a secondary structure model based on archaeal sequences, we have cloned the genes encoding RNase P RNA from eight additional species, Halococcus morrhuae, Natronobacterium gregoryi, Halobacterium cutirubrum, Halobacterium trapanicum, Methanobacterium thermoautotrophicum strain deltaH, Methanobacterium thermoautotrophicum strain Marburg, Methanothermus fervidus, and Thermococcus celer strain AL-1, and used these sequences in a phylogenetic comparative analysis of secondary structure.

The primary sequences and secondary structures of the archaeal RNase P RNAs largely resemble their bacterial counterparts, and those nucleotides which are most conservative in the bacterial RNAs are also generally conserved in the archaeal sequences. Despite these similarities, the archaeal RNAs are unlike their bacterial counterparts in that they are not capable of catalysis in the absence of other enzyme components. The structural basis of this deficiency must reside in the differences in the bacterial and archaeal sequences or higher-order structure.

The archaeal consensus secondary structure contains all but one helix present in the bacterial consensus structure, the 2bp helix (P11) adjacent to large regions in which the structure remains unknown even in Bacteria. The structure of the P15/P16 region varies amongst the archaeal RNAs, despite the conservation of this region in Bacteria (in which it has been implicated in recognition of the substrate pre-tRNA 3' terminus). However, in the methanobacteria and T. celer, this region conforms to the sequence and structure consensus of the bacterial RNAs, but nevertheless lack catalytic proficiency in vitro, and so it seems unlikely that this region is entirely responsible for this 'defect' in the archaeal RNAs.