RNase P RNAs from some Archaea are catalytically active

Abstract

The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.RNase P is an endoribonuclease best known for its role in tRNA biosynthesis, in which it is the enzyme responsible for the removal of 5Ј leader sequences from transfer RNA precursors (for reviews see refs. 1 and 2). In Bacteria, RNase P consists of two subunits: a large (Ϸ140-kDa, 400-nt) RNA and a small (Ϸ14-kDa, 120-amino acid) protein. Both RNA and protein are required in vivo and for optimal activity in vitro in reactions at low ionic strength (3, 4). The RNA is the catalytic subunit of the bacterial enzyme; at elevated ionic strength in vitro, it is by itself capable of processing pre-tRNAs catalytically; i.e., it is a ribozyme (5). The protein component of the bacterial enzyme alters substrate recognition by directly contacting the leader region of the pre-tRNA (6). The RNase P enzymes of Archaea (formerly archaebacteria) and Eukarya (the nuclear͞cytoplasmic portion of the eukaryotic cell) also contain RNA subunits, but these RNAs have not been shown to be catalytically active. Although it seems likely that the catalytic function of the archaeal and eukaryal enzymes resides in the RNA, the expression of this activity apparently requires the presence of the protein subunits.RNase P enzymes have been characterized from only two archaeal species: the thermoacidophilic crenarchaeote Sulfolobus acidocaldarius (7) and the extremely halophilic euryarchaeote Haloferax volcanii (8). The S. acidocaldarius RNase P is resistant to micrococcal nuclease treatment and contains a 315-nt RNA that persists after nuclease treatment (9). The enzyme is large (Ϸ400 kDa apparent molecular mass) and has a low density in Cs 2 SO 4 (1.27 g͞cm 3 ), similar to the densities of the eukaryotic nuclear enzyme and implying a high protein:RNA content. The H. volcanii RNase P, on the other hand, resembles the bacterial enzyme in density in Cs 2 SO 4 (1.61...

Ribonucleases P/MRP and the Expanding Ribonucleoprotein World

“…Universally, the RNA subunit is able to independently perform catalysis (49)(50)(51) although its enzymatic activity is greatly enhanced in the presence of the protein subunits. By inference, it is assumed that the RNA subunit of MRP is also responsible for catalysis (13).…”

Solution structure of RNase P RNA

“…In archaeal and eucaryal RNase P, additional proteins unrelated to the bacterial protein are present and correlate with a decrease in the size and structural complexity of the RNA moiety (Evans et al 2006;Ellis and Brown 2009). The specific functions of the protein components of RNase P remain subjects for debate (Marvin and Engelke 2009;Esakova and Krasilnikov 2010), but the role of the RNA is clearly catalytic: The RNase P RNA components from all three domains of life are evolutionary homologs and can catalyze tRNA maturation in vitro independently of protein cofactors (Guerrier-Takada et al 1983;Pannucci et al 1999;Kikovska et al 2007). …”

Ribosomal protein L7Ae is a subunit of archaeal RNase P

“…Except for some unique organellar variants, RNase P functions in all three domains of life as a ribonucleoprotein (RNP) (1,2). Although catalysis rests with the essential RNase P RNA (RPR) in all three domains of life (4)(5)(6), the RNase P protein (RPP) cofactors play essential roles. In the simple one RPR-one RPP bacterial RNase P, the RPP aids RPR catalysis by enhancing cleavage efficiency and affinity for substrate and Mg 2þ (7)(8)(9).…”