itochondrial RNase P database

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Introduction (Seif et al., 2003)

RNase P is a ribo-nucleoprotein (for exceptions, see below) that is universally present in eubacteria, archaebacteria, and eukaryotes, and in mitochondria and chloroplasts. It participates in the processing of tRNAs, 4.5 S RNAs, and other small RNAs, by endonucleolytic removal of 5' leader sequences from RNA precursors (Peck-Miller and Altman 1991).

Eubacterial RNase P

 The RNA subunits of eubacterial RNase P (P-RNA) have been intensely studied, and are currently best understood. E. coli P-RNA is essential for the enzymatic activity in vivo, and is the only subunit necessary for activity in vitro (Stark et al. 1978; Kole and Altman 1981; Guerrier-Takada et al. 1983). Comparisons of all known P-RNAs have revealed significant primary and secondary structure similarities, indicating that these molecules evolved from a common, ancestral RNA.
The in vitro activity of P-RNAs in the absence of a protein component has been demonstrated in numerous instances (Guerrier-Takada et al. 1983; Gardiner et al. 1985; Wagner et al. 2001). Nevertheless, the single eubacterial protein component of RNase P (P-protein) is essential for the enzymatic activity in vivo. It has been suggested that the protein participates in formation of an active-site-architecture, by interacting with the 5’leader of tRNAs (Crary et al. 1998), and that it increases the catalytic activity of RNase P by acting as an electrostatic shield between the negatively charged P-RNA and tRNAs (Guerrier-Takada et al. 1983; Gardiner et al. 1985; Christian et al.  2002). The P-protein also broadens the substrate specificity of RNase P, by enhancing its affinity for non-tRNA substrates. For example, 4.5 S RNA and C4 RNA precursors are processed more efficiently  by a P-RNA/P-protein complex, than by P-RNA alone (Peck-Miller and Altman 1991; Hartmann et al. 1995).

Archeabacterial RNase P

The P-RNA secondary structure model of archaebacteria is strikingly similar to that of eubacteria, except for the lack of the P13, P14 and P18 helices (Brown and Haas 1995; Brown 1999). Archaeal P-RNAs were long thought to be inactive without their protein partner (e.g., Brown and Haas 1995). However, the P-RNAs of Methanobacteria, Thermococci, and Halobacteria do have catalytic activity under extreme ionic conditions (Pannucci et al. 1999). In fact, deletion mutants show that the structural elements missing in archaeal P-RNAs are also dispensable for in vitro catalysis by the E. coli RNA molecule (Darr et al. 1992; Haas et al. 1994). Although archaebacterial P-RNA structures resemble those of eubacteria, the archaeal holoenzyme is much larger. It has at least four protein subunits that appear to be homologs of the eukaryotic P-proteins (Hall and Brown 2002).

Nuclear RNase P

Eukaryotic nuclear P-RNAs have been investigated in detail in ascomycete fungi and in animals. They have no catalytic activity in vitro, and as in archaebacteria, consist of an RNA subunit and several proteins, at least 9 in yeast and 10 in human (Guerrier-Takada et al. 2002; Gopalan et al. 2002). A secondary structure model of the eukaryotic P-RNA conforms convincingly to the bacterial consensus structure with only minor deviations (Chen and Pace 1997; Frank et al. 2000). In plants, RNase P has been purified, and a P-RNA component has been suggested based on the sensitivity of the carrot RNase P activity to micrococcal nuclease treatment (Franklin et al. 1995). Although the nuclear RNase P from wheat is resistant to nuclease treatment, its density as well as its low isoelectric point also suggest the presence of a P-RNA subunit (Arends and Schön 1997). In fact, RNase P from rat liver (Jayanthi and Van Tuyle 1992) and the archaebacterium Sulfolobus solfataricus (Darr et al. 1990) resist micrococcal nuclease treatment, but do contain a P-RNA subunit (Altman et al. 1993; Harris et al. 2001). This suggests that the RNA subunit is protected from digestion by P-proteins.

Organellar RNase P

Mitochondria and chloroplasts contain distinct, organelle-specific RNase P activities. The analysis of organellar P-RNAs has been complicated by the patchy occurrence of the rnpB gene, both in chloroplast and mitochondrial DNAs. The chloroplast-encoded P-RNA of Cyanophora paradoxa folds into a cyanobacteria-like secondary structure (in agreement with the cyanobacterial origin of chloroplasts), and is essential for RNase P activity (Baum et al. 1996). Chloroplast DNA-encoded rnpB genes have been found only in the green alga Nephroselmis olivacea (Turmel et al. 1999), the red algae Porphyra purpurea (Reith and Munholland 1995), and Cyanidium caldarium. We identified the latter, previously unrecognized rnpB gene, at positions 99959-100305 of GenBank record AF022186, (Glöckner et al. 2000). All other known cpDNAs do not seem to encode a P-RNA. A recent prediction of a maize chloroplast rnpB gene (Collins et al. 2000) is based on rather weak secondary structure similarities to known homologs, does not consider otherwise highly conserved primary sequence motifs, and has not been confirmed experimentally. Inferences that do not take primary sequence conservation into account are compromised because A+T rich chloroplast sequences can fit almost any given consensus structure and are, therefore, of little predictive value. Moreover, several biochemical studies suggest that chloroplast RNase P (cpRNase P) may not contain an organelle coded P-RNA. For instance, spinach chloroplast RNase P activity resists micrococcal nuclease treatment, and has physical properties consistent with the presence of a protein-only enzyme. These characteristics suggest that spinach chloroplast RNase P is indeed a protein-only enzyme (Thomas et al. 2000).
Mitochondrial RNase P activities have been studied in various yeasts (see below), the ascomycete fungus Aspergillus nidulans (Lee et al. 1996a), human (Doersen et al. 1985; Rossmanith and Karwan 1998; Puranam and Attardi 2001; Rossmanith and Potuschak 2001), Trypanosoma brucei (Salavati et al. 2001), potato (Marchfelder and Brennicke 1994), wheat (Hanic-Joyce and Gray 1990) and carrot (Franklin et al. 1995). The most detailed information on the biochemical and genetic properties of mitochondrial RNase P is available for S. cerevisiae. Its RNA subunit was first identified as a mitochondrially encoded molecule by analyzing yeast mitochondrial mutants deficient in mitochondrial tRNA processing and protein synthesis (Underbrink-Lyon et al. 1983; Miller and Martin 1983). The unusually large protein subunit has been shown to be nucleus-encoded (Morales et al. 1992; Dang and Martin 1993).
Further rnpB genes have been identified by sequence similarity, in mtDNAs of numerous budding yeasts (T. glabrata, Clark-Walker et al. 1985; Saccharomycopsis  fibuligera, Wise  and Martin 1991a; Kluyveromyces lactis; Wilson et al. 1989; Saccharomyces exiguus; Wise and Martin 1991b; Saccharomyces douglasii; Ragnini et al. 1991; Saccharomyces chevalieri, Saccharomyces ellipsoideous, Saccharomyces diastaticus, Sbisa et al. 1996; and Saccharomyces castellii, Petersen et al. 2002), the protist Reclinomonas americana (Lang et al. 1997), the prasinophyte green alga N. olivacea (Turmel et al. 1999), but not in the mtDNAs of plants, animals, a great number of protists or non-ascomycete fungi (Lang et al. 1999). From an evolutionary standpoint, it is puzzling that the occurrence of mitochondrially encoded rnpB genes is so patchy. Have these genes been lost from the mtDNAs of plants, animals, most fungi and protists, or do we fail to identify them because they are so extremely derived? In fact, highly derived, extremely A+U-rich mtP-RNAs are characteristic in yeast. Consequently, predictions of yeast mtP-RNA secondary structures are difficult, despite the availability of comparative data. In addition, the drastic size variations of these RNA molecules obscure the identification of RNA secondary structure elements (Wise and Martin 1991a). For example, the respective lengths of predicted mtP-RNAs are 423 nucleotides (nt) for S. cerevisiae (Stribinskis et al. 1996), 227 nt for Torulopsis glabrata (Shu et al. 1991a), and as short as 140 nt for Saccharomycopsis fibuligera (Wise and Martin, 1991a).
The mitochondrially-encoded mtP-RNA of the protist Reclinomonas americana was the first identified to contain all structural elements defined in the eubacterial P-RNA consensus structure (Lang et al. 1997). Its features served as a hallmark for re-analyzing the mtP-RNA secondary structure of A. nidulans. This analysis reveals a secondary structure that is substantially more similar to both the Reclinomonas mitochondrial and to the eubacterial consensus (Martin and Lang 1997) than the previously published model (Lee et al. 1996b).


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