itochondrial RNase P database



Secondary structure models and alignments      Related articles      Links       For suggestions or submissions


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).



References

Altman, S., Wesolowski, D., and Puranam, P.S. 1993. Nucleotide sequences of the RNA subunit of RNase P from
        several mammals. Genomics 18: 418-422.
Arends, S. and Schön, A. 1997. Partial purification and characterization of nuclear ribonuclease P from wheat.
        Eur. J. Biochem. 244: 635-645.
Baum, M., Cordier, A., and Schön, A. 1996. RNase P from a photosynthetic organelle contains an RNA homologous
        to the cyanobacterial counterpart.  J. Mol. Biol. 257: 43-52.
Brown, J.W. 1999. The Ribonuclease P Database. Nucleic Acids Res. 27: 314.
Brown, J.W. and Haas, E.S. 1995. Ribonuclease P structure and function in Archaea. Mol. Biol. Rep. 22: 131-134.
Chen, J.L. and Pace, N.R. 1997. Identification of the universally conserved core of ribonuclease P RNA. RNA 3: 557 560.
Christian, E.L., Zahler, N.H., Kaye, N.M., and Harris, M.E. 2002. Analysis of substrate recognition by the
        ribonucleoprotein endonuclease RNase P. Methods 28: 307-322.
Collins, L.J., Moulton, V., and Penny, D. 2000. Use of RNA secondary structure for studying the evolution of RNase P
        and  RNase MRP. J Mol Evol. 51:194-204.
Crary, S.M., Niranjanakumari, S., and Fierke, C.A. 1998. The protein component of Bacillus subtilis ribonuclease P
        increases catalytic efficiency by enhancing interactions with the 5' leader sequence of pre tRNAAsp. Biochemistry.
        37: 9409 9416.
Clark-Walker, G.D., McArthur, C.R., and Sriprakash, K.S., 1985. Location of transcriptional control signals and
        transfer RNA sequences in Torulopsis glabrata mitochondrial DNA. EMBO J. 4: 465-473.
Dang, Y.L. and Martin, N.C., 1993. Yeast mitochondrial RNase P sequence of the RPM2 gene and demonstration that its
       product is a protein subunit of the enzyme. J. Biol. Chem. 269: 19791-19796.
Darr, S.C., Zito, K., Smith, D., and Pace, N.R. 1992. Contributions of phylogenetically variable structural elements to the
        function of the ribozyme ribonuclease P. Biochemistry 31: 328-333.
Darr, S.C., Pace, B., and Pace, N.R. 1990. Characterization of ribonuclease P from the archaebacterium Sulfolobus
        solfataricus. J. Biol. Chem. 265: 12927 12932.
Frank, D.N., Adamidi, C., Ehringer, M.A., Pitulle, C., and Pace, N.R. 2000. Phylogenetic-comparative analysis of the
        eukaryal ribonuclease P RNA. RNA 6: 1895-1904.
Franklin, S.E., Zwick, M.G., and Johnson, J.D. 1995. Characterization and partial purification of two pre tRNA 5'
        processing activities from Daucus carrota (carrot) suspension cells. Plant J. 7: 553 563.
Gardiner, K.J., Marsh, T.L., and Pace, N.R. 1985. Ion dependence of the Bacillus subtilis RNase P reaction. J. Biol. Chem.
        260: 5415 5419.
Glöckner, G., Rosenthal, A., and Valentin, K. 2000. The structure and gene repertoire of an ancient red algal plastid
        genome. J. Mol. Evol. 51: 382-390.
Gopalan, V., Vioque, A., and Altman, S. 2002. RNase P: variations and uses. J. Biol. Chem. 277: 6759-6762.
Guerrier-Takada, C., Eder, P.S., Gopalan, V., and Altman, S. 2002. Purification and characterization of Rpp25, an
        RNA-binding protein subunit of human ribonuclease P. RNA. 8: 290-295.
Guerrier-Takada, C., and Altman, S. 1992. Reconstitution of enzymatic activity from fragments of M1 RNA. Proc. Natl.
        Acad. Sci. U S A. 89: 1266-1270.
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S. 1983. The RNA Moiety of ribonuclease P is the
        catalytic subunit of the enzyme. Cell 35: 849-857.
Haas, E.S., Brown, J.W., Pitulle, C., and Pace, N.R. 1994. Further perspective on the catalytic core and secondary structure
        of ribonuclease P RNA. Proc. Natl. Acad. Sci. USA 91: 2527-2531.
Hall, T.A. and Brown, J.W. 2002. Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear
        RNase P proteins. RNA 8: 296-306.
Hanic Joyce, P.J. and Gray, M.W. 1990. Processing of transfer RNA precursors in a wheat mitochondrial extract.
        J. Biol. Chem. 265: 13782 13791.
Harris, J.K., Haas, E.S., Williams, D., Frank, D.N., and Brown, J.W. 2001. New insight into RNase P RNA structure from
        comparative analysis of the archaeal RNA. RNA 7: 220-232.
Hartmann, R.K., Heinrich, J., Schlegl, J., and Schuster, H. 1995. Precursor of C4 antisense RNA of bacteriophages P1 and
        P7 is a substrate for RNase P of Escherichia coli. Proc. Natl. Acad. Sci. U S A. 92: 5822-5826.
Jayanthi, G.P. and Van Tuyle, G.C. 1992. Characterization of ribonuclease P isolated from rat liver cytosol. Arch. Biochem.
        Biophys. 296: 264 270.
Kole, R. and Altman, S. 1981. Properties of purified ribonuclease P from Escherichia coli. Biochemistry 20: 1902-1906.
LaGrandeur, T.E., Darr, S.C., Hass, E.S., and Pace, N.R. 1993. Characterization of the RNase P RNA of Sulfolobus
        acidocaldarius. J. Bacteriology 175: 5043-5048.
Lang, B.F., Gray, M.W., and Burger, G. 1999. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev.
        Genet. 33: 351-397.
Lang, B.F., Burger, G., O'Kelly, C.J., Cedergren, R., Golding, G.B., Lemieux, C., Sankoff, D., Turmel, M., and Gray, M.W.
        1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387: 493-497.
Lee, Y.C., Lee, B.J., Hwang, D.S., and Kang, H.S. 1996a. Purification and characterization of mitochondrial ribonuclease P
        from Aspergillus nidulans. Eur. J. Biochem. 235: 289 296.
Lee, Y.C., Lee, B.J., and Kang, H.S. 1996b. The RNA component of mitochondrial ribonuclease P from Aspergillus
        nidulans. Eur. J. Biochem. 235: 297-303.
Marchfelder, A. and Brennicke, A. 1994. Characterization and partial purification of tRNA processing activities from
        potato mitochondria. Plant Physiol. 105: 1247-1254.
Martin, C.A. and Lang, B.F. 1997. Mitochondrial RNase P: the RNA family grows. Nucleic Acids Symp. Ser. 36: 42-44.
Miller, D.L. and Martin, N.C. 1983. Characterization of the yeast mitochondrial locus necessary for tRNA biosynthesis:
        DNA sequence analysis and identification of a new transcript.  Cell 3: 911-917.
Morales, M.J., Dang, Y.L., Lou, Y.C., Sulo, P., and Martin, N.C. 1992. A 105 k-Da protein is required  for yeast
        mitochondrial RNase P activity.  Proc. Natl. Acad. Sci. USA  89: 9875-9879.
Pannucci, J.A., Haas, E.S., Hall, T.A., Harris, J.K., and Brown, J.W. 1999. RNase P RNAs from some archaea are
        catalytically active. Proc. Natl. Acad. Sci. U S A 96: 7803 7808.
Pascual, A. and Vioque, A. 1999. Functional reconstitution of RNase P activity from a plastid RNA subunit and a
        cyanobacterial protein subunit. FEBS Lett. 442: 7 10.
Peck-Miller, K.A. and Altman, S. 1991. Kinetics of the processing of the precursor to 4.5S RNA, a naturally occurring
        substrate for RNase P from Escherichia coli. J. Mol. Biol. 221: 1-5.
Puranam R.S. and Attardi G. 2001. The RNase P associated with HeLa cell mitochondria contains an essential RNA
        component identical in sequence to that of the nuclear RNase P. Mol. Cell. Biol. 21: 548 61.
Ragnini, A., Grisanti, P., Rinaldi, T., Frontali, L., and Palleschi, C. 1991. Mitochondrial genome of Saccharomyces
        douglasii: genes coding for components of the protein synthetic apparatus. Curr. Genet. 19: 169-174.
Reith, M. and Munholland, J. 1995. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome.
        Plant Mol. Biol. Reptr. 13: 333-335.
Rossmanith, W. and Karwan, R.M. 1998. Characterization of human mitochondrial RNase P: novel aspects in tRNA
        processing. Biochem. Biophys. Res. Commun. 247: 234 241.
Rossmanith, W. and Potushak, T. 2001. Difference between mitochondrial RNase P and nuclear RNase P.
        Mol. Cell. Biol. 21: 8236-8237.
Salavati, R., Panigrahi, A.K., and Stuart, K.D. 2001. Mitochondrial ribonuclease P activity of Trypanosoma brucei.
        Mol. Biochem. Parasitol. 115: 109-117.
Sbisa, E., Pesole, G., Tullo, A., and Saccone, C. 1996. The evolution of the RNase P- and RNase MRP- associated RNAs:
        phylogenetic analysis and nucleotide substitution rate. J. Mol. Evol. 43: 46-57.
Seif ER, Forget L, Martin NC, and Lang BF. 2003. Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific
        variations in RNA secondary structure. RNA 9: 1073-1083.
Sekito, T., Okamoto, K., Kitano, H., and Yoshida, K. 1995. The complete mitochondrial DNA sequence of Hansenula
        wingei reveals new characteristic of yeast mitochondria. Curr. Genet.  28:  39-53.
Shu, H.H., Wise, C.A., Clark Walker, G.D., and Martin, N.C. 1991a. A gene required for RNase P activity in Candida
        (Torulopsis) glabrata mitochondria codes for a 227 nucleotide RNA with homology to bacterial RNase P RNA. Mol.
        Cell. Biol. 11: 1662 1667.
Shu, H.H. and Martin, N.C. 1991b. RNase P RNA in Candida glabrata mitochondria is transcribed  with substrate
        tRNAs.Nucleic Acids Res. 19: 6221-6226.
Stark, B.C., Kole, R., Bowman, E.J., and Altman, S. 1978. Ribonuclease P: an enzyme with an essential RNA component.
        Proc. Natl. Acad. Sci. USA 75: 3717-3721.
Stribinskis, V., Gao, G.J., Ellis, S.R., and Martin, N.C. 2001. Rpm2, the protein subunit of mitochondrial RNase P in
        Saccharomyces cerevisiae, also has a role in the translation of mitochondrially encoded subunits of cytochrome c
        oxidase. Genetics. 158: 573-585.
Stribinskis, V., Gao, G.J., Sulo, P., Dang, Y.L., and Martin, N.C. 1996. Yeast mitochondrial RNase P RNA synthesis is
        altered in an RNase P protein subunit mutant insights into the biogenesis of a mitochondrial RNA-processing enzyme.
        Mol. Cell. Biol. 16: 3429-3436.
Thomas, B.C., Li X., and Gegenheimer, P. 2000. Chloroplast ribonuclease P does not utilize the ribozyme-type pre-tRNA
        cleavage mechanism. RNA 6: 545-553.
Turmel, M., Lemieux, C., Burger, G., Lang, B.F., Otis, C., Plante, I., and Gray, M.W. 1999. The complete mitochondrial
        DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary
        patterns within green algae. Plant Cell 11: 1717-1730.
Underbrink-Lyon, K., Miller, D.L., Ross, N.A., Fukuhara, H., and Martin, N.C. 1983. Characterization of a yeast
        mitochondrial locus necessary for tRNA biosynthesis. Deletion mapping and restriction mapping studies. Mol. Gen.
        Genet. 191: 512-518.
Wagner, M., Fingerhut, C., Gross, H.J., and Schon, A. 2001. The first phytoplasma RNase P RNA provides new insights
        into the sequence requirements of this ribozyme. Nucleic Acids Res. 29: 2661-2665.
Wilson, C., Ragnini, A., and Fukuhara, H. 1989. Analysis of the regions coding for transfer RNAs in Kluyveromyces lactis
        mitochondrial DNA. Nucleic Acids Res. 17: 4485-4491.
Wise, C.A. and Martin, N.C. 1991a. Dramatic size variation of yeast mitochondrial RNAs suggests that RNase P RNAs can
        be quite small.  J. Biol. Chem. 266: 19154-19157.
Wise, C. and Martin, N.C. 1991b. Sequence analysis of Saccharomyces exiguus mitochondrial DNA reveals an RNase P
        RNA flanked by two tRNA genes. Nucleic Acids Res. 19: 4773.