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Gene Review

rnpA  -  ribonuclease P

Escherichia coli O157:H7 str. Sakai

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Disease relevance of rnpA


High impact information on rnpA

  • RNase E, an essential endoribonuclease in Escherichia coli, is involved in 9S rRNA processing, the degradation of many mRNAs, and the processing of the M1 RNA subunit of RNase P. However, the reason that RNase E is required for cell viability is still not fully understood [6].
  • Evidence that substrate-specific effects of C5 protein lead to uniformity in binding and catalysis by RNase P [7].
  • The bacterial RNase P protein is required to activate bacterial RNase P RNA in vivo, but previous studies have yielded contradictory conclusions regarding its specific functions [8].
  • Together, these data are consistent with a cluster of metal ion interactions in the P1-P4 multi-helix junction that defines the catalytic core of the RNase P ribozyme [9].
  • Most sites of interference are at strongly conserved nucleotides and nine reside within a long-range base-pairing interaction present in all known RNase P RNAs [10].

Chemical compound and disease context of rnpA


Biological context of rnpA

  • Although helix P4 in the catalytic domain of the RNase P ribozyme is known to coordinate magnesium ions important for activity, distinguishing between direct and indirect roles in catalysis has been difficult [16].
  • Our finding that a single base change is sufficient to alter the metal preference of RNase P is further evidence that the J3/4-P4-J2/4 domain forms a portion of the ribozyme's active site [17].
  • The inhibition of gene expression was virtually abolished at restrictive temperatures in strains that were temperature-sensitive for RNase P (EC [18].
  • A mechanism is proposed for the RNA-catalyzed reactions involved in RNA splicing and RNase P hydrolysis of precursor tRNA [19].
  • Certain fragments of M1 RNA, the catalytic subunit of RNase P from Escherichia coli, either have no enzymatic activity at all or have altered substrate specificity compared with that of the intact catalytic RNA [20].

Anatomical context of rnpA

  • RNase P from human (HeLa) cells cannot catalyze the cleavage in vitro of the 5'-proximal oligoribonucleotide that contains the leader sequence in such simple complexes but can do so when the 3'-proximal oligoribonucleotide (external guide sequence) is altered to resemble three-quarters of a tRNA molecule [21].
  • The properties of RNase P purified according to the procedure developed in this laboratory have been compared with those of the enzyme purified from ribosomes according to the procedure described by Robertson et al [22].
  • Mitochondrial RNase P is probably a part of the mitochondrial RNA processing machinery of mammalian mitochondria, being responsible for the endonucleolytic cleavage of the RNA transcripts at the 5'-side of the tRNA sequences [23].
  • Although the ionic requirements of mtRNase P are similar to those of the RNase P activity isolated from the post-mitochondrial cytosol fraction, the chromatographic properties of mtRNase P are distinct [23].
  • RNase P-like activity can be quantitatively recovered from intact mitochondrial preparations treated with micrococcal nuclease, strongly suggesting that the enzyme is localized within the organelles [23].

Associations of rnpA with chemical compounds

  • Activity assays with mutant RNase P holoenzymes assembled in vivo or in vitro revealed that the C292/293 mutations cause a severe functional defect at low Mg(2+) concentrations (2 mM), which we infer to be on the level of catalytically important Mg(2+) recruitment [24].
  • RNase P activity can be reconstituted by mixing separated RNA and protein components in buffer containing 7M urea followed by dialysis of this mixture to remove the urea [25].
  • Highly purified RNase P exhibits one prominent RNA and one prominent polypeptide component when examined in polyacrylamide gels containing sodium dodecyl sulfate [26].
  • Metal ions are essential cofactors for precursor tRNA (ptRNA) processing by bacterial RNase P. The ribose 2'-OH at nucleotide (nt) -1 of ptRNAs is known to contribute to positioning of catalytic Me2+ [27].
  • Experiments were conducted to investigate structural features of the aminoacyl stem region of precursor histidine tRNA critical for the proper cleavage by the catalytic RNA component of RNase P that is responsible for 5' maturation [28].

Physical interactions of rnpA

  • The photoagent (azidophenacyl) was coupled uniquely to the 5'-thiophosphate of the tRNA, the site of action by RNase P. The photoagent-containing tRNA binds to RNase P RNA and is cross-linked by UV irradiation to it at high efficiency (10-30%) [29].

Enzymatic interactions of rnpA

  • An analysis of the in vitro processing of leuX precursor revealed that the processing of the 5' end took place in a single-step reaction catalysed by RNase P while the 3' processing involved two successive reactions [30].
  • Moreover, a deletion of the RNase P protein motif significantly reduces the ability of Hera to hydrolyze ATP in the presence of RNase P RNA [31].

Other interactions of rnpA

  • DNA sequences affecting the transcription of the Escherichia coli rnpB transcript encoding the catalytic M1 RNA subunit of RNase P have been analyzed [32].
  • Analysis of mutants revealed that the cleavages are mediated by endonucleases which do not seem to be identical to RNase III, RNase E or RNase P [33].
  • These large precursors were cleaved by cell extracts first into intermediate size pieces which were subsequently processed by RNase P. On the basis of heat stability of mutant cell extracts, the endonuclease responsible for the initial cleavage appears to be distinct from RNase P and is designated RNase O [34].
  • In vitro and in vivo processing of cyanelle tmRNA by RNase P [35].

Analytical, diagnostic and therapeutic context of rnpA

  • We report here for the first time specific and growth-inhibitory drug targeting of RNase P in live bacteria [1].
  • Microarray analysis reveals the expression of several noncoding intergenic regions that are increased at 43 degrees C compared with 30 degrees C. These regions are substrates for RNase P, and they are cleaved less efficiently than, for example, tRNA precursors [36].
  • Engineered RNase P ribozymes are promising gene-targeting agents that can be used in both basic research and clinical applications [37].
  • These results also demonstrate the feasibility of engineering highly effective RNase P ribozymes for gene targeting applications, including anti-HCMV gene therapy [38].
  • RNase P ribozymes selected in vitro to cleave a viral mRNA effectively inhibit its expression in cell culture [39].


  1. Antisense Inhibition of RNase P: MECHANISTIC ASPECTS AND APPLICATION TO LIVE BACTERIA. Gruegelsiepe, H., Brandt, O., Hartmann, R.K. J. Biol. Chem. (2006) [Pubmed]
  2. Comparative photocross-linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs. Chen, J.L., Nolan, J.M., Harris, M.E., Pace, N.R. EMBO J. (1998) [Pubmed]
  3. Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA. LaGrandeur, T.E., Hüttenhofer, A., Noller, H.F., Pace, N.R. EMBO J. (1994) [Pubmed]
  4. Ribonuclease P substrate specificity: cleavage of a bacteriophage phi80-induced RNA. Bothwell, A.L., Stark, B.C., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (1976) [Pubmed]
  5. Effective inhibition of human cytomegalovirus gene expression and replication by a ribozyme derived from the catalytic RNA subunit of RNase P from Escherichia coli. Trang, P., Lee, M., Nepomuceno, E., Kim, J., Zhu, H., Liu, F. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  6. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Ow, M.C., Kushner, S.R. Genes Dev. (2002) [Pubmed]
  7. Evidence that substrate-specific effects of C5 protein lead to uniformity in binding and catalysis by RNase P. Sun, L., Campbell, F.E., Zahler, N.H., Harris, M.E. EMBO J. (2006) [Pubmed]
  8. Protein activation of a ribozyme: the role of bacterial RNase P protein. Buck, A.H., Dalby, A.B., Poole, A.W., Kazantsev, A.V., Pace, N.R. EMBO J. (2005) [Pubmed]
  9. Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA. Christian, E.L., Kaye, N.M., Harris, M.E. EMBO J. (2002) [Pubmed]
  10. Rp-phosphorothioate modifications in RNase P RNA that interfere with tRNA binding. Hardt, W.D., Warnecke, J.M., Erdmann, V.A., Hartmann, R.K. EMBO J. (1995) [Pubmed]
  11. An immunological determinant of RNase P protein is conserved between Escherichia coli and humans. Mamula, M.J., Baer, M., Craft, J., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  12. RNase P cleaves transient structures in some riboswitches. Altman, S., Wesolowski, D., Guerrier-Takada, C., Li, Y. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  13. Precursor of C4 antisense RNA of bacteriophages P1 and P7 is a substrate for RNase P of Escherichia coli. Hartmann, R.K., Heinrich, J., Schlegl, J., Schuster, H. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  14. The additional guanylate at the 5' terminus of Escherichia coli tRNAHis is the result of unusual processing by RNase P. Orellana, O., Cooley, L., Söll, D. Mol. Cell. Biol. (1986) [Pubmed]
  15. Maturation of pre-tRNA(fMet) by Escherichia coli RNase P is specified by a guanosine of the 5'-flanking sequence. Meinnel, T., Blanquet, S. J. Biol. Chem. (1995) [Pubmed]
  16. The P4 metal binding site in RNase P RNA affects active site metal affinity through substrate positioning. Christian, E.L., Smith, K.M., Perera, N., Harris, M.E. RNA (2006) [Pubmed]
  17. In vitro selection for altered divalent metal specificity in the RNase P RNA. Frank, D.N., Pace, N.R. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  18. Artificial regulation of gene expression in Escherichia coli by RNase P. Guerrier-Takada, C., Li, Y., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (1995) [Pubmed]
  19. A general two-metal-ion mechanism for catalytic RNA. Steitz, T.A., Steitz, J.A. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  20. Reconstitution of enzymatic activity from fragments of M1 RNA. Guerrier-Takada, C., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  21. Targeted cleavage of mRNA by human RNase P. Yuan, Y., Hwang, E.S., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  22. In vitro synthesis of transfer RNA. II. Identification of required enzymatic activities. Bikoff, E.K., LaRue, B.F., Gefter, M.L. J. Biol. Chem. (1975) [Pubmed]
  23. Characterization of an RNase P activity from HeLa cell mitochondria. Comparison with the cytosol RNase P activity. Doersen, C.J., Guerrier-Takada, C., Altman, S., Attardi, G. J. Biol. Chem. (1985) [Pubmed]
  24. The precursor tRNA 3'-CCA interaction with Escherichia coli RNase P RNA is essential for catalysis by RNase P in vivo. Wegscheid, B., Hartmann, R.K. RNA (2006) [Pubmed]
  25. Reconstitution of RNase P activity from inactive RNA and protein. Kole, R., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (1979) [Pubmed]
  26. Ribonuclease P: an enzyme with an essential RNA component. Stark, B.C., Kole, R., Bowman, E.J., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (1978) [Pubmed]
  27. Catalysis by RNase P RNA: unique features and unprecedented active site plasticity. Persson, T., Cuzic, S., Hartmann, R.K. J. Biol. Chem. (2003) [Pubmed]
  28. Structural requirements for processing of synthetic tRNAHis precursors by the catalytic RNA component of RNase P. Green, C.J., Vold, B.S. J. Biol. Chem. (1988) [Pubmed]
  29. Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent. Burgin, A.B., Pace, N.R. EMBO J. (1990) [Pubmed]
  30. A novel function of RNase P from Escherichia coli: processing of a suppressor tRNA precursor. Nomura, T., Ishihama, A. EMBO J. (1988) [Pubmed]
  31. Hera from Thermus thermophilus: the first thermostable DEAD-box helicase with an RNase P protein motif. Morlang, S., Weglöhner, W., Franceschi, F. J. Mol. Biol. (1999) [Pubmed]
  32. Sites of initiation and pausing in the Escherichia coli rnpB (M1 RNA) transcript. Lee, Y., Ramamoorthy, R., Park, C.U., Schmidt, F.J. J. Biol. Chem. (1989) [Pubmed]
  33. In vivo and in vitro identity of site specific cleavages in the 5' non-coding region of ompA and bla mRNA in Escherichia coli. Nilsson, G., Lundberg, U., von Gabain, A. EMBO J. (1988) [Pubmed]
  34. Sequential processing of precursor tRNA molecules in Escherichia coli. Sakano, H., Shimura, Y. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  35. In vitro and in vivo processing of cyanelle tmRNA by RNase P. Gimple, O., Schön, A. Biol. Chem. (2001) [Pubmed]
  36. A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs. Li, Y., Altman, S. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  37. Engineered RNase P ribozymes increase their cleavage activities and efficacies in inhibiting viral gene expression in cells by enhancing the rate of cleavage and binding of the target mRNA. Zou, H., Lee, J., Kilani, A.F., Kim, K., Trang, P., Kim, J., Liu, F. J. Biol. Chem. (2004) [Pubmed]
  38. Engineered RNase P ribozymes are efficient in cleaving a human cytomegalovirus mRNA in vitro and are effective in inhibiting viral gene expression and growth in human cells. Zou, H., Lee, J., Umamoto, S., Kilani, A.F., Kim, J., Trang, P., Zhou, T., Liu, F. J. Biol. Chem. (2003) [Pubmed]
  39. RNase P ribozymes selected in vitro to cleave a viral mRNA effectively inhibit its expression in cell culture. Kilani, A.F., Trang, P., Jo, S., Hsu, A., Kim, J., Nepomuceno, E., Liou, K., Liu, F. J. Biol. Chem. (2000) [Pubmed]
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