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Gene Review

rnpB  -  miscRNA

Escherichia coli O157:H7 str. Sakai

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Disease relevance of rnpB

  • Mutant RNase P RNA alleles (rnpBC292 and rnpBC293) caused severe growth defects in the E. coli rnpB mutant strain DW2 and abolished growth in the newly constructed mutant strain BW, in which chromosomal rnpB expression strictly depended on the presence of arabinose [1].
  • Modification of nucleotides 330-332 in the J15/16 loop of Synechocystis RNase P RNA from GGU to CCA has a modest effect on kcat for CCA-containing substrates and has no effect on cleavage-site selection [2].
  • Phylogenetic comparative analyses of RNase P RNA-encoding gene sequences from Chlorobium limicola, Chlorobium tepidum, Bacteroides thetaiotaomicron, and Flavobacterium yabuuchiae refine the secondary structure model of the general (eu)bacterial RNase P RNA and show that a highly conserved feature of that RNA is not essential [3].
  • To verify that the RNase P RNA gene was analyzed, a modified, putative gene was cloned adjacent to a bacteriophage T7 promoter and various transcripts were tested for RNase P activity [4].
  • RNase P RNA from T. thermophilus cleaved a pre-tRNA(Tyr) from E. coli with highest efficiency between 55 degrees C and 65 degrees C. The T. thermophilus RNA, which has a G-C content of 86% in helical regions, displays several structural idiosyncrasies, although its secondary structure is similar to that of proteobacteria [5].

High impact information on rnpB


Chemical compound and disease context of rnpB


Biological context of rnpB

  • Cell growth could be rescued when expressing a second bacterial RNase P RNA with an unrelated sequence in the target region [16].
  • The P4 metal binding site in RNase P RNA affects active site metal affinity through substrate positioning [17].
  • Unlike 16S rRNA phylogeny that has placed the Aquificales as the deepest lineage of the bacterial phylogenetic tree, RNase P RNA-based phylogeny groups S. azorense and P. marina with the green sulfur, cyanobacterial, and delta/epsilon proteobacterial branches [18].
  • Base pairing between the substrate and the ribozyme has previously been shown to be essential for catalytic activity of most ribozymes, but not for RNase P RNA [9].
  • The nucleotide sequence of the gene and its surroundings was determined from the cloned DNA and by directly sequencing or reverse transcribing the RNase P RNA [4].

Anatomical context of rnpB


Associations of rnpB with chemical compounds


Physical interactions of rnpB

  • 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%) [23].

Enzymatic interactions of rnpB


Other interactions of rnpB


  1. 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]
  2. Substrate binding and catalysis by ribonuclease P from cyanobacteria and Escherichia coli are affected differently by the 3' terminal CCA in tRNA precursors. Pascual, A., Vioque, A. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  3. Further perspective on the catalytic core and secondary structure of ribonuclease P RNA. Haas, E.S., Brown, J.W., Pitulle, C., Pace, N.R. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  4. The RNA component of the Bacillus subtilis RNase P. Sequence, activity, and partial secondary structure. Reich, C., Gardiner, K.J., Olsen, G.J., Pace, B., Marsh, T.L., Pace, N.R. J. Biol. Chem. (1986) [Pubmed]
  5. Analysis of the gene encoding the RNA subunit of ribonuclease P from T. thermophilus HB8. Hartmann, R.K., Erdmann, V.A. Nucleic Acids Res. (1991) [Pubmed]
  6. Long-range structure in ribonuclease P RNA. Haas, E.S., Morse, D.P., Brown, J.W., Schmidt, F.J., Pace, N.R. Science (1991) [Pubmed]
  7. 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]
  8. 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]
  9. Base pairing between Escherichia coli RNase P RNA and its substrate. Kirsebom, L.A., Svärd, S.G. EMBO J. (1994) [Pubmed]
  10. 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]
  11. Efficient cleavage of pre-tRNAs by E. coli RNAse P RNA requires the 2'-hydroxyl of the ribose at the cleavage site. Kleineidam, R.G., Pitulle, C., Sproat, B., Krupp, G. Nucleic Acids Res. (1993) [Pubmed]
  12. The pre-tRNA nucleotide base and 2'-hydroxyl at N(-1) contribute to fidelity in tRNA processing by RNase P. Zahler, N.H., Sun, L., Christian, E.L., Harris, M.E. J. Mol. Biol. (2005) [Pubmed]
  13. Kinetic analysis of the M1 RNA folding pathway. Kent, O., Chaulk, S.G., MacMillan, A.M. J. Mol. Biol. (2000) [Pubmed]
  14. Purine N7 groups that are crucial to the interaction of Escherichia coli rnase P RNA with tRNA. Heide, C., Feltens, R., Hartmann, R.K. RNA (2001) [Pubmed]
  15. Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P. Crary, S.M., Kurz, J.C., Fierke, C.A. RNA (2002) [Pubmed]
  16. Antisense Inhibition of RNase P: MECHANISTIC ASPECTS AND APPLICATION TO LIVE BACTERIA. Gruegelsiepe, H., Brandt, O., Hartmann, R.K. J. Biol. Chem. (2006) [Pubmed]
  17. 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]
  18. Thermostable RNase P RNAs lacking P18 identified in the Aquificales. Marszalkowski, M., Teune, J.H., Steger, G., Hartmann, R.K., Willkomm, D.K. RNA (2006) [Pubmed]
  19. Functional reconstitution of RNase P activity from a plastid RNA subunit and a cyanobacterial protein subunit. Pascual, A., Vioque, A. FEBS Lett. (1999) [Pubmed]
  20. Inhibition of RNase P RNA cleavage by aminoglycosides. Mikkelsen, N.E., Brännvall, M., Virtanen, A., Kirsebom, L.A. Proc. Natl. Acad. Sci. U.S.A. (1999) [Pubmed]
  21. G350 of Escherichia coli RNase P RNA contributes to Mg2+ binding near the active site of the enzyme. Rasmussen, T.A., Nolan, J.M. Gene (2002) [Pubmed]
  22. Lead-ion-induced cleavage of RNase P RNA. Ciesiolka, J., Hardt, W.D., Schlegl, J., Erdmann, V.A., Hartmann, R.K. Eur. J. Biochem. (1994) [Pubmed]
  23. 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]
  24. 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]
  25. Complementation of an RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubacteria. Waugh, D.S., Pace, N.R. J. Bacteriol. (1990) [Pubmed]
  26. NAIM and site-specific functional group modification analysis of RNase P RNA: magnesium dependent structure within the conserved P1-P4 multihelix junction contributes to catalysis. Kaye, N.M., Christian, E.L., Harris, M.E. Biochemistry (2002) [Pubmed]
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