Genomes and Genes
Gene Symbol: rnpA
Description: protein C5 component of RNase P
Alias: ECK3696, JW3681
Species: Escherichia coli str. K-12 substr. MG1655
- Hansen A, Pfeiffer T, Zuleeg T, Limmer S, Ciesiolka J, Feltens R, et al. Exploring the minimal substrate requirements for trans-cleavage by RNase P holoenzymes from Escherichia coli and Bacillus subtilis. Mol Microbiol. 2001;41:131-43 pubmed..7 min-1. All cleavage sites were at least 2 nt away from the 5' and 3' ends of the oligonucleotides. Some cleavage site preferences were observed dependent on the identity of the RNase P RNA subunit. ..
- Li Y, Altman S. A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs. Proc Natl Acad Sci U S A. 2003;100:13213-8 pubmedThe rnpA mutation, A49, in Escherichia coli reduces the level of RNase P at 43 degrees C because of a temperature-sensitive mutation in C5 protein, the protein subunit of the enzyme...
- Guerrier Takada C, Haydock K, Allen L, Altman S. Metal ion requirements and other aspects of the reaction catalyzed by M1 RNA, the RNA subunit of ribonuclease P from Escherichia coli. Biochemistry. 1986;25:1509-15 pubmed..Many aspects of the reaction catalyzed by M1 RNA are compatible with a mechanism in which phosphodiester bond cleavage is mediated by metal ion. ..
- Vioque A, Arnez J, Altman S. Protein-RNA interactions in the RNase P holoenzyme from Escherichia coli. J Mol Biol. 1988;202:835-48 pubmed..Regions of M1 RNA required for interaction with C5 protein have been defined by deletion analysis and footprinting techniques. These interactions are localized primarily between nucleotides 82 to 96 and 170 to 270 of M1 RNA. ..
- Kufel J, Kirsebom L. Residues in Escherichia coli RNase P RNA important for cleavage site selection and divalent metal ion binding. J Mol Biol. 1996;263:685-98 pubmed..These results support a model in which base-pairing between M1 RNA and its substrate results in a re-coordination of a divalent metal ion(s) such that cleavage at the correct position is accomplished. ..
- Guerrier Takada C, Gardiner K, Marsh T, Pace N, Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 1983;35:849-57 pubmed..When the precursor to E. coli 4.5S RNA is used as a substrate, only the enzyme complexes formed with M1 RNA from E. coli and the protein moieties from either bacterial species are active. ..
- Kirsebom L, Baer M, Altman S. Differential effects of mutations in the protein and RNA moieties of RNase P on the efficiency of suppression by various tRNA suppressors. J Mol Biol. 1988;204:879-88 pubmed..efficiency of suppression by tRNA suppressors in vivo in strains of Escherichia coli that harbor a mutation in the rnpA gene, the gene for the protein component (C5) of RNase P, and in strains that carry several different alleles of ..
- Sun L, Campbell F, Zahler N, Harris M. Evidence that substrate-specific effects of C5 protein lead to uniformity in binding and catalysis by RNase P. EMBO J. 2006;25:3998-4007 pubmed..Together, these data suggest that an important biological function of RNase P protein is to offset differences in pre-tRNA structure such that binding and catalysis are uniform. ..
- Perreault J, Altman S. Important 2'-hydroxyl groups in model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J Mol Biol. 1992;226:399-409 pubmed
- Talbot S, Altman S. Kinetic and thermodynamic analysis of RNA-protein interactions in the RNase P holoenzyme from Escherichia coli. Biochemistry. 1994;33:1406-11 pubmed..7 +/- 0.1). The dependence of Kd on the ionic strength and the positive delta S suggests that hydrophobic and stacking interactions contribute significantly to the formation of the RNase P holoenzyme. ..
- Kufel J, Kirsebom L. Cleavage site selection by M1 RNA the catalytic subunit of Escherichia coli RNase P, is influenced by pH. J Mol Biol. 1994;244:511-21 pubmed..These data are discussed in terms of metal ion binding near the cleavage sites in the enzyme-substrate complex. ..
- Mohanty B, Kushner S. Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Res. 2007;35:7614-25 pubmed..Our data indicate that RNase P substrate recognition is more complex than previously envisioned. ..
- Ando T, Tanaka T, Hori Y, Kikuchi Y. Kinetics of hyperprocessing reaction of human tyrosine tRNA by ribonuclease P ribozyme from Escherichia coli. Biosci Biotechnol Biochem. 2002;66:1967-71 pubmed..These results indicated that the occurrence of hyperprocessing depends on the magnesium ion concentration, and suggested that magnesium ions contribute to the recognition of the shape of the substrate by bacterial RNase P enzymes. ..
- Warnecke J, Fürste J, Hardt W, Erdmann V, Hartmann R. Ribonuclease P (RNase P) RNA is converted to a Cd(2+)-ribozyme by a single Rp-phosphorothioate modification in the precursor tRNA at the RNase P cleavage site. Proc Natl Acad Sci U S A. 1996;93:8924-8 pubmed..Dramatic inhibition of the chemical step by both the Rp- and Sp-phosphorothioate modification is unprecedented among known ribozymes and points to unique features of transition state geometry in the RNase P RNA-catalyzed reaction. ..
- Kirsebom L, Svard S. The kinetics and specificity of cleavage by RNase P is mainly dependent on the structure of the amino acid acceptor stem. Nucleic Acids Res. 1992;20:425-32 pubmed..In addition, it appears that the C5 protein of RNase P is involved in the interaction between the enzyme and its substrate in a substrate-dependent manner, as previously suggested. ..
- Li Y, Cole K, Altman S. The effect of a single, temperature-sensitive mutation on global gene expression in Escherichia coli. RNA. 2003;9:518-32 pubmed..The expression pattern of essential genes and gene discovery from intergenic regions, for which other new transcripts are found, are also discussed. ..
- Tallsjo A, Kufel J, Kirsebom L. Interaction between Escherichia coli RNase P RNA and the discriminator base results in slow product release. RNA. 1996;2:299-307 pubmed..This interaction is suggested to play an important role in determining the rate of product release during multiple turnover cleavage of tRNA precursors by M1 RNA as well as in cleavage site selection. ..
- Li Z, Deutscher M. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA. 2002;8:97-109 pubmed..coli tRNA transcripts, providing substrates for final maturation by RNase P and the 3' exoribonucleases. Based on this new information, a detailed model for tRNA maturation is proposed. ..
- Mohanty B, Kushner S. Processing of the Escherichia coli leuX tRNA transcript, encoding tRNA(Leu5), requires either the 3'-->5' exoribonuclease polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator. Nucleic Acids Res. 2010;38:597-607 pubmed publisher..RNase E, G and Z are not involved in terminator removal. These results provide further evidence that the E. coli tRNA processing machinery is far more diverse than previously envisioned. ..
- Kirsebom L, Svard S. Base pairing between Escherichia coli RNase P RNA and its substrate. EMBO J. 1994;13:4870-6 pubmed..Our data also suggest possible base pairing between U294 in M1 RNA and the discriminator base at position +73 of the precursor. Our findings are also discussed in terms of evolution. ..
- Nomura T, Ishihama A. A novel function of RNase P from Escherichia coli: processing of a suppressor tRNA precursor. EMBO J. 1988;7:3539-45 pubmed..The self-cleaved precursor tRNA was no longer processed by the 3' endonuclease, suggesting that the 3' endonuclease recognizes a specific conformation of the precursor tRNA for action. ..
- Hartmann R, Heinrich J, Schlegl J, Schuster H. 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. 1995;92:5822-6 pubmed..in vivo from a plasmid carrying the P1 c4 gene revealed that 5'-mature C4 RNA was the predominant species in rnpA+ bacteria, whereas virtually no mature C4 RNA was found in the temperature-sensitive rnpA49 strain at the ..
- Kazakov S, Altman S. Site-specific cleavage by metal ion cofactors and inhibitors of M1 RNA, the catalytic subunit of RNase P from Escherichia coli. Proc Natl Acad Sci U S A. 1991;88:9193-7 pubmed..coli. There is also a center for the binding of metal ions in the substrate, close to the site of cleavage by M1 RNA. ..
- Kufel J, Kirsebom L. Different cleavage sites are aligned differently in the active site of M1 RNA, the catalytic subunit of Escherichia coli RNase P. Proc Natl Acad Sci U S A. 1996;93:6085-90 pubmed..We discuss a model in which the interaction between the 3'-terminal "RCCA" motif (first three residues interact) of a tRNA precursor and M1 RNA plays a significant role in this process. ..
- Zahler N, Christian E, Harris M. Recognition of the 5' leader of pre-tRNA substrates by the active site of ribonuclease P. RNA. 2003;9:734-45 pubmed..These results provide the first direct evidence for RNase P RNA interactions with the substrate cleavage site, and show that RNA and protein cooperate in leader sequence recognition. ..
- Persson T, Cuzic S, Hartmann R. Catalysis by RNase P RNA: unique features and unprecedented active site plasticity. J Biol Chem. 2003;278:43394-401 pubmed
- Hartmann E, Hartmann R. The enigma of ribonuclease P evolution. Trends Genet. 2003;19:561-9 pubmed
- Peck Miller K, Altman S. Kinetics of the processing of the precursor to 4.5 S RNA, a naturally occurring substrate for RNase P from Escherichia coli. J Mol Biol. 1991;221:1-5 pubmed..5S, is cleaved with greater efficiency than the parent molecule. The 3'-terminal CCC sequence of p4.5 S may be as important for cleavage of this substrate as the 3'-terminal CCA sequence is for cleavage of tRNA precursors. ..
- Mohanty B, Kushner S. Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli. Nucleic Acids Res. 2008;36:364-75 pubmed..Taken together it is clear that there are multiple pathways involved in the maturation of tRNAs in E. coli. ..
- Ikemura T, Shimura Y, Sakano H, Ozeki H. Precursor molecules of Escherichia coli transfer RNAs accumulated in a temperature-sensitive mutant. J Mol Biol. 1975;96:69-86 pubmed
- Sun L, Campbell F, Yandek L, Harris M. Binding of C5 protein to P RNA enhances the rate constant for catalysis for P RNA processing of pre-tRNAs lacking a consensus (+ 1)/C(+ 72) pair. J Mol Biol. 2010;395:1019-37 pubmed publisher..Additionally, these observations suggest that C5 protein has evolved to compensate for tRNA variation at positions important for binding to P RNA, allowing for tRNA specialization. ..
- Ilgen C, Kirk L, Carbon J. Isolation and characterization of large transfer ribonucleic acid precursors from Escherichia coli. J Biol Chem. 1976;251:922-9 pubmed..Many of these precursor RNA molecules contain multiple copies of the same tRNA sequence, indicating a tandem arrangement of the corresponding tRNA genes in the E. coli genome. ..
- Tsai H, Masquida B, Biswas R, Westhof E, Gopalan V. Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme. J Mol Biol. 2003;325:661-75 pubmed..These models are consistent with results from previous studies and provide both structural and mechanistic insights into the functioning of this unique catalytic RNP complex. ..
- Koutmou K, Zahler N, Kurz J, Campbell F, Harris M, Fierke C. Protein-precursor tRNA contact leads to sequence-specific recognition of 5' leaders by bacterial ribonuclease P. J Mol Biol. 2010;396:195-208 pubmed publisher..Furthermore, bioinformatic analyses suggest that sequence-specific contacts between the protein subunit and the leader sequences of pre-tRNAs may be common in bacterial RNase P and may lead to species-specific substrate recognition. ..
- Park B, Lee J, Kim M, Lee Y. Effects of C5 protein on Escherichia coli RNase P catalysis with a precursor tRNA(Phe) bearing a single mismatch in the acceptor stem. Biochem Biophys Res Commun. 2000;268:136-40 pubmed
- Kikovska E, Mikkelsen N, Kirsebom L. The naturally trans-acting ribozyme RNase P RNA has leadzyme properties. Nucleic Acids Res. 2005;33:6920-30 pubmed..Our data suggest that Pb2+ can promote cleavage of RNA by activating either an inner sphere H2O or a neighboring 2'OH to act as nucleophile. ..
- Burkard U, Soll D. The unusually long amino acid acceptor stem of Escherichia coli selenocysteine tRNA results from abnormal cleavage by RNase P. Nucleic Acids Res. 1988;16:11617-24 pubmed..coli tRNA(SeCys) does contain this additional basepair, and that its formation results from abnormal cleavage by RNase P. ..
- Surratt C, Lesnikowski Z, Schifman A, Schmidt F, Hecht S. Construction and processing of transfer RNA precursor models. J Biol Chem. 1990;265:22506-12 pubmed..McClain, W. H., Guerrier-Takada, C., and Altman, S. (1987) Science 238, 527-530) that identifies the T stem and loop as a possible recognition site. ..
- Apirion D. Genetic mapping and some characterization of the rnpA49 mutation of Escherichia coli that affects the RNA-processing enzyme ribonuclease P. Genetics. 1980;94:291-9 pubmed..coli map, with the suggested order rnpA bglB phoS rbsP ilv. As expected, the rnpA49 mutation is recessive...
- Rivera León R, Green C, Vold B. High-level expression of soluble recombinant RNase P protein from Escherichia coli. J Bacteriol. 1995;177:2564-6 pubmed..Mass spectrometry confirmed the molecular weight of the purified protein and indicated a purity of > 95%. Protein functionality was demonstrated by reconstitution of active holoenzyme. ..
- Schlegl J, Fürste J, Bald R, Erdmann V, Hartmann R. Cleavage efficiencies of model substrates for ribonuclease P from Escherichia coli and Thermus thermophilus. Nucleic Acids Res. 1992;20:5963-70 pubmed..In addition, acceptor stem--T arm substrates, composed of two synthetic RNA fragments, have been designed to mimic internal cleavage of any target RNA molecule available for base pairing. ..
- Guerrier Takada C, Altman S. A physical assay for and kinetic analysis of the interactions between M1 RNA and tRNA precursor substrates. Biochemistry. 1993;32:7152-61 pubmed..Direct measurements of the concentrations of all the components in the reaction catalyzed by M1 RNA facilitated a new approach to the kinetic analysis of the action of the enzyme. ..
- Fujita M, Yoshikawa H, Ogasawara N. Structure of the dnaA region of Micrococcus luteus: conservation and variations among eubacteria. Gene. 1990;93:73-8 pubmed..The dnaA gene and at least three other genes, rnpA, rpmH and dnaN were found to be conserved in M. luteus...
- Subbarao M, Makam H, Apirion D. A site in a tRNA precursor that can be processed by the whole RNase P enzyme but not by the RNA alone. J Biol Chem. 1984;259:14339-42 pubmed..The possible function of the protein of RNase P in the enzymatic reaction is discussed. ..
- Schmitz M. Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy. Nucleic Acids Res. 2004;32:6358-66 pubmed..The change of the metal ion binding site is compared with results obtained on corresponding mutant RNase P RNA molecules as reported by Harris and co-workers (RNA, 1, 210-218). ..
- Kirsebom L, Svard S. Identification of a region within M1 RNA of Escherichia coli RNase P important for the location of the cleavage site on a wild-type tRNA precursor. J Mol Biol. 1993;231:594-604 pubmed..We discuss the possibility that the conformation of M1 RNA in the enzyme-substrate complex is dependent on the identity of the substrate. ..
- Kaye N, Christian E, Harris M. 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. Biochemistry. 2002;41:4533-45 pubmed
- Hardt W, Schlegl J, Erdmann V, Hartmann R. Gel retardation analysis of E. coli M1 RNA-tRNA complexes. Nucleic Acids Res. 1993;21:3521-7 pubmed..This indicates that tight binding of the tRNA to the catalytic RNA at higher magnesium concentrations retards product release and therefore substrate turnover. ..
- Bikoff E, LaRue B, Gefter M. In vitro synthesis of transfer RNA. II. Identification of required enzymatic activities. J Biol Chem. 1975;250:6248-55 pubmed..Robertson, H.D., Altman, S., and Smith, F.D. (1972) J.Biol. Chem. 247, 5243-5251.). ..
- Miyata M, Sano K, Okada R, Fukumura T. Mapping of replication initiation site in Mycoplasma capricolum genome by two-dimensional gel-electrophoretic analysis. Nucleic Acids Res. 1993;21:4816-23 pubmed..The arrangement and directions of rnpA, rpmH, dnaA, dnaN were conserved, but no other open reading frames were found that were homologous to those that ..
- Gopalan V, Kuhne H, Biswas R, Li H, Brudvig G, Altman S. Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy. Biochemistry. 1999;38:1705-14 pubmed..The results from this EPR spectroscopy-based approach together with those from earlier studies identify residues in C5 protein which are proximal to M1 RNA in the RNase P holoenzyme complex. ..
- Talbot S, Altman S. Gel retardation analysis of the interaction between C5 protein and M1 RNA in the formation of the ribonuclease P holoenzyme from Escherichia coli. Biochemistry. 1994;33:1399-405 pubmed..Our data show that regions of M1 RNA that interact with C5 protein are clustered into three main areas that are localized between nucleotides 41-99, 168-198, and 266-287. ..
- Haga S, Tanaka T, Kikuchi Y. Mutational analysis of the length of the J3/4 domain of Escherichia coli ribonuclease P ribozyme. Biosci Biotechnol Biochem. 2004;68:2630-2 pubmed..Our data indicate that the conserved AGGA sequence was important for efficient ribozyme reactions, and suggested that the length mutations affected ribozyme activity through metal ion binding steps. ..
- Vioque A. Protein synthesis inhibitors and catalytic RNA. Effect of puromycin on tRNA precursor processing by the RNA component of Escherichia coli RNase P. FEBS Lett. 1989;246:137-9 pubmed..Puromycin has an inhibitory effect that could be related to similar substrate recognition mechanisms by rRNA in the ribosome and by M1 RNA in RNase P. ..
- Sharin E, Schein A, Mann H, Ben Asouli Y, Jarrous N. RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis. Nucleic Acids Res. 2005;33:5120-32 pubmed..The results suggest that distinct protein folds in two unrelated protein cofactors can facilitate transition from RNA- to ribonucleoprotein-based catalysis by RNase P. ..
- Nagai Y, Ando T, Tanaka T, Kikuchi Y. Recognition of tRNA bottom half by bacterial ribonuclease P. Nucleic Acids Res Suppl. 2003;:281-2 pubmed..We also found that RNase P holoenzyme prefered somewhat mutated tRNA precursor to the wild-type tRNA precursor. ..
- Jung Y, Park I, Lee Y. Alteration of RNA I metabolism in a temperature-sensitive Escherichia coli rnpA mutant strain. Biochem Biophys Res Commun. 1992;186:1463-70 pubmedE. coli strain A49 carries the themosensitive mutation in the rnpA gene encoding the protein component of RNase P, a tRNA-processing enzyme...
- Biswas R, Ledman D, Fox R, Altman S, Gopalan V. Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe. J Mol Biol. 2000;296:19-31 pubmed
- Skovgaard O. Nucleotide sequence of a Proteus mirabilis DNA fragment homologous to the 60K-rnpA-rpmH-dnaA-dnaN-recF-gyrB region of Escherichia coli. Gene. 1990;93:27-34 pubmed..coli chromosome containing a part of the gene encoding a 60-kDa membrane-associated protein (60K), the rnpA-rpmH-dnaA-dnaN-recF genes, and the N-terminal part of the gyrB gene...
- Cuzic Feltens S, Weber M, Hartmann R. Investigation of catalysis by bacterial RNase P via LNA and other modifications at the scissile phosphodiester. Nucleic Acids Res. 2009;37:7638-53 pubmed publisher..The presence of the protein cofactor suppressed the ground state binding defects, but not the catalytic defects. ..
- Schmidt F, Seidman J, Bock R. Transfer ribonucleic acid biosynthesis. Substrate specificity of ribonuclease P. J Biol Chem. 1976;251:2440-5 pubmed..The enzymic specificity of RNase P in vitro therefore reflects the in vivo pathway for serine tRNA biosynthesis, where the C-C-A sequence is synthesized while the serine tRNA sequence is still a part of the large precursor RNA. ..
- Guerrier Takada C, Lumelsky N, Altman S. Specific interactions in RNA enzyme-substrate complexes. Science. 1989;246:1578-84 pubmed..These data demonstrate that in RNA's with very different cellular functions, there are domains with similar structural and functional properties and that there is a nucleotide in M1 RNA that affects the site of cleavage by the enzyme. ..
- Reilly R, RajBhandary U. A single mutation in loop IV of Escherichia coli SuIII tRNA blocks processing at both 5'- and 3'-ends of the precursor tRNA. J Biol Chem. 1986;261:2928-35 pubmed..Only the approximately 85-nucleotide-long precursor, which represents a small fraction of the total tRNA precursors, has the correct 5'-end of the mature tRNA. ..
- Svard S, Kirsebom L. Determinants of Escherichia coli RNase P cleavage site selection: a detailed in vitro and in vivo analysis. Nucleic Acids Res. 1993;21:427-34 pubmed..With respect to the function of the subunits of RNase P our data suggest that the nucleotide at position 333 in M1 RNA, and the C5 protein, are important for the identification of the cleavage site. ..
- Pomeranz Krummel D, Kent O, MacMillan A, Altman S. Evidence for helical unwinding of an RNA substrate by the RNA enzyme RNase P: use of an interstrand disulfide crosslink in substrate. J Mol Biol. 2000;295:1113-8 pubmed..Therefore, helical unwinding of the analog of the aminoacyl stem of the substrate near its site of cleavage may be necessary for efficient processing by E. coli RNase P. ..
- Tanaka T, Nagai Y, Kikuchi Y. Substrate shape preference of Escherichia coli ribonuclease P ribozyme and holo enzyme using bottom-half part-shifting variants of pre-tRNA. Biosci Biotechnol Biochem. 2005;69:1992-4 pubmed
- Orellana O, Cooley L, Soll D. The additional guanylate at the 5' terminus of Escherichia coli tRNAHis is the result of unusual processing by RNase P. Mol Cell Biol. 1986;6:525-9 pubmed..The results show that the extra guanylate at the 5' end of mature E. coli tRNAHis is encoded in the gene and is found in tRNA as the result of an unusual cleavage by RNase P. ..
- Ohnishi K. Possible evolutionary origin of primitive protein-encoding mRNAs as a virusoid-like ribo-organism. Nucleic Acids Symp Ser. 1990;:39-40 pubmedE. coli rnpA and rpmH genes encoding the protein portion of ribonuclease (RNase) P and L34 ribosomal protein were found to be homologous to the entire sequence of M1 RNA and virusoids...
- Gurevitz M, Apirion D. Interplay among processing and degradative enzymes and a precursor ribonucleic acid in the selective maturation and maintenance of ribonucleic acid molecules. Biochemistry. 1983;22:4000-5 pubmed
- Harris M, Kazantsev A, Chen J, Pace N. Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking. RNA. 1997;3:561-76 pubmed..The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme. ..
- Hori Y, Bichenkova E, Wilton A, El Attug M, Sadat Ebrahimi S, Tanaka T, et al. Synthetic inhibitors of the processing of pretransfer RNA by the ribonuclease P ribozyme: enzyme inhibitors which act by binding to substrate. Biochemistry. 2001;40:603-8 pubmed..They provide novel, small-molecule, inhibitor frameworks for this endoribonuclease ribozyme. ..