1
|
Novel inhibitors of Staphylococcus aureus RnpA that synergize with mupirocin. Bioorg Med Chem Lett 2018; 28:1127-1131. [PMID: 29463447 DOI: 10.1016/j.bmcl.2018.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 11/23/2022]
Abstract
We recently discovered RnpA as a promising new drug discovery target for methicillin-resistant S. aureus (MRSA). RnpA is an essential protein that is thought to perform two required cellular processes. As part of the RNA degrasome Rnpa mediates RNA degradation. In combination with rnpB it forms RNase P haloenzymes which are required for tRNA maturation. A high throughput screen identified RNPA2000 as an inhibitor of both RnpA-associated activities that displayed antibacterial activity against clinically relevant strains of S. aureus, including MRSA. Structure-activity studies aimed at improving potency and replacing the potentially metabotoxic furan moiety led to the identification of a number of more potent analogs. Many of these new analogs possessed overt cellular toxicity that precluded their use as antibiotics but two derivatives, including compound 5o, displayed an impressive synergy with mupirocin, an antibiotic used for decolonizing MSRA whose effectiveness has recently been jeopardized by bacterial resistance. Based on our results, compounds like 5o may ultimately find use in resensitizing mupirocin-resistant bacteria to mupirocin.
Collapse
|
2
|
Walczyk D, Willkomm DK, Hartmann RK. Bacterial type B RNase P: functional characterization of the L5.1-L15.1 tertiary contact and antisense inhibition. RNA (NEW YORK, N.Y.) 2016; 22:1699-1709. [PMID: 27604960 PMCID: PMC5066622 DOI: 10.1261/rna.057422.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/06/2016] [Indexed: 06/06/2023]
Abstract
Ribonuclease P is the ubiquitous endonuclease that generates the mature 5'-ends of precursor tRNAs. In bacteria, the enzyme is composed of a catalytic RNA (∼400 nucleotides) and a small essential protein subunit (∼13 kDa). Most bacterial RNase P RNAs (P RNAs) belong to the architectural type A; type B RNase P RNA is confined to the low-G+C Gram-positive bacteria. Here we demonstrate that the L5.1-L15.1 intradomain contact in the catalytic domain of the prototypic type B RNase P RNA of Bacillus subtilis is crucial for adopting a compact functional conformation: Disruption of the L5.1-L15.1 contact by antisense oligonucleotides or mutation reduced P RNA-alone and holoenzyme activity by one to two orders of magnitude in vitro, largely retarded gel mobility of the RNA and further affected the structure of regions P7/P8/P10.1, P15 and L15.2, and abolished the ability of B. subtilis P RNA to complement a P RNA-deficient Escherichia coli strain. We also provide mutational evidence that an L9-P1 tertiary contact, as found in some Mycoplasma type B RNAs, is not formed in canonical type B RNAs as represented by B. subtilis P RNA. We finally explored the P5.1 and P15 stem-loop structures as targets for LNA-modified antisense oligonucleotides. Oligonucleotides targeting P15, but not those directed against P5.1, were found to efficiently anneal to P RNA and to inhibit activity (IC50 of ∼2 nM) when incubated with preassembled B. subtilis RNase P holoenzymes.
Collapse
Affiliation(s)
- Dennis Walczyk
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany
| | - Dagmar K Willkomm
- Klinik für Infektiologie und Mikrobiologie, Universitätsklinikum Schleswig-Holstein Campus Lübeck, D-23538 Lübeck, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany
| |
Collapse
|
3
|
Wu S, Mao G, Kirsebom LA. Inhibition of Bacterial RNase P RNA by Phenothiazine Derivatives. Biomolecules 2016; 6:biom6030038. [PMID: 27618117 PMCID: PMC5039424 DOI: 10.3390/biom6030038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/19/2022] Open
Abstract
There is a need to identify novel scaffolds and targets to develop new antibiotics. Methylene blue is a phenothiazine derivative, and it has been shown to possess anti-malarial and anti-trypanosomal activities. Here, we show that different phenothiazine derivatives and pyronine G inhibited the activities of three structurally different bacterial RNase P RNAs (RPRs), including that from Mycobacterium tuberculosis, with Ki values in the lower μM range. Interestingly, three antipsychotic phenothiazines (chlorpromazine, thioridazine, and trifluoperazine), which are known to have antibacterial activities, also inhibited the activity of bacterial RPRs, albeit with higher Ki values than methylene blue. Phenothiazines also affected lead(II)-induced cleavage of bacterial RPR and inhibited yeast tRNA(Phe), indicating binding of these drugs to functionally important regions. Collectively, our findings provide the first experimental data showing that long, noncoding RNAs could be targeted by different phenothiazine derivatives.
Collapse
Affiliation(s)
- Shiying Wu
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
| |
Collapse
|
4
|
Drainas D. Antibiotics and RNase P. Antibiotics (Basel) 2016; 5:antibiotics5020015. [PMID: 27164152 PMCID: PMC4929430 DOI: 10.3390/antibiotics5020015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 04/22/2016] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
RNase P is an essential endonuclease in tRNA biogenesis, which generates the mature 5′-termini of tRNAs. Most forms of RNase P are ribonucleoproteins, i.e., they consist of an essential RNA and protein subunits. The catalytic function of ribonucleoprotein RNase P enzymes resides entirely in the RNA subunit. Its high structural and functional diversity among representatives of a vast variety of phylogenetic domains indicates that RNase P could serve as a molecular target and a useful screening system for the development of new drugs in the battle against bacterial drug resistance.
Collapse
Affiliation(s)
- Denis Drainas
- Department of Biological Chemistry, School of Medicine, University of Patras, Rio-Patras 26504, Greece.
| |
Collapse
|
5
|
Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
Collapse
|
6
|
Liu X, Chen Y, Fierke CA. A real-time fluorescence polarization activity assay to screen for inhibitors of bacterial ribonuclease P. Nucleic Acids Res 2014; 42:e159. [PMID: 25249623 PMCID: PMC4227764 DOI: 10.1093/nar/gku850] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribonuclease P (RNase P) is an essential endonuclease that catalyzes the 5′ end maturation of precursor tRNA (pre-tRNA). Bacterial RNase P is an attractive potential antibacterial target because it is essential for cell survival and has a distinct subunit composition compared to the eukaryal counterparts. To accelerate both structure-function studies and discovery of inhibitors of RNase P, we developed the first real-time RNase P activity assay using fluorescence polarization/anisotropy (FP/FA) with a 5′ end fluorescein-labeled pre-tRNAAsp substrate. This FP/FA assay also detects binding of small molecules to pre-tRNA. Neomycin B and kanamycin B bind to pre-tRNAAsp with a Kd value that is comparable to their IC50 value for inhibition of RNase P, suggesting that binding of these antibiotics to the pre-tRNA substrate contributes to the inhibitory activity. This assay was optimized for high-throughput screening (HTS) to identify specific inhibitors of RNase P from a 2880 compound library. A natural product derivative, iriginol hexaacetate, was identified as a new inhibitor of Bacillus subtilis RNase P. The FP/FA methodology and inhibitors reported here will further our understanding of RNase P molecular recognition and facilitate discovery of antibacterial compounds that target RNase P.
Collapse
Affiliation(s)
- Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
7
|
Toumpeki C, Stamatopoulou V, Bikou M, Grafanaki K, Kallia-Raftopoulou S, Papaioannou D, Stathopoulos C, Drainas D. Targeting Ribonuclease P. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
8
|
Lu Q, Wierzbicki S, Krasilnikov AS, Schmitt ME. Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components. RNA (NEW YORK, N.Y.) 2010; 16:529-37. [PMID: 20086051 PMCID: PMC2822918 DOI: 10.1261/rna.1893710] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 11/20/2009] [Indexed: 05/22/2023]
Abstract
RNase MRP is a ribonucleoprotein endoribonuclease found in three cellular locations where distinct substrates are processed: the mitochondria, the nucleolus, and the cytoplasm. Cytoplasmic RNase MRP is the nucleolar enzyme that is transiently relocalized during mitosis. Nucleolar RNase MRP (NuMRP) was purified to homogeneity, and we extensively purified the mitochondrial RNase MRP (MtMRP) to a single RNA component identical to the NuMRP RNA. Although the protein components of the NuMRP were identified by mass spectrometry successfully, none of the known NuMRP proteins were found in the MtMRP preparation. Only trace amounts of the core NuMRP protein, Pop4, were detected in MtMRP by Western blot. In vitro activity of the two enzymes was compared. MtMRP cleaved only mitochondrial ORI5 substrate, while NuMRP cleaved all three substrates. However, the NuMRP enzyme cleaved the ORI5 substrate at sites different than the MtMRP enzyme. In addition, enzymatic differences in preferred ionic strength confirm these enzymes as distinct entities. Magnesium was found to be essential to both enzymes. We tested a number of reported inhibitors including puromycin, pentamidine, lithium, and pAp. Puromycin inhibition suggested that it binds directly to the MRP RNA, reaffirming the role of the RNA component in catalysis. In conclusion, our study confirms that the NuMRP and MtMRP enzymes are distinct entities with differing activities and protein components but a common RNA subunit, suggesting that the RNA must be playing a crucial role in catalytic activity.
Collapse
Affiliation(s)
- Qiaosheng Lu
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, USA
| | | | | | | |
Collapse
|
9
|
Vourekas A, Stamatopoulou V, Toumpeki C, Tsitlaidou M, Drainas D. Insights into functional modulation of catalytic RNA activity. IUBMB Life 2008; 60:669-83. [PMID: 18636557 DOI: 10.1002/iub.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
RNA molecules play critical roles in cell biology, and novel findings continuously broaden their functional repertoires. Apart from their well-documented participation in protein synthesis, it is now apparent that several noncoding RNAs (i.e., micro-RNAs and riboswitches) also participate in the regulation of gene expression. The discovery of catalytic RNAs had profound implications on our views concerning the evolution of life on our planet at a molecular level. A characteristic attribute of RNA, probably traced back to its ancestral origin, is the ability to interact with and be modulated by several ions and molecules of different sizes. The inhibition of ribosome activity by antibiotics has been extensively used as a therapeutical approach, while activation and substrate-specificity alteration have the potential to enhance the versatility of ribozyme-based tools in translational research. In this review, we will describe some representative examples of such modulators to illustrate the potential of catalytic RNAs as tools and targets in research and clinical approaches.
Collapse
Affiliation(s)
- Anastassios Vourekas
- Department of Biological Chemistry, School of Medicine, University of Patras, Rio-Patras, Greece
| | | | | | | | | |
Collapse
|
10
|
Kalavrizioti D, Vourekas A, Tekos A, Tsagla A, Stathopoulos C, Drainas D. Kinetics of inhibition of ribonuclease P activity by peptidyltransferase inhibitors. Effect of antibiotics on RNase P. Mol Biol Rep 2003; 30:9-14. [PMID: 12688530 DOI: 10.1023/a:1022290110116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A cell-free system derived from Dictyostelium discoideum has been used to study the kinetics of inhibition of RNase P by puromycin, amicetin and blasticidin S. Detailed kinetic analysis showed that the type of inhibition of RNase P activity by puromycin is simple competitive, whereas the type of inhibition by amicetin and blasticidin S is simple non-competitive. On the basis of Ki values amicetin is stronger inhibitor than puromycin and blasticidin S.
Collapse
Affiliation(s)
- Dimitra Kalavrizioti
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
| | | | | | | | | | | |
Collapse
|
11
|
Affiliation(s)
- T A Hall
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | |
Collapse
|
12
|
Salavati R, Panigrahi AK, Stuart KD. Mitochondrial ribonuclease P activity of Trypanosoma brucei. Mol Biochem Parasitol 2001; 115:109-17. [PMID: 11377745 DOI: 10.1016/s0166-6851(01)00273-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ribonuclease P (RNase P) is an essential enzyme that cleaves the 5' leader sequences of precursor tRNAs (pre-tRNAs) to generate mature tRNAs. The RNase P-like activity from Trypanosoma brucei mitochondria (mtRNase P) was purified over 10000-fold by sequential column chromatography. This is the first demonstration of such activity from mitochondria of parasitic protozoa. Its apparent molecular weight is approximately 70 kDa, considerably less than bacterial RNase P. Preliminary characterizations revealed no RNA component that is essential for this activity. Like other RNase P activities, the cleavage generates mature tRNAs with a terminal 5'-phosphate at the cleavage site and the 5' leader sequence with a 3'-hydroxyl. Disruption of the pre-tRNA tertiary structure inhibits the cleavage of the substrates. These data suggest that although all mitochondrial tRNAs are encoded in nuclear DNA in T. brucei, these cells contain an RNase P in the mitochondrion that cleaves the 5' terminal leader sequences of pre-tRNAs to generate mature tRNAs. Cleavage by mtRNase P of a pre-tRNA substrate that was divided into two fragments was demonstrated. This shows the feasibility of artificial regulation of gene expression that can be achieved by creating a complex made of target mRNA and a complementary small oligonucleotide that resembles natural substrates for RNase P.
Collapse
Affiliation(s)
- R Salavati
- Department of Pathobiology, Seattle Biomedical Research Institute, University of Washington, 4, Nickerson Street, 98109, Seattle, WA, USA
| | | | | |
Collapse
|
13
|
|
14
|
Stathopoulos C, Tsagla A, Tekos A, Drainas D. Effect of peptidyltransferase inhibitors on ribonuclease P activity from Dictyostelium discoideum. Effect of antibiotics on RNase P. Mol Biol Rep 2000; 27:107-11. [PMID: 11092557 DOI: 10.1023/a:1007183306082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The effect of several peptidyltransferase inhibitors on ribonuclease P activity from Dictyostelium discoideum was investigated. Among the inhibitors tested puromycin, amicetin and blasticidin S revealed a dose-dependent inhibition of tRNA maturation. Blasticidin S and amicetin do not compete with puromycin for the same site on the enzyme, suggesting the existence of distinct antibiotic binding sites on D. discoideum RNase P. Inhibition experiments further indicate that binding sites for blasticidin S and amicetin overlap.
Collapse
Affiliation(s)
- C Stathopoulos
- Deparment of Biochemistry, School of Medicine, University of Patras, Greece
| | | | | | | |
Collapse
|
15
|
Abstract
The structural and physico-chemical parameters promoting the binding of aminoglycosides to RNAs are becoming clear. The strength of the interaction is dominated by electrostatics, with the positively charged aminoglycosides displacing metal ions. Although aminoglycosides inhibit most known ribozymes, aminoglycosides or polyamines are able to catalyze specific RNA cleavage in the absence of metal ions.
Collapse
Affiliation(s)
- F Walter
- UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, F-67084, France
| | | | | |
Collapse
|
16
|
Mikkelsen NE, Brännvall M, Virtanen A, Kirsebom LA. Inhibition of RNase P RNA cleavage by aminoglycosides. Proc Natl Acad Sci U S A 1999; 96:6155-60. [PMID: 10339557 PMCID: PMC26851 DOI: 10.1073/pnas.96.11.6155] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A number of aminoglycosides have been reported to interact and interfere with the function of various RNA molecules. Among these are 16S rRNA, the group I intron, and the hammerhead ribozymes. In this report we show that cleavage by RNase P RNA in the absence as well as in the presence of the RNase P protein is inhibited by several aminoglycosides. Among the ones we tested, neomycin B was found to be the strongest inhibitor with a Ki value in the micromolar range (35 microM). Studies of lead(II)-induced cleavage of RNase P RNA suggested that binding of neomycin B interfered with the binding of divalent metal ions to the RNA. Taken together, our findings suggest that aminoglycosides compete with Mg2+ ions for functionally important divalent metal ion binding sites. Thus, RNase P, which is an essential enzyme, is indeed a potential drug target that can be used to develop new drugs by using various aminoglycosides as lead compounds.
Collapse
Affiliation(s)
- N E Mikkelsen
- Department of Cell and Molecular Biology, Box 596, Biomedical Center, Uppsala University, SE-751 24 Uppsala, Sweden
| | | | | | | |
Collapse
|
17
|
Rossmanith W, Karwan RM. Characterization of human mitochondrial RNase P: novel aspects in tRNA processing. Biochem Biophys Res Commun 1998; 247:234-41. [PMID: 9642109 DOI: 10.1006/bbrc.1998.8766] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human mitochondrial RNase P does not distinguish itself from other RNase P enzymes by most of its basic properties. 5' phosphates on tRNA products, strict dependence on a divalent cation, independence of ATP or other cofactors, and sensitivity to puromycin are generally characteristic for RNase P. Slow sedimentation of human mitochondrial RNase P in glycerol gradients suggests a molecular weight considerably lower than that of bacterial or nuclear RNase P. In contrast to fungi, all putative components of mammalian mitochondrial RNase P are encoded by the nucleus. Intriguingly, no indication of the involvement of a trans-acting RNA was found in mammalian mitochondrial tRNA processing. Mitochondrial RNase P is resistant to rigorous treatments with nucleases and exhibits a protein-like density in Cs2SO4 gradients. Moreover, an analysis of copurifying RNAs revealed no putative RNase P RNA candidates. These data suggest that mammalian mitochondrial RNase P, unlike its nuclear counterpart or its bacterial relatives, is not a ribonucleoprotein but a protein enzyme.
Collapse
Affiliation(s)
- W Rossmanith
- Institut für Tumorbiologie-Krebsforschung der Universität Wien, Borschkegasse 8a, Vienna, A-1090, Austria.
| | | |
Collapse
|
18
|
Abstract
Dramatic technical progress in RNA synthesis and structure determination has allowed several difficulties inherent to the preparation, handling and structural analysis of RNA to be overcome, and this has led to a wealth of information about RNA structure and its relationship with biological function. It is now fully recognized that RNA molecules intervene at all stages of cell life, not only because of key sequence motifs but also because of intricate three-dimensional folds. This realization has promoted RNA to a potential therapeutic target. As in protein motifs recognizing nucleic acids, groups of the molecule interacting with RNA contribute to specific binding through defined hydrogen bonds and van der Waals docking, while other parts contribute to the driving force of binding via less specific electrostatic interactions accompanied by water and ion displacement.
Collapse
Affiliation(s)
- T Hermann
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | | |
Collapse
|
19
|
Abstract
Ribonuclease P (RNase P) is responsible for the generation of mature 5' termini of tRNA. The RNA component of this complex encodes the enzymatic activity in bacteria and is itself catalytically active under appropriate conditions in vitro. The role of the subunits in eucaryotes has not yet been established. We have partially purified RNase P activity from the ciliate protozoan Tetrahymena thermophila to learn more about the biochemical characteristics of RNase P from a lower eucaryote. The Tetrahymena RNase P displays a pH optimum and temperature optimum characteristic of RNase P enzymes isolated from other organisms. The Km of the T. thermophila enzyme for pre-tRNAGln is 1.6 x 10(-7)M, which is comparable to the values reported for other examples of RNase P. The Tetrahymena RNase P is a ribonucleoprotein complex, as supported by its sensitivity to micrococcal nuclease and proteinase K. The buoyant density of the enzyme in Cs2SO4 is 1.42 g/ml, which suggests that the RNA component of the Tetrahymena enzyme comprises a significantly greater percentage of the holoenzyme than that determined for RNase P of other Eucarya or Archaea. The holoenzyme has a requirement for divalent cations displaying characteristics that are unique for RNase P but closely resemble preferences reported for the Tetrahymena group I intron RNA. Puromycin inhibits pre-tRNA processing by the Tetrahymena complex, and implications of the similarities between recognition of tRNA by ribosomal components and RNase P are discussed.
Collapse
MESH Headings
- Animals
- Base Sequence
- Cations, Divalent
- Chromatography, Affinity
- Chromatography, Ion Exchange
- DNA Primers
- Endoribonucleases/antagonists & inhibitors
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Puromycin/pharmacology
- RNA Precursors/chemistry
- RNA Precursors/metabolism
- RNA, Catalytic/antagonists & inhibitors
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Transfer, Gln/chemistry
- RNA, Transfer, Gln/metabolism
- Ribonuclease P
- Substrate Specificity
- Tetrahymena thermophila/enzymology
Collapse
Affiliation(s)
- H L True
- Department of Microbiology and College of Medicine, University of Illinois, Urbana, Illinois 61801, USA
| | | |
Collapse
|
20
|
Kirsebom LA, Vioque A. RNase P from bacteria. Substrate recognition and function of the protein subunit. Mol Biol Rep 1996; 22:99-109. [PMID: 8901495 DOI: 10.1007/bf00988713] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNase P recognizes many different precursor tRNAs as well as other substrates and cleaves all of them accurately at the expected position. RNase P recognizes the tRNA structure of the precursor tRNA by a set of interactions between the catalytic RNA subunit and the T- and acceptor-stems mainly, although residues in the 5'-leader sequence as well as the 3'-terminal CCA are important. These conclusions have been reached by several studies on mutant precursor tRNAs as well as cross-linking studies between RNase P RNA and precursor tRNAs. The protein subunit of RNase P seems also to affect the way that the substrate is recognized as well as the range of substrates that can be used by RNase P, although the protein does not seem to interact directly with the substrates. The interaction between the protein and RNA subunits of RNase P has been extensively studied in vitro. The protein subunit sequence is not highly conserved among bacteria, however different proteins are functionally equivalent as heterologous reconstitution of the RNase P holoenzyme can be achieved in many cases.
Collapse
Affiliation(s)
- L A Kirsebom
- Department of Microbiology, Biomedical Center, Uppsala, Sweden
| | | |
Collapse
|
21
|
Potuschak T, Rossmanith W, Karwan R. RNase MRP and RNase P share a common substrate. Nucleic Acids Res 1993; 21:3239-43. [PMID: 7688115 PMCID: PMC309761 DOI: 10.1093/nar/21.14.3239] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
RNase MRP is a site-specific ribonucleoprotein endoribonuclease that processes RNA from the mammalian mitochondrial displacement loop containing region. RNase P is a site-specific ribonucleoprotein endoribonuclease that processes pre-tRNAs to generate their mature 5'-ends. A similar structure for the RNase P and RNase MRP RNAs and a common cleavage mechanism for RNase MRP and RNase P enzymes have been proposed. Experiments with protein synthesis antibiotics have shown that both RNase MRP and RNase P are inhibited by puromycin. We also show that E. coli RNase P cleaves the RNase MRP substrate, mouse mitochondrial primer RNA, exactly at a site that is cleaved by RNase MRP.
Collapse
Affiliation(s)
- T Potuschak
- Institut für Tumorbiologie-Krebsforschung, Universität Wien, Austria
| | | | | |
Collapse
|
22
|
von Ahsen U, Schroeder R. Streptomycin inhibits splicing of group I introns by competition with the guanosine substrate. Nucleic Acids Res 1991; 19:2261-5. [PMID: 1710351 PMCID: PMC329428 DOI: 10.1093/nar/19.9.2261] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Streptomycin is an aminocyclitol glycoside antibiotic, which interferes with prokaryotic protein synthesis by interacting with the ribosomal RNA. We report here that streptomycin is also able to inhibit self splicing of the group I intron of the thymidylate synthase gene of phage T4. The inhibition is kinetically competitive with the substrate guanosine. Streptomycin and guanosine have in common a guanidino group, which has been shown to undergo hydrogen bonds with the ribozyme (Bass & Cech, Biochemistry, 25, 1986, 4473). The inhibitory effect of streptomycin extends to other group I introns, but does not affect group II introns. Mutating the bulged nucleotide in the conserved P7 secondary structure element of the td intron alters the affinity of the ribozyme for both guanosine and streptomycin. Myomycin, an antibiotic with similar effects on protein synthesis as streptomycin, is also able to inhibit splicing. In contrast, bluensomycin, which is structurally related to streptomycin, but contains only one guanidino group does not inhibit splicing. We discuss these findings in support of an evolutionary model that stresses the antiquity of antibiotics (J. Davies, Molecular Microbiology 4, 1990, 1227).
Collapse
Affiliation(s)
- U von Ahsen
- Institut für Mikrobiologie und Genetik, Universität Wien, Vienna, Austria
| | | |
Collapse
|
23
|
|
24
|
Abstract
Analysis of crosslinked complexes of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli, and transfer RNA precursor substrates has led to the identification of regions in the enzyme and in the substrate that are in close physical proximity to each other. The nucleotide in M1 RNA, residue C92, which participates in a crosslink with the substrate was deleted and the resulting mutant M1 RNA was shown to cleave substrates lacking the 3' terminal CCAUCA sequence at sites several nucleotides away from the normal site of cleavage. The presence or absence of the 3' terminal CCAUCA sequence in transfer RNA precursor substrates markedly affects the way in which these substrates interact with the catalytic RNA in the enzyme-substrate complex. The contacts between wild-type M1 RNA and its substrate are in a region that resembles part of the transfer RNA "E" (exit) site in 23S ribosomal RNA. 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.
Collapse
|