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Davies-Sala C, Jani S, Zorreguieta A, Tolmasky ME. Identification of the Acinetobacter baumannii Ribonuclease P Catalytic Subunit: Cleavage of a Target mRNA in the Presence of an External Guide Sequence. Front Microbiol 2018; 9:2408. [PMID: 30349524 PMCID: PMC6186949 DOI: 10.3389/fmicb.2018.02408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/20/2018] [Indexed: 11/17/2022] Open
Abstract
The bacterial ribonuclease P or RNase P holoenzyme is usually composed of a catalytic RNA subunit, M1, and a cofactor protein, C5. This enzyme was first identified for its role in maturation of tRNAs by endonucleolytic cleavage of the pre-tRNA. The RNase P endonucleolytic activity is characterized by having structural but not sequence substrate requirements. This property led to development of EGS technology, which consists of utilizing a short antisense oligonucleotide that when forming a duplex with a target RNA induces its cleavage by RNase P. This technology is being explored for designing therapies that interfere with expression of genes, in the case of bacterial infections EGS technology could be applied to target essential, virulence, or antibiotic resistant genes. Acinetobacter baumannii is a problematic pathogen that is commonly resistant to multiple antibiotics, and EGS technology could be utilized to design alternative therapies. To better understand the A. baumannii RNase P we first identified and characterized the catalytic subunit. We identified a gene coding for an RNA species, M1Ab, with the expected features of the RNase P M1 subunit. A recombinant clone coding for M1Ab complemented the M1 thermosensitive mutant Escherichia coli BL21(DE3) T7A49, which upon transformation was able to grow at the non-permissive temperature. M1Ab showed in vitro catalytic activity in combination with the C5 protein cofactor from E. coli as well as with that from A. baumannii, which was identified, cloned and partially purified. M1Ab was also able to cleave a target mRNA in the presence of an EGS with efficiency comparable to that of the E. coli M1, suggesting that EGS technology could be a viable option for designing therapeutic alternatives to treat multiresistant A. baumannii infections.
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Affiliation(s)
- Carol Davies-Sala
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States.,Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, University of Buenos Aires, Buenos Aires, Argentina
| | - Saumya Jani
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, University of Buenos Aires, Buenos Aires, Argentina
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
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Loveland JL, Rice J, Turrini PCG, Lizotte-Waniewski M, Dorit RL. Essential is Not Irreplaceable: Fitness Dynamics of Experimental E. coli RNase P RNA Heterologous Replacement. J Mol Evol 2014; 79:143-52. [DOI: 10.1007/s00239-014-9646-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 09/11/2014] [Indexed: 11/27/2022]
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Altman S. Ribonuclease P: an enzyme with a catalytic RNA subunit. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 62:1-36. [PMID: 2471397 DOI: 10.1002/9780470123089.ch1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- S Altman
- Department of Biology, Yale University, New Haven, Connecticut 06520
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Kim S, Kim H, Park I, Lee Y. Mutational analysis of RNA structures and sequences postulated to affect 3' processing of M1 RNA, the RNA component of Escherichia coli RNase P. J Biol Chem 1996; 271:19330-7. [PMID: 8702618 DOI: 10.1074/jbc.271.32.19330] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
When the rnpB gene encoding M1 RNA, the RNA component of Escherichia coli RNase P, is transcribed, the primary M1 RNA transcript (pM1 RNA) is produced and subsequently processed at the 3' end to generate the mature M1 RNA. To study features of pM1 RNA thought to be involved in RNA processing, systematic mutations were introduced in sequence elements and secondary structures surrounding the processing site using p23 RNA, a truncated pM1 RNA transcribed from the internally deleted rnpB gene, as a model substrate and the processing of its mutant derivatives was analyzed in vivo and in vitro. Neither the alteration of two bases forming the processing site nor the disruption of secondary structures surrounding the site significantly affected the processing efficiency although the secondary structures were required for maintaining RNA stability. In contrast, mutations at the rne-dependent site, GAUUU, immediately 3' to the processing site inhibited the processing and the extent of the inhibition varied with the altered sequences. Furthermore, the processing of the mutants of the rne-dependent site as well as wild-type p23 RNA was inhibited in an E. coli rnets strain at the nonpermissive temperature.
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Affiliation(s)
- S Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Taejon 305-701, Korea
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Haas ES, Armbruster DW, Vucson BM, Daniels CJ, Brown JW. Comparative analysis of ribonuclease P RNA structure in Archaea. Nucleic Acids Res 1996; 24:1252-9. [PMID: 8614627 PMCID: PMC145784 DOI: 10.1093/nar/24.7.1252] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Although the structure of the catalytic RNA component of ribonuclease P has been well characterized in Bacteria, it has been little studied in other organisms, such as the Archaea. We have determined the sequences encoding RNase P RNA in eight euryarchaeal species: Halococcus morrhuae, Natronobacterium gregoryi, Halobacterium cutirubrum, Halobacteriurn trapanicum, Methanobacterium thermoautotrophicum strains deltaH and Marburg, Methanothermus fervidus and Thermococcus celer strain AL-1. On the basis of these and previously available sequences from Sulfolobus acidocaldarius, Haloferax volcanii and Methanosarcina barkeri the secondary structure of RNase P RNA in Archaea has been analyzed by phylogenetic comparative analysis. The archaeal RNAs are similar in both primary and secondary structure to bacterial RNase P RNAs, but unlike their bacterial counterparts these archaeal RNase P RNAs are not by themselves catalytically proficient in vitro.
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Affiliation(s)
- E S Haas
- Department of Microbiology, North Carolina State University, Raleigh 27695, USA
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Chamberlain JR, Tranguch AJ, Pagán-Ramos E, Engelke DR. Eukaryotic nuclear RNase P: structures and functions. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 55:87-119. [PMID: 8787607 DOI: 10.1016/s0079-6603(08)60190-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J R Chamberlain
- Program in Cellular and Molecular Biology, The University of Michigan Medical School, Ann Arbor 48109, USA
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Svärd SG, Mattsson JG, Johansson KE, Kirsebom LA. Cloning and characterization of the RNase P RNA genes from two porcine mycoplasmas. Mol Microbiol 1994; 11:849-59. [PMID: 7517485 DOI: 10.1111/j.1365-2958.1994.tb00363.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report the cloning of the RNase P RNA genes from the primary aetiological agent of porcine pneumonia, Mycoplasma hyopneumoniae, and the closely related commensal, Mycoplasma flocculare. The monocistronic genes each have promoters with AT-rich -35 regions and Rho-independent-like transcription terminators which are retained in the RNase P RNA. Both of these RNase P RNA variants are shown to be catalytically active in vitro in spite of a low overall GC content (30%). Our results suggest a new example of a stable mini-helix in the conserved core of the mycoplasmal RNase P RNAs. Deletion of the corresponding structural element in Escherichia coli RNase P RNA (M1 RNA) generated an RNase P RNA with an impaired substrate interaction. Displacement of this structural element with the mycoplasmal mini-helix resulted in an enzyme with a phenotype similar to that of wild-type M1 RNA. In addition, this structural element is important for lead ion-induced cleavage at specific sites in M1 RNA.
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Affiliation(s)
- S G Svärd
- Department of Microbiology, University of Uppsala, Sweden
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Pagán-Ramos E, Tranguch AJ, Kindelberger DW, Engelke DR. Replacement of the Saccharomyces cerevisiae RPR1 gene with heterologous RNase P RNA genes. Nucleic Acids Res 1994; 22:200-7. [PMID: 8121805 PMCID: PMC307772 DOI: 10.1093/nar/22.2.200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Phylogenetic studies of yeast nuclear RNase P RNA genes have shown a striking conservation of secondary structure for the Saccharomyces and Schizosaccharomyces RNase P RNAs, yet much of the primary sequence and many substructures vary among the RNAs examined. To investigate which sequences and structural features can be varied and still allow function in a heterologous organism, RNase P genes from several yeast species were tested for the ability to substitute for the Saccharomyces cerevisiae RNA. The RNase P genes from Saccharomyces carlsbergensis and Saccharomyces kluyveri could act as the sole source of RNase P RNA within S. cerevisiae cells, whereas the genes from Saccharomyces globosus and Schizosaccharomyces pombe could not. Although heterologous RNase P RNAs were synthesized by the cells in all cases, the RNAs that complemented tended to be processed from longer precursor transcripts into mature-sized RNase P RNA, while the RNAs that did not complement tended to accumulate as the longer precursor form. The results identified sequences and structures in the RNA that are not essential for interaction with species-specific proteins, processing or localization, and suggested other positions that may be candidates for such processes.
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Affiliation(s)
- E Pagán-Ramos
- Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-0606
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Affiliation(s)
- J W Brown
- Department of Biology, Indiana University, Bloomington 47405
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Waugh DS, Pace NR. Complementation of an RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubacteria. J Bacteriol 1990; 172:6316-22. [PMID: 1699929 PMCID: PMC526815 DOI: 10.1128/jb.172.11.6316-6322.1990] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report the construction of a strain of Escherichia coli in which the only functional gene for the RNA moiety of RNase P (rnpB) resides on a plasmid that is temperature sensitive for replication. The chromosomal RNase P RNA gene was replaced with a chloramphenicol acetyltransferase gene. The conditionally lethal phenotype of this strain was suppressed by plasmids that carry RNase P RNA genes from some distantly related eubacteria, including Alcaligenes eutrophus, Bacillus subtilis, and Chromatium vinosum. Thus, the rnpB genes from these organisms are capable of functioning as the sole source of RNase P RNA in E. coli. The rnpB genes of some other organisms (Agrobacterium tumefaciens, Pseudomonas fluorescens, Bacillus brevis, Bacillus megaterium, and Bacillus stearothermophilus) could not replace the E. coli gene. The significance of these findings as they relate to RNase P RNA structure and function and the utility of the described strain for genetic studies are discussed.
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Affiliation(s)
- D S Waugh
- Department of Biology, Indiana University, Bloomington 47405
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Abstract
The discovery and characterization of the catalytic RNA subunit of the enzyme ribonuclease P of Escherichia coli is described.
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Affiliation(s)
- S Altman
- Dept. of Biology, Yale University, New Haven, CT 06520
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Bartkiewicz M, Gold H, Altman S. Identification and characterization of an RNA molecule that copurifies with RNase P activity from HeLa cells. Genes Dev 1989; 3:488-99. [PMID: 2470644 DOI: 10.1101/gad.3.4.488] [Citation(s) in RCA: 164] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An RNA molecule, 340 nucleotides in length and designated H1 RNA, copurifies with RNase P activity from extracts of HeLa cells or isolated HeLa cell nuclei. When the genomic DNA of various organisms is probed with H1 cDNA in Southern hybridization assays, only mammalian DNA gives a positive signal. The gene coding for H1 RNA in human cells is present in one to three copies per cell. The nucleotide sequence of H1 RNA, which shows little homology to the known sequences of its analogs from prokaryotes and yeast, can be drawn as a two-dimensional, hydrogen-bonded structure that resembles similar structures proposed for the RNA subunit of RNase P from these other sources. Part of the hypothetical structure is virtually identical to structures that can be drawn for analogous RNAs from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and S. octosporus.
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Affiliation(s)
- M Bartkiewicz
- Department of Biology, Yale University, New Haven, Connecticut 06520
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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. [PMID: 2468523 DOI: 10.1016/0014-5793(89)80269-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RNase P and ribosomes must interact with similar substrate molecules, tRNA precursors in the case of RNase P and aminoacyl-, peptidyl- or free tRNAs in the case of ribosomes. In order to compare the substrate recognition mechanisms between ribosomes and RNase P, protein synthesis inhibitors have been assayed for their effect on the catalytic activity of the RNA component of Escherichia coli RNase P (M1 RNA). 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.
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Baer M, Lumelsky N, Guerrier-Takada C, Altman S. Structure and Function of Bacterial RNase P. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 1989. [DOI: 10.1007/978-3-642-83709-8_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Biocatalysts by Design. Nat Biotechnol 1988. [DOI: 10.1038/nbt0788-826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Baer MF, Reilly RM, McCorkle GM, Hai TY, Altman S, RajBhandary UL. The recognition by RNase P of precursor tRNAs. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)69212-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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