51
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Li Y, Altman S. Partial reconstitution of human RNase P in HeLa cells between its RNA subunit with an affinity tag and the intact protein components. Nucleic Acids Res 2002; 30:3706-11. [PMID: 12202755 PMCID: PMC137421 DOI: 10.1093/nar/gkf499] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An RNA affinity tag was incorporated into the RNA subunit of human nuclear RNase P. The tagged RNA assembled with the protein components of RNase P inside HeLa cells to generate an active enzyme. Because of the specificity of the RNA tag to streptavidin, the reconstituted complex could be separated from the native enzyme and other ribonucleoproteins (particularly RNase MRP) by streptavidin agarose chromatography and could be recovered by the eluting agent, biotin. A mutant, tagged RNase P RNA, whose P3 domain was partially replaced, could not reconstitute with the proteins to yield an active enzyme. The P3 domain, therefore, is critical for the structure and function of RNase P.
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Affiliation(s)
- Yong Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA
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52
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Nadal A, Martell M, Lytle JR, Lyons AJ, Robertson HD, Cabot B, Esteban JI, Esteban R, Guardia J, Gómez J. Specific cleavage of hepatitis C virus RNA genome by human RNase P. J Biol Chem 2002; 277:30606-13. [PMID: 12060655 DOI: 10.1074/jbc.m203595200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have found that RNase P from HeLa cells specifically and efficiently cleaves hepatitis C virus (HCV) transcripts in vitro. The evidence includes identification of the 5'-phosphate polarity of the newly generated termini at position A(2860) as well as immunological and biochemical assays. Active cleavage has been shown in five dominant sequences of HCV "quasispecies" differing at or near the position of cleavage, demonstrating that this is a general property of HCV RNA. During the analysis, a second cleavage event was found in the 3' domain of the internal ribosome entry site. We have found that HCV RNA competitively inhibits pre-tRNA cleavage by RNase P, suggesting that HCV RNA has structural similarities to tRNA. This finding sets HCV apart from other pathogens causing serious human diseases and represents the first description of human RNase P-viral RNA cleavage. Here we discuss the possible meaning of these RNase P-accessible structures built into the viral genome and their possible role in vivo. Moreover, such structures within the viral genome might be vulnerable to attack by therapeutic strategies.
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Affiliation(s)
- Anna Nadal
- Servicio de Medicina Interna-Hepatologia, Area de Investigación Básica, Hospital Vall d'Hebrón, Paseo Vall d'Hebrón 119-129, Barcelona 08035, Spain
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53
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Jiang T, Altman S. A protein subunit of human RNase P, Rpp14, and its interacting partner, OIP2, have 3'-->5' exoribonuclease activity. Proc Natl Acad Sci U S A 2002; 99:5295-300. [PMID: 11929972 PMCID: PMC122763 DOI: 10.1073/pnas.072083699] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2002] [Indexed: 11/18/2022] Open
Abstract
The processing of precursor tRNAs at their 5' and 3' termini is a fundamental event in the biosynthesis of tRNA. RNase P is generally responsible for endonucleolytic removal of a leader sequence of precursor tRNA to generate the mature 5' terminus. However, much less is known about the RNase P counterparts or other proteins that are active at the tRNA 3' terminus. Here we show that one of the human RNase P subunits, Rpp14, together with one of its interacting protein partners, OIP2, is a 3'-->5' exoribonuclease with a phosphorolytic activity that processes the 3' terminus of precursor tRNA. Immunoprecipitates of a crude human RNase P complex can process both ends of precursor tRNA by hydrolysis, but purified RNase P has no exonuclease activity. Rpp14 and OIP2 may be part of an exosome activity.
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Affiliation(s)
- Taijiao Jiang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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54
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Hall TA, Brown JW. Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins. RNA (NEW YORK, N.Y.) 2002; 8:296-306. [PMID: 12003490 PMCID: PMC1370252 DOI: 10.1017/s1355838202028492] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Although archaeal RNase P RNAs are similar in both sequence and structure to those of Bacteria rather than eukaryotes, and heterologous reconstitution between the Bacillus subtilis RNase P protein and some archaeal RNase P RNAs has been demonstrated, no archaeal protein sequences with similarity to any known bacterial RNase P protein subunit have been identified, and the density of Methanothermobacter thermoautotrophicus RNase P in Cs2SO4 (1.42 g/mL) is inconsistent with a single small bacterial-like protein subunit. Four hypothetical open reading frames (MTH11, MTH687, MTH688, and MTH1618) were identified in the genome of M. thermoautotrophicus that have sequence similarity to four of the nine Saccharomyces cerevisiae RNase P protein subunits: Pop4p, Pop5p, Rpp1p, and Rpr2p, respectively. Polyclonal antisera generated to recombinant Mth11p, Mth687p, Mth688p, and Mth1618p each recognized a protein of the predicted molecular weight in western blots of partially purified M. thermoautotrophicus RNase P, and immunoprecipitated RNase P activity from the same partially purified preparation. RNase P in Archaea is therefore composed of an RNA subunit similar to bacterial RNase P RNA and multiple protein subunits similar to those in the eukaryotic nucleus.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibody Formation
- Blotting, Western
- Cell Nucleus/enzymology
- Centrifugation, Density Gradient
- Cesium/chemistry
- Chlorides/chemistry
- Chromatography, Affinity
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Eukaryotic Cells/enzymology
- Humans
- Methanobacterium/enzymology
- Molecular Sequence Data
- Precipitin Tests
- Protein Subunits
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/metabolism
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- Rabbits
- Recombinant Proteins/immunology
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Ribonuclease P
- Saccharomyces cerevisiae/enzymology
- Sequence Homology, Amino Acid
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Affiliation(s)
- Thomas A Hall
- Department of Microbiology, North Carolina State University, Raleigh 27695-7615, USA
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55
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Guerrier-Takada C, Eder PS, Gopalan V, Altman S. Purification and characterization of Rpp25, an RNA-binding protein subunit of human ribonuclease P. RNA (NEW YORK, N.Y.) 2002; 8:290-295. [PMID: 12003489 PMCID: PMC1370251 DOI: 10.1017/s1355838202027954] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In HeLa cells, ribonuclease P (RNase P), the tRNA processing enzyme consists of an RNA subunit (H1 RNA) associated with at least nine protein subunits, Rpp14, Rpp20, Rpp21, Rpp29 (hPop4), Rpp30, Rpp38, Rpp40, hPop1, and hPop5 (18.8 kDa). We report here the cloning and immuno-biochemical analysis of Rpp25, another protein subunit of RNase P. Polyclonal rabbit antibodies raised against recombinant Rpp25 recognize their corresponding antigens in RNase P-containing fractions purified from HeLa cells, and they also precipitate active holoenzyme. Furthermore, this protein has general RNA binding properties.
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Affiliation(s)
- Cecilia Guerrier-Takada
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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56
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Affiliation(s)
- N Jarrous
- Department of Molecular Biology, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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57
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Eubank TD, Biswas R, Jovanovic M, Litovchick A, Lapidot A, Gopalan V. Inhibition of bacterial RNase P by aminoglycoside-arginine conjugates. FEBS Lett 2002; 511:107-12. [PMID: 11821058 DOI: 10.1016/s0014-5793(01)03322-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential of RNAs and RNA-protein (RNP) complexes as drug targets is currently being explored in various investigations. For example, a hexa-arginine derivative of neomycin (NeoR) and a tri-arginine derivative of gentamicin (R3G) were recently shown to disrupt essential RNP interactions between the trans-activator protein (Tat) and the Tat-responsive RNA (trans-activating region) in the human immunodeficiency virus (HIV) and also inhibit HIV replication in cell culture. Based on certain structural similarities, we postulated that NeoR and R3G might also be effective in disrupting RNP interactions and thereby inhibiting bacterial RNase P, an essential RNP complex involved in tRNA maturation. Our results indicate that indeed both NeoR and R3G inhibit RNase P activity from evolutionarily divergent pathogenic bacteria and do so more effectively than they inhibit partially purified human RNase P activity.
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Affiliation(s)
- Timothy D Eubank
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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58
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Jarrous N. Human ribonuclease P: subunits, function, and intranuclear localization. RNA (NEW YORK, N.Y.) 2002; 8:1-7. [PMID: 11871657 PMCID: PMC1370226 DOI: 10.1017/s1355838202011184] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Catalytic complexes of nuclear ribonuclease P (RNase P) ribonucleoproteins are composed of several protein subunits that appear to have specific roles in enzyme function in tRNA processing. This review describes recent progress made in the characterization of human RNase P, its relationship with the ribosomal RNA processing ribonucleoprotein RNase MRP, and the unexpected evolutionary conservation of its subunits. A new model for the biosynthesis of human RNase P is presented, in which this process is dynamic, transcription-dependent, and implicates functionally distinct nuclear compartments in tRNA biogenesis.
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Affiliation(s)
- Nayef Jarrous
- Department of Molecular Biology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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59
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Abstract
Ribonuclease P (RNase P) is an essential endonuclease that acts early in the tRNA biogenesis pathway. This enzyme catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs. RNase P activities have been identified in Bacteria, Archaea, and Eucarya, as well as organelles. Most forms of RNase P are ribonucleoproteins, i.e., they consist of an essential RNA subunit and protein subunits, although the composition of the enzyme in mitochondria and chloroplasts is still under debate. The recent purification of the eukaryotic nuclear RNase P has demonstrated a significantly larger protein content compared to the bacterial enzyme. Moreover, emerging evidence suggests that the eukaryotic RNase P has evolved into at least two related nuclear enzymes with distinct functions, RNase P and RNase MRP. Here we review current information on RNase P, with emphasis on the composition, structure, and functions of the eukaryotic nuclear holoenzyme, and its relationship with RNase MRP.
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Affiliation(s)
- Shaohua Xiao
- Department of Biological Chemistry, 3200 MSRB III, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - Felicia Scott
- Department of Biological Chemistry, 3200 MSRB III, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606
| | - David R. Engelke
- Department of Biological Chemistry, 3200 MSRB III, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, Michigan 48109-0606
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60
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van Eenennaam H, van der Heijden A, Janssen RJ, van Venrooij WJ, Pruijn GJ. Basic domains target protein subunits of the RNase MRP complex to the nucleolus independently of complex association. Mol Biol Cell 2001; 12:3680-9. [PMID: 11694598 PMCID: PMC60285 DOI: 10.1091/mbc.12.11.3680] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The RNase MRP and RNase P ribonucleoprotein particles both function as endoribonucleases, have a similar RNA component, and share several protein subunits. RNase MRP has been implicated in pre-rRNA processing and mitochondrial DNA replication, whereas RNase P functions in pre-tRNA processing. Both RNase MRP and RNase P accumulate in the nucleolus of eukaryotic cells. In this report we show that for three protein subunits of the RNase MRP complex (hPop1, hPop4, and Rpp38) basic domains are responsible for their nucleolar accumulation and that they are able to accumulate in the nucleolus independently of their association with the RNase MRP and RNase P complexes. We also show that certain mutants of hPop4 accumulate in the Cajal bodies, suggesting that hPop4 traverses through these bodies to the nucleolus. Furthermore, we characterized a deletion mutant of Rpp38 that preferentially associates with the RNase MRP complex, giving a first clue about the difference in protein composition of the human RNase MRP and RNase P complexes. On the basis of all available data on nucleolar localization sequences, we hypothesize that nucleolar accumulation of proteins containing basic domains proceeds by diffusion and retention rather than by an active transport process. The existence of nucleolar localization sequences is discussed.
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Affiliation(s)
- H van Eenennaam
- Department of Biochemistry, University of Nijmegen, NL-6500 HB Nijmegen, The Netherlands
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61
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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: 30] [Impact Index Per Article: 1.3] [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.
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Affiliation(s)
- R Salavati
- Department of Pathobiology, Seattle Biomedical Research Institute, University of Washington, 4, Nickerson Street, 98109, Seattle, WA, USA
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62
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van Eenennaam H, Lugtenberg D, Vogelzangs JH, van Venrooij WJ, Pruijn GJ. hPop5, a protein subunit of the human RNase MRP and RNase P endoribonucleases. J Biol Chem 2001; 276:31635-41. [PMID: 11413139 DOI: 10.1074/jbc.m103399200] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNase MRP and RNase P particles both function as endoribonucleases. RNase MRP has been implicated in the processing of precursor-rRNA, whereas RNase P has been shown to function in the processing of pre-tRNA. Both ribonucleoprotein particles have an RNA component that can be folded into a similar secondary structure and share several protein components. We have identified human, rat, mouse, cow, and Drosophila homologues of the Pop5p protein subunit of the yeast RNase MRP and RNase P complexes. The human Pop5 cDNA encodes a protein of 163 amino acids with a predicted molecular mass of 18.8 kDa. Polyclonal antibodies raised against recombinant hPop5 identified a 19-kDa polypeptide in HeLa cells and showed that hPop5 is associated with both RNase MRP and RNase P. Using affinity-purified anti-hPop5 antibodies, we demonstrated that the endogenous hPop5 protein is localized in the nucleus and accumulates in the nucleolus, which is consistent with its association with RNase MRP and RNase P. Catalytically active RNase P was partially purified from HeLa cells, and hPop5 was shown to be associated with it. Finally, the evolutionarily conserved acidic C-terminal tail of hPop5 appeared to be required neither for complex formation nor for RNase P activity.
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Affiliation(s)
- H van Eenennaam
- Department of Biochemistry, University of Nijmegen, P. O. Box 9101, NL-6500 HB Nijmegen, The Netherlands
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63
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Jarrous N, Reiner R, Wesolowski D, Mann H, Guerrier-Takada C, Altman S. Function and subnuclear distribution of Rpp21, a protein subunit of the human ribonucleoprotein ribonuclease P. RNA (NEW YORK, N.Y.) 2001; 7:1153-1164. [PMID: 11497433 PMCID: PMC1370162 DOI: 10.1017/s1355838201010469] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Rpp21, a protein subunit of human nuclear ribonuclease P (RNase P) was cloned by virtue of its homology with Rpr2p, an essential subunit of Saccharomyces cerevisiae nuclear RNase P. Rpp21 is encoded by a gene that resides in the class I gene cluster of the major histocompatibility complex, is associated with highly purified RNase P, and binds precursor tRNA. Rpp21 is predominantly localized in the nucleoplasm but is also observed in nucleoli and Cajal bodies when expressed at high levels. Intron retention and splice-site selection in Rpp21 precursor mRNA regulate the intranuclear distribution of the protein products and their association with the RNase P holoenzyme. Our study reveals that dynamic nuclear structures that include nucleoli, the perinucleolar compartment and Cajal bodies are all involved in the production and assembly of human RNase P.
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MESH Headings
- 3T3 Cells
- Alternative Splicing
- Amino Acid Sequence
- Animals
- Blotting, Western
- Cell Nucleus/chemistry
- Cell Nucleus/metabolism
- Cells, Cultured
- Cloning, Molecular
- DNA, Complementary/metabolism
- Endoribonucleases/chemistry
- Endoribonucleases/metabolism
- Fibroblasts/metabolism
- HeLa Cells
- Humans
- Introns
- Major Histocompatibility Complex
- Mice
- Microscopy, Fluorescence
- Models, Genetic
- Molecular Sequence Data
- Precipitin Tests
- Protein Binding
- RNA Splicing
- RNA, Catalytic/chemistry
- RNA, Catalytic/metabolism
- RNA, Messenger/metabolism
- RNA, Transfer/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Ribonuclease P
- Saccharomyces cerevisiae/chemistry
- Saccharomyces cerevisiae/genetics
- Sequence Homology, Amino Acid
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Affiliation(s)
- N Jarrous
- Department of Molecular Biology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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64
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Jiang T, Guerrier-Takada C, Altman S. Protein-RNA interactions in the subunits of human nuclear RNase P. RNA (NEW YORK, N.Y.) 2001; 7:937-41. [PMID: 11455963 PMCID: PMC1370153 DOI: 10.1017/s1355838201010299] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A yeast three-hybrid system was employed to analyze interactions in vivo between H1 RNA, the RNA subunit of human nuclear RNase P, and eight of the protein subunits of the enzyme. The genetic analysis indicates that subunits Rpp21, Rpp29, Rpp30, and Rpp38 interact directly with H1 RNA. The results of direct UV crosslinking studies of the purified RNase P holoenzyme confirm the results of the three-hybrid assay.
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Affiliation(s)
- T Jiang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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65
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Ziehler WA, Morris J, Scott FH, Millikin C, Engelke DR. An essential protein-binding domain of nuclear RNase P RNA. RNA (NEW YORK, N.Y.) 2001; 7:565-75. [PMID: 11345435 PMCID: PMC1370110 DOI: 10.1017/s1355838201001996] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Eukaryotic RNase P and RNase MRP are endoribonucleases composed of RNA and protein subunits. The RNA subunits of each enzyme share substantial secondary structural features, and most of the protein subunits are shared between the two. One of the conserved RNA subdomains, designated P3, has previously been shown to be required for nucleolar localization. Phylogenetic sequence analysis suggests that the P3 domain interacts with one of the proteins common to RNase P and RNase MRP, a conclusion strengthened by an earlier observation that the essential domain can be interchanged between the two enzymes. To examine possible functions of the P3 domain, four conserved nucleotides in the P3 domain of Saccharomyces cerevisiae RNase P RNA (RPR1) were randomized to create a library of all possible sequence combinations at those positions. Selection of functional genes in vivo identified permissible variations, and viable clones that caused yeast to exhibit conditional growth phenotypes were tested for defects in RNase P RNA and tRNA biosynthesis. Under nonpermissive conditions, the mutants had reduced maturation of the RPR1 RNA precursor, an expected phenotype in cases where RNase P holoenzyme assembly is defective. This loss of RPR1 RNA maturation coincided, as expected, with a loss of pre-tRNA maturation characteristic of RNase P defects. To test whether mutations at the conserved positions inhibited interactions with a particular protein, specific binding of the individual protein subunits to the RNA subunit was tested in yeast using the three-hybrid system. Pop1p, the largest subunit shared by RNases P and MRP, bound specifically to RPR1 RNA and the isolated P3 domain, and this binding was eliminated by mutations at the conserved P3 residues. These results indicate that Pop1p interacts with the P3 domain common to RNases P and MRP, and that this interaction is critical in the maturation of RNase P holoenzyme.
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Affiliation(s)
- W A Ziehler
- Department of Biological Chemistry, University of Michigan, Ann Arbor 48109-0606, USA
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66
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XIAO SHAOHUA, HOUSER-SCOTT FELICIA, ENGELKE DAVIDR. Eukaryotic ribonuclease P: increased complexity to cope with the nuclear pre-tRNA pathway. J Cell Physiol 2001; 187:11-20. [PMID: 11241345 PMCID: PMC3758117 DOI: 10.1002/1097-4652(200104)187:1<11::aid-jcp1055>3.0.co;2-k] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ribonuclease P is an ancient enzyme that cleaves pre-tRNAs to generate mature 5' ends. It contains an essential RNA subunit in Bacteria, Archaea, and Eukarya, but the degree to which the RNA subunit relies on proteins to supplement catalysis is highly variable. The eukaryotic nuclear holoenzyme has recently been found to contain almost twenty times the protein content of the bacterial enzymes, in addition to having split into at least two related enzymes with distinct substrate specificity. In this review, recent progress in understanding the molecular architecture and functions of nuclear forms of RNase P will be considered.
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Affiliation(s)
| | | | - DAVID R. ENGELKE
- Correspondence: David R. Engelke, Department of Biological Chemistry, The University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA.
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67
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Wilson MD, Riemer C, Martindale DW, Schnupf P, Boright AP, Cheung TL, Hardy DM, Schwartz S, Scherer SW, Tsui LC, Miller W, Koop BF. Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5. Nucleic Acids Res 2001; 29:1352-65. [PMID: 11239002 PMCID: PMC29746 DOI: 10.1093/nar/29.6.1352] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning ACHE: to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by ACHE: and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse-human comparison can be viewed at http://web.uvic.ca/~bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.
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Affiliation(s)
- M D Wilson
- Department of Biology, Centre for Environmental Health, PO Box 3020, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
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68
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Abstract
A yeast two-hybrid system was used to analyze interactions among the protein subunits of human nuclear RNase P themselves and with other interacting partners encoded in a HeLa cell cDNA library. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 are involved in extensive, but weak, protein-protein interactions in the holoenzyme complex. Rpp14, Rpp20, and Rpp30 were found to have strong interactions with proteins encoded in the cDNA library. The small heat shock protein 27, which interacts with Rpp20 in the two-hybrid assay, binds to Rpp20 during affinity chromatography and can be found to be associated with, and enhances the activity of, highly purified RNase P. RNase P activity in HeLa cell nuclei also increases under the stress of heat shock.
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69
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Jiang T, Altman S. Protein-protein interactions with subunits of human nuclear RNase P. Proc Natl Acad Sci U S A 2001; 98:920-5. [PMID: 11158571 PMCID: PMC14685 DOI: 10.1073/pnas.98.3.920] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yeast two-hybrid system was used to analyze interactions among the protein subunits of human nuclear RNase P themselves and with other interacting partners encoded in a HeLa cell cDNA library. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 are involved in extensive, but weak, protein-protein interactions in the holoenzyme complex. Rpp14, Rpp20, and Rpp30 were found to have strong interactions with proteins encoded in the cDNA library. The small heat shock protein 27, which interacts with Rpp20 in the two-hybrid assay, binds to Rpp20 during affinity chromatography and can be found to be associated with, and enhances the activity of, highly purified RNase P. RNase P activity in HeLa cell nuclei also increases under the stress of heat shock.
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Affiliation(s)
- T Jiang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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70
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Ridanpää M, van Eenennaam H, Pelin K, Chadwick R, Johnson C, Yuan B, vanVenrooij W, Pruijn G, Salmela R, Rockas S, Mäkitie O, Kaitila I, de la Chapelle A. Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia. Cell 2001; 104:195-203. [PMID: 11207361 DOI: 10.1016/s0092-8674(01)00205-7] [Citation(s) in RCA: 325] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The recessively inherited developmental disorder, cartilage-hair hypoplasia (CHH) is highly pleiotropic with manifestations including short stature, defective cellular immunity, and predisposition to several cancers. The endoribonuclease RNase MRP consists of an RNA molecule bound to several proteins. It has at least two functions, namely, cleavage of RNA in mitochondrial DNA synthesis and nucleolar cleaving of pre-rRNA. We describe numerous mutations in the untranslated RMRP gene that cosegregate with the CHH phenotype. Insertion mutations immediately upstream of the coding sequence silence transcription while mutations in the transcribed region do not. The association of protein subunits with RNA appears unaltered. We conclude that mutations in RMRP cause CHH by disrupting a function of RNase MRP RNA that affects multiple organ systems.
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Affiliation(s)
- M Ridanpää
- Folkhälsan Institute of Genetics, 00280-Helsinki, Finland
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71
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Abstract
Human nuclear RNase P purified from HeLa cells has ATPase activity. This activity is associated with one of the protein subunits of the enzyme, Rpp20. Thus, human nuclear RNase P, which contains several proteins and one essential RNA, has at least one other enzymatic activity in addition to cleavage of phosphoester bonds in RNA. The amino acid sequence of Rpp20 has a signature motif found in an ATPase-containing subunit of a family of protein complexes (ABC transporters) that mediate a variety of trans-membrane traffic, as well as a segment, DIxxN, that resembles the DEAD box motif of many ATPases: together, these might represent an ATPase signature motif.
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72
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Abstract
Human nuclear RNase P purified from HeLa cells has ATPase activity. This activity is associated with one of the protein subunits of the enzyme, Rpp20. Thus, human nuclear RNase P, which contains several proteins and one essential RNA, has at least one other enzymatic activity in addition to cleavage of phosphoester bonds in RNA. The amino acid sequence of Rpp20 has a signature motif found in an ATPase-containing subunit of a family of protein complexes (ABC transporters) that mediate a variety of trans-membrane traffic, as well as a segment, DIxxN, that resembles the DEAD box motif of many ATPases: together, these might represent an ATPase signature motif.
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Affiliation(s)
- Y Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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73
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Puranam RS, Attardi G. The RNase P associated with HeLa cell mitochondria contains an essential RNA component identical in sequence to that of the nuclear RNase P. Mol Cell Biol 2001; 21:548-61. [PMID: 11134342 PMCID: PMC86618 DOI: 10.1128/mcb.21.2.548-561.2001] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mitochondrion-associated RNase P activity (mtRNase P) was extensively purified from HeLa cells and shown to reside in particles with a sedimentation constant ( approximately 17S) very similar to that of the nuclear enzyme (nuRNase P). Furthermore, mtRNase P, like nuRNase P, was found to process a mitochondrial tRNA(Ser(UCN)) precursor [ptRNA(Ser(UCN))] at the correct site. Treatment with micrococcal nuclease of highly purified mtRNase P confirmed earlier observations indicating the presence of an essential RNA component. Furthermore, electrophoretic analysis of 3'-end-labeled nucleic acids extracted from the peak of glycerol gradient-fractionated mtRNase P revealed the presence of a 340-nucleotide RNA component, and the full-length cDNA of this RNA was found to be identical in sequence to the H1 RNA of nuRNase P. The proportions of the cellular H1 RNA recovered in the mitochondrial fractions from HeLa cells purified by different treatments were quantified by Northern blots, corrected on the basis of the yield in the same fractions of four mitochondrial nucleic acid markers, and shown to be 2 orders of magnitude higher than the proportions of contaminating nuclear U2 and U3 RNAs. In particular, these experiments revealed that a small fraction of the cell H1 RNA (of the order of 0.1 to 0.5%), calculated to correspond to approximately 33 to approximately 175 intact molecules per cell, is intrinsically associated with mitochondria and can be removed only by treatments which destroy the integrity of the organelles. In the same experiments, the use of a probe specific for the RNA component of RNase MRP showed the presence in mitochondria of 6 to 15 molecules of this RNA per cell. The available evidence indicates that the levels of mtRNase P detected in HeLa cells should be fully adequate to satisfy the mitochondrial tRNA synthesis requirements of these cells.
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MESH Headings
- Biomarkers/analysis
- Catalysis
- Cell Nucleus/enzymology
- Cell Nucleus/genetics
- Cloning, Molecular
- Digitonin/metabolism
- Endoribonucleases/chemistry
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli Proteins
- HeLa Cells
- Humans
- Micrococcal Nuclease/metabolism
- Mitochondria/enzymology
- Mitochondria/genetics
- RNA/analysis
- RNA/genetics
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Catalytic/metabolism
- RNA, Mitochondrial
- RNA, Nuclear/analysis
- RNA, Nuclear/genetics
- RNA, Small Nuclear/analysis
- RNA, Small Nucleolar/analysis
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribonuclease P
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/genetics
- Ribonucleoproteins/isolation & purification
- Ribonucleoproteins/metabolism
- Saccharomyces cerevisiae/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- R S Puranam
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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74
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Houser-Scott F, Ziehler WA, Engelke DR. Saccharomyces cerevisiae nuclear ribonuclease P: structure and function. Methods Enzymol 2001; 342:101-17. [PMID: 11586886 DOI: 10.1016/s0076-6879(01)42539-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- F Houser-Scott
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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75
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Altman S, Gopalan V, Vioque A. Varieties of RNase P: a nomenclature problem? RNA (NEW YORK, N.Y.) 2000; 6:1689-94. [PMID: 11142368 PMCID: PMC1370038 DOI: 10.1017/s1355838200001783] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
MESH Headings
- Archaea/enzymology
- Archaea/genetics
- Archaeal Proteins/chemistry
- Archaeal Proteins/classification
- Archaeal Proteins/genetics
- Archaeal Proteins/isolation & purification
- Bacteria/enzymology
- Bacteria/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/classification
- Bacterial Proteins/genetics
- Bacterial Proteins/isolation & purification
- Base Sequence
- Chloroplasts/enzymology
- Endoribonucleases/chemistry
- Endoribonucleases/classification
- Endoribonucleases/genetics
- Endoribonucleases/isolation & purification
- Evolution, Molecular
- Fungal Proteins/chemistry
- Fungal Proteins/classification
- Fungal Proteins/genetics
- Fungal Proteins/isolation & purification
- HeLa Cells/enzymology
- Humans
- Molecular Sequence Data
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/classification
- Neoplasm Proteins/genetics
- Neoplasm Proteins/isolation & purification
- Nucleic Acid Conformation
- Organelles/enzymology
- Plant Proteins/chemistry
- Plant Proteins/classification
- Plant Proteins/isolation & purification
- Protein Subunits
- RNA, Archaeal/chemistry
- RNA, Archaeal/classification
- RNA, Archaeal/genetics
- RNA, Archaeal/isolation & purification
- RNA, Bacterial/chemistry
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Catalytic/chemistry
- RNA, Catalytic/classification
- RNA, Catalytic/genetics
- RNA, Catalytic/isolation & purification
- RNA, Fungal/chemistry
- RNA, Fungal/classification
- RNA, Fungal/genetics
- RNA, Fungal/isolation & purification
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/classification
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Ribonuclease P
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/classification
- Ribonucleoproteins/genetics
- Ribonucleoproteins/isolation & purification
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Terminology as Topic
- Zea mays/enzymology
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Affiliation(s)
- S Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
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76
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Tekos A, Tsagla A, Stathopoulos C, Drainas D. Inhibition of eukaryotic ribonuclease P activity by aminoglycosides: kinetic studies. FEBS Lett 2000; 485:71-5. [PMID: 11086168 DOI: 10.1016/s0014-5793(00)02190-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of several aminoglycoside antibiotics on ribonuclease P (RNase P) was investigated using an in vitro experimental system from Dictyostelium discoideum. Detailed kinetic analysis showed that all aminoglycosides tested (tobramycin, gentamicin, kanamycin, paromomycin, neomycin) behave as classical non-competitive inhibitors, with neomycin being the strongest inhibitor. The inhibition effect is attributed to the electrostatic competition of the cationic aminoglycosides with magnesium ions required for catalysis. Increasing Mg(2+) ion concentrations reduced the effect of aminoglycosides on RNase P activity. Detailed kinetic analysis showed that aminoglycosides compete with Mg(2+) for common binding sites on RNase P holoenzyme.
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Affiliation(s)
- A Tekos
- Department of Biochemistry, School of Medicine, University of Patras, 26500 Patras, Greece
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77
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Papadimou E, Monastirli A, Tsambaos D, Merk HF, Drainas D. Inhibitory effects of arotinoids on tRNA biogenesis. SKIN PHARMACOLOGY AND APPLIED SKIN PHYSIOLOGY 2000; 13:345-51. [PMID: 11096376 DOI: 10.1159/000029942] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The effects of five arotinoids (Ro 13-7410, Ro 15-0778, Ro 15-1570, Ro 13-6298, Ro 40-8757) on ribonuclease P (RNase P) activity were studied in a cell-free system derived from Dictyostelium discoideum. RNase P is a ribonucleoprotein that endonucleolytically cleaves all tRNA precursors to produce the mature 5' end. Kinetic analysis showed that these compounds behave as classical competitive inhibitors with Ki values 4.35, 3.6, 2.8 and 0.045 mM for Ro 13-6298, Ro 15-1570, Ro 15-0778 and Ro 13-7410, respectively. Ro 13-7410 was 62, 80 and 97 times more potent in inhibiting the enzyme activity as compared to Ro 15-0778, Ro 15-1570 and Ro 13-6298, respectively, whereas Ro 40-8757 showed no effect on RNase P activity. These results project the significance of the acidic polar terminus in the arotinoid molecule binding to the enzyme. The kinetics of inhibition reflects allosteric interactions of arotinoids with D. discoideum RNase P. Moreover, our findings indicate that the inhibitory effects of arotinoids on tRNA biogenesis can be mediated through mechanisms not involving the retinoid nuclear receptors.
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Affiliation(s)
- E Papadimou
- Department of Biochemistry, School of Medicine, University of Patras, Greece
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78
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Papadimou E, Monastirli A, Tsambaos D, Drainas D. Additive inhibitory effect of calcipotriol and anthralin on ribonuclease P activity. Biochem Pharmacol 2000; 60:91-4. [PMID: 10807949 DOI: 10.1016/s0006-2952(00)00298-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The effects of two antipsoriatic compounds, calcipotriol and anthralin, separately or in combination on ribonuclease P (RNase P), were investigated using a cell-free system from the slime mold Dictyostelium discoideum. RNase P is an ubiquitous and essential enzyme which endonucleolytically cleaves all tRNA precursors to produce the mature 5' end. The substrate for RNase P assays was an in vitro (32)P-labeled transcript of the Schizosaccharomyces pombe tRNA(Ser) gene supS1. Enzyme assays were carried out at 37 degrees in 20 microL 50 mM Tris-HCL 7.6 buffer, containing 10 mM NH(4)Cl, 5 mM MgCl(2), and 10% isopropanol. Calcipotriol or anthralin alone exerted a dose-dependent inhibitory effect on RNase P activity, with the former being more active than the latter in this respect. Simultaneous exposure of the enzyme to both drugs resulted in an enhancement of RNase P inhibition, which was additive. Considering the lack of structural similarities between the substrate (precursor tRNA) of RNase P and the tested drugs, it seems reasonable to suggest that their effects may be due to binding to allosteric inhibition sites of the enzyme. Although our in vitro findings cannot be directly extrapolated to the in vivo human condition, they do suggest that the inhibitory effects of calcipotriol and anthralin on tRNA biogenesis may be implicated in the mechanisms of their antipsoriatic action. Moreover, the additive inhibitory effect of these compounds on RNase P activity provides an experimental basis for their possible combined therapeutic application in the management of psoriasis.
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Affiliation(s)
- E Papadimou
- Department of Biochemistry, School of Medicine, University of Patras, G26500, Patras, Greece
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79
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Shadel GS, Buckenmeyer GA, Clayton DA, Schmitt ME. Mutational analysis of the RNA component of Saccharomyces cerevisiae RNase MRP reveals distinct nuclear phenotypes. Gene 2000; 245:175-84. [PMID: 10713458 DOI: 10.1016/s0378-1119(00)00013-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The 340-nucleotide RNA component of Saccharomyces cerevisiae RNase MRP is encoded by the single-copy essential gene, NME1. To gain additional insight into the proposed structure and functions of this endoribonuclease, we have extensively mutagenized the NME1 gene and characterized yeast strains expressing mutated forms of the RNA using a gene shuffle technique. Strains expressing each of 26 independent mutations in the RNase MRP RNA gene were characterized for their ability to grow at various temperatures and on various carbon sources, stability of the RNase MRP RNA and processing of the 5.8S rRNA (a nuclear function of RNase MRP). 11 of the mutations resulted in a lethal phenotype, six displayed temperature-conditional lethality, and several preferred a non-fermentable carbon source for growth. In those mutants that exhibited altered growth phenotypes, the severity of the growth defect was directly proportional to the severity of the 5.8S rRNA processing defect in the nucleus. Together this analysis has defined essential regions of the RNase MRP RNA and provides evidence that is consistent with the proposed function of the RNase MRP enzyme.
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Affiliation(s)
- G S Shadel
- Department of Biochemistry, Emory University School of Medicine, Rollins Research Center, 1510 Clifton Road, Atlanta, GA, USA
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80
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Jarrous N, Wolenski JS, Wesolowski D, Lee C, Altman S. Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P. J Cell Biol 1999; 146:559-72. [PMID: 10444065 PMCID: PMC2150555 DOI: 10.1083/jcb.146.3.559] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/1999] [Accepted: 07/01/1999] [Indexed: 01/24/2023] Open
Abstract
The precise location of the tRNA processing ribonucleoprotein ribonuclease P (RNase P) and the mechanism of its intranuclear distribution have not been completely delineated. We show that three protein subunits of human RNase P (Rpp), Rpp14, Rpp29 and Rpp38, are found in the nucleolus and that each can localize a reporter protein to nucleoli of cells in tissue culture. In contrast to Rpp38, which is uniformly distributed in nucleoli, Rpp14 and Rpp29 are confined to the dense fibrillar component. Rpp29 and Rpp38 possess functional, yet distinct domains required for subnucleolar localization. The subunit Rpp14 lacks such a domain and appears to be dependent on a piggyback process to reach the nucleolus. Biochemical analysis suggests that catalytically active RNase P exists in the nucleolus. We also provide evidence that Rpp29 and Rpp38 reside in coiled bodies, organelles that are implicated in the biogenesis of several other small nuclear ribonucleoproteins required for processing of precursor mRNA. Because some protein subunits of RNase P are shared by the ribosomal RNA processing ribonucleoprotein RNase MRP, these two evolutionary related holoenzymes may share common intranuclear localization and assembly pathways to coordinate the processing of tRNA and rRNA precursors.
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Affiliation(s)
- Nayef Jarrous
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Joseph S. Wolenski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Donna Wesolowski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Christopher Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520
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81
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Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW. RNase P RNAs from some Archaea are catalytically active. Proc Natl Acad Sci U S A 1999; 96:7803-8. [PMID: 10393902 PMCID: PMC22142 DOI: 10.1073/pnas.96.14.7803] [Citation(s) in RCA: 177] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.
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Affiliation(s)
- J A Pannucci
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
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82
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Pluk H, van Eenennaam H, Rutjes SA, Pruijn GJ, van Venrooij WJ. RNA-protein interactions in the human RNase MRP ribonucleoprotein complex. RNA (NEW YORK, N.Y.) 1999; 5:512-524. [PMID: 10199568 PMCID: PMC1369778 DOI: 10.1017/s1355838299982079] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The eukaryotic nucleolus contains a large number of small RNA molecules that, in the form of small nucleolar ribonucleoprotein complexes (snoRNPs), are involved in the processing and modification of pre-rRNA. One of the snoRNPs that has been shown to possess enzymatic activity is the RNase MRP. RNase MRP is an endoribonuclease involved in the formation of the 5' end of 5.8S rRNA. In this study the association of the hPop1 protein with the RNase MRP complex was investigated. The hPop1 protein seems not to be directly bound to the RNA component, but requires nt 1-86 and 116-176 of the MRP RNA to associate with the RNase MRP complex via protein-protein interactions. UV crosslinking followed by ribonuclease treatment and immunoprecipitation with anti-Th/To antibodies revealed three human proteins of about 20, 25, and 40 kDa that can associate with the RNase MRP complex. The 20- and 25-kDa proteins appear to bind to stem-loop I of the MRP RNA whereas the 40-kDa protein requires the central part of the MRP RNA (nt 86-176) for association with the RNase MRP complex. In addition, we show that the human RNase P proteins Rpp30 and Rpp38 are also associated with the RNase MRP complex. Expression of Vesicular Stomatitis Virus- (VSV) tagged versions of these proteins in HeLa cells followed by anti-VSV immunoprecipitation resulted in coprecipitation of both RNase P and RNase MRP complexes. Furthermore, UV crosslinking followed by anti-Th/To and anti-Rpp38 immunoprecipitation revealed that the 40-kDa protein we detected in UV crosslinking is probably identical to Rpp38.
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Affiliation(s)
- H Pluk
- Department of Biochemistry, University of Nijmegen, The Netherlands
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83
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Jarrous N, Eder PS, Wesolowski D, Altman S. Rpp14 and Rpp29, two protein subunits of human ribonuclease P. RNA (NEW YORK, N.Y.) 1999; 5:153-157. [PMID: 10024167 PMCID: PMC1369747 DOI: 10.1017/s135583829800185x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In HeLa cells, the tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. Five of these proteins (hPop1p, Rpp20, Rpp30, Rpp38, and Rpp40) have been partially characterized. Here we report on the cDNA cloning and immunobiochemical analysis of Rpp14 and Rpp29. Polyclonal rabbit antibodies raised against recombinant Rpp14 and Rpp29 recognize their corresponding antigens in HeLa cells and precipitate catalytically active RNase P. Rpp29 shows 23% identity with Pop4p, a subunit of yeast nuclear RNase P and the ribosomal RNA processing enzyme RNase MRP. Rpp14, by contrast, exhibits no significant homology to any known yeast gene. Thus, human RNase P differs in the details of its protein composition, and perhaps in the functions of some of these proteins, from the yeast enzyme.
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Affiliation(s)
- N Jarrous
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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84
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Abstract
Ribonuclease P (RNase P) is the endoribonuclease that generates the mature 5'-ends of tRNA by removal of the 5'-leader elements of precursor-tRNAs. This enzyme has been characterized from representatives of all three domains of life (Archaea, Bacteria, and Eucarya) (1) as well as from mitochondria and chloroplasts. The cellular and mitochondrial RNase Ps are ribonucleoproteins, whereas the most extensively studied chloroplast RNase P (from spinach) is composed solely of protein. Remarkably, the RNA subunit of bacterial RNase P is catalytically active in vitro in the absence of the protein subunit (2). Although RNA-only activity has not been demonstrated for the archael, eucaryal, or mitochondrial RNAs, comparative sequence analysis has established that these RNAs are homologous (of common ancestry) to bacterial RNA. RNase P holoenzymes vary greatly in organizational complexity across the phylogenetic domains, primarily because of differences in the RNase P protein subunits: Mitochondrial, archaeal, and eucaryal holoenzymes contain larger, and perhaps more numerous, protein subunits than do the bacterial holoenzymes. However, that the nonbacterial RNase P RNAs retain significant structural similarity to their catalytically active bacterial counterparts indicates that the RNA remains the catalytic center of the enzyme.
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Affiliation(s)
- D N Frank
- Department of Plant and Microbial Biology, University of California, Berkeley 94720-3102, USA.
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85
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Plehn-Dujowich D, Altman S. Effective inhibition of influenza virus production in cultured cells by external guide sequences and ribonuclease P. Proc Natl Acad Sci U S A 1998; 95:7327-32. [PMID: 9636148 PMCID: PMC22606 DOI: 10.1073/pnas.95.13.7327] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/1998] [Indexed: 02/07/2023] Open
Abstract
The polymerase (PB2) and nucleocapsid (NP) genes encoded by the genome of influenza virus are essential for replication of the virus. When synthetic genes that express RNAs for external guide sequences targeted to the mRNAs of the PB2 and NP genes are stably incorporated into mouse cells in tissue culture, infection of these cells with influenza virus is nonproductive. Endogenous RNase P cleaves the targeted influenza virus mRNAs when they are in a complex with the external guide sequences. Targeting two different mRNAs simultaneously inhibits viral particle production more efficiently than does targeting only one mRNA.
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Affiliation(s)
- D Plehn-Dujowich
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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86
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Stolc V, Katz A, Altman S. Rpp2, an essential protein subunit of nuclear RNase P, is required for processing of precursor tRNAs and 35S precursor rRNA in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 1998; 95:6716-21. [PMID: 9618478 PMCID: PMC22609 DOI: 10.1073/pnas.95.12.6716] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/1998] [Indexed: 02/07/2023] Open
Abstract
RPP2, an essential gene that encodes a 15.8-kDa protein subunit of nuclear RNase P, has been identified in the genome of Saccharomyces cerevisiae. Rpp2 was detected by sequence similarity with a human protein, Rpp20, which copurifies with human RNase P. Epitope-tagged Rpp2 can be found in association with both RNase P and RNase mitochondrial RNA processing in immunoprecipitates from crude extracts of cells. Depletion of Rpp2 protein in vivo causes accumulation of precursor tRNAs with unprocessed introns and 5' and 3' termini, and leads to defects in the processing of the 35S precursor rRNA. Rpp2-depleted cells are defective in processing of the 5.8S rRNA. Rpp2 immunoprecipitates cleave both yeast precursor tRNAs and precursor rRNAs accurately at the expected sites and contain the Rpp1 protein orthologue of the human scleroderma autoimmune antigen, Rpp30. These results demonstrate that Rpp2 is a protein subunit of nuclear RNase P that is functionally conserved in eukaryotes from yeast to humans.
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Affiliation(s)
- V Stolc
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
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87
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Chamberlain JR, Lee Y, Lane WS, Engelke DR. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev 1998; 12:1678-90. [PMID: 9620854 PMCID: PMC316871 DOI: 10.1101/gad.12.11.1678] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/1998] [Accepted: 04/03/1998] [Indexed: 02/07/2023]
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein enzyme that cleaves precursor tRNA transcripts to give mature 5' ends. RNase P in eubacteria has a large, catalytic RNA subunit and a small protein subunit that are required for precursor tRNA cleavage in vivo. Although the eukaryotic holoenzymes have similar, large RNA subunits, previous work in a number of systems has suggested that the eukaryotic enzymes require a greater protein content. We have purified the Saccharomyces cerevisiae nuclear RNase P to apparent homogeneity, allowing the first comprehensive analysis of an unexpectedly complex subunit composition. Peptide sequencing by ion trap mass spectrometry identifies nine proteins that copurify with the nuclear RNase P RNA subunit, totaling 20-fold more protein than in the bacterial enzyme. All of these proteins are encoded by genes essential for RNase P activity and for cell viability. Previous genetic studies suggested that four proteins might be subunits of both RNase P and RNase MRP, the related rRNA processing enzyme. We demonstrate that all four of these proteins, Pop1p, Pop3p, Pop4p, and Rpp1p, are integral subunits of RNase P. In addition, four of the five newly identified protein subunits, Pop5p, Pop6p, Pop7p, and Pop8p, also appear to be shared between RNase P and RNase MRP. Only one polypeptide, Rpr2p, is unique to the RNase P holoenzyme by genetic depletion and immunoprecipitation studies. The large increase in the number of protein subunits over eubacterial RNase P is consistent with an increase in functional complexity in eukaryotes. The degree of structural similarity between nuclear RNase P and RNase MRP suggests that some aspects of their functions in pre-tRNA and pre-rRNA processing pathways might overlap or be coordinated.
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Affiliation(s)
- J R Chamberlain
- Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606 USA
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88
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Jarrous N, Eder PS, Guerrier-Takada C, Hoog C, Altman S. Autoantigenic properties of some protein subunits of catalytically active complexes of human ribonuclease P. RNA (NEW YORK, N.Y.) 1998; 4:407-417. [PMID: 9630247 PMCID: PMC1369627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
At least six proteins co-purify with human ribonuclease P (RNase P), a tRNA processing ribonucleoprotein. Two of these proteins, Rpp30 and Rpp38, are Th autoantigens. Recombinant Rpp30 and Rpp38 are also recognized by Th sera from systemic sclerosis patients. Two of the other proteins associated with RNase P, Rpp20 and Rpp40, do not cross-react with Th sera. Polyclonal antibodies raised against all four recombinant proteins recognize the corresponding proteins associated with RNase P and precipitate active holoenzyme. Catalytically active RNase P holoenzyme can be separated from the nucleolar and mitochondrial RNA processing endoribonuclease, RNase MRP, even though these two enzymes may share some subunits.
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Affiliation(s)
- N Jarrous
- Department of Biology, Yale University, New Haven, Connecticut 06520, USA
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89
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True HL, Celander DW. Protein components contribute to active site architecture for eukaryotic ribonuclease P. J Biol Chem 1998; 273:7193-6. [PMID: 9516409 DOI: 10.1074/jbc.273.13.7193] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, ribonuclease P (RNase P) requires both RNA and protein components for catalytic activity. The eukaryotic RNase P RNA, unlike its bacterial counterparts, does not possess intrinsic catalytic activity in the absence of holoenzyme protein components. We have used a sensitive photoreactive cross-linking assay to explore the substrate-binding environment for different eukaryotic RNase P holoenzymes. Protein components from the Tetrahymena thermophila and human RNase P holoenzymes form specific products in photoreactions containing [4-thio]-uridine-labeled pre-tRNAGln. The HeLa RNase P RNA in neither the presence nor the absence of holoenzyme protein components formed cross-link products to the pre-tRNAGln probe. Parallel photo-cross-linking experiments with the Escherichia coli RNase P holoenzyme revealed that only the bacterial RNase P RNA forms specific substrate photoadducts. A protein-rich active site for the eukaryotic RNase P represents one unique feature that distinguishes holoenzyme organization between bacteria and eukaryotes.
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Affiliation(s)
- H L True
- Department of Microbiology, University of Illinois at Urbana-Champaign, Chemical and Life Sciences Laboratory, Urbana, Illinois 61801, USA
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90
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Stolc V, Altman S. Rpp1, an essential protein subunit of nuclear RNase P required for processing of precursor tRNA and 35S precursor rRNA in Saccharomyces cerevisiae. Genes Dev 1997; 11:2926-37. [PMID: 9353260 PMCID: PMC316654 DOI: 10.1101/gad.11.21.2926] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/1997] [Accepted: 07/25/1997] [Indexed: 02/05/2023]
Abstract
The gene for an essential protein subunit of nuclear RNase P from Saccharomyces cerevisiae has been cloned. The gene for this protein, RPP1, was identified by virtue of its homology with a human scleroderma autoimmune antigen, Rpp30, which copurifies with human RNase P. Epitope-tagged Rpp1 can be found in association with both RNase P RNA and a related endoribonuclease, RNase MRP RNA, in immunoprecipitates from crude extracts of cells. Depletion of Rpp1 in vivo leads to the accumulation of precursor tRNAs with unprocessed 5' and 3' termini and reveals rRNA processing defects that have not been described previously for proteins associated with RNase P or RNase MRP. Immunoprecipitated complexes cleave both yeast precursor tRNAs and precursor rRNAs.
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Affiliation(s)
- V Stolc
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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91
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Stolc V, Altman S. Rpp1, an essential protein subunit of nuclear RNase P required for processing of precursor tRNA and 35S precursor rRNA in Saccharomyces cerevisiae. Genes Dev 1997; 11:2414-25. [PMID: 9308968 PMCID: PMC316520 DOI: 10.1101/gad.11.18.2414] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/1997] [Accepted: 07/25/1997] [Indexed: 02/05/2023]
Abstract
The gene for an essential protein subunit of nuclear RNase P from Saccharomyces cerevisiae has been cloned. The gene for this protein, RPP1, was identified by virtue of its homology with a human scleroderma autoimmune antigen, Rpp30, which copurifies with human RNase P. Epitope-tagged Rpp1 can be found in association with both RNase P RNA and a related endoribonuclease, RNase MRP RNA, in immunoprecipitates from crude extracts of cells. Depletion of Rpp1 in vivo leads to the accumulation of precursor tRNAs with unprocessed 5' and 3' termini and reveals rRNA processing defects that have not been described previously for proteins associated with RNase P or RNase MRP. Immunoprecipitated complexes cleave both yeast precursor tRNAs and precursor rRNAs.
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Affiliation(s)
- V Stolc
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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92
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Jacobson MR, Cao LG, Taneja K, Singer RH, Wang YL, Pederson T. Nuclear domains of the RNA subunit of RNase P. J Cell Sci 1997; 110 ( Pt 7):829-37. [PMID: 9133670 DOI: 10.1242/jcs.110.7.829] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The ribonucleoprotein enzyme RNase P catalyzes the 5′ processing of pre-transfer RNA, and has also recently been implicated in pre-ribosomal RNA processing. In the present investigation, in situ hybridization revealed that RNase P RNA is present throughout the nucleus of mammalian cells. However, rhodamine-labeled human RNase P RNA microinjected into the nucleus of rat kidney (NRK) epithelial cells or human (HeLa) cells initially localized in nucleoli, and subsequently became more evenly distributed throughout the nucleus, similar to the steadystate distribution of endogenous RNase P RNA. Parallel microinjection and immunocytochemical experiments revealed that initially nucleus-microinjected RNase P RNA localized specifically in the dense fibrillar component of the nucleolus, the site of pre-rRNA processing. A mutant RNase P RNA lacking the To antigen binding domain (nucleotides 25–75) did not localize in nucleoli after nuclear microinjection. In contrast, a truncated RNase P RNA containing the To binding domain but lacking nucleotides 89–341 became rapidly localized in nucleoli following nuclear microinjection. However, unlike the full-length RNase P RNA, this 3′ truncated RNA remained stably associated with the nucleoli and did not translocate to the nucleoplasm. These results suggest a nucleolar phase in the maturation, ribonucleoprotein assembly or function of RNase P RNA, mediated at least in part by the nucleolar To antigen. These and other recent findings raise the intriguing possibility of a bifunctional role of RNase P in the nucleus: catalyzing pre-ribosomal RNA processing in the nucleolus and pre-transfer RNA processing in the nucleoplasm.
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Affiliation(s)
- M R Jacobson
- Cell Biology Group, Worcester Foundation for Biomedical Research, Shrewsbury, MA 01545, USA
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