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Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing. Genes Dev 2017; 31:59-71. [PMID: 28115465 PMCID: PMC5287113 DOI: 10.1101/gad.286963.116] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/20/2016] [Indexed: 12/03/2022]
Abstract
In this study, Goldfarb et al. used CRISPR–Cas9 genome editing to eliminate MRP RNA—a ribonucleoprotein complex with an RNA subunit that is conserved across eukarya—in the majority of cells. Analysis by RNA FISH, Northerns, and RNA sequencing demonstrates an accumulation of ribosomal RNA precursor and thus establishes a role for RNase MRP in human pre-rRNA processing. MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR–Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor—analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing—implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation.
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McClain WH, Lai LB, Gopalan V. Trials, travails and triumphs: an account of RNA catalysis in RNase P. J Mol Biol 2010; 397:627-46. [PMID: 20100492 DOI: 10.1016/j.jmb.2010.01.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 01/12/2010] [Accepted: 01/19/2010] [Indexed: 12/16/2022]
Abstract
Last December marked the 20th anniversary of the Nobel Prize in Chemistry to Sidney Altman and Thomas Cech for their discovery of RNA catalysts in bacterial ribonuclease P (an enzyme catalyzing 5' maturation of tRNAs) and a self-splicing rRNA of Tetrahymena, respectively. Coinciding with the publication of a treatise on RNase P, this review provides a historical narrative, a brief report on our current knowledge, and a discussion of some research prospects on RNase P.
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Affiliation(s)
- William H McClain
- Department of Bacteriology, College of Agriculture & Life Sciences, University of Wisconsin, Madison, WI 53706, USA.
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Uzan M. RNA processing and decay in bacteriophage T4. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:43-89. [PMID: 19215770 DOI: 10.1016/s0079-6603(08)00802-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteriophage T4 is the archetype of virulent phage. It has evolved very efficient strategies to subvert host functions to its benefit and to impose the expression of its genome. T4 utilizes a combination of host and phage-encoded RNases and factors to degrade its mRNAs in a stage-dependent manner. The host endonuclease RNase E is used throughout the phage development. The sequence-specific, T4-encoded RegB endoribonuclease functions in association with the ribosomal protein S1 to functionally inactivate early transcripts and expedite their degradation. T4 polynucleotide kinase plays a role in this process. Later, the viral factor Dmd protects middle and late mRNAs from degradation by the host RNase LS. T4 codes for a set of eight tRNAs and two small, stable RNA of unknown function that may contribute to phage virulence. Their maturation is assured by host enzymes, but one phage factor, Cef, is required for the biogenesis of some of them. The tRNA gene cluster also codes for a homing DNA endonuclease, SegB, responsible for spreading the tRNA genes to other T4-related phage.
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Affiliation(s)
- Marc Uzan
- Institut Jacques Monod, CNRS-Universites Paris, Paris, France
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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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Surratt CK, Carter BJ, Payne RC, Hecht SM. Metal ion and substrate structure dependence of the processing of tRNA precursors by RNase P and M1 RNA. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)45735-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Surratt CK, Lesnikowski Z, Schifman AL, Schmidt FJ, Hecht SM. Construction and processing of transfer RNA precursor models. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)45734-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Deutscher MP. Ribonucleases, tRNA nucleotidyltransferase, and the 3' processing of tRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1990; 39:209-40. [PMID: 2247609 DOI: 10.1016/s0079-6603(08)60628-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- M P Deutscher
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06032
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9
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Nichols L, Schmidt FJ. Dependence of M1 RNA substrate specificity on magnesium ion concentration. Nucleic Acids Res 1988; 16:2931-42. [PMID: 2453026 PMCID: PMC336442 DOI: 10.1093/nar/16.7.2931] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We have constructed a plasmid expressing E. coli M1 RNA, the catalytic RNA subunit of ribonuclease P, under the control of a phage T7 promoter. The active M1 RNA species synthesized in vitro by T7 RNA polymerase from this vector was reacted with the tRNA(Gln) - tRNA(Leu) precursor RNA (Band K) encoded by phage T4. Only the tRNA(Leu) moiety of this dimeric precursor RNA contains the 3' terminal C-C-A sequence common to all tRNAs. We observed that protein-free M1 RNA was capable of processing the precursor RNA at the 5' ends of both tRNA tRNA sequences. The rate of cleavage of the tRNA(Gln) sequence was more strongly dependent on [Mg2+] than that of tRNA(Leu), increasing severalfold between 100 and 500 mM Mg2+, conditions under which the rate of cleavage at the tRNA(Leu) sequence was constant.
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Affiliation(s)
- L Nichols
- Department of Biochemistry, University of Missouri-Columbia 65212
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Abstract
The cloverleaf stem segments of the suppressor gene of bacteriophage T4 tRNA(Gln) contain ten G.C and ten A.U base-pairs. To gain a better appreciation of the G.C base-pair requirement, we isolated multiple mutants of this suppressor gene in which base-pairs of G.C were replaced by A.U. One active suppressor gene contained only A.U base-pairs on the anticodon stem, indicating that G.C base-pairs in this region of tRNA(Gln) are not essential for function. In contrast, replacement was not possible at two base-pairs on the D stem and at one base-pair on the T stem.
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Affiliation(s)
- W H McClain
- Department of Bacteriology, University of Wisconsin, Madison 53706
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Broida J, Abelson J. Sequence organization and control of transcription in the bacteriophage T4 tRNA region. J Mol Biol 1985; 185:545-63. [PMID: 4057254 DOI: 10.1016/0022-2836(85)90071-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacteriophage T4 contains genes for eight transfer RNAs and two stable RNAs of unknown function. These are found in two clusters at 70 X 10(3) base-pairs on the T4 genetic map. To understand the control of transcription in this region we have completed the sequencing of 5000 base-pairs in this region. The sequence contains a part of gene 3, gene 1, gene 57, internal protein I, the tRNA genes and five open reading frames which most likely code for heretofore unidentified proteins. We have used subclones of the region to investigate the kinetics of transcription in vivo. The results show that transcription in this region consists of overlapping early, middle and late transcripts. Transcription is directed from two early promoters, one or two middle promoters and perhaps two late promoters. This region contains all of the features that are seen in T4 transcription and as such is a good place to study the phenomenon in more detail.
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Engelke DR, Gegenheimer P, Abelson J. Nucleolytic processing of a tRNAArg-tRNAAsp dimeric precursor by a homologous component from Saccharomyces cerevisiae. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(20)71239-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Subbarao MN, Makam H, Apirion D. A site in a tRNA precursor that can be processed by the whole RNase P enzyme but not by the RNA alone. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42600-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Guerrier-Takada C, McClain WH, Altman S. Cleavage of tRNA precursors by the RNA subunit of E. coli ribonuclease P (M1 RNA) is influenced by 3'-proximal CCA in the substrates. Cell 1984; 38:219-24. [PMID: 6380759 DOI: 10.1016/0092-8674(84)90543-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
tRNA precursor molecules that contain the CCA sequence found at the 3' termini of all mature tRNAs are cleaved in vitro more readily by M1 RNA, the catalytic subunit of E. coli RNAase P, than precursors that lack this sequence. The sensitivity to the CCA sequence is not apparent when precursors are cleaved by the reconstituted RNAase P holoenzyme that contains both M1 RNA and the protein subunit. These results have been obtained with monomeric precursor molecules encoded by the E. coli and human chromosomes and with three dimeric precursor molecules encoded by the bacteriophage T4 genome. The data are in agreement with previous results concerning T4 tRNA biosynthesis in vivo and show that the CCA sequence is important for the processing of precursors to tRNAs.
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Abstract
We describe the isolation and characterization of two unusual amber suppressor forms of T4 tRNALeu. The sequences of the suppressor tRNAs can be described as hybrids of wild-type tRNALeu and suppressor tRNAGln molecules: the chain lengths and majority of the nucleotide residues corresponded to tRNALeu, but CUA anticodons flanked by 2-14 residues were identical to tRNAGln. The uncertainty as to the exact number of flanking residues correlated with tRNAGln is due to the similarity of the two tRNA sequences in this region. No evidence was found for changes in other T4 tRNAs. We propose that genes for the hybrid tRNAs were produced by mispairing of DNAs at anticodon segments of tRNALeu and tRNAGln with a double crossover flanking those segments.
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Abstract
We found that a precursor of an RNA molecule from T4-infected Escherichia coli cells (p2Spl; precursor of species 1) has the capacity to cleave itself in a specific position. This cleavage is similar to a cleavage carried out by the aid of a protein, RNase F, that has been previously identified. This cleavage could lead to the maturation of an RNA (species 1) found in T4-infected E. coli cells. The reaction is time and temperature-dependent and is relatively slow as compared to the protein-dependent reaction. It requires at least a monovalent cation and is aided by non-ionic detergents. In the absence of detergent the cleavage can occur but at a reduced rate. The substrate does not contain hidden nicks and a variety of experiments suggest that it does not contain a protein. Moreover, we found no indication that the cleavage is due to contaminating nucleases in the substrate or in the reagents. The intact secondary and tertiary structures of the molecule are necessary for the cleavage to occur. The finding of a self cleaving RNA molecule has interesting evolutionary implications.
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Dallmann G, Quinn T, Apirion D. A gene affecting accumulation of the RNA moiety of the processing enzyme RNase P. J Bacteriol 1983; 156:529-36. [PMID: 6195144 PMCID: PMC217864 DOI: 10.1128/jb.156.2.529-536.1983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The level of 10Sb (M1) RNA, the RNA of RNase P, is very low in growing cultures of rnpB mutants. Northern transfer experiments suggested that these strains accumulate no more than 10% of the wild-type level of 10Sb RNA. However, there is no indication that there is a limiting amount of RNase P activity in these mutants in vivo. A plasmid that directs the synthesis of 10Sb RNA does not complement the rnpB mutants, even though there is only a single gene for 10Sb RNA in the Escherichia coli genome. The 10Sb RNA synthesized from this plasmid is equivalent to wild-type 10Sb RNA since it can replace it in the reconstitution of RNase P. The 10Sb RNA, which is a rather stable molecule, is unstable in the presence of the rnpB mutation. This could explain why rnpB mutants do not accumulate 10Sb RNA. An F' plasmid that contains DNA from the rnpB region of the chromosome complements an rnpB mutant in vivo and in vitro, and it also contains the 10Sb RNA gene. A number of possible explanations for these phenomena are discussed.
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Szeberényi J, Roy MK, Apirion D. 7 S RNA: a single site substrate for the RNA processing enzyme ribonuclease E of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1983; 740:282-90. [PMID: 6347257 DOI: 10.1016/0167-4781(83)90137-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
7 S RNA accumulates at non-permissive temperatures in an RNAase E strain containing the recombinant plasmid pJR3 delta which carries a single 5 S rRNA gene and expression sequences. 7 S RNA is a processing intermediate that contains the complete sequence of 5 S rRNA as well as a stem-and-loop structure encoded by the terminator of rrnD. 7 S RNA can be processed in vitro by RNAase E. Structural analysis of the products (5 S rRNA and the stem) of in vitro processing of 7 S RNA revealed that the cleavage site of RNAase E in 7 S RNA is 3 nucleotides downstream from the 3' end of the mature 5 S rRNA. The cleavage generates 3'-hydroxyl and 5'-phosphate termini.
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Miczak A, Ford J, Marian M, Apirion D. RNA processing: new mutants that affect endonucleolytic processing of RNA. Biochem Biophys Res Commun 1983; 114:690-8. [PMID: 6192822 DOI: 10.1016/0006-291x(83)90836-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A strain of Escherichia coli carrying the rne-3071 mutation that affects the RNA processing enzyme ribonuclease E, was mutagenized, and double mutants deficient in RNA processing were isolated. The isolation was based on the appearance of a particular RNA precursor molecule upon infection of an rne mutant with a specific bacteriophage T4 deletion strain. From one of the double mutants the rne mutation was removed, and the new single mutant, designated rng, was examined. In this mutant the maturation of host RNA as well as of bacteriophage T4 RNA is affected. The effect of the rng mutation on RNA synthesis is unique and can be distinguished from the effects of the other established mutations in RNA processing. The effects of the rng mutation can be recognized in vivo and in vitro.
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Gurevitz M, Jain SK, Apirion D. Identification of a precursor molecular for the RNA moiety of the processing enzyme RNase P. Proc Natl Acad Sci U S A 1983; 80:4450-4. [PMID: 6192433 PMCID: PMC384056 DOI: 10.1073/pnas.80.14.4450] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A precursor molecule for 10Sb (M1) RNA, the RNA moiety of the RNA processing enzyme ribonuclease P (EC 3.1.26.5), is accumulated transiently in an Escherichia coli strain containing a plasmid that carries the 10Sb RNA gene. The same RNA precursor molecule is accumulated, in relatively large quantities, in a temperature-sensitive RNase E- mutant at the nonpermissive temperature. The RNA precursor includes 10Sb RNA and an extra 3' fragment that contains a termination stem and loop. It can be processed in vitro to a molecule the size of 10Sb RNA. None of the four endoribonucleases of E. coli--RNase III, RNase E, RNase F, or RNase P--takes part in this cleavage reaction. Therefore, we suggest that the processing of the precursor-10Sb RNA to 10Sb RNA is carried out by a thus-far unidentified endoribonuclease. The accumulation of a RNA molecule in a RNase E- mutant that does not contain a cleavage site for RNase E has been encountered previously and can be explained by assuming the existence of a RNA processing complex in the E. coli cell.
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Apirion D. RNA processing in a unicellular microorganism: implications for eukaryotic cells. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 30:1-40. [PMID: 6364230 DOI: 10.1016/s0079-6603(08)60682-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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22
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Jain SK, Gurevitz M, Apirion D. A small RNA that complements mutants in the RNA processing enzyme ribonuclease P. J Mol Biol 1982; 162:515-33. [PMID: 6187924 DOI: 10.1016/0022-2836(82)90386-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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23
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Jain SK, Pragai B, Apirion D. A possible complex containing RNA processing enzymes. Biochem Biophys Res Commun 1982; 106:768-78. [PMID: 6180743 DOI: 10.1016/0006-291x(82)91777-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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24
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Pragai B, Apirion D. Processing of bacteriophage T4 transfer RNAs. Structural analysis and in vitro processing of precursors that accumulate in RNase E-strains. J Mol Biol 1982; 154:465-84. [PMID: 7042984 DOI: 10.1016/s0022-2836(82)80007-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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26
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de Wachter R. The number of repeats expected in random nucleic acid sequences and found in genes. J Theor Biol 1981; 91:71-98. [PMID: 7029145 DOI: 10.1016/0022-5193(81)90375-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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27
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Kline L, Nishikawa S, Söll D. Partial purification of RNase P from Schizosaccharomyces pombe. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69366-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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28
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Goldfarb A, Daniel V. Mapping of transcription units in the bacteriophage T4 tRNA gene cluster. J Mol Biol 1981; 146:393-412. [PMID: 7024554 DOI: 10.1016/0022-2836(81)90039-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Martin NC, Miller D, Hartley J, Moynihan P, Donelson JE. The tRNAAGYSer and tRNACGYArg genes from a gene cluster in yeast mitochondrial DNA. Cell 1980; 19:339-43. [PMID: 6244104 DOI: 10.1016/0092-8674(80)90508-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Yeast mitochondrial DNA-pBR322 recombinant DNA molecules screened for rRNA genes were used as a source of DNA for mitochondrial tRNA gene sequence analysis. We report here the sequences of yeast mitochondrial tRNA genes coding for a tRNAAGYSer and a tRNACGYArg. The tRNAAGYSer sequence deduced from the gene is the first reported sequence of a yeast tRNAAGYSer. It is also the second yeast mitochondrial tRNASer gene to be sequenced, and demonstrates unequivocally the presence of mitochondrial encoded serine tRNA isoacceptors. The tRNACGYArg sequence deduced from the gene is the most AT-rich (82%) tRNA sequence ever reported. Whereas all the mitochondrial genes sequenced to date exist singly on the genome and are separated by long stretches of AT-rich DNA, the tRNAACYSer and tRNAcgyarg genes exist in tandem, separated by only 3 bp. This gene arrangement strongly suggests that mitochondrial tRNA genes may be transcribed into multicistronic precursors.
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35
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36
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Hagenbüchle O, Larson D, Hall GI, Sprague KU. The primary transcription product of a silkworm alanine tRNA gene: identification of in vitro sites of initiation, termination and processing. Cell 1979; 18:1217-29. [PMID: 519766 DOI: 10.1016/0092-8674(79)90234-4] [Citation(s) in RCA: 112] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A 13.5 Kb fragment of Bombyx mori DNA containing a single tRNA2Ala gene has been cloned, and transcribed in vitro with Xenopus germinal vesicle extracts. The primary transcription product of the tRNA2Ala gene has been isolated and shown to possess an unprocessed triphosphorylated 5' terminus. Products resulting from processing of this transcript have also been isolated and characterized. Complete nucleotide sequence analysis of this cloned alanine tRNA gene and its primary transcript shows that transcription initiates three nucleotides away from the mature tRNA2Ala 5' end and terminates in a U cluster 22 nucleotides beyond the last encoded 3' nucleotide of the mature species. Sequence determination of the products of in vitro maturation shows that in contrast to the tRNA processing mechanism characteristic of procaryotes, the extra 3'-nucleotides in this silkworm tRNA precursor are removed by a single endonucleolytic cleavage.
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37
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Young RA, Macklis R, Steitz JA. Sequence of the 16 S-23 s spacer region in two ribosomal RNA operons of Escherichia coli. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50754-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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38
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Kaplan DA, Nierlich DP. Isolation of the transfer RNA genes of bacteriophage T4 and transfer RNA synthesis in vitro. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 561:184-93. [PMID: 420849 DOI: 10.1016/0005-2787(79)90501-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Non-glucosylated T4 DNA was restricted with the endonuclease EcoRI and the mixture of DNA fragments separated by gel electrophoresis and transcribed with purified Escherichia coli RNA polymerase. Three purified fragments were shown to act as templates for tRNA synthesis. A smaller fragment, shown to be hybridizable to 32P-labeled T4 tRNA was not transcribable. It was concluded that the promoter for T4 tRNA synthesis had been separated from the structural genes in the smaller fragment by EcoRI and that the distal portion of the tRNA gene cluster lacks internal promoters which display in vitro activity. Preparations of non-glucosylated T4 DNA were never fully restricted with EcoRI and when the larger purified fragments carrying the tRNA were restricted with excess enzyme only a slight cleavage to yield the smaller fragments was obtained. The property of the DNA-limiting complete restriction is not know.
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39
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Schmidt FJ, McClain WH. An Escherichia coli ribonuclease which removes an extra nucleotide from a biosynthetic intermediate of bacteriophage T4 proline transfer RNA. Nucleic Acids Res 1978; 5:4129-39. [PMID: 364422 PMCID: PMC342738 DOI: 10.1093/nar/5.11.4129] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The biosynthesis of bacteriophage T4 tRNAPro, tRNASer, and tRNAIle requires enzymatic removal of extra nucleotides from the 3' terminus of the respective precursor RNAs. A ribonuclease activity capable of catalyzing such reactions has been partially purified from uninfected Escherichia coli using an artificial precursor RNA as substrate. A number of ribonuclease activities were resolved during purification. Use of E. coli strain BN, a mutant known to be deficient in the relevant ribonuclease activity, permitted us to identify it in wild-type cells. This activity was designated the BN ribonuclease. BN ribonuclease had an apparent molecular weight of 35,000 as measured by Sephadex gel filtration. Mg2+ was required for activity, which was optimal at [Mg2+] of 2mM. Activity did not require monovalent cations K+ or Na+. BN ribonuclease was less efficient at removing extra residues in the biosynthesis of tRNASer and tRNAIle than in the biosynthesis of tRNAPro.
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40
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Sakano H, Shimura Y. Characterization and in vitro processing of transfer RNA precursors accumulated in a temperature-sensitive mutant of Escherichia coli. J Mol Biol 1978; 123:287-326. [PMID: 357735 DOI: 10.1016/0022-2836(78)90082-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Wasiak T, Gniazdowski M. Turnover of the 5'-end phosphate in yeast tRNA in vivo. FEBS Lett 1978; 89:260-2. [PMID: 350625 DOI: 10.1016/0014-5793(78)80231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Shimura Y, Sakano H, Nagawa F. Specific ribonucleases involved in processing of tRNA precursors of Escherichia coli. Partial purification and some properties. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 86:267-81. [PMID: 350582 DOI: 10.1111/j.1432-1033.1978.tb12308.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ribonucleases O and Q, the two putative nucleolytic activities which we detected previously in the crude extract from a thermosensitive ribonuclease P mutant (TS241) of Escherichia coli and which were shown to function in the processing of tRNA precursors in vitro, were partially purified from the 1000000 x g supernatant fraction of E. coli Q13. In the course of purification of these enzymes, the total RNAs synthesized in the thermosensitive mutant at the restrictive temperature were used as the substrates and the activities were identified from disappearance or alteration of specific tRNA precursor molecules in polyacrylamide gel electrophoresis. The purified ribonuclease O preparation cleaved specifically the multimeric tRNA precursors at the spacer regions. The purified ribonuclease Q preparation removed, in accordance with the definition of this enzyme, extra nucleotides from the 3'-terminal ends of monomeric tRNA precursors. Some properties of these two nucleases were investigated. In addition to these nucleases, another exonuclease (tentatively designated ribonuclease Y) and ribonuclease P, a well-characterized endonuclease, were also purified. The sequential mode of the processing of tRNA precursors, originally observed in the cleavage reactions with the crude extracts in vitro, was supported by studies with the purified enzyme preparations.
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McClain WH, Seidman JG, Schmidt FJ. Evolution of the biosynthesis of 3'-terminal C-C-A residues in T-even bacteriophage transfer RNAs. J Mol Biol 1978; 119:519-36. [PMID: 642000 DOI: 10.1016/0022-2836(78)90200-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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44
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Goddard JP. The structures and functions of transfer RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978. [DOI: 10.1016/0079-6107(78)90021-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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45
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Deutscher MP, Lin JJ, Evans JA. Transfer RNA metabolism in Escherichia coli cells deficient in tRNA nucleotidyltransferase. J Mol Biol 1977; 117:1081-94. [PMID: 342706 DOI: 10.1016/s0022-2836(77)80014-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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46
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Mazzara GP, McClain WH. Cysteine transfer RNA of Escherichia coli: nucleotide sequence and unusual metabolic properties of the 3' C-C-A terminus. J Mol Biol 1977; 117:1061-79. [PMID: 342705 DOI: 10.1016/s0022-2836(77)80013-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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47
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Mazzara G, Seidman J, McClain W, Yesian H, Abelson J, Guthrie C. Nucleotide sequence of an arginine transfer ribonucleic acid from bacteriophage T4. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40963-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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48
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Comer MM. Correlation between genetic and nucleotide distances in a bacteriophage T4 transfer, RNA gene. J Mol Biol 1977; 113:267-71. [PMID: 881737 DOI: 10.1016/0022-2836(77)90054-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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49
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Vögeli G, Stewart TS, McCutchan T, Söll D. Isolation of Escherichia coli precursor tRNAs containing modified nucleoside Q. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40556-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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50
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Kitamura N, Ikeda H, Yamada Y, Ishikura H. Processing by ribonuclease II of the tRNATyr precursor of Escherichia coli synthesized in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 73:297-306. [PMID: 320007 DOI: 10.1111/j.1432-1033.1977.tb11319.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The tRNATyr precursor molecule, synthesized from phi 80 psu3+ DNA (containing a single tRNA gene) by DNA-dependent RNA polymerase and q factor, was about 205 nucleotides long. The main product of its digestion with a ribonuclease tii preparation from Escherichia coli showed the same electrophoretic mobility as tRNAtyr precursor isolated in vivo and was found to be identical to it when analysed using fingerprint techniques. This intermediate precursor synthesized in vitro was converted further by processing with ribonuclease P into an RNA identical size to mature tRNATyr. It was concluded that the initiation of transcription of the tRNATyr gene in vitro occurs at the same site as that of transcription in vivo and a termination occurs at about 80 nucleotides beyond the CCA end of tRNATyr.
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