1
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Pinker F, Bonnard G, Gobert A, Gutmann B, Hammani K, Sauter C, Gegenheimer PA, Giegé P. PPR proteins shed a new light on RNase P biology. RNA Biol 2013; 10:1457-68. [PMID: 23925311 PMCID: PMC3858429 DOI: 10.4161/rna.25273] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A fast growing number of studies identify pentatricopeptide repeat (PPR) proteins as major players in gene expression processes. Among them, a subset of PPR proteins called PRORP possesses RNase P activity in several eukaryotes, both in nuclei and organelles. RNase P is the endonucleolytic activity that removes 5′ leader sequences from tRNA precursors and is thus essential for translation. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins, although some evidence implied that some eukaryotes or cellular compartments did not use RNA for RNase P activity. The characterization of PRORP reveals a two-domain enzyme, with an N-terminal domain containing multiple PPR motifs and assumed to achieve target specificity and a C-terminal domain holding catalytic activity. The nature of PRORP interactions with tRNAs suggests that ribonucleoprotein and protein-only RNase P enzymes share a similar substrate binding process.
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Affiliation(s)
- Franziska Pinker
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France; Institut de Biologie Moléculaire et Cellulaire du CNRS; Architecture et Réactivité de l'ARN; Université de Strasbourg; Strasbourg, France
| | - Géraldine Bonnard
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Anthony Gobert
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Bernard Gutmann
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Kamel Hammani
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
| | - Claude Sauter
- Institut de Biologie Moléculaire et Cellulaire du CNRS; Architecture et Réactivité de l'ARN; Université de Strasbourg; Strasbourg, France
| | | | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes du CNRS; Université de Strasbourg; Strasbourg, France
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2
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Schierling K, Rösch S, Rupprecht R, Schiffer S, Marchfelder A. tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii. J Mol Biol 2002; 316:895-902. [PMID: 11884130 DOI: 10.1006/jmbi.2001.5395] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' processing pathway. The archaeal RNase Z has a KCl optimum at 5mM, which is in contrast to the intracellular KCl concentration being as high as 4M KCl. The archaeal RNase Z does process 5' extended and intron-containing pretRNAs but with a much lower efficiency than 5' matured, intronless pretRNAs. At least in vitro there is thus no defined order for 5' and 3' processing and splicing. A heterologous precursor tRNA is cleaved efficiently by the archaeal RNase Z. Experiments with precursors containing mutated tRNAs revealed that removal of the anticodon arm reduces cleavage efficiency only slightly, while removal of D and T arm reduces processing effciency drastically, even down to complete inhibition. Comparison with its nuclear and mitochondrial homologs revealed that the substrate specificity of the archaeal RNase Z is narrower than that of the nuclear RNase Z but broader than that of the mitochondrial RNase Z.
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MESH Headings
- Anticodon/genetics
- Base Sequence
- Cell Nucleus/enzymology
- Endoribonucleases/isolation & purification
- Endoribonucleases/metabolism
- Eukaryotic Cells/enzymology
- Evolution, Molecular
- Haloferax volcanii/enzymology
- Haloferax volcanii/genetics
- Hydrogen-Ion Concentration
- Introns/genetics
- Mitochondria/enzymology
- Mutation/genetics
- Nucleic Acid Conformation
- Osmolar Concentration
- Potassium Chloride/pharmacology
- RNA 3' End Processing
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- RNA, Transfer, Tyr/metabolism
- Substrate Specificity
- Temperature
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3
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Schiffer S, Helm M, Théobald-Dietrich A, Giegé R, Marchfelder A. The plant tRNA 3' processing enzyme has a broad substrate spectrum. Biochemistry 2001; 40:8264-72. [PMID: 11444972 DOI: 10.1021/bi0101953] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To elucidate the minimal substrate for the plant nuclear tRNA 3' processing enzyme, we synthesized a set of tRNA variants, which were subsequently incubated with the nuclear tRNA 3' processing enzyme. Our experiments show that the minimal substrate for the nuclear RNase Z consists of the acceptor stem and T arm. The broad substrate spectrum of the nuclear RNase Z raises the possibility that this enzyme might have additional functions in the nucleus besides tRNA 3' processing. Incubation of tRNA variants with the plant mitochondrial enzyme revealed that the organellar counterpart of the nuclear enzyme has a much narrower substrate spectrum. The mitochondrial RNase Z only tolerates deletion of anticodon and variable arms and only with a drastic reduction in cleavage efficiency, indicating that the mitochondrial activity can only cleave bona fide tRNA substrates efficiently. Both enzymes prefer precursors containing short 3' trailers over extended 3' additional sequences. Determination of cleavage sites showed that the cleavage site is not shifted in any of the tRNA variant precursors.
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Affiliation(s)
- S Schiffer
- Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany
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4
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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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5
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Kunzmann A, Brennicke A, Marchfelder A. 5' end maturation and RNA editing have to precede tRNA 3' processing in plant mitochondria. Proc Natl Acad Sci U S A 1998; 95:108-13. [PMID: 9419337 PMCID: PMC18142 DOI: 10.1073/pnas.95.1.108] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report the characterization and partial purification of potato mitochondrial RNase Z, an endonuclease that generates mature tRNA 3' ends. The enzyme consists of one (or more) protein(s) without RNA subunits. Products of the processing reaction are tRNA molecules with 3' terminal hydroxyl groups and 3' trailers with 5' terminal phosphates. The main processing sites are located immediately 3' to the discriminator and one nucleotide further downstream. This endonucleolytic processing at and close to the tRNA 3' end in potato mitochondria suggests a higher similarity to the eukaryotic than to the prokaryotic tRNA 3' processing pathway. Partial purification and separation of RNase Z from the 5' processing activity RNase P allowed us to determine biochemical characteristics of the enzyme. The activity is stable over broad pH and temperature ranges, with peak activity at pH 8 and 30 degrees C. Optimal concentrations for MgCl2 and KCl are 5 mM and 30 mM, respectively. The potato mitochondrial RNase Z accepts only tRNA precursors with mature 5' ends. The precursor for tRNAPhe requires RNA editing for efficient processing by RNase Z.
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Affiliation(s)
- A Kunzmann
- Allgemeine Botanik, Universität Ulm, Albert-Einstein-Allee 11, D-89069 Ulm, Germany
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6
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Wu CY, Lin CH, Chen LJ. Identification of the transcription start site for the spinach chloroplast serine tRNA gene. FEBS Lett 1997; 418:157-61. [PMID: 9414117 DOI: 10.1016/s0014-5793(97)01373-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Deleting part of the 3' end of the spinach chloroplast serine tRNA coding region, which destroyed the proper folding of its RNA transcript and resulted in the inhibition of tRNA processing, allowed the detection of a serine tRNA primary transcript. The transcription start site for this primary transcript, synthesized from the internal promoter, was mapped to -12 upstream from the mature tRNA coding region. Transcription analysis with various 5' deletion mutants suggested that the AT-rich region between -31 and -11, immediately upstream of the serine tRNA transcription start site, affects the transcription efficiency, and possibly the selection of transcription start site. Identification of the transcription start site for the spinach chloroplast serine tRNA gene in this study represents the first example of 5' end mapping of a tRNA precursor transcribed from chloroplast tRNA genes containing an internal promoter.
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MESH Headings
- Base Sequence
- Chloroplasts/metabolism
- Cloning, Molecular
- Genes, Plant
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plasmids
- RNA Caps/metabolism
- RNA, Plant/biosynthesis
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Transfer, Ser/biosynthesis
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- Sequence Deletion
- Spinacia oleracea/genetics
- Transcription, Genetic
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Affiliation(s)
- C Y Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan, ROC
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7
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Cheng YS, Lin CH, Chen LJ. Transcription and processing of the gene for spinach chloroplast threonine tRNA in a homologous in vitro system. Biochem Biophys Res Commun 1997; 233:380-5. [PMID: 9144543 DOI: 10.1006/bbrc.1997.6464] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An in vitro system was established to study the transcription and processing of threonine tRNA using spinach chloroplast enzyme extract. Experiments using a series of 5' deletion mutants demonstrated that the transcription of trnT gene required no 5' upstream promoter elements. Four plasmid DNA templates containing trnT were constructed for tRNA processing assay. The processing reaction was carried out either with exogenously added precursor-tRNAs made by T7 RNA polymerase or with RNAs synthesized by the transcription activity in the same processing enzyme extract. Both assays demonstrated that the 5' and 3' ends of mature tRNA were processed endonucleolytically and the processing of the 5' end preceded the maturation of the 3' end. The activity of nucleotidyl transferase that adds CCA nucleotides to the 3' end of tRNA was also observed. The use of a coupled transcription and processing system provides us with a better insight to the tRNA processing mechanism of the chloroplast.
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Affiliation(s)
- Y S Cheng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan, ROC
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8
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Papadimitriou A, Gross HJ. Pre-tRNA 3'-processing in Saccharomyces cerevisiae. Purification and characterization of exo- and endoribonucleases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:747-59. [PMID: 9022706 DOI: 10.1111/j.1432-1033.1996.0747r.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We investigated ribonucleases from Saccharomyces cerevisiae which are active in pre-tRNA 3'-processing in vitro. Two pre-tRNA 3'-exonucleases with molecular masses of 33 and 60 kDa, two pre-tRNA 3'-endonucleases with molecular masses of 45 kDa/60 kDa and 55 kDa and 70-kDa 3'-pre-tRNase were purified from yeast whole cell extracts by several successive chromatographic purification steps. The purified exonucleases are non-processive 3'-exonucleases that catalyze the exonucleolytic processing of 3'-trailer sequences of pre-tRNAs to produce mature tRNAs. The 45-kDa/60-kDa 3'-endonuclease is tRNA-specific and catalyzes the processing of pre-tRNAs in a single endonucleolytic step. Two isoenzymes of this activity (p45 and p60) were identified by chromatography. The second endonuclease, p55, is dependent on monovalent ions and cleaves about three nucleotides downstream the mature 3'-end. All of the purified 3'-pre-tRNases accept homologous as well as heterologous pre-tRNA substrates. Pre-tRNAs carrying a 5'-leader are processed with almost the same efficiency as those lacking this 5'-leader. Mature tRNAs carrying the CCA 3'-sequence and tRNA pseudogene products carrying mutations in the mature domain are processed by the 3'-exonucleases, not by the 3'-endonucleases. The specific endonuclease p45/p60 discriminates between UUUOH as a 3'-flank, which is cleaved, and the CCA 3'-end of mature tRNAs, which is not cleaved. This study suggests that several 3'-pre-tRNases are active on tRNA precursors in vitro and might therefore in pre-tRNA 3'-processing in yeast, partly in a cooperative manner.
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Affiliation(s)
- A Papadimitriou
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Biozentrum, Würzburg, Germany
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9
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Sugita M, Sugiura M. Regulation of gene expression in chloroplasts of higher plants. PLANT MOLECULAR BIOLOGY 1996; 32:315-26. [PMID: 8980485 DOI: 10.1007/bf00039388] [Citation(s) in RCA: 152] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Chloroplasts contain their own genetic system which has a number of prokaryotic as well as some eukaryotic features. Most chloroplast genes of higher plants are organized in clusters and are cotranscribed as polycistronic pre-RNAs which are generally processes into many shorter overlapping RNA species, each of which accumulates of steady-state RNA levels. This indicates that posttranscriptional RNA processing of primary transcripts is an important step in the control of chloroplast gene expression. Chloroplast RNA processing steps include RNA cleavage/trimming, RNA splicing, ENA editing and RNA stabilization. Several chloroplast genes are interrupted by introns and therefore require processing for gene function. In tobacco chloroplasts, 18 genes contain introns, six for tRNA genes and 12 for protein-encoding genes. A number of specific proteins and RNA factors are believed to be involved in splicing and maturation of pre-RNAs in chloroplasts. Processing enzymes and RNA-binding proteins which could be involved in posttranscriptional steps have been identified in the last several years. Our current knowledge of the regulation of gene expression in chloroplasts of higher plants is overviewed and further studies on this matter are also considered.
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Affiliation(s)
- M Sugita
- Center for Gene Research, Nagoya University, Japan
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10
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Baum M, Schön A. Localization and expression of the closely linked cyanelle genes for RNase P RNA and two transfer RNAs. FEBS Lett 1996; 382:60-4. [PMID: 8612765 DOI: 10.1016/0014-5793(96)00148-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The genomic region encoding the RNA subunit of the cyanelle RNase P has been characterized. rnpB, which has no homologue in chloroplasts, is flanked by two tRNA genes on the complementary DNA strand. Transcriptional control elements of all three genes have been experimentally determined. Comparison of the sequenced region with the corresponding loci of chloroplast genomes from vascular plants suggests that major inversions may have led to a possible loss or severe truncation of the RNase P RNA coding region during the course of plastid evolution.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- Endoribonucleases/genetics
- Eukaryota/enzymology
- Eukaryota/genetics
- Gene Expression/physiology
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plastids/enzymology
- Plastids/genetics
- Promoter Regions, Genetic/genetics
- RNA, Catalytic/genetics
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/genetics
- RNA, Transfer, His/chemistry
- RNA, Transfer, His/genetics
- Ribonuclease P
- Sequence Analysis, DNA
- Transcription, Genetic/genetics
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Affiliation(s)
- M Baum
- Institut für Biochemie, Bayerische Julius-Maximilans-Universität, Würzburg, Germany
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11
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Abstract
RNase P consists of both protein and RNA subunits in all organisms and organelles investigated so far, with the exception of chloroplasts and plant nuclei where no enzyme-associated RNA has been detected to date. Studies on substrate specificity revealed that cleavage by plant nuclear RNase P is critically dependent on a complete and intact structure of the substrate. No clearcut answer is yet possible regarding the order of processing events at the 5' or 3' end of tRNAs in the case of nuclear or chloroplast processing enzymes. RNase P from a phylogenetically ancient photosynthetic organelle will be discussed in greater detail: The enzyme from the Cyanophora paradoxa cyanelle is the first RNase P from a photosynthetic organelle which has been shown to contain an essential RNA subunit. This RNA is strikingly similar to its counterpart from cyanobacteria, yet it lacks catalytic activity. Properties of the holoenzyme suggest an intermediate position in RNA enzyme evolution, with an Eukaryotic-type, inactive RNA and a prokaryotic-type small protein subunit. The possible presence of an RNA component in RNase P from plant nuclei and modern chloroplasts will be discussed, including a critical evaluation of some criteria that have been frequently applied to elucidate the subunit composition of RNase P from different organisms.
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Affiliation(s)
- A Schön
- Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Würzburg, Germany
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12
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Liere K, Link G. Structure and expression characteristics of the chloroplast DNA region containing the split gene for tRNA(Gly) (UCC) from mustard (Sinapis alba L.). Curr Genet 1994; 26:557-63. [PMID: 7874753 DOI: 10.1007/bf00309950] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The mustard chloroplast gene trnG-UCC is split by a 717-bp group-II intron. Northern hybridization and RNase protection experiments suggest cotranscription with the upstream psbK-psbI operon, but not with the downstream trnR-UCU gene. The ends of most RNase-protected fragments between psbI and trnG correlate with the position of two potential stem-loop structures in this region, which could act as RNA processing elements. However, one RNA 5' end, approximately 75 bp upstream of the trnG 5' exon, does not so correlate and is preceded by prokaryotic-type '-10' and '-35' sequence elements. This suggests the possibility that a fraction of the trnG transcripts is initiated here. All precursor transcripts spanning the trnG region seem to have a common 3' end, which was located 117 bp downstream from the 3' exon, immediately after a stem-loop region. During seedling development, the major 0.8-0.9-kb trnG precursor transcripts show a transient maximum level at around 48 h after sowing, at a time when the mature tRNA begins to accumulate to constant levels. No significant differences in transcript patterns were observed either in the light or in darkness.
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Affiliation(s)
- K Liere
- Arbeitsgruppe Pflanzliche Zellphysiologie und Molekularbiologie, Fakultät für Biologie, Ruhr-Universität Bochum, Germany
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13
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Nickelsen J, Link G. RNA-protein interactions at transcript 3' ends and evidence for trnK-psbA cotranscription in mustard chloroplasts. MOLECULAR & GENERAL GENETICS : MGG 1991; 228:89-96. [PMID: 1715978 DOI: 10.1007/bf00282452] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In vitro transcripts from the 3' flanking regions of mustard chloroplast genes were tested for protein binding in a chloroplast extract. Efficient and sequence-specific RNA-protein interaction was detected with transcripts of the genes trnK, rps16 and trnH, but not with the 3' terminal region of trnQ RNA. The transacting component required for specific complex formation is probably a single 54 kDa polypeptide. The protein-binding region of the rps16 3' terminal region was mapped and compared with that of the trnK transcript determined previously. Both regions reveal a conserved 7-mer UUUAUCU followed by a stretch of U residues. Deletion of the trnK 3' U cluster resulted in more than 80% reduction in the binding activity, and after deletion of both the U stretch and the 7-mer motif no binding at all was detectable. RNase protection experiments indicate that the protein-binding regions of both the rps16 and trnK transcripts correlate with the positions of in vivo 3' ends, suggesting an essential role for the 54 kDa binding protein in RNA 3' end formation. In the case of the trnK gene, evidence was obtained for read-through transcripts that extend into the psbA coding region, thus pointing to the possibility of trnK-psbA cotranscription.
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14
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Hanic-Joyce P, Gray M. Processing of transfer RNA precursors in a wheat mitochondrial extract. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)77417-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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Affiliation(s)
- W Gruissem
- Department of Botany, University of California, Berkeley 94720
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16
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Biosynthesis of tRNA in yeast mitochondria. An endonuclease is responsible for the 3′-processing of tRNA precursors. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68294-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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17
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Boyer SK, Mullet JE. Pea chloroplast tRNA(Lys) (UUU) gene: transcription and analysis of an intron-containing gene. PHOTOSYNTHESIS RESEARCH 1988; 17:7-22. [PMID: 24429659 DOI: 10.1007/bf00047679] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/1987] [Accepted: 12/15/1987] [Indexed: 06/03/2023]
Abstract
The pea chloroplast trnK gene which encodes tRNA(Lys) (UUU) was sequenced. TrnK is located 210 bp upstream from the promoter of psbA and immediately downstream from the 3'-end of rbcL. The gene is transcribed from the same DNA strand as psbA and rbcL. A 2447 bp intron with class II features is located in the trnK anticodon loop. The intron contains a 506 amino acid open reading frame which could encode an RNA maturase. The primary transcript of trnK is 2.9 kb long; its 5'-end was identified as a site of transcription initiation by in vitro transcription experiments. The 5'-terminus is adjacent to DNA sequences previously identified as transcription promoter elements. The most abundant trnK transcript is 2.5 kb long with termini corresponding to the 5' and 3' ends of the trnK exons. Intron specific RNAs were not detected. This suggests that RNA processing which produces tRNA(Lys) leads to rapid degradation of intron sequences.
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Affiliation(s)
- S K Boyer
- Biological Sciences Department, Purdue University, Lilly hall of Life Sciences, 47907, West Lafayette, Indiana, USA
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18
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Burkard U, Söll D. The 5′-terminal guanylate of chloroplast histidine tRNA is encoded in its gene. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)81555-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Marion-Poll A, Hibbert CS, Radebaugh CA, Hallick RB. Processing of mono-, di- and tricistronic transfer RNAs precursors in a spinach or pea chloroplast soluble extract. PLANT MOLECULAR BIOLOGY 1988; 11:45-56. [PMID: 24272157 DOI: 10.1007/bf00016013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/1988] [Accepted: 03/18/1988] [Indexed: 06/02/2023]
Abstract
Monomeric, dimeric and trimeric chloroplast tRNA precursors from Euglena gracilis were synthesized by Sp6, T7 or T3 RNA polymerases using an in vitro transcription system. The length of the 3' and 5' ends of these precursors was varied to facilitate the identification of processing intermediates, and to study the effect of the structure of the tRNA precursors on the processing reactions. All the tRNA precursors studied, independent of their structure, are processed to mature tRNAs in both spinach and pea chloroplast soluble extracts. 5'-and 3' endonucleases are involved in the cleavage of 5' and 3' ends of the pre-tRNAs. These two reactions are not ordered in vitro. Other enzymatic activities can be detected in the chloroplast soluble extract including exonucleases, and CCA-adding enzyme.
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Affiliation(s)
- A Marion-Poll
- Laboratoire de Biologie Cellulaire, INRA, Route de Saint Cyr, 78000, Versailles, France
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20
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Stern DB, Gruissem W. Control of plastid gene expression: 3' inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription. Cell 1987; 51:1145-57. [PMID: 3690662 DOI: 10.1016/0092-8674(87)90600-3] [Citation(s) in RCA: 332] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have examined the function of inverted repeat sequences found at the 3' ends of plastid DNA transcription units in higher plants, using a homologous in vitro transcription extract. The inverted repeat sequences are ineffective as transcription terminators, but serve as efficient RNA processing elements. Synthetic RNAs are processed in a 3'-5' direction by a nuclease activity present in the transcription extract, generating nearly homogeneous 3' ends distal to the inverted repeat sequence. S1 nuclease protection experiments demonstrate that the 3' ends generated in vitro coincide with those found for plastid mRNAs in vivo. RNA molecules possessing inverted repeats near their 3' ends are substantially more stable than control RNAs in the chloroplast extract, and kinetic measurements indicate that each RNA has a unique decay rate. Coupled with previously published information suggesting that the differential accumulation of plastid RNAs during development is effectively controlled by post-transcriptional mechanisms, these results raise the possibility that RNA processing and stability, specifically involving 3' end inverted repeats, are important regulatory features of plastid gene expression.
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Affiliation(s)
- D B Stern
- Department of Botany, University of California, Berkeley 94720
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21
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22
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