TRNA precursor transcribed from a mutant human gene inserted into a SV40 vector is processed incorrectly

A new mitochondrial DNA mutation (A3288G) in the tRNA(Leu(UUR)) gene associated with familial myopathy

We describe a family with a maternally inherited mitochondrial myopathy and an A3288G mutation in the tRNA(Leu(UUR)) gene. The proband had muscle cramping and mild weakness while her brother had long-standing limb and respiratory muscle weakness and her daughter had elevated serum CK. The mutation, which was nearly homoplasmic in muscle and heteroplasmic in blood, affects the TpsiC loop at a conserved site and was not found in 107 controls. This report confirms the frequent association of tRNA(Leu(UUR)) mutations with respiratory muscle involvement and bolsters the concept that tRNA(Leu(UUR)) is a hotspot for mtDNA mutations.

RNA transport

RNA molecules synthesized in the nucleus are transported to their sites of function throughout the eukaryotic cell by specific transport pathways. This review focuses on transport of messenger RNA, small nuclear RNA, ribosomal RNA, and transfer RNA between the nucleus and the cytoplasm. The general molecular mechanisms involved in nucleocytoplasmic transport of RNA are only beginning to be understood. However, during the past few years, substantial progress has been made. A major theme that emerges from recent studies of RNA transport is that specific signals mediate the transport of each class of RNA, and these signals are provided largely by the specific proteins with which each RNA is associated.

Sequence-specific binding of transfer RNA by glyceraldehyde-3-phosphate dehydrogenase

A transfer RNA (tRNA) binding protein present in HeLa cell nuclear extracts was purified and identified as the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Studies with mutant tRNAs indicated that GAPDH recognizes both sequence and structural features in the RNA. GAPDH discriminated between wild-type tRNA and two tRNA mutants that are defective in nuclear export, which suggests that the protein may participate in RNA export. The cofactor nicotinamide adenine dinucleotide disrupted complex formation between tRNA and GAPDH and thus may share a common binding site with the RNA. Indirect immunofluorescence experiments showed that GAPDH is present in the nucleus as well as in the cytoplasm.

Pleiotropic effect of a point mutation in the yeast SUP4-o tRNA gene: in vivo pre-tRNA processing in S. cerevisiae

The expression of mutant tyrosine-inserting ochre suppressor SUP4-o tRNA genes in vivo in S. cerevisiae was examined as a basis for further studies of tRNA transcription and processing. In vivo yeast precursor tRNAs have been identified by filter hybridization and primer extension analysis. We have previously shown that a mutant SUP4-o tRNA gene with a C52----A52 transversion at positive 52 (C52----A52(+IVS) allele) was transcribed but that the primary transcript was not processed correctly. We show here that 5' and 3' end processing as well as splicing are defective for this mutant but that the 5' end processing is restored when the intron is removed from the gene by oligonucleotide directed mutagenesis (C52----A52(-IVS) allele). Our results imply that the C52----A52 transversion by itself cannot account for the lack of susceptibility to RNase P cleavage but that the overall tertiary structure of the mutant tRNA precursor is destabilized by the intron/anticodon stem. A second consequence of the C52----A52 transversion is to prevent complete maturation of the tRNA precursor at its 3' end since intermediates containing incompletely processed 3' trailers accumulate in the yeast cells transformed with the C52----A52(-IVS) allele. A correct structure of the T stem might therefore define a structural feature required for the recognition of the 3' processing activity.

Genes, variant genes, and pseudogenes of the human tRNA(Val) gene family are differentially expressed in HeLa cells and in human placenta

Pre-tRNAs(Val) were identified in unfractionated tRNA preparations from HeLa cells and human placenta and their 5' leader structures were deduced from the nucleotide sequences of the corresponding cDNAs. Several of these precursors can be assigned to nine out of the eleven members of the human tRNA(Val) gene family characterized so far, which demonstrates that these gene loci are actively transcribed in vivo. Among the expressed genes there are (a) genes for the two known tRNA(Val) isoacceptor species from human placenta, (b) gene variants that exhibit sequence alterations as compared to conventional genes, and (c) pseudogenes that produce processing-deficient precursors which are not matured to tRNAs. The transcription products of several yet unknown tRNA(Val) genes have also been detected. Furthermore, different expression patterns are observed in the two cell types studied. These data allow for the first time an insight into the in vivo expression of a human tRNA gene family.

Structure and transcription of the mitochondrial genome in heteroplasmic strains of Saccharomyces cerevisiae

Saccharomyces cerevisiae strain FF1210-6C/170 is respiratory deficient due to a mutation of the penultimate base of the mitochondrial tRNA(Asp) gene. We have identified a number of progeny from this strain which have reverted to respiratory sufficiency by the excision and tandem amplification of a small region of the mitochondrial (mt) DNA carrying the tRNA(Asp) gene, while also maintaining the full-length mtDNA. We have studied the structure of the mtDNA and mitochondrial transcription in a number of these heteroplasmic strains. The exact site of the recombination involved in the excision of the repeating unit of the amplified mtDNA has been determined for five of the revertants. Recombination occurs between identical sequences 4-13 base pairs in length. Each of the different repeating units of the amplified DNA retains an active promoter which has been moved to a site just upstream of the tRNA(Asp) gene by the excision/amplification. Transcripts from the heteroplasmic strains have been characterized to determine the sites of mitochondrial RNA termini. We find that in addition to the 5' and 3' processing of the tRNAs, many of the transcripts terminate at a position about 300 base pairs downstream of the gene for tRNA(Asp). We also find that 3' processing of tRNA(Asp) precursors is absent in petite strains which lack 5' processing indicating that 5' processing of tRNA(Asp) may be a prerequisite for 3' processing in this mutant.

Genes, variant genes and pseudogenes of the human tRNA(Val) gene family. Expression and pre-tRNA maturation in vitro

Nine different members of the human tRNA(Val) gene family have been cloned and characterized. Only four of the genes code for one of the known tRNA(Val) isoacceptors. The remaining five genes carry mutations, which in two cases even affect the normal three-dimensional tRNA structure. Each of the genes is transcribed by polymerase III in a HeLa cell nuclear extract, but their transcription efficiencies differ by up to an order of magnitude. Conserved sequences immediately flanking the structural genes that could serve as extragenic control elements were not detected. However, short sequences in the 5' flanking region of two genes show striking similarity with sequences upstream from two Drosophila melanogaster tRNA(Val) genes. Each of the human tRNA(Val) genes has multiple, i.e. two to four, transcription initiation sites. In most cases, transcription termination is caused by oligo(T) sequences downstream from the structural genes. However, the signal sequences ATCTT and CTTCTT also serve as effective polymerase III transcription terminators. The precursors derived from the four tRNA(Val) genes coding for known isoacceptors and those derived from two mutant genes are processed first at their 3' and subsequently at their 5' ends to yield mature tRNAs. The precursor derived from a third mutant gene is incompletely maturated at its 3' end, presumably as a consequence of base-pairing between 5' and 3' flanking sequences. Finally, precursors encoded by the genes that carry mutations affecting the tRNA tertiary structure are completely resistant to 5' and 3' processing.

A point mutation in a mitochondrial tRNA gene abolishes its 3' end processing

A temperature sensitive mutation mapping in the tRNA region of the mitochondrial genome of S. cerevisiae has been found to abolish 3' processing of tRNA(asp). Mutant cells grown for a few generations at the non-permissive temperature were found to specifically lack mature tRNA(asp) and to accumulate 3' unprocessed precursors of this tRNA. The accumulation of precursors of other mitochondrial tRNAs was also observed under the same conditions. After longer incubation times, a generalized decrease of mitochondrial transcripts could be observed. The mutation was genetically mapped in a limited region surrounding the tRNA(asp) gene and found, by sequencing, to consist of a C- greater than T transition at position 61 of the tRNA(asp) gene.

Initiator tRNAMet genes from the nematode Caenorhabditis elegans

Five different members of the initiator tRNAMet gene family have been isolated and characterized from the nematode Caenorhabditis elegans. All five show identical tRNA coding sequences, followed by a block of T residues associated with termination by RNA polymerase III. Nucleotide sequences flanking the tDNAs are completely divergent, except for two distinct members with identical flanking sequences, which may have arisen from a recent gene duplication event. Each tDNA is also flanked by middle-repetitive DNA, but the lack of cross-hybridization to each other suggests that these repetitive sequences have no common functional significance. The tRNAMeti genes do not appear to be closely linked to each other, although in vitro transcription reveals a putative tDNA adjacent to one member. Finally, there are large differences in the extent to which the five genes are transcribed by a homologous C. elegans cell-free extract, suggesting that flanking sequences have a significant effect on transcription by RNA polymerase III.

tRNA nuclear transport: defining the critical regions of human tRNAimet by point mutagenesis

We recently described a carrier-mediated nuclear transport system for tRNA in Xenopus laevis oocytes. A natural human tRNAimet variant with a G to T transversion in position 57 is defective in transport across the nuclear membrane. In addition, processing of the primary transcript of the variant gene is much less efficient than the wild type. We now describe the nuclear transport and processing phenotypes of 30 different point mutants generated by in vitro mutagenesis of a wild-type human tRNAimet gene. The effects of each nucleotide change on processing and transport were analyzed in X. laevis oocytes following nuclear microinjection of each mutant gene. Mutants exhibiting transport-defective behavior were further characterized by measuring transport kinetics of the purified mature tRNA. Our studies demonstrate that many mutations affect tRNAimet nuclear transport, although those with the most deleterious effects are clustered in the highly conserved D stem-loop and T stem-loop regions.

Transcription, processing and nuclear transport of a B1 Alu RNA species complementary to an intron of the murine alpha-fetoprotein gene

The Alu sequence family comprises the major dispersed repeat sequences of rodent and primate genomes, numbering greater than 300,000 copies in the human haploid genome. The function of these elements is unknown. The sequences can be transcribed by RNA polymerase III and represent a substantial fraction of total heterogeneous nuclear RNA. Alu sequences can be found both in the flanking regions and within the transcription units of several well-characterized genes. Here we show that some members of the mouse B1 Alu sequence family encode a small cytoplasmic RNA. The mouse B1 sequence is congruent to 130 nucleotides long and shows homology with the monomeric units of the dimeric 300-nucleotide primate sequence. By means of microinjection studies in the Xenopus laevis oocyte, we have elucidated a novel pathway leading to the appearance of a processed B1-type Alu RNA species in the cytoplasm. The abundance of this small Alu RNA differs between various mouse tissues, suggesting a role in tissue-specific gene expression.

Stable transcription complex on a class III gene in a minichromosome

We have constructed recombinant simian virus 40 molecules containing Xenopus 5S RNA and tRNA genes. Recombinant minichromosomes containing these genes were isolated to study the interaction of RNA polymerase III transcription factors with these model chromatin templates. Minichromosomes containing a tRNAMet gene can be isolated in a stable complex with transcription factors (IIIB and IIIC) and are active in vitro templates for purified RNA polymerase III. In contrast, minichromosomes containing a 5S RNA gene are refractory to transcription by purified RNA polymerase III in either the absence or the presence of other factors.

Structure and transcription of eukaryotic tRNA genes

The availability of cloned tRNA genes and a variety of eukaryotic in vitro transcription systems allowed rapid progress during the past few years in the characterization of signals in the DNA-controlling gene transcription and in the processing of the precurser RNAs formed. This will be the subject matter discussed in this review.

Stable transcription complex on a class III gene in a minichromosome

We have constructed recombinant simian virus 40 molecules containing Xenopus 5S RNA and tRNA genes. Recombinant minichromosomes containing these genes were isolated to study the interaction of RNA polymerase III transcription factors with these model chromatin templates. Minichromosomes containing a tRNAMet gene can be isolated in a stable complex with transcription factors (IIIB and IIIC) and are active in vitro templates for purified RNA polymerase III. In contrast, minichromosomes containing a 5S RNA gene are refractory to transcription by purified RNA polymerase III in either the absence or the presence of other factors.

Construction and functional analysis of a series of synthetic RNA polymerase III promoters

RNA polymerase III promoters were constructed by cloning chemically synthesized double stranded analogues of the box A and box B consensus sequences into suitable vectors. In contrast to approaches adopted previously for the analysis of RNA polymerase III promoters, this method has no limitation on the structure and number of variants generated, and allows critical sequences in various permutations to be studied. Furthermore, the series of synthetic polymerase III promoters created constitute a collection of point mutation variants and hence provide a powerful tool for the analysis of nucleotides essential for promoter function. The results demonstrate that these two boxes, when separated by approximately 50 base pairs, are sufficient to direct efficient transcription, and that substitution of certain nucleotides causes reduced template activity.

Mature methyl-deficient tRNA isolated from a mammary adenocarcinoma

A transplantable rat tumor, mammary adenocarcinoma 13762, accumulates tRNA which can be methylated in vitro by mammalian tRNA (adenine-1) methyltransferase. This unusual ability of the tumor RNA to serve as substrate for a homologous tRNA methylating enzyme is correlated with unusually low levels of the A 58-specific adenine-1 methyltransferase. The nature of the methyl-accepting RNA has been examined by separating tumor tRNA on two-dimensional polyacrylamide gels. Comparisons of ethidium bromide-stained gels of tumor vs. liver tRNA show no significant quantitative differences and no accumulation of novel tRNAs or precursor tRNAs in adenocarcinoma RNA. Two-dimensional separations of tumor RNA after in vitro [14C]methylation using purified adenine-1 methyltransferase indicate that about 25% of the tRNA species are strongly methyl-accepting RNAs. Identification of six of the tRNAs separated on two-dimensional gels has been carried out by hybridization of cloned tRNA genes to Northern blots. Three of these, tRNALys3 , tRNAGln and tRNAMeti , are among the adenocarcinoma methyl-accepting RNAs. The other three RNAs, all of which are leucine-specific tRNAs, show no methyl-accepting properties. Our results suggest that low levels of a tRNA methyltransferase in the adenocarcinoma cause selected species of tRNA to escape the normal A58 methylation, resulting in the appearance of several mature tRNAs which are deficient in 1-methyladenine. The methyl-accepting tRNAs from the tumor appear as ethidium bromide-stained spots of similar intensity to those seen for RNA from rat liver; therefore, methyladenine deficiency does not seem to impair processing of these tRNAs.

Homologous in vitro transcription of linear DNA fragments containing the tRNAArg-tRNAAsp gene pair from Saccharomyces cerevisiae

Transcription of a tRNAArg-tRNAAsp gene pair from Saccharomyces cerevisiae by an homologous yeast extract results in a dimeric percursor molecule which is processed to mature-sized tRNAArg and tRNAAsp molecules. We have transcribed linear DNA fragments cleaved within the gene sequences to show that precursor synthesis is not dependent on the internal promoter of the second gene (tRNAAsp). Furthermore, the second gene does not support independent transcription when the normal upstream initiation site is removed.

Generation of long read-through transcripts in vivo and in vitro by deletion of 3' termination and processing sequences in the human tRNAimet gene

The effects of 3' deletions of the coding and flanking regions of the human tRNAimet gene on its transcription and subsequent processing have been studied both in vitro and in vivo. We demonstrate that in the absence of the oligo T stop signal, polymerase III will read-through efficiently to the next available downstream stop signal. In mutations preserving the 3' terminal sequence of the coding region these read-through transcripts are efficiently processed, irrespective of their length and sequence by an endonucleolytic cleavage to yield both a mature tRNA and an intact trailer RNA. However, deletions involving the terminal regions up to +62 in the coding sequence produce an unprocessed co-transcript of tRNA and downstream sequences. Deletions further within the B promoter box abolish transcription. The use of these mutants as possible "portable" promoters is discussed.

Directed semisynthetic point mutational analysis of an RNA polymerase III promoter

The transcription of tRNA and Alu repeat genes in vitro by RNA polymerase III has been shown to be dependent on the presence of two intragenic regions, which contain the consensus sequences RGYNNRRYGG (box A) and GA/TTCRANNC (box B), located 30-60 nucleotides apart. The role of box B and some of its variants was analyzed by a novel method involving the chemical synthesis of double stranded analogues of box B which were subsequently cloned into recombinant vectors carrying box A alone. This method creates a series of semi-synthetic RNA polymerase III promoters and has no limitation on the structure and number of variants which can be generated. The results showed the "wild type" sequence GTTCGAGAC and the sequence GTTCGTGAC (an A to T transversion of the 6th position) were active in promoting RNA polIII transcription. However, the box B sequences CTTCGAGAC and GTACGAGA, where the only departures from the consensus are a G to C and an A to T transversion in the 1st and 3rd positions respectively, were unable to restore promoter function.

tRNA transport from the nucleus in a eukaryotic cell: carrier-mediated translocation process

The mechanism by which a tRNA molecule is delivered from the nucleus of a cell to the cytoplasm has been studied in the Xenopus laevis oocyte utilizing nuclear microinjection and manual microdissection techniques. tRNA nuclear transport in this cell resembles a carrier-mediated translocation process rather than diffusion through a simple pore or channel. tRNA transport is saturable by tRNA, with a maximal rate measured to be about 190 X 10(7) molecules per min per nucleus (21 degrees C) in the mature oocyte. Competitive inhibition between two different tRNA species can be demonstrated, suggesting that many tRNA species share a common carrier system. tRNA nuclear transport is sharply dependent on temperature, with an optimal rate observed at 31 degrees C. A single G-to-U substitution at position 57 in the vertebrate tRNAMeti molecule reduces the transport rate of this tRNA by a factor of about 20, implicating this highly conserved region of the tRNA molecule (loop IV) as critical for recognition by the transport mechanism. On morphologic grounds I propose that ribosome-like components surrounding the nuclear pore may function as the tRNA translocation "motor." The tRNA nuclear transport mechanism represents a distinctly eukaryotic process and a site of potential control over cell growth and proliferation.

The promoter sequence of a yeast tRNAtyr gene

Thirty-one base substitution mutations within the yeast SUP4 tRNAtyr gene were used to probe the effects of different intragenic sequences on promoter activity. The various mutant plasmids were tested quantitatively for their in vitro template activity and for their ability to block competitively the transcription of a reference gene. Five mutations within the coding sequence of SUP4 decreased template activity for pre-tRNAtyr synthesis. The competition assays revealed 11 mutant genes that behaved differently than SUP4-o. Six were weaker competitors and five were stronger. The 12 mutations affecting template activity or competition are clustered in three regions: those encoding the dihydrouracil (D) arm, the extra loop, and the T psi arm of the tRNA. All of the mutations that reduce competition involve base changes that decrease homology to a eucaryotic tRNA consensus sequence in the highly conserved D and T psi regions. Three of the five up mutations increased homology to the tRNA consensus sequence.

Mutation in the a block of the yeast tRNAleu3 gene that allows transcription but abolishes splicing and 5'-end maturation

A three-base substitution mutant of the yeast tRNALeu3 has been constructed. The mutation, introduced through the use of a heptadecanucleotide as a site-specific mutagen, is localized in the anterior portion of the promoter and results in the inability to form a D stem. The mutant is active in transcription, but maturation of the 5' terminus and splicing are abolished. The results are discussed in the light of a recently proposed model for initiation of transcription of eucaryotic tRNA genes.

Specific interactions of Saccharomyces cerevisiae proteins with a promoter region of eukaryotic tRNA genes

The specific binding of one or several Saccharomyces cerevisiae proteins to a segment of genes that code for different yeast tRNAs has been demonstrated with the use of the DNase I-protection "footprint" assay of Galas and Schmitz. The analyzed binding occurs near the 3' ends of the genes and is centered on an 11-base-pair DNA sequence that has been well conserved among eukaryotic tRNA genes. Others have shown the involvement of this sequence in initiating the transcription of tRNA genes by RNA polymerase III. The adenovirus gene that codes for VAI RNA also contains this conserved sequence element, and we detect binding of yeast protein(s) to this gene. Competition experiments show that a common set of proteins binds to different tRNA genes. The DNA-protein complex is quite stable at 20 degrees C and low ionic strength.

Enzymatic replacement in vitro of the first anticodon base of yeast tRNAAsp: application to the study of tRNA maturation in vivo, after microinjection into frog oocytes

A combination of several enzymes, RNase-T1, nuclease S1, T4-polynucleotide kinase and T4-RNA ligase were used to prepare and modify different fragments of yeast tRNAAsp (normal anticodon G U C). This allowed us to reconstitute, in vitro, a chimeric tRNA that has any of the four bases G, A, U or C, as the first anticodon nucleotide, labelled with (32p) in its 3' position. Such reconstituted (32p) labelled yeast tRNAAsp were microinjected into the cytoplasm or the nucleus of the frog oocyte and checked for their stability as well as for their potential to work as a substrate for the maturation (modifying) enzymes under in vivo conditions. Our results indicate that the chimeric yeast tRNAsAsp were quite stable inside the frog oocyte. Also, the G34 was effectively transformed inside the cytoplasm of frog oocyte into Q34 and mannosyl-Q34; U34 into mcm5s2U and mcm5U. In contrast, C34 and A34 were not transformed at all neither in the cytoplasm nor in the nucleus of the frog oocyte. The above procedure constitutes a new approach in order to detect the presence of a given modifying enzyme inside the frog oocyte; also it provides informations about its cellular location and possibility about its specificity of interaction with foreign tRNA.