[Overexpression of genes encoding tRNA(Tyr) AND tRNA(Gln) improves viability of nonsense mutants in SUP45 gene in yeast Saccharomyces cerevisiae].

The variety of mechanisms providing viability of organisms bearing nonsense-mutations in the essential genes is unknown at present. In yeast Saccharomyces cerevisiae nonsense-mutants containing premature stop-codon in mRNA of the essential SUP45 gene were obtained. These strains are viable in the absence of mutant suppressor tRNA, therefore it is supposed that there are alternative mechanisms providing nonsense-suppression and mutants viability. Analysis of transformants obtained by transformation of strain bearing nonsense-mutant allele of SUP45 gene with multicopy yeast genomic library revealed three genes encoding wild type tRNA(Tyr) and four genes encoding wild type tRNA(Gln) that improve nonsense-mutants viability. Moreover, overexpression of these genes leads to the increase in the amount of full-length eRF1 protein in cell and compensates nonsense-mutants sensitivity to high temperature. Probable mechanisms of tRNA(Tyr) and tRNA(Gln) influence on the increase of viability of nonsense-mutants in SUP45 gene are discussed in this work.

In vitro analysis of elongation and termination by mutant RNA polymerases with altered termination behavior.

We have studied the in vitro elongation and termination properties of several yeast RNA polymerase III (pol III) mutant enzymes that have altered in vivo termination behavior (S. A. Shaaban, B. M. Krupp, and B. D. Hall, Mol. Cell. Biol. 15:1467-1478, 1995). The pattern of completed-transcript release was also characterized for three of the mutant enzymes. The mutations studied occupy amino acid regions 300 to 325, 455 to 521, and 1061 to 1082 of the RET1 protein (P. James, S. Whelen, and B. D. Hall, J. Biol. Chem. 266:5616-5624, 1991), the second largest subunit of yeast RNA pol III. In general, mutant enzymes which have increased termination require a longer time to traverse a template gene than does wild-type pol III; the converse holds true for most decreased-termination mutants. One increased-termination mutant (K310T I324K) was faster and two reduced termination mutants (K512N and T455I E478K) were slower than the wild-type enzyme. In most cases, these changes in overall elongation kinetics can be accounted for by a correspondingly longer or shorter dwell time at pause sites within the SUP4 tRNA(Tyr) gene. Of the three mutants analyzed for RNA release, one (T455I) was similar to the wild type while the two others (T455I E478K and E478K) bound the completed SUP4 pre-tRNA more avidly. The results of this study support the view that termination is a multistep pathway in which several different regions of the RET1 protein are actively involved. Region 300 to 325 likely affects a step involved in RNA release, while the Rif homology region, amino acids 455 to 521, interacts with the nascent RNA 3' end. The dual effects of several mutations on both elongation kinetics and RNA release suggest that the protein motifs affected by them have multiple roles in the steps leading to transcription termination.

Strategies for the suppression of peroxidase gene expression in tobacco. II. In vivo suppression of peroxidase activity in transgenic tobacco using ribozyme and antisense constructs.

Several strategies involving the use of antisense and ribozyme constructs in different expression vectors were investigated as methods of suppressing gene expression in planta. We had previously identified an efficiently cleaving ribozyme (Rz), with two catalytic units and 60 nucleotide (nt) of complementary sequence, to the lignin-forming peroxidase of tobacco (TPX). This Rz was cloned behind the 35S CaMV (35S) and nopaline synthase (NOS) promoters, and into a vector utilising the tobacco tyrosine tRNA for expression. For comparison with more traditional antisense strategies, full-length TPX antisense (AS) constructs were also constructed behind the NOS and 35S promoters. Populations of transgenic tobacco containing these constructs were produced and compared to control plants transformed with the vector only. Significant suppression of peroxidase expression in the range of 40-80% was seen in the T0 and T1 populations carrying 35S-AS, 35S-Rz and tRNA-Rz constructs. Co-segregation of the suppressed peroxidase phenotype and the tRNA-Rz transgenes was demonstrated. Northern blot analysis indicated that levels of TPX mRNA were lower in the Rz plants. No evidence of mRNA cleavage was observed and thus it was unclear if the Rz constructs were acting as Rzs in vivo. Transgenic plants containing the tRNA-Rz construct had significantly lower levels of peroxidase than the other transgenic plants. There was no significant difference in levels of suppression of TPX between the short Rz in the 35S vector and the full-length AS constructs. Although peroxidase levels were significantly reduced in transgenic plants carrying 35S-AS, 35S-Rz and tRNA-Rz constructs, no significant difference in lignin levels was observed.

Effective ribozyme delivery in plant cells.

Hammerhead ribozyme sequences were incorporated into a tyrosine tRNA (tRNA(Tyr)) and compared with nonembedded molecules. To increase the levels of ribozyme and control antisense in vivo, sequences were expressed from an autonomously replicating vector derived from African cassava mosaic geminivirus. In vitro, the nonembedded ribozyme cleaved more target RNA, encoding chloramphenicol acetyltransferase (CAT), than the tRNA(Tyr) ribozyme. In contrast, the tRNA(Tyr) ribozyme was considerably more effective in vivo than either the nonembedded ribozyme or antisense sequences, reducing CAT activity to < 20% of the control level. A target sequence (CM2), mutated to be noncleavable, showed no reduction in CAT activity in the presence of the tRNA(Tyr) ribozyme beyond that for the antisense construct. The reduction in full-length CAT mRNA and the presence of specific cleavage products demonstrated in vivo cleavage of the target mRNA by the tRNA(Tyr) ribozyme. The high titer of tRNA(Tyr) ribozyme was a result of transcription from the RNA polymerase III promoter and led to the high ribozyme/substrate ratio essential for ribozyme efficiency.

Human mitochondrial tRNA processing.

tRNA processing is a central event in mammalian mitochondrial gene expression. We have identified key enzymatic activities (ribonuclease P, precursor tRNA 3'-endonuclease, and ATP(CTP)-tRNA-specific nucleotidyltransferase) that are involved in HeLa cell mitochondrial tRNA maturation. Different mitochondrial tRNA precursors are cleaved precisely at the tRNA 5'- and 3'-ends in a homologous mitochondrial in vitro processing system. The cleavage at the 5'-end precedes that at the 3'-end, and the tRNAs are substrates for the specific CCA addition in the same in vitro system. Using a comparative enzymatic approach as well as biochemical and immunological techniques, we furthermore demonstrate that human cells contain two distinct enzymes that remove 5'-extensions from tRNA precursors, the previously characterized nuclear and the newly identified mitochondrial ribonuclease P. These two cellular isoenzymes have different substrate specificities that seem to be well adapted to their structurally disparate mitochondrial and nuclear tRNA substrates. This kind of approach may also help to understand the structural diversities and commonalities of tRNAs.

A nuclear encoded tRNA of Trypanosoma brucei is imported into mitochondria.

The mitochondrial genome of trypanosomes, unlike that of most other eukaryotes, does not appear to encode any tRNAs. Therefore, mitochondrial tRNAs must be either imported into the organelle or created through a novel mitochondrial process, such as RNA editing. Trypanosomal tRNA(Tyr), whose gene contains an 11-nucleotide intron, is present in both the cytosol and the mitochondrion and is encoded by a single-copy nuclear gene. By site-directed mutagenesis, point mutations were introduced into this tRNA gene, and the mutated gene was reintroduced into the trypanosomal nuclear genome by DNA transfection. Expression of the mutant tRNA led to the accumulation of unspliced tRNA(Tyr) (A. Schneider, K. P. McNally, and N. Agabian, J. Biol. Chem. 268:21868-21874, 1993). Cell fractionation revealed that a significant portion of the unspliced mutant tRNA(Tyr) was recovered in the mitochondrial fraction and was resistant to micrococcal nuclease treatment in the intact organelle. Expression of the nuclear integrated, mutated tRNA gene and recovery of its gene product in the mitochondrial fraction directly demonstrated import. In vitro experiments showed that the unspliced mutant tRNA(Tyr), in contrast to the spliced wild-type form, was no longer a substrate for the cognate aminoacyl synthetase. The presence of uncharged tRNA in the mitochondria demonstrated that aminoacylation was not coupled to import.

Minimum intron requirements for tRNA splicing and nuclear transport in Xenopus oocytes.

The presence or absence of an intron defines two classes of eukaryotic nuclear tRNA genes whose transcripts differ in a requirement for splicing. Using quantitative nuclear microinjection, we have previously found that nucleocytoplasmic transport of these two classes of tRNAs involves pathways which differ in one or more limiting components. To examine substrate features which distinguish these two pathways, a series of variants of a Xenopus tRNA(Tyr) gene were constructed in which the intron size was altered. The splicing and transport properties of the resulting transcripts were examined in oocyte microinjection and in vitro processing assays. The addition of one or two nucleotides at the splice site equivalent in an intronless gene produced transcripts which could be transported without splicing. However, transport was reduced relative to the mature-sequence tRNA, suggesting the anticodon loop (interrupted in pre-tRNAs) may be recognized by the intronless tRNA transport apparatus. Transcripts with four- or six-nucleotide intervening sequences were incompletely spliced with cleavage at only the 3' splice site. Neither unspliced precursor nor partially processed intermediates were efficiently transported. The results of coinjection experiments using tRNA and pre-tRNA competitors suggest that simple retention by the splicing apparatus may not account for failure to export these RNAs. Finally, a requirement for splicing is not unique to transport of pre-tRNA(Tyr) since a pre-tRNA(3Leu) variant which was not spliced was also not exported.

Repression and redirection of Saccharomyces cerevisiae tRNA synthesis from upstream of the transcriptional start site.

Derivatives of the Saccharomyces cerevisiae SUP4 tRNATyr gene with binding sites for the transcription regulatory protein GCN4 located upstream of the transcriptional start site have been constructed. The effect of GCN4 on transcription of these genes by purified RNA polymerase III and transcription factors (TF) IIIB and IIIC has been analyzed. GCN4 effectively blocks initiation of transcription only when prebound to sites that overlap with the binding site of TFIIIB. Residual GCN4-repressed transcription is significantly redirected to nearby downstream sites, the selection of which depends on the location of bound GCN4. That prebound repressing GCN4 redirects, instead of merely blocking, the TFIIIC-dependent interaction of TFIIIB with DNA has been directly demonstrated by footprinting. The effect of GCN4 on transcription persists after it has been stripped off its DNA-binding site: once it has been redirected, DNA-bound TFIIIB remains in place, a consequence of the fact that it binds extraordinarily tightly to DNA without recognizing specific DNA sequence.

Non-enzymatic excision of pre-tRNA introns?

We used human tRNA(Tyr) precursor as a substrate to study self-excision of a pre-tRNA intron. This RNA was synthesized in vitro in a HeLa cell extract. It contains a 5' leader, an intron of 20 nucleotides and a 3' trailer. Self-cleavage of pre-tRNA(Tyr) occurs in 100 mM NH4OAc at a pH ranging from 6 to 8.5 in the presence of spermine, MgCl2 and Triton X-100 under conditions very similar to enzymatic intron excision. The reaction is temperature-dependent, relatively fast as compared to the enzyme-catalysed reaction and leads to fragments which resist further degradation. The detailed structure of all major and minor cleavage products was established by fingerprint analyses. Non-enzymatic cleavage occurs predominantly at the 3' splice site and to a minor extent at the 5' splice site. Other minor cleavage sites are located within the intron and in the 3' trailer. Putative 5' and 3' tRNA halves resulting from pre-tRNA(Tyr) self-cleavage are substrates for wheat germ RNA ligase, suggesting that the cleavage reaction yields 2',3'-cyclic phosphate and 5'-hydroxyl termini. Pre-tRNA splicing endonuclease is believed to cleave both the 5' and the 3' splice site. However, on the basis of our results we propose that this enzyme may support the formation of a pre-tRNA tertiary structure favourable for autocatalytic intron excision and impair unspecific self-cleavage.