Steady-state kinetic analysis of transcription of cloned tRNASer genes from Drosophila melanogaster

Differential transcription of multiple copies of a silk worm gene encoding tRNA(Gly1)

Ten different tRNA(Gly1) genes from the silk worm, Bombyx mori, have been cloned and characterized. These genes were transcribed in vitro in homologous nuclear extracts from the posterior silk gland (PSG) or nuclear extracts derived from the middle silk gland or ovarian tissues. Although the transcription levels were much higher in the PSG nuclear extracts, the transcriptional efficiency of the individual genes followed a similar pattern in all the extracts. Based on the levels of in vitro transcription, the ten tRNA(Gly1) genes could be divided into three groups, viz., those which were transcribed at very high levels (e.g., clone pR8), high to medium levels (e.g., pBmi1, pBmp1, pBmh1, pBmt1) and low to barely detectable levels (e.g., pBms1, pBmj1 and pBmk1). The coding sequences of all these tRNA genes being identical, the differential transcription suggested that the flanking sequences modulate their transcriptional efficiency. The presence of positive and negative regulatory elements in the 5' flanking regions of these genes was confirmed by transcription competition experiments. A positive element was present in the immediate upstream A+T-rich sequences in all the genes, but no consensus sequences correlating to the transcriptional status could be generated. The presence of negative elements on the other hand was indicated only in some of the genes and therefore may have a role in the differential transcription of these tRNA(Gly1) genes in vivo.

Informational redundancy of tRNA(4Ser) and tRNA(7Ser) genes in Drosophila melanogaster and evidence for intergenic recombination

Variant tRNA genes have been widely observed in multicellular eukaryotes. Recent biochemical studies have shown that some of them are expressed in a tissue- or a stage-specific manner. These findings would thus imply that certain modified tRNAs may be crucial for the development of the organism. Using Drosophila melanogaster as a model, we have taken a combined genetic and molecular approach to examine critically the possible biological functions of tRNA(4, 7Ser) genes. We showed that at least 50% of the total templates can be deleted from the genome without inducing abnormal phenotypes such as Minute, or a decrease in viability. In addition, two of the tRNASer variant genes that are unique in sequence are also completely dispensable. This strongly implies that even though they may be expressed in vivo, they play no essential role in the development of the fruitfly. By comparison with some of the corresponding tRNA genes in another sibling species, Drosophila erecta, our results suggest strongly that the variants are products non-reciprocal exchanges among the tRNA(4, 7Ser), genes. Such intergenic recombination events may have a major influence in the concerted evolution of the two gene families.

Drosophila melanogaster tRNA(Ser) suppressor genes function with strict codon specificity when introduced into Saccharomyces cerevisiae

The anticodon of the wild-type tRNA(7Ser) gene of Drosophila melanogaster was mutated using oligodeoxyribonucleotide-directed, site-specific mutagenesis, and all three nonsense suppressor derivatives of the gene were constructed. These constructs were cloned into an Escherichia coli-yeast shuttle vector (YRp7), and used to transform a Saccharomyces cerevisiae strain [JG 369-3B(alpha)] containing an array of nonsense alleles. When tested on appropriate omission media, the D. melanogaster suppressor genes were found to function in the yeast with strict codon specificity. Subsequent Northern hybridization analyses revealed that the D. melanogaster suppressor genes were transcribed and processed well, when in S. cerevisiae.

A human tRNA gene heterocluster encoding threonine, proline and valine tRNAs

A cluster of three tRNA genes encoding a tRNA(UGUThr), a tRNA(UGGPro), and a tRNA(AACVal), and two Alu-elements occur in a 6.0-kb human DNA fragment. The tRNA(Thr) gene is 2.7-kb upstream from the tRNA(Pro) gene, which is separated by 367 bp from the tRNA(Val) gene. One Alu-element actually overlaps the tRNA(Val) gene and is of opposite polarity to all three tRNA genes. All three tRNA genes are accurately transcribed in a homologous HeLa cell extract, since the ribonuclease T1 fingerprints of the tRNA transcripts are consistent with the nucleotide sequences of the tRNAs. The upstream region flanking the tRNA(Thr) gene has two tracts of alternating purine/pyrimidine residues potentially capable of adopting the Z-DNA conformation, and presumptive binding sites for two RNA polymerase II transcription factors. The tRNA(Thr) gene apparently has a substantially higher in vitro transcriptional efficiency than the other two tRNA genes in this cluster, and a tRNA(GCCGly) gene from another human DNA segment. Deletion constructs of the tRNA(Thr) gene retaining 272, 168, and 33 bp of original 5'-flanking DNA had about the same in vitro transcriptional efficiency, whereas that of the construct with only 2 bp of 5'-flanking human DNA was drastically reduced. The tRNA(Thr) gene constructs with 272 and 168 bp of original 5'-flanking DNA apparently reduce the transcriptional efficiencies of the proline and glycine tRNA genes, implicating the upstream region from the tRNA(Thr) gene as being crucial for its high transcriptional efficiency.

Heterologous 5' flanking regions do not support in vitro template activity of a Drosophila melanogaster tRNA(Val3b) gene

The 5' and 3' structure of a Drosophila tRNA(Val3b) gene was investigated to examine the defect which caused the extremely low in vitro transcription template activity of the gene. Recombinant genes were constructed linking 5' and 3' flanking regions from tRNA genes which were active in vitro templates (tRNA(Val4), tRNA(Arg), tRNA(Ser7)) to the tRNA(Val3b) gene. None of the recombinant genes were effective in vitro templates. The defect in tRNA(Val3b) was demonstrated to reside in the 5' flanking region of the gene and deletion analysis indicated that no specific transcription inhibitor sequence was present 5' to the gene. The data suggest that the effect of 5' flanking sequences on in vitro transcription of the tRNA(Val3b) gene requires a specific relationship between the tRNA gene and the flanking sequence.

Sequences between the internal control regions of tRNAArg of Drosophila melanogaster influence stimulation of transcription of the 5' flanking DNA

Recombinants between 5' deletion mutants of a tRNA(3bVal) gene which is inactive as an in vitro transcription template and a tRNAArg gene, which is an active in vitro template were made. The 5' flanking region of tRNA(Arg) including 36 nucleotides of the coding sequence of the gene stimulated transcription of the tRNA(3bVal), deleted to the +17 position, gene by over 50 fold. When the 5' flanking region of the tRNA(Arg) gene included 22 nucleotides of the coding sequence stimulation was reduced by a factor of 3. Thus the sequences between +22 and +36 of tRNA(Arg) are required to permit maximum stimulation of tRNA(3bVal) in vitro template activity.

The 5'-flanking sequence of yeast tRNA(Leu3) genes enhances the rate of transcription from stable pre-initiation complexes

A conserved sequence that enhances transcription is present at or near the 5'-end of genes which code for several abundant yeast tRNAs, one of which is tDNA(Leu3). Mutants with alterations in this region have been compared to the parent tDNA(Leu3) and a yeast tDNA(Ser) that normally lacks the conserved sequence. The apparent KM of the transcription apparatus is insensitive to 5'-flanking sequence variation. Replacement of the normal 5'-flanking sequence does result in 3-18 fold reductions in VMAX and a 7-13 fold loss of transcription in tests with competitor genes. A second template exclusion assay revealed that sequences upstream of the conserved region effect a 2 fold change in the ability of the genes to stably sequester a component(s) of the obligatory pre-initiation complex while positions -22 to +9 have little or no effect.

Extensive microheterogeneity of serine tRNA genes from Drosophila melanogaster

The nucleotide sequences of nine genes corresponding to tRNA(Ser)4 or tRNA(Ser)7 of Drosophila melanogaster were determined. Eight of the genes compose the major tRNA(Ser)4,7 cluster at 12DE on the X chromosome, while the other is from 23E on the left arm of chromosome 2. Among the eight X-linked genes, five different, interrelated, classes of sequence were found. Four of the eight genes correspond to tRNA(Ser)4 and tRNA(Ser)7 (which are 96% homologous), two appear to result from single crossovers between tRNA(Ser)4 and tRNA(Ser)7 genes, one is an apparent double crossover product, and the last differs from a tRNA(Ser)4 gene by a single C to T transition at position 50. The single autosomal gene corresponds to tRNA(Ser)7. Comparison of a pair of genes corresponding to tRNA(Ser)4 from D. melanogaster and Drosophila simulans showed that, while gene flanking sequences may diverge considerably by accumulation of point changes, gene sequences are maintained intact. Our data indicate that recombination occurs between non-allelic tRNA(Ser) genes, and suggest that at least some recombinational events may be intergenic conversions.

Modulation of a Drosophila melanogaster tRNA gene transcription in vitro by a sequence TNNCT in its 5' flank

We have previously demonstrated the existence of both positive and negative transcription modulatory sequences in the 5' flank of a Drosophila melanogaster tRNA(4Val) gene using deletion analysis. The deletion of a pentadeoxynucleotide TCGCT between nucleotides (nt) -34 and -38 relative to the mature coding sequences resulted in a 90% decrease in template activity. In the present study, we have created a number of site-specific changes in the sequence TCGCT. Results indicate a significant decrease in the level of template activity when nt -38(T), -35(C) and -34(T) were mutated. In contrast, a change at nt -37(C) resulted in a slight increase in transcription and a change at nt -36(G) reduced template activity by only 1%. Sequences flanking other tRNA genes which are efficient templates for transcription were examined and found to contain a sequence closely related to TCGCT. We propose that a general form of the sequence TNNCT is a positive transcription modulator for a class of Drosophila tRNA genes.

Identification and nucleotide sequence determination of a potential primer tRNA for reverse transcription of a Drosophila retrotransposon, 297

Drosophila retrotransposons have been shown to have genes for enzymes similar to the reverse transcriptase of retroviruse. They may possibly be involved in genome replication on translocation (15). Identification was made of a primer tRNA for the putative reverse transcription of a Drosophila retrotransposon, 297, and its genomic counterparts using a homology to the putative primer binding site of 297. Our nucleotide sequence analysis indicated a species of Drosophila serine tRNA to have two distinct properties similar to those characteristic of retroviral primer tRNA: its 3'terminal 18 nucleotides are exactly complementary to the putative primer binding site of 297 and its 19th base from the 3' end is modified. These results appear to support the notion stated above and suggest this serine tRNA to be the most likely candidate for a potential primer tRNA of 297.

Upstream sequences confer distinctive transcriptional properties on genes encoding silkgland-specific tRNAAla

To understand the molecular basis for the tissue-specific accumulation of alanine tRNAs in silkworms, we have compared the transcriptional properties of genes that encode constitutive and silkgland-specific type alanine tRNA. Genes for each class of alanine tRNA behave very differently when used as templates for homologous in vitro transcription. Since these properties are likely related to the activities of the corresponding genes in vivo, we wished to identify the cis-acting elements responsible for them. We have therefore constructed hybrid silkgland-specific/constitutive genes and have analyzed their capacity to direct transcription in vitro. We find a simple pattern: the distinctive transcriptional properties of the two kinds of tRNAAla genes are the result of different positive signals upstream from their sites of transcription initiation.