A rat tRNA gene cluster containing the genes for tRNAPro and tRNALys. Analysis of nucleotide sequences of the genes and the surrounding regions

Inhibition of nascent-peptide release at translation termination

The transcript leader of the human cytomegalovirus (CMV) gpUL4 (gp48) gene contains a 22-codon upstream open reading frame (uORF2) that represses translation of the downstream cistron. Previous work demonstrated that ribosomes stall at the termination codon of uORF2 and, remarkably, that the coding information of uORF2 is required for both the translational repression and ribosomal stalling. We now provide evidence that the peptide product of uORF2 is synthesized and is retained in the ribosome in the form of a peptidyl-tRNA. Translation of the gp48 transcript leader in cell extracts produces the 2.4-kDa uORF2 peptide and a second product migrating with an apparent molecular mass of 20 kDa that represents the uORF2 peptide covalently linked to tRNA(Pro), the tRNA predicted to decode the carboxy-terminal codon of uORF2. The uORF2 peptidyl-tRNA is only detected after translation of RNAs containing uORF2 sequences that also inhibit downstream translation and cause ribosomal stalling. These data support a model in which the nascent uORF2 peptide blocks translation termination prior to hydrolysis of the peptidyl-tRNA bond. This blockade results in ribosomal stalling on the transcript leader which in turn impedes the access of ribosomes to the downstream cistron. This system illustrates that translation termination may be a critical step controlling expression of some eukaryotic genes.

The processing of wild type and mutant forms of rat nuclear pre-tRNA(Lys) by the homologous RNase P

The 5' processing of rat pre-tRNA(Lys) and a series of mutant derivatives by rat cytosolic RNase P was examined. In standard, non-kinetic assays, mutant precursors synthesized in vitro with 5' leader sequences of 10, 17, 24, 25, and 46 nucleotides were processed to approximately equal levels and yielded precisely cleaved 5' processed intermediates with the normal 7-base pair aminoacyl stems. The construct containing the tRNA(Lys) with the 46-nucleotide leader was modified by PCR to give a series of pre-tRNA(Lys) mutants designed to measure the effect on processing by (1) substituting the nucleotide at the +1 position, (2) pairing and unpairing the +1 and +72 bases, (3) elongating the aminoacyl stem, and (4) disrupting the helix of the aminoacyl stem. Comparative kinetic analyses revealed that changing the wild type +1G to A, C, or U was well tolerated by the RNase P provided that compensatory changes at +72 created a base pair or a G.U noncanonical pair. Mutants with elongated aminoacyl stems that were produced either by inserting an additional base pair at +3:a + 69:a or by pairing the -1A with a +73U, were processed to yield 7-base pair aminoacyl stems, but with different efficiencies. The efficiency seen with the double insertion mutant was higher than even the wild type precursor, but the -1A-U + 73 mutant was a relatively poor substrate. Disrupting the aminoacyl stem helix by introducing a +7G G + 66 mispairing or by inserting a single G at the +3:a position dramatically reduced the processing efficiency, although the position of cleavage occurred precisely at the wild type cleavage site. However, the single insertion of a C at the +69:a position resulted in an efficiently cleaved precursor, but permitted a minor, secondary cleavage within the leader between the -6 and -5 nucleotides in addition to the dominant wild type scission.

Transfer RNA genes from Dictyostelium discoideum are frequently associated with repetitive elements and contain consensus boxes in their 5' and 3'-flanking regions

A total of 68 different tRNA genes from the cellular slime mold Dictyostelium discoideum have been isolated and characterized. Although these tRNA genes show features common to typical nuclear tRNA genes from other organisms, several unique characteristics are apparent: (1) the 5'-proximal flanking region is very similar for most of the tRNA genes; (2) more than 80% of the tRNA genes contain an "ex-B motif" within their 3'-flanking region, which strongly resembles characteristics of the consensus sequence of a T-stem/T-loop region (B-box) of a tRNA gene; (3) probably more than 50% of the tRNA genes in certain D. discoideum strains are associated with a retrotransposon, termed DRE (Dictyostelium repetitive element), or with a transposon, termed Tdd-3 (Transposon Dictyostelium discoideum). DRE always occurs 50 (+/- 3) nucleotides upstream and Tdd-3 always occurs 100 (+/- 20) nucleotides downstream from the tRNA gene. D. discoideum tRNA genes are organized in multicopy gene families consisting of 5 to 20 individual genes. Members of a particular gene family are identical within the mature tRNA coding region while flanking sequences are idiosyncratic.

Eukaryotic tRNAs(Pro): primary structure of the anticodon loop; presence of 5-carbamoylmethyluridine or inosine as the first nucleoside of the anticodon

The modified nucleoside U*, located in the first position of the anticodon of yeast, chicken liver and bovine liver tRNA(Pro) (anticodon U*GG), has been determined by means of TLC, HPLC, ultraviolet spectrum and gas chromatography-mass spectrometry. The structure was established as 5-carbamoylmethyluridine (ncm5U). In addition, we report on the primary structures of the above-mentioned tRNAs as well as those which have the IGG anticodon. In yeast, the two tRNA(Pro) (anticodons U*GG and IGG) differ by eight nucleotides, whereas in chicken and in bovine liver, both anticodons are carried by the same 'body tRNA' with one posttranscriptional exception at position 32, where pseudouridine is associated with ncm5U (position 34) in tRNA(Pro) (U*GG) and 2'-O-methylpseudouridine is associated with inosine (position 34) in tRNA(Pro) (IGG).

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 human tRNA gene cluster encoding the major and minor valine tRNAs and a lysine tRNA

A human genomic DNA clone hybridizing to mammalian valine tRNA(IAC) contained a cluster of three tRNA genes. Two valine tRNA genes with anticodons of AAC and CAC, encoding the major and minor cytoplasmic valine tRNA isoacceptors, respectively, and a lysine tRNA(CUU) gene were identified by Southern blot hybridization and DNA sequence analysis of a 7.1-kb region. At least nine Alu family members were interspersed throughout the 18.5-kb human DNA fragment, with three Alu elements in the intergenic region between the valine tRNA(AAC) gene and the lysine tRNA gene. Each of the five Alu family members in the sequenced region can be categorized into one of the four Alu subfamilies. The coding regions of all three tRNA genes contain characteristic internal split promoter sequences and typical RNA polymerase III termination signals in the 3'-flanking regions. The tRNA genes are accurately transcribed by RNA polymerase III in a HeLa cell extract, since the RNase T1 fingerprints of the mature-sized tRNA transcription products are consistent with the structural genes. The lysine tRNA(CUU) gene was transcribed only slightly more efficiently than the valine tRNA(CAC) gene in the homologous in vitro transcription system. Surprisingly, the valine tRNA(CAC) gene was transcribed about eightfold more efficiently than the valine tRNA(AAC) gene, implicating the presence of a modulatory element in the upstream region flanking the tRNA(CAC) gene.

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.

tRNAGlu(GAA) genes from the cellular slime mold Dictyostelium discoideum

The haploid genome of the cellular slime mold Dictyostelium discoideum contains at least 18 gene copies coding for a tRNAGlu(GAA). Using a combination of parasexual genetic analysis and molecular biology techniques, 14 of the 18 individual members of this gene family could be assigned to particular linkage groups. According ot this analysis four tRNAGlu genes are located on group I (C, H, I, K), two genes on group II (D,J), seven genes on either group III or VI (A, B, E, F, L, M, N), and one gene on group VII (G). Eight of the tRNAGlu(GAA) genes have been cloned and characterized. All genes are identical in that part of the gene which corresponds to the mature tRNA, thus representing true nonallelic members of this gene family. Different members of this gene family can be distinguished from each other because they reside on restriction fragments of different lengths and because each gene contains unique 5'- and 3'-flanking regions. Nevertheless, a certain degree of sequence conservation within these flanking regions is apparent for members of this gene family. According to in vivo expression analyses of individual genes in Saccharomyces cerevisiae, all isolated tRNAGlu(GAA) copies represent functional transcription units.

Modulation of transcriptional activity and stable complex formation by 5'-flanking regions of mouse tRNAHis genes

We determined the nucleotide sequences of three mouse tRNAHis genes and a tRNAGly gene present in two different lambda clones. One lambda clone contained two tRNAHis genes 600 base pairs (bp) apart in opposite orientations. The other clone contained a tRNAHis and a tRNAGly gene 569 bp apart in the same orientation. The coding regions of the three tRNAHis genes were identical to sequenced mammalian tRNAHis if posttranscriptional modifications are not considered. Notably, the three tRNAHis genes and a fourth gene previously sequenced by us contained within the flanking regions, various amounts of short, conserved 5' leader sequences and 3' trailer sequences directly abutting the coding regions. Otherwise the flanking regions were not homologous. Deletion mutants of one of the tRNAHis genes were constructed which contained 228, 99, 9, and 3 bp of the wild-type 5'-flanking region, respectively. Deletion of 5'-flanking sequences from positions -9 to -4 reduced transcriptional activity substantially (ca. fivefold) in a HeLa cell S-100 lysate. This effect was independent of the vector sequences in the deletion clone, implying that the region from -4 to -9 of the intact gene contains a positive modulatory element for transcription in vitro. The deletion mutant containing 3 bp of wild-type 5'-flanking sequence also had a greatly reduced ability to inhibit the transcription of a second tRNA gene in a competition assay. Thus, the normal 5'-flanking region influences the ability of the gene to form stable complexes with transcription factors. These data further indicate that a mammalian transcription extract is sensitive to 5'-flanking-region effects if a suitable tRNA gene is assayed.

Structure and in vitro transcription of tRNA gene clusters containing the primers of MuLV reverse transcriptase

Three genes coding for mouse tRNAPro have been isolated from a genomic library and characterized both structurally and functionally. Two of these (tPro52 and tPro53) code for the tRNA primer of reverse transcriptase of MuLV. The third one (tPro51) shows several differences (mutations and deletions) that probably prevent the folding of the matured transcript into the cloverleaf structure, and is therefore a pseudogene. This pseudogene gives rise to a RNA transcription product in vitro. tPro52 is clustered with a tRNALys gene and with a tRNAAla gene, which is strongly homologous to the rat identifier repeated sequence. tPro53 is clustered with a tRNAAsp and a tRNAGly gene. Other tRNA-hybridizing sequences are present in the lambda clones that contain tPro51 and tPro53.

The sequences of two nuclear genes and a pseudogene for tRNA(Pro) from the higher plant Phaseolus vulgaris

A genomic bank of nuclear DNA (nDNA) from the higher plant Phaseolus vulgaris, constructed using the lambda EMBL-4 vector, has been screened for the presence of tRNA genes. One of the many positive recombinants was found to hybridise several times stronger than the other positives, and has been shown to contain several tRNA genes. We report the structure of two nuclear tRNA genes for tRNA(Pro), namely tRNA(Pro)(UGG) and tRNA(Pro)(AGG), and that of a 'pseudogene' for tRNA(Pro). This 'pseudogene', despite showing 95% homology with the other tRNA(Pro) species presented here, has several features which are likely to affect its transcription or its functioning as a tRNA.

The human tRNAVal gene family: organization, nucleotide sequences and homologous transcription of three single-copy genes

At least 13 independent tRNAVal gene loci were detected in the human genome. Three of these genes were isolated and shown to occur only once in the haploid genome. No further functional tRNA genes are located on the isolated clones. Two tRNAVal genes encode the known major and minor tRNAVal isoacceptors, the third may be a pseudogene because a corresponding tRNAVal is not yet known. Comparison of extragenic sequences did not reveal significant homologies, indicating the separation of these genes early in vertebrate evolution. An Alu-type repeat was found in two of the clones within several hundred bp distance from the tDNA. All three genes are transcriptionally active in a HeLa nuclear extract. We show here for the first time that homologous in vitro transcription of mammalian tRNA genes strongly depends on extragenic control regions: interestingly, as a consequence of different flanking regions, the transcription efficiencies vary by an order of magnitude among the genes for the major and the minor tRNAVal and thus reflect the concentrations of these tRNAs in vivo.

Modulation of transcriptional activity and stable complex formation by 5'-flanking regions of mouse tRNAHis genes

We determined the nucleotide sequences of three mouse tRNAHis genes and a tRNAGly gene present in two different lambda clones. One lambda clone contained two tRNAHis genes 600 base pairs (bp) apart in opposite orientations. The other clone contained a tRNAHis and a tRNAGly gene 569 bp apart in the same orientation. The coding regions of the three tRNAHis genes were identical to sequenced mammalian tRNAHis if posttranscriptional modifications are not considered. Notably, the three tRNAHis genes and a fourth gene previously sequenced by us contained within the flanking regions, various amounts of short, conserved 5' leader sequences and 3' trailer sequences directly abutting the coding regions. Otherwise the flanking regions were not homologous. Deletion mutants of one of the tRNAHis genes were constructed which contained 228, 99, 9, and 3 bp of the wild-type 5'-flanking region, respectively. Deletion of 5'-flanking sequences from positions -9 to -4 reduced transcriptional activity substantially (ca. fivefold) in a HeLa cell S-100 lysate. This effect was independent of the vector sequences in the deletion clone, implying that the region from -4 to -9 of the intact gene contains a positive modulatory element for transcription in vitro. The deletion mutant containing 3 bp of wild-type 5'-flanking sequence also had a greatly reduced ability to inhibit the transcription of a second tRNA gene in a competition assay. Thus, the normal 5'-flanking region influences the ability of the gene to form stable complexes with transcription factors. These data further indicate that a mammalian transcription extract is sensitive to 5'-flanking-region effects if a suitable tRNA gene is assayed.

Nucleotide sequence and transcription of a gene encoding human tRNAGlyCCC

A phage lambda clone containing a 13.1-kb human DNA fragment was isolated and found to contain a tRNA gene encoding a glycine tRNA. The nucleotide sequence of the gene and its flanking regions has been determined. The gene does not have an intervening sequence nor does it encode the 3'-terminal CCA sequence found in mature tRNAs. Although this tRNA gene has an anticodon sequence of CCC, it has a striking homology (96%) with a human glycine tRNA which has an anticodon of GCC. As in other eukaryotic tRNA genes, the coding region contains a characteristic internal split promoter sequence, and the 3'-flanking region has a typical RNA polymerase III termination site of five consecutive T residues. There is no apparent sequence in the 5'-flanking region which could serve as a regulatory element. This gene is accurately transcribed in vitro by RNA polymerase III using a HeLa cell-free system. During the course of in vitro transcription, larger precursor tRNAGlyCCC transcripts are processed to yield a mature-sized tRNA product. A precursor-product relationship was established by comparing the ribonuclease A fingerprints of the precursor and product tRNA transcripts.

Genes and pseudogenes in a reiterated rat tRNA gene cluster

A 13.4 kb rat genomic DNA fragment containing two related tRNA gene clusters was isolated from a rat lambda recombinant and analyzed for gene arrangement and nucleotide sequence. One cluster was found to contain a tRNALeuCUG gene while the second contained a tRNALeuCUA pseudogene with multiple base substitutions. The tRNALeu gene was found to possess an intact coding region and a functional transcription termination signal at the 3' end as demonstrated by in vitro transcription and processing of precursors to mature size tRNA. The first tRNA gene cluster was found to contain in addition to tRNALeu, three other transcribable genes coding for tRNAAspGAC(U), tRNAGlyGGA(G) and tRNAGluGAG; the second cluster contained in addition to tRNALeu pseudogene, the tRNAAsp tRNAGly and tRNAGlu genes. Examination of flanking sequences of the corresponding tRNA genes in the two clusters shows no homology at the 5' ends and partial conservation of sequences at the 3'-end region. Genomic rat DNA blot hybridizations show that the tRNALeu gene is distributed together with the tRNAAsp, tRNAGly and tRNAGlu on a 10 fold repeat of 3.2 kb EcoRI fragment.

Lysine tRNAs from rat liver: lysine tRNA sequences are highly conserved

The two major lysine tRNAs from rat liver, tRNA2Lys and tRNA5Lys, were sequenced by rapid gel or chromatogram readout methods. The major tRNA2Lys differs from a minor form only by a base pair in positions 29 and 41; both tRNAs have an unidentified nucleotide, U**, in the third position of the anticodon. Although highly related, the major tRNA2Lys and tRNA5Lys differ in four base pairs and four unpaired nucleotides, including the first position of the anticodons, but have the same base pair in positions 29 and 41. The three tRNAs maintain a m2G-U pair in the acceptor stem. Detection of this m2G is in contrast to other reports of lysine tRNAs. Sequences of lysine tRNAs are strongly conserved in higher eukaryotes.

Nucleotide sequences of two regions of the human genome containing tRNAAsn genes

The primary structures of two human tRNAAsn genes and 600-700 nucleotides of their flanking regions have been determined from two separate isolates of a fetal DNA library in phage lambda vector. The tRNA gene from one clone differs from the major mammalian tRNAAsn by a single base substitution at position 47, with an A replacing a G, while the tRNAAsn gene from the second clone has base substitutions at positions 17 and 65, with a G replacing a C and a T replacing a C, respectively. The sequences of the noncoding 5'- and 3'-flanking regions of both clones are over 90% homologous. As with other mammalian tRNA genes, these two human tRNAAsn genes contain CTTTTPu, which might act as a transcription termination signal, 11 bp 3' to the structural gene. In vitro transcription experiments in a HeLa cell extract demonstrate that both cloned tRNAAsn genes can be transcribed and processed to mature-sized tRNAs.

Structure and evolution of a mouse tRNA gene cluster encoding tRNAAsp, tRNAGly and tRNAGlu and an unlinked, solitary gene encoding tRNAAsp

We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al., 1981, Nucleic Acids Res. 9, 2239-2250). The mouse and rat tRNAAsp and tRNAGly coding regions are identical. The tRNAGlu coding regions differ at two positions. The flanking sequences contain 3 non-homologous areas: a c. 100 bp insertion in the first mouse spacer, short tandemly repeated sequences in the second spacers and unrelated sequences at the 3' ends of the clusters. In contrast, most of the flanking regions are homologous, consisting of strings of consecutive, identical residues (5-17 bp) separated by single base differences and short insertions/deletions. The latter are often associated with short repeats. The homology of the flanking regions is c. 75%, similar to other murine genes. The second lambda clone contains a solitary mouse tRNAAsp gene. The coding region is identical to that of the clustered tRNAAsp gene. The 5' flanking regions of the two genes contain homologous areas (10-25 bp) separated by unrelated sequences. Overall, the flanking regions of the two mouse tRNAAsp genes are less homologous than those of the mouse and rat clusters.

Isolation and characterization of genomic mouse DNA clones containing sequences homologous to tRNAs and 5S rRNA

We have cloned and characterized three fragments of Balb/c mouse DNA which hybridize to mouse cell tRNAs. Fractionation of the tRNAs which hybridize to these clones reveals that two of the clones, lambda Mt-4A and lambda Mt-6A hybridize to only one or two tRNAs, while one clone, lambda Mt-4B, hybridizes to at least seven tRNAs. Two of the tRNAs were identified as tRNAProCCG and tRNAGlyGGA, and others have been identified as tRNAs which are selectively encapsidated into virions of murine leukemia virus and avian reticuloendotheliosis virus. The DNA sequences of putative genes for tRNAProCCG and tRNAGlyGGA, plus flanking regions, were determined. A clone of Balb/c mouse DNA which selectively hybridized to 5S rRNA was also isolated and partially characterized.

Isolation and characterization of three cloned fragments of human DNA coding for tRNAs and small nuclear RNA U1

Employing a human fetal liver library in lambda Charon 4A phage vector, we have isolated and characterized three clones of human DNA containing genes for tRNAs. One clone contains at least three tRNA genes (tRNALys, tRNAGln and tRNALeu) within 2 kb of each other. The other two clones contain two different single genes for tRNAAsn. One of these latter two DNAs also contains a gene for U1 small nuclear RNA.

Using iodinated single-stranded M13 probes to facilitate rapid DNA sequence analysis--nucleotide sequence of a mouse lysine tRNA gene

From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. However, the mouse gene contains a 14 bp region comprising 13 A-T base pairs, 30-44 bp from the 5' end of the coding region. Cognate A-T rich regions are present in human and Drosophila genes. The coding region is flanked by two 11 bp direct repeats, similar to those associated with alu family sequences. The sequence was determined by a "walking" protocol that employs, as a novel feature, iodinated single-stranded M13 probes to identify M13 subclones which contain sequences partially overlapping and contiguous to an initially determined sequence. The probes can also be used to screen lambda phage and in Southern and dot blot experiments.