Primary structure of yeast mitochondrial DNA-coded phenylalanine-tRNA

tRNA biology in mitochondria

Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.

Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5

Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3'-adjacent to the anticodon, generates the modified nucleoside m(1)G37. In archaea and eukaryotes, m(1)G37 synthesis is catalyzed by tRNA(m(1)G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 A resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class-I methyltransferases. The a/eTrm5-defining domain, D2, exhibits structural similarity to some class-I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2-D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2-D3 fragment or the tRNA. The NMR analysis of the D2-D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2-D3 fragment was as active as the full-length enzyme for tRNA methylation. The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation.

Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase

The TRM5 gene encodes a tRNA (guanine-N1-)-methyltransferase (Trm5p) that methylates guanosine at position 37 (m(1)G37) in cytoplasmic tRNAs in Saccharomyces cerevisiae. Here we show that Trm5p is also responsible for m(1)G37 methylation of mitochondrial tRNAs. The TRM5 open reading frame encodes 499 amino acids containing four potential initiator codons within the first 48 codons. Full-length Trm5p, purified as a fusion protein with maltose-binding protein, exhibited robust methyltransferase activity with tRNA isolated from a Delta trm5 mutant strain, as well as with a synthetic mitochondrial initiator tRNA (tRNA(Met)(f)). Primer extension demonstrated that the site of methylation was guanosine 37 in both mitochondrial tRNA(Met)(f) and tRNA(Phe). High pressure liquid chromatography analysis showed the methylated product to be m(1)G. Subcellular fractionation and immunoblotting of a strain expressing a green fluorescent protein-tagged version of the TRM5 gene revealed that the enzyme was localized to both cytoplasm and mitochondria. The slightly larger mitochondrial form was protected from protease digestion, indicating a matrix localization. Analysis of N-terminal truncation mutants revealed that a Trm5p active in the cytoplasm could be obtained with a construct lacking amino acids 1-33 (Delta1-33), whereas production of a Trm5p active in the mitochondria required these first 33 amino acids. Yeast expressing the Delta1-33 construct exhibited a significantly lower rate of oxygen consumption, indicating that efficiency or accuracy of mitochondrial protein synthesis is decreased in cells lacking m(1)G37 methylation of mitochondrial tRNAs. These data suggest that this tRNA modification plays an important role in reading frame maintenance in mitochondrial protein synthesis.

Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting

Mutations in the acceptor stem, the 5-methyluridine-pseudouridine-cytidine (TFC) arm, and the anticodon of Salmonella tRNA2Gly can cause -1 frameshifting. The potential for standard base pairing between acceptor stem positions 1 and 72 is disrupted in the mutant sufS627. This disruption may interfere with the interaction of the tRNA with elongation factor-Tu.GTP or an as-yet-unspecified domain of the ribosome. The potential for standard base pairing in part of the TFC stem is disrupted in mutant sufS625. The nearly universal C-61 base of the TFC stem is altered in mutant sufS617, and the TFC loop is extended in mutant sufS605. These changes are expected to interfere with the stability of the TFC loop and its interaction with the D arm. The mutation in mutant sufS605, and possibly other mutants, alters nucleoside modification in the D arm. Three mutants, sufS601, sufS607, and sufS609, have a cytidine substituted for the modified uridine at position 34, the first anticodon position. None of the alterations grossly disrupts in-frame triplet decoding by the mutant tRNAs. The results show that -1 frameshifting in vivo can be caused by tRNAs with normal anticodon loop size and suggest that alternative conformational states of the mutant tRNAs may allow them to read a codon in frame or to shift reading frame.

Codon reading patterns in Saccharomyces cerevisiae mitochondria based on sequences of mitochondrial tRNAs

The sequences of Saccharomyces cerevisiae mitochondrial tRNA Arg1, tRNA Arg2, tRNA Gly, tRNA Lys2, tRNA Leu amd tRNA Pro are reported. Special structural features were found in tRNA Pro, which has A8, C21, A48 instead of the constant residues U8, A21 and pyrimidine 48, and in tRNA Lys2, which has a U excluded from base-paring and bulging out from the TpsiC stem. The tRNA Arg1, tRBA Lys2 and tRNA Leu, which belong to two-codon families ending in a purine, have a modified uridine in the wobble position, which prevents misreading of C and U. It is likely to be 5-carboxymethylaminomethyluridine. tRNA Gly and tRNA Pro have an unmodified uridine in the wobble position allowing the reading of all four codons of a four-codon family. However, tRNA Arg2, which is a minor species and belongs to the CGN four-codon family, has an unmodified A in the wobble position. This unusual feature raises the problem of the mechanism by which the codons CGA, CGG and CGC are recognized.

Phenylalanine and tyrosine transfer RNAs encoded by Tetrahymena pyriformis mitochondrial DNA: primary sequence, post-transcriptional modifications, and gene localization

We have isolated Phe and Tyr tRNAs from Tetrahymena pyriformis mitochondria and have determined that these are "native" species, encoded by the mtDNA. A single gene for the tRNA(Phe) has been positioned 12-14 kbp from the left end of the linear Tetrahymena mtDNA, while duplicate tRNA(Tyr) genes have been localized within the inverted terminal repeats of this genome. Primary sequence analysis demonstrates that the tRNA(Tyr) has all of the characteristic primary and secondary structural features of a normal tRNA; however, the tRNA(Phe) displays several atypical features, including (i) replacement of the usual T psi sequence by UC, (ii) a U.U pair in the T psi C stem, and (iii) an extra 5'-nucleotide (U).

Yeast mitochondrial tRNAIle and tRNAMetm: nucleotide sequence and codon recognition patterns

The nucleotide sequence of yeast mitochondrial isoleucine- and methionine-elongator tRNA have been determined. Interestingly, long stretches of almost identical nucleotide sequences are found within these two tRNAs and also within the yeast mt tRNAMetf, suggesting that the 3 tRNAs may have arisen from a common ancestor. Both mt tRNAMetm and tRNAIle contain all the structural characteristics which are present in the standard cloverleaf, except that the mt tRNAMetm contains an extra unpaired nucleotide within the base-paired T psi C stem. This rather unusual feature may have an influence on the decoding properties of the C-A-U anticodon of mt tRNAMetm by conferring the ability to translate not only the codon A-U-G but also A-U-A.

The primary structure of yeast mitochondrial tyrosine tRNA

The mitochondrial tyrosine tRNA from Saccharomyces cerevisiae has been sequenced. It has two interesting structural features: (i) it lacks two semi-invariant purine residues in the D-loop which are involved in tertiary interactions in the yeast cytoplasmic tRNAPhe; (ii) it has a large variable loop and therefore resembles procaryotic tRNAsTyr rather than eucaryotic cytoplasmic ones.

Transcripts of mitochondrial tRNA genes in Saccharomyces cerevisiae

The transcription of a group of tRNA genes from the large tRNA gene cluster of mitochondrial DNA from Saccharomyces cerevisiae has been investigated by hybridization with DNA probes carrying tRNA coding sequences and small portions of the A + T rich intergenic regions. Results have shown that in some rho- mutants (DS502, F11) mature tRNA was absent, but a few transcripts could be detected. Some high molecular weight species actually hybridized with DNA probes carrying different tRNA coding sequences. Low molecular weight transcripts (100-150 nucleotides, carrying one tRNA sequence) were also present in these mutants. A high molecular weight transcript was also observed in the wild type, though in much more limited amount. The low molecular weight transcripts were analysed by the S1 mapping technique and found to include both a tRNA sequence and the upstream 5' flanking region extending as far as the 3' end of the preceding tRNA gene. The results suggest the existence of a common transcript bearing several tRNA sequences and indicate a possible mechanism of processing, which might be defective in mutants.

The primary structures of three yeast mitochondrial serine tRNA isoacceptors

Yeast mitochondria contain several isoaccepting species of serine-tRNA. The relative amount of these isoacceptors varies according to the conditions used to grow the yeast cells. In order to gain insight into the structural differences among these isoacceptors, the three mitochondrial tRNAsSer, which are present in derepressed yeast cells, have been sequenced. The primary structure of tRNASer1 differs considerably from that of tRNASer2; these two isoacceptors have only 39 nucleotides in common. In contrast, tRNASer3 differs from tRNASer2 by only one post-transcriptional modification: the psi residue in position 28 of tRNASer2 is replaced by a normal U in tRNASer3. Unlike tRNASer2 and tRNASer3, the primary sequence of tRNASer1 shows two unusual structural features: it has a D in position 14 instead of the "universal" A14 of the standard tRNA cloverleaf and it contains two G residues between the D-stem and the anticodon-stem. Considering their respective anticodons, tRNASer1 should recognize the two serine codons A-G-C and A-G-U, whereas both tRNASer2 and tRNASer3 should recognize all four serine codons of the U-C-N series.

The nucleotide sequence of the maize and spinach chloroplast isoleucine transfer RNA encoded in the 16S to 23S rDNA spacer

The sequence of maize chloroplast tRNAIle2, encoded in the 16S to 23S rDNA spacer, was determined using in vitro labeling techniques. The sequence is: pG-G-G-C-U-A-U-U-A-G-C-U-C-A-G-U-Gm-G-D-A-G-A-G-C-m22G-C-G-C-C-C-C-U-G-A-U-t6A- A-G-G-G-C-G-A-G-m7G-acp3U-C-U-C-U-G-G-T-psi-C-A-A-G-U-C-C-A-G-G-A-U-G-G-C-C-C-A -C-C-AOH. This sequence is identical to that predicted from the corresponding gene sequence, after excision of a long intervening sequence (1), but shows the post-transcriptional modifications of this tRNA. Furthermore it demonstrates that the excision of the intron occurs after the second base following the anticodon and that this gene, which is over 1000 base-pair long, is transcribed and processed into a mature functional chloroplast-tRNA. The sequence of maize (a monocot) and spinach (a dicot) tRNAIle2 are shown to be identical.

In vitro reconstruction of the mitochondrial translation system of yeast

We have isolated the translation system from yeast mitochondria and have reconstructed it in vitro. This submitochondrial system, composed of mitochondrial ribosomes, tRNA, pH 5 fraction and mRNA, is maximally active at 10 mM Mg2+ and 100 mM KCl or NH4Cl. NH4+ is more stimulatory than K+. Added Escherichia coli tRNA gives less than half the activity obtained with added mitochondrial tRNA. Activity is enhanced with protease inhibitors but not with Ca2+, spermine, or spermidine. In contrast to heterologous translation systems, the present system produces products with molecular weights similar to those of products synthesized by yeast mitochondria in vivo and by intact yeast mitochondria in vitro. The results support the idea that the unique coding features of the mitochondrial genome require a unique translation system for accurate translation of mitochondrial mRNAs.

Structure and properties of a bovine liver UGA suppressor serine tRNA with a tryptophan anticodon

A bovine liver serine tRNA with a variety of unusual features has been sequenced and characterized. This tRNA is aminoacylated with serine, although it has a tryptophan anticodon CmCA. In ribosome binding assays, this tRNA (tRNASERCmCA) binds to the termination codon UGA and shows little or no binding in response to a variety of other codons including those for tryptophan and serine. The unusual codon recognition properties of this molecule were confirmed in an in vitro assay where this tRNA suppressed UGA termination. This is the first naturally occurring eucaryotic suppressor tRNA to be so characterized. Other unusual features, possibly related to the ability of this tRNA to read UGA, are the presence of two extra nucleotides, compared to all other tRNAs, between the universal residues U at position 8 and A at position 14 and the presence of an extra unpaired nucleotide within the double-stranded loop IV stem. This tRNA is also the largest eucaryotic tRNA sequenced to date (90 nucleotides). Despite its size, however, it contains only six modified residues, tRNASerCmCA shows extremely low homology to other mammalian serine (47-52% homology) or tryptophan (49% homology) tRNAs.

The nucleotide sequence of spinach chloroplast methionine elongator tRNA

The nucleotide sequence of spinach chloroplast methionine elongator tRNA (sp. chl. tRNAm Met) has been determined. This tRNA is considerably more homologous to E. coli tRNAm Met (67% homology) than to the three known eukaryotic tRNAm Met (50-55% homology). Sp. chl. tRNAm Met, like the eight other chloroplast tRNAs sequenced, contains a methylated GG sequence in the dihydrouridine loop and lacks unusual structural features which have been found in several mitochondrial tRNAs.

Transfer RNA genes in the cap-oxil region of yeast mitochondrial DNA

A cytoplasmic "petite" (rho-) clone of Saccharomyces cerevisiae has been isolated and found through DNA sequencing to contain the genes for cysteine, histidine, leucine, glutamine, lysine, arginine, and glycine tRNAs. This clone, designated DS502, has a tandemly repeated 3.5 kb segment of the wild type genome from 0.7 to 5.6 units. All the tRNA genes are transcribed from the same strand of DNA in the direction cap to oxil. The mitochondrial DNA segment of DS502 fills a sequence gap that existed between the histidine and lysine tRNAs. The new sequence data has made it possible to assign accurate map positions to all the tRNA genes in the cap-oxil span of the yeast mitochondrial genome. A detailed restriction map of the region from 0 to 17 map units along with the locations of 16 tRNA genes have been determined. The secondary structures of the leucine and glutamine tRNAs have been deduced from their gene sequences. The leucine tRNA exhibits 64% sequence homology to an E. coli leucine tRNA.

Leaky +1 and -1 frameshift mutations at the same site in a yeast mitochondrial gene

Two mutations in a mitochondrial structural gene, which cause leaky premature polypeptide chain termination and leaky growth, are +1 and -1 frameshifts in the same run of five T residues. The partial restoration of reading frame is probably due to ribosomal frameshifting at this site, and may be promoted by the unique structure of the yeast mitochondrial t RNAPhe.

Distinctive sequence of human mitochondrial ribosomal RNA genes

The nucleotide sequence spanning the ribosomal RNA (rRNA) genes of cloned human mitochondrial DNA reveals an extremely compact genome organization wherein the putative tRNA genes are probably 'butt-jointed' around the two rRNA genes. The sequences of the rRNA genes are significantly homologous in some regions to eukaryotic and prokaryotic sequences, but distinctive; the tRNA genes also have unusual nucleotide sequences. It seems that human mitochondria did not originate from recognizable relatives of present day organisms.

Hamster mitochondrial transfer RNA lacks T and the universal GUUCG sequence

Earlier inferences (based on incorporation of radio-activity from methyl-labeled methionine) that mammalian mitochondrial tRNA lacks ribothymidine ('T') have been confirmed using [14C]uridine as precursor. Moreover, oligonucleotide fingerprint analysis of 32P-labeled samples have shown that hamster mitochondrial tRNA lacks the 'universal' pentanucleotide of conventional tRNA in which T normally occurs, CTpsiCG, in modified or unmodified form.

Yeast mitochondrial methionine initiator tRNA: characterization and nucleotide sequence

Two methionine tRNAs from yeast mitochondria have been purified. The mitochondrial initiator tRNA has been identified by formylation using a mitochondrial enzyme extract. E. coli transformylase however, does not formylate the yeast mitochondrial initiator tRNA. The sequence was determined using both 32P-in vivo labeled and 32P-end labeled mt tRNAf(Met). This tRNA, unlike N. crassa mitochondrial tRNAf(Met), has two structural features typical of procaryotic initiator tRNAs: (i) it lacks a Watson-Crick base-pair at the end of the acceptor stem and (ii) has a T-psi-C-A sequence in loop IV. However, both yeast and N. crassa mitochondrial initiator tRNAs have a U11:A24 base-pair in the D-stem unlike procaryotic initiator tRNAs which have A11:U24. Interestingly, both mitochondrial initiator tRNAs, as well as bean chloroplast tRNAf(Met), have only two G:C pairs next to the anticodon loop, unlike any other initiator tRNA whatever its origin. In terms of overall sequence homology, yeast mitochondrial tRNA(Met)f differs from both procaryotic or eucaryotic initiator tRNAs, showing the highest homology with N. crassa mitochondrial initiator tRNA.

The nucleotide sequence of phenylalanine tRNA from the cytoplasm of Neurospora crassa

The phenylalanine tRNA from the cytoplasm of Neurospora crassa has been purified and sequenced. The sequence is: pGCGGGUUUAm2GCUCA (N) GDDGGGAGAGCm22GpsiCAGACmUGmAAYApsim5CUGAAGm7GDm5CGUGUGTpsiCGm1AUCCACACAAACCGCACCAOH. Both in the nature of modified nucleotides which are present in this tRNA and in the overall sequence, this tRNA resembles more closely phenylalanine tRNAs of eukaryotic cytoplasm than those of prokaryotes. The sequence of this tRNA differs from those of the corresponding tRNAs of wheat germ and yeast by only 6 and 7 nucleotides respectively out of 76 nucleotides.U

The tRNAAGYSer and tRNACGYArg genes from a gene cluster in yeast mitochondrial DNA

Yeast mitochondrial DNA-pBR322 recombinant DNA molecules screened for rRNA genes were used as a source of DNA for mitochondrial tRNA gene sequence analysis. We report here the sequences of yeast mitochondrial tRNA genes coding for a tRNAAGYSer and a tRNACGYArg. The tRNAAGYSer sequence deduced from the gene is the first reported sequence of a yeast tRNAAGYSer. It is also the second yeast mitochondrial tRNASer gene to be sequenced, and demonstrates unequivocally the presence of mitochondrial encoded serine tRNA isoacceptors. The tRNACGYArg sequence deduced from the gene is the most AT-rich (82%) tRNA sequence ever reported. Whereas all the mitochondrial genes sequenced to date exist singly on the genome and are separated by long stretches of AT-rich DNA, the tRNAACYSer and tRNAcgyarg genes exist in tandem, separated by only 3 bp. This gene arrangement strongly suggests that mitochondrial tRNA genes may be transcribed into multicistronic precursors.

Evolution of methionine initiator and phenylalanine transfer RNAs

Sequence data from methionine initiator and phenylalanine transfer RNAs were used to construct phylogenetic trees by the maximum parsimony method. Although eukaryotes, prokaryotes and chloroplasts appear related to a common ancestor, no firm conclusion can be drawn at this time about mitochondrial-coded transfer RNAs. tRNA evolution is not appropriately described by random hit models, since the various regions of the molecule differ sharply in their mutational fixation rates. "Hot" mutational spots are identified in the Tpsic, the amino acceptor and the upper anticodon stems; the D arm and the loop areas on the other hand are highly conserved. Crucial tertiary interactions are thus essentially preserved while most of the double helical domain undergoes base pair interchange. Transitions are about half as costly as transversions, suggesting that base pair interchanges proceed mostly through G-U and A-C intermediates. There is a preponderance of replacements starting from G and C but this bias appears to follow the high G + C content of the easily mutated base paired regions.

Accessibility of guanine at position 44 in the invariant sequence 5'CCG44AAC3' of Escherichia coli 5S RNA to reaction with kethoxal

The reaction of Escherichia coli ribosomes with beta-ethoxy-alpha-ketobutyraldehyde (kethoxal) in a buffer containing 50--100 mM Tris.HCl at pH 7.4, 50 mM NH4Cl, and 5 mM Mg(OAc)2 readily released the 5S RNA from the ribosomes. When liberated, the 5S RNA is in a conformation such that position 44 is selectively reactive, in addition to the normally reactive quanines at positions 41 and 13. Positions 41 and 13 have been previously shown to react in the 5S RNA in situ. The resulting new RNase T1 resistant oligonucleotides 5'CCG 44K AAUCAG51(3') and 5'ACCCCAUG 41KCCG 44KAACUCAG51(3') have been isolated and identified. These oligonucleotides have not been found in RNase T1 digests of 5S RNA that is not released from the ribosome. The guanine at position 44 is part of the invariant sequence 5'CCG44AAC3' which includes that portion of the molecule thought to interact with the invariant 5'GT psi C3' of tRNAs in the ribosomal A site. This invariant sequence of the 5S RNA may also form part of the binding site for protein L5.

Assembly of the mitochondrial membrane system: sequences of yeast mitochondrial valine and an unusual threonine tRNA gene

The mitochondrial DNA segments of two independently isolated rho- clones of S. cerevisiae carrying a genetic marker for a threonine tRNA have been characterized by restriction endonuclease analysis and DNA sequencing. The DNA sequences of the two segments have been used to deduce the primary and secondary structures of the tRNA. The threonine tRNA is unusual in having a leucine anticodon (3'-GAU-5'). Despite the anomalous anticodon, the tRNA is proposed to function in mitochondrial protein synthesis. One of the rho- clones contains an additional coding sequence that has been identified as a valine tRNA genes have been located on the wild-type physical map and determined to be transcribed from two different strands.

Rapid RNA sequencing: nucleases from Staphylococcus aureus and Neurospora crassa discriminate between uridine and cytidine

Using end-labelled RNA, significant changes in base specificity of three nucleases have been detected under defined conditions. Staphylococcus aureus nuclease at pH 3.5 without Ca++ cleaves all Pyr-N bonds more uniformly and efficiently than RNase A, without any preference for Pyr-A bonds. At pH 7.5 in 10 mM Ca++ this enzyme cleaves all N-C and N-G bonds slowly, whereas N-U and N-A bonds are hydrolyzed rapidly. Hence, the base at the 3'- or at the 5'-side of a phosphodiester bond can determine the base specificity of S. aureus nuclease. - In absence of urea, Neurospora crassa endonuclease cleaves all phosphodiester bonds, but leaves all C-N bonds intact in 7 M urea. - RNase U2 at pH 3.5 cleaves A-N bonds more efficiently than at pH 5.0.

Nucleotide sequence of the mitochondrial structural genes for cysteine-tRNA and histidine-tRNA of yeast

We have determined the nucleotide sequence of a segment of Saccharomyces cerevisiae mtDNA that contains the structural genes for a cysteine-tRNA and a histidine-tRNA. The genes are approximately 85 bp apart, they do not contain intervening sequences or sequences coding for the 3'-CCA terminus and they are surrounded by nearly pure AT segments. The tRNAs deduced are very AT-rich, 74 and 75 nucleotides long, respectively, and contain one or more unusual features not found in tRNAs from other sources.

Nucleotide sequence of three isoaccepting lysine tRNAs from rabbit liver and SV40-transformed mouse fibroblasts

The lysine isoacceptor tRNAs differ in two aspects from the majority of the other mammalian tRNA species: they do not contain ribosylthymine (T) in loop IV, and a 'new' lysine tRNA, which is practically absent in non-dividing tissue, appears at elevated levels in proliferating cells. We have therefore purified the three major isoaccepting lysine tRNAs from rabbit liver and the 'new' lysine tRNA isolated from SV40-transformed mouse fibroblasts, and determined their nucleotide sequences. Our basic findings are as follows. a) The three major lysine tRNAs (species 1, 2 and 3) from rabbit liver contain 2'-O-methylribosylthymine (Tm) in place of T. tRNA1Lys and tRNA2Lys differ only by a single base pair in the middle of the anticodon stem; the anticodon sequence C-U-U is followed by N-threonyl-adenosine (t6A). TRNA3Lys has the anticodon S-U-U and contains two highly modified thionucleosides, S (shown to be 2-thio-5-carboxymethyl-uridine methyl ester) and a further modified derivative of t6 A (2-methyl-thio-N6-threonyl-adenosine) on the 3' side of the anticodon. tRNA3Lys differs in 14 and 16 positions, respectively, from the other two isoacceptors. b) Protein synthesis in vitro, using synthetic polynucleotides of defined sequence, showed that tRNA2Lys with anticodon C-U-U recognized A-A-G only, whereas tRNA3Lys, which contains thio-nucleotides in and next to the anticodon, decodes both lysine codons A-A-G and A-A-A, but with a preference for A-A-A. In a globin-mRNA-translating cell-free system from ascites cells, both lysine tRNAs donated lysine into globin. The rate and extent of lysine incorporation, however, was higher with tRNA2Lys than with tRNA3Lys, in agreement with the fact that alpha-globin and beta-globin mRNAs contain more A-A-G than A-A-A- codons for lysine. c) A comparison of the nucleotide sequences of lysine tRNA species 1, 2 and 3 from rabbit liver, with that of the 'new' tRNA4Lys from transformed and rapidly dividing cells showed that this tRNA is not the product of a new gene or group of genes, but is an undermodified tRNA derived exclusively from tRNA2Lys. Of the two dihydrouridines present in tRNA2Lys, one is found as U in tRNA4Lys; the purine next to the anticodon is as yet unidentified but is known not be t6 A. In addition we have found U, T and psi besides Tm as the first nucleoside in loop IV.