The primary structure of two mammalian tRNAs Phe: identity of calf liver and rabbit liver tRNAs Phe

Discovery of a Gene Family Critical to Wyosine Base Formation in a Subset of Phenylalanine-specific Transfer RNAs

A large number of post-transcriptional base modifications in transfer RNAs have been described (Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. (1998) Nucleic Acids Res. 26, 148-153). These modifications enhance and expand tRNA function to increase cell viability. The intermediates and genes essential for base modifications in many instances remain unclear. An example is wyebutosine (yW), a fluorescent tricyclic modification of an invariant guanosine situated on the 3'-side of the tRNA(Phe) anticodon. Although biosynthesis of yW involves several reaction steps, only a single pathway-specific enzyme has been identified (Kalhor, H. R., Penjwini, M., and Clarke, S. (2005) Biochem. Biophys. Res. Commun. 334, 433-440). We used comparative genomics analysis to identify a cluster of orthologous groups (COG0731) of wyosine family biosynthetic proteins. Gene knock-out and complementation studies in Saccharomyces cerevisiae established a role for YPL207w, a COG0731 ortholog that encodes an 810-amino acid polypeptide. Further analysis showed the accumulation of N(1)-methylguanosine (m(1)G(37)) in tRNA from cells bearing a YPL207w deletion. A similar lack of wyosine base and build-up of m(1)G(37) is seen in certain mammalian tumor cell lines. We proposed that the 810-amino acid COG0731 polypeptide participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.

Changes of post-transcriptional modification of wye base in tumor-specific tRNAPhe

Nucleotide sequences of normal mouse liver tRNAPhe and tumor-specific tRNAPhes isolated from Ehrlich ascites tumor and neuroblastoma cells were examined by post-labeling techniques. The results showed that their sequences are identical, except for changes in post-transcriptional modifications that are located in the anticodon region. Normal mouse liver tRNAPhe contained Cm32, Gm34 and YOH37. On the other hand, tumor-specific tRNAPhes were found in one of two possible configurations: 1) Cm32, Gm34 and Y*OH37 (under-modified YOH) or 2) C32, G34 and m1G37. The ratio of the two forms of tRNAPhes differed in different tumor cells; Ehrlich ascites tumor tRNAPhe had mainly Y*OH-containing tRNAPhe whereas neuroblastoma tRNAPhe has predominantly m1G-containing tRNAPhe. It was concluded that tumor-specific tRNAPhes are products of different extents of modification, rather than of new tRNA transcription.

The nucleotide sequence of phenylalanine tRNA of Xenopus laevis

The nucleotide sequence of Xenopus laevis phenylalanine tRNA extracted from oocytes was determined to be: pGCCGAAAUAm2GCUCm1AG DDGGGAGAGCm22 G psi psi AGACmUGmAAYA psi C UAAAGm7GDCm5CCUGGT psi CGm1AUCCCGG GUUUCGGCACCAoH. This result was achieved by analysing, with classical procedures [6], the oligonucleotides obtained after digestion by T1 or pancreatic ribonuclease. This sequence is identical to the mammalian sequence. It has been entirely conserved during 10(8) years, the time lapse between the divergence of amphibians and mammals in evolution. In contrast to 5S RNA, no important heterogeneity has been found in the oocyte sequence, suggesting that there is only a single sequence for tRNAphe in X. laevis. Small differences are seen in the elution pattern from RPC-5 columns for immature oocyte and somatic tRNAphe. They are probably due to a submodification of methyl-5-cytidine residues, which appear to be about half methylated in tRNAphe as well as in total tRNA from immature oocytes.

The nucleotide sequence of Euglena cytoplasmic phenylalanine transfer RNA. Evidence for possible classifications of Euglena among the animal rather than the plant kingdom

The nucleotide sequence of cytoplasmic phenylalanine tRNA from Euglena gracilis has been elucidated using procedures described previously for the corresponding chloroplastic tRNA [Cell, 9, 717 (1976)]. The sequence is: pG-C-C-G-A-C-U-U-A-m(2)G-C-U-Cm-A-G-D-D-G-G-G-A-G-A-G-C-m(2)2G-psi-psi-A-G-A-Cm -U-Gm-A-A-Y-A-psi-C-U-A-A-A-G-m(7)G-U-C-*C-C-U-G-G-T-psi-C-G-m(1)A-U-C-C-C-G-G- G-A-G-psi-C-G-G-C-A-C-C-A. Like other tRNA Phes thus far sequenced, this tRNA has a chain length of 76 nucleotides. The sequence of E. gracilis cytoplasmic tRNA Phe is quite different (27 nucleotides out of 76 different) from that of the corresponding chloroplastic tRNA but is surprisingly similar (72 out of 76 nucleotides identical) to that of tRNA Phe from mammalian cytoplasm. This extent of sequence homology even exceeds that found between E. gracilis and wheat germ cytoplasmic tRNA Phe. These findings raise interesting questions on the evolution of tRNAs and the taxonomy of Euglena.

The primary structure of rabbit, calf and bovine liver tRNAPhe

Highly purified tRNAPhe from rabbit liver, calf liver and bovine liver were completely digested with pancreatic ribonuclease and ribonuclease T1. The oligonucleotides were separated and identified. The tRNAPhe from rabbit liver and calf liver were partially cleaved with ribonuclease T1 or by action of lead acetate. We describe the analyses of the large fragments and the derivation of the primary structure of these mammalian tRNAsPhe.

Tumour-specific phenylalanine tRNA contains two supernumerary methylated bases

Every malignant tumour examined contains aberrant tRNA methyltransferases and a few tRNAs which are absent from the normal tissue of origin. To determine whether tumour-specific tRNAs have different modifications from those in normal tissue, we purified the most frequently occurring tumour-specific isoaccepting tRNA from two malignant tissues. The isoaccepting phenylalanine tRNA from Novikoff hepatoma and Ehrlich ascites cells both contain two supernumerary methylated bases. One of these l-methylguanine, is absent from the phenylalanine tRNA of normal rat, mouse, rabbit and calf liver. An increase in the levels of 5-methylcytidine and dihydrouridine was also detected.

Multiple chromatographic peaks of phenylalanyl-tRNA associated with spontaneous hydrolysis of Y base during isolation

In contrast to the single phenylalanyl-tRNA found in normal cells, some tumours are known to have more than one phenylalanine isoacceptor. However, during certain steps in tRNA isolation from normal or tumour tissue, additional chromatographic peaks can be artificially produced which may be confused with the tumour-specific Phe-tRNA. Such procedures as extraction with unbuffered phenol and unbuffered gel filtration chromatography appear to produce adventitious isoacceptors by hydrolysis of Y base.

Rabbit liver tRNA1Val:I. Primary structure and unusual codon recognition

The major valine acceptor tRNA1Val from rabbit liver was purified and its nucleotide sequence determined by in vitro [32P] - labeling with T4 phage induced polynucleotide kinase and finger-printing techniques. Its primary structure was found to be identical with the major valine tRNA from mouse myeloma cells. According to the wobble hypothesis this tRNA, which exclusively has an IAC anticodon, should decode the valine codons GUU, GUC and GUA only. However, this tRNA recognizes all four valine codons with a surprising preference for GUG. It is unknown whether this is due to the lack of A37 modification next to the 3' end of the anticodon IAC. The nature of the inosine-guanosine interaction remains to be clarified.

Isolation and comparison of ribothymidine-lacking tRNAs of fetal, newborn and adult bovine tissues

Although ribothymidine (rT) is the most common methylated nucleoside in tRNA, a wide variety of bovine tissues have now been found to contain a class of tRNAs which totally lack rT and have an unmodified uridine in its place. The tissues studied include bovine brain, kidney, liver, thymus and testicles from adult, newborn and fetal stages. The class of tRNA was detected by its ability to be methylated with Escherichia coli rT-forming uracil methylase with radioactive S-adenosyl-L-methionine as the methyl donor. In each case rT was shown to account for at least 95% of the methylated products produced. In vitro methylated tRNA populations were compared by fractionation of double-labeled tRNAs on RPC-5 columns. Three major methyl-accepting tRNA peaks were found for all mammalian tissues studied. The level of methyl acceptance in these peaks was found to vary considerably between tRNAs of different tissues. A major difference in the methyl-accepting tRNA populations of bovine liver and calf thymus was observed. Little similarity was found in the rT-lacking class of tRNAs of bovine liver and wheat germ. Three members of the rT-lacking class of bovine liver tRNA were isolated and found to be two species of valine tRNA and one species of threonine tRNA. All three tRNA's completely lacked rT and could be quantitatively methylated with E. coli uracil methylase.

Structural studies on RNA from Bombyx mori L. I. Nucleoside composition of enriched tRNA species from the posterior silkgland purified by coutercurrent distribution

A large scale fractionation of tRNA from the posterior silkgland of the silkworm Bombyx mori L. by countercurrent distribution is described. One single 1,500 transfer distribution carried out with Phosphate buffer-Fromamide-Isopropanol (PFI) solvent system yields highly enriched isoaccepting species with increasing mobility order: tRNA1Gly, tRNA1-2Ala, tRNATyr, tRNA2Gly, tRNA1Ser and tRNA2Ser with 75%, 70%, 90%, 60%, 60%, and 90% purities respectively. Nucleosides fingerprint analysis of each iso-tRNA species confirms the anticodon structures previously suggested for tRNA2Ala (IGC), tRNA2bGly (U-CC) (U-CC) and tRNA2bSer (IGA). Twenty two minor nucleosides, three of them with unknown structure, have been detected. They are: m5C in tRNA1Gly, m1I in all tRNAAla species, polar A and U called X in tRNATyr, polar U derivative in tRNAGly2, mt6A in tRNASer1 and i6A tRNA2Ser. Both tRNASer species have m3C and ac7C. We do not detect Q, Y and thiol derivatives. The elution characteristics of silkgland tRNA species may be expressed in a semilogarithmic diagram where log K (K is the partition coefficient) is related to the base ratio A/Y) and the coding properties. The distribution pattern of silkgland tRNAs has been compared with that of Yeast and Rat liver tRNAs fractionated by countercurrent distribution with the PFI and PMB (Potassium phosphate buffer, 2-methoxy ethanol, 2-butoxy ethanol) solvent systems.

Nucleotide sequence of phenylalanine transfer ribonucleic acid from pea (Pisum sativum, Alaska)

Phenylalanine transfer ribonucleic acid from peas (Pisum sativum, Alaska) was completely digested with beef pancreatic ribonuclease (RNase I) and with ribonuclease T1. The resulting oligonucleotides were compared with those from the corresponding hydrolyses of phenylalanine transfer ribonucleic acid from wheat germ. The structures of both ribonucleic acids appeared to be identical. This report is the first to show that identical structures for the same specific acceptor transfer ribonucleic acid are present in two different plant species.

An improved method for the separation and quantitation of the modified nucleosides of transfer RNA

A method is described which allows a very efficient determination of the modified nucleosides of tRNA. The technique involves enzymatic degradation of the tRNA to nucleosides at pH 7.6 and their separation by two-dimensional thin-layer chromatography on cellulose-coated aluminum foils. Based on the analysis of two mammalian tRNAs it is shown that the technique is suitable for the determination of chemically unstable nucleosides as well as the ribose-methylated compounds. At least 36 of the 45 known modified nucleosides can be separated and quantitatively determined by the method described. This procedure is especially suitable for the estimation of the nucleoside composition of unlabeled tRNAs as well as for studying the post-transcriptional modifications of tRNA.

Purification of human placenta phenylalanine, valine, methionine, glucine, and serine transfer ribonucleic acids

By using column chromatography on varied media, the purification of several individual tRNAs from human placenta has been achieved. The crude human placenta tRNA was isolated using phenol extraction at pH 4.5 followed by DEAE-cellulose chromatography (B. Roe (1975), Nucleic Acids Res. 2, 21-42) and initially fractionated on BD-cellulose at neutral pH. Subsequent chromatography of the partially purified tRNA using high-speed, high-pressure liquid chromatography on RPC-5 and Aminex A-28 coupled with chromatography on BD-cellulose at acidic pH and on DEAE-Sephadex A-50 significantly shortened isolation time for milligram quantities of several pure tRNA species. Those tRNAs from human placenta obtained in a purity greater than 1.2 nmol/A260 unit are tRNAPhe, tRNAMet(i), tRNAVal(1a), tRNAVal(1b), and tRNAGly(1), while those obtained at purity of at least 0.8 nmol/A260 unit are tRNASer2 and tRNASer3. In addition, the use of Aminex A-28 as a chromatographic system for the isolation of tRNA is discussed.

Nucleotide sequence of human placenta cytoplasmic initiator tRNA

Cytoplasmic initiator tRNA from human placenta has been purified. The nucleotide sequence of this tRNA has been determined and found identical to that of initiator tRNA from mammalian cytoplasm.

Nucleotide sequence of salmon testes and salmon liver cytoplasmic initiator tRNA

Initiator tRNAs from the cytoplasm of salmon testes and salmon liver have been purified. The nucleotide sequence of these initiator tRNAs has been determined and found identical to that of initiator tRNA from mammalian cytoplasm. The only difference is the extent of modification of the nuceloside located between the dihydrouridine and the anticodon stems. In the salmon tRNAs, this modified nucleoside is predominantly N2N2-dimethyl guanosine, whereas in the mammalian initiator tRNA it is N2-methyl guanosine.

Reversed phase chromatography of isoaccepting tRNA's from healthy and crown gall tissues from Nicotiana tabacum

RPC 5 (Reversed Phase Chromatography) of aminoacyl-tRNA's from healthy and crown gall (induced by Agrobacterium tume-faciens strain B6) tobacco tissues were compared for eleven amino acids. For ten amino acids: alanine, arginine, glutamic acid, glycine, isoleucine, leucine, lysine, methionine, tyrosine, and valine, no qualitative or quantitative differences could be detected between aminoacyl-tRNA's from both sources. Phenylalanyl-tRNA's from crown gall tissues gave two peaks on RPC 5; the minor early eluting species (peak 1) was always absent in elution profiles of phenylalanyl-tRNA's from healthy tissues or from tobacco leaves. After the "Y" base was removed by pH 2.9 treatment, peak 2 of phenylalanine tRNA was shifted to the position of peak 1.