The primary structure of rabbit liver tRNA Phe and its comparison with known tRNA Phe sequences

History of tRNA research in strasbourg

The tRNA molecules, in addition to translating the genetic code into protein and defining the second genetic code via their aminoacylation by aminoacyl-tRNA synthetases, act in many other cellular functions and dysfunctions. This article, illustrated by personal souvenirs, covers the history of ~60 years tRNA research in Strasbourg. Typical examples point up how the work in Strasbourg was a two-way street, influenced by and at the same time influencing investigators outside of France. All along, research in Strasbourg has nurtured the structural and functional diversity of tRNA. It produced massive sequence and crystallographic data on tRNA and its partners, thereby leading to a deeper physicochemical understanding of tRNA architecture, dynamics, and identity. Moreover, it emphasized the role of nucleoside modifications and in the last two decades, highlighted tRNA idiosyncrasies in plants and organelles, together with cellular and health-focused aspects. The tRNA field benefited from a rich local academic heritage and a strong support by both university and CNRS. Its broad interlinks to the worldwide community of tRNA researchers opens to an exciting future. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1066-1087, 2019.

TRMT2A is a novel cell cycle regulator that suppresses cell proliferation

During the maturation of transfer RNA (tRNA), a variety of chemical modifications can be introduced at specific nucleotide positions post-transcriptionally. 5-Methyluridine (m⁵U) is one of the most common and conserved modifications from eubacteria to eukaryotes. Although TrmA protein in Escherichia coli and Trm2p protein in Saccharomyces cerevisiae, which are responsible for the 5-methylation of uracil at position 54 (m⁵U54) on tRNA, are well characterized, the biological function of the U54 methylation responsible enzyme in mammalian species remains largely unexplored. Here, we show that the mammalian tRNA methyltransferase 2 homolog A (TRMT2A) protein harbors an RNA recognition motif in the N-terminus and the conserved uracil-C5-methyltransferase domain of the TrmA family in the C-terminus. TRMT2A predominantly localizes to the nucleus in HeLa cells. TRMT2A-overexpressing cells display decreased cell proliferation and altered DNA content, while TRMT2A-deficient cells exhibit increased growth. Thus, our results reveal the inhibitory role of TRMT2A on cell proliferation and cell cycle control, providing evidence that TRMT2A is a candidate cell cycle regulator in mammals.

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.

Nucleotide sequence and transcription of a rat tRNA(Phe) gene and a neighboring Alu-like element

A bacteriophage gamma Ch4A clone containing a 22-kb rat DNA insert was isolated and found to contain a solitary tRNA(Phe)GAA gene and, 436 bp downstream of it, an Alu-like element. The nucleotide sequence of a 1141-bp DNA fragment containing these genes was determined. The rat tRNA(Phe)GAA gene, with the exception of an additional A in the extra arm, has a sequence identical to that of a rabbit liver tRNA(Phe). The Alu-like element belongs to the rodent B2 family of short interspersed repetitive nucleotide sequences. This repetitive element, B2Phe, is flanked by 12-bp direct repeats, contains an internal split promoter (block A and block B) for RNA polymerase III and is devoid of an A-rich segment at the 3' end. Like other members of the B2 family, the B2Phe element presents 64% sequence homology with rat serine tRNA and contains a serine (GCT) anticodon. Both tRNA(Phe)GAA gene and B2Phe element were found to be transcriptionally active in HeLa cell and Xenopus oocyte nuclear extracts. The tRNA(Phe) gene transcripts were processed during the course of transcription to form mature-size tRNA(Phe). The transcription efficiency of the B2Phe element was found to be an order of magnitude higher than that of the tRNA(Phe) gene. Competition experiments demonstrate that the B2Phe DNA can form a more stable transcription complex than the tRNA(Phe) gene and compete with it for binding of transcription factors.

Metabolism of 1-methyladenosine

1-[methyl-8-14C] Adenosine was synthesized and its metabolic fate was determined in intact rat. It was found that approximately 57% of 1-[methyl-8-14C] adenosine administered iv was excreted unchanged in the urine and 33% of the excreted radioactivity in the urine was associated with the major metabolite 1-methyl-hypoxanthine and about 4.5% was associated with 1-methylinosine. Very little adenosine or N6-methyladenosine was formed. It is concluded that 1-methyladenosine is initially deaminated by adenosine deaminase to 1-methylinosine which is then cleaved by nucleoside phosphorylase to 1-methylhypoxanthine.

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.

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.

A acid-stable analogue of the 3-beta-D-ribofuranoside of Y-base

A cyclonucleoside analogue of Y(TU) riboside has been prepared and shown to be relatively stable in M-hydrochloric acid solution at room temperature.

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.

Purification and characterization of tRNAMet-f, tRNAPhe and tRNATyr2 from Baccillus subtilis

Three tRNAs specific for methionine, phenylalanine and tyrosine were isolated from the total tRNA of Bacillus subtilis by chromatographic procedures using BD-cellulose and reversed-phase (5) chromatography. The acceptor activities of the purified tRNAs are 1160, 1260 and 1320 pmoles per A260nm unit for tRNAMetf, tRNAPhe and tRNATyr2 respectively. In tRNAMetf and tRNAPhe ribothymidine, pseudouridine and dihydrouridine are present, in addition, in tRNAPhe 7-methyguanosine and a 2'-O-methylated nucleoside were found. The modified nucleosides of tRNATyr2 are ribothymidine, pseudouridine, dihydrouridine, 4-thiouridine and 1-methyladenosine. The results suggest the presence of 2-methylthio-N6(delta 2-isopentenyl)adenosine in tRNAPhe and tRNATyr2. The thermal denaturation profiles of the three tRAN species are presented.

The nucleotide sequence of cysteine transfer ribonucleic acid from baker's yeast. Identification of the products from partial degradation of the molecule and derivation of the complete sequence

1. A series of large oligonucleotide fragments derived from tRNA Cys, were separated chromatographically and the sequence of each was deduced by examination of the products of digestion with pancreatic and T1 ribonucleases. 2. The location of the specific cleavage points in the nucleotide chain was similar to that produced by brief treatment with pancreatic ribonuclease. 3. The fragments could be arranged into two alternative sequences. The correct sequence was deduced by the sequential removal and identification of the first nine nucleotides from the 3'-end of the terminal half of the molecules.

Doublet frequencies in sequenced nucleic acids

A doublet frequency count (set of frequencies of the 16 possible two-base sequences) can be calculated from the experimentally determined overall sequence of a nucleic acid. In this paper, a statistical methodology is developed for comparing such counts with random, with others of the same type or with doublet proportions found in whole DNAs. The methods are applied to two major categories of sequenced RNAs. It is found that vertebrate ribosomal and transfer RNAs show significant differences from the overall vertebrate DNA pattern, especially in the frequency of the doublet CG. Bacterial rRNA and tRNA, on the other hand, show less dissimilarity from total DNA. In the RNA of the small bacteriophage MS2, the doublet frequencies of the translated regions of the genome resemble those in the host E. coli, whereas those in the intercistronic regions differ substantially. All these findings are discussed in relation to the origin, evolution and selection of the nucleic acids concerned.

The primary structure of the major cytoplasmic valine tRNA of mouse myeloma cells

This paper describes the derivation of the primary structure of the major valine tRNA in the cytoplasm of mouse myeloma cells. Approximately 75% of the nucleotide sequence of this tRNA is also shared by the tRNA1-Val of yeast, this homology serving as a further indication of the extreme conservation of the structures of the tRNAs of different eukaryotic organisms. A novel feature of mouse myeloma tRNA1-Val is its loop IV sequence: -U-PSI-C-G-M1A-A-A-. This particular loop IV sequence has not previously been found in a tRNA structure. In addition, tRNA1-Val possesses some unusual nucleoside modifications. 5-Methyluridine (T) was not found to occur within loop IV of this tRNA, although this minor nucleoside is also absent from certain other mammalian tRNAs. Only one other tRNA, mammalian tRNAf-Met, has been found to possess 2-methylguanosine (m2G) in the position between the (b) and (c) stems of the cloverleaf. Numerous tRNAs have m2-2G in this location, and it would appear that the second methylation of this guanosine is characteristically absent from certain mammalian tRNA species.

Studies on human tRNA. I. The rapid, large scale isolation and partial fractionation of placenta and liver tRNA

A procedure for the large scale isolation of mammalian tRNA has been applied to the isolation of several grams of human liver, human placenta, rabbit liver and rat liver tRNA. This procedure entails an initial grinding of the tissue in phenol-sodium acetate at acidic pH, followed by DEAE cellulose chromatography. Procedures are also described for analysis of the purified tRNA on the basis of size, using controlled pore glass bean columns. In addition, the acceptor activity of isolated tRNAs has been determined using both the heterologous and homologous synthetases. The chromatographic profile of individual isoaccepting species using BD cellulose chromatography is shown and the 3' terminal nucleoside content was also determined. The methods described now make it feasible for large scale studies of mammalian tRNA enabling us to better understand the relationships between the structure of mammalian tRNA and its many diversified functions.

Isolation and chromatographic behaviour of phenylalanine tRNA from barley embryos

Two fractions of phenylalanine tRNA (tRNA(Phe) (1) and tRNA(Phe) (2)) were purified by BD-cellulose and RPC-5 chromatography of crude tRNA isolated from barley embryos. Successive RPC-5 rechromatography runs of tRNA(Phe) (2) showed its conversion into more stable tRNA(Phe) (1), suggesting that the two fractions have essentially the same primary structure. Both tRNA(Phe) (1) and tRNA(Phe) (2) had about the same acceptor activity, but tRNA(Phe) (2) was aminoacylated much faster than tRNA(Phe) (1). RPC-5 chromatography of crude aminoacylated tRNA showed higher contents of phe-tRNA(Phe) (2) than of phe-tRNA(Phe) (1) but the ratio of these two fractions estimated by relative fluorescence intensity was about 1. Fluorescence spectra of tRNA(Phe) from barley embryos suggest that it contains Y base similar to Y(w) from wheat tRNA(Phe).

Studies on the fractionation of total transfer ribonucleic acid and purification of an alanine transfer ribonucleic acid from chick embryo

Chick embryo tRNA, prepared by a simple large-scale method, was fractionated on three different ion-exchange columns. In all cases simple chromatographic patterns for various tRNA species were observed, indicating the presence of only a few major species of tRNA for each amino acid. By repeated chromatography one species of alanine tRNA was purified to approx. 80% purity. T(1) ribonuclease digest of this purified tRNA gave a simple chromatographic pattern. Because of the simplicity of the method of preparation of tRNA from this readily available source and the presence of only a few species of tRNA for each amino acid, chick embryo is suited for the study of tRNA and its various functions in higher systems.

2'-O-methyl ribothymidine: a component of rabbit liver lysine transfer RNA

One of the lysine transfer RNAs of rabbit liver is shown to contain 2'-O-methyl ribothymidine in place of ribothymidine. This represents the first demonstration of the presence of 2'-O-methyl ribothymidine in a nucleic acid.