Separation of aminoacyl-transfer RNAs by polyacrylamide gel electrophoresis

A polyacrylamide gel electrophoresis system for separating $\text{E.}$$\text{coli}$ tRNAs and aminoacyl-tRNAs is described. The tRNA was separated into 6 discrete bands which contained varyin aamounts of tRNA and therefore varying numbers of tRNA species. In order to locate specific tRNAs, tRNA was charged with a ¹⁴C amino acid and the aminoacyl-tRNA was located by autoradiography. With several amino acids, 2 isoaccepting species were found. In total, 30 aminoacyl-tRNAs were located.     

Alteration of the intracellular concentration of aminoacyl-tRNA synthetases and isoaccepting tRNAs during amino-acid limited growth in Escherichia coli.

Growth of Escherichia coli AB 2271 under threonine or isoleucine deficiency leads to a depression of the threonyl-tRNA synthetase and isoleucyl-tRNA synthetase respectively. During this amino-acid-limited growth the concentrations of isoaccepting fractions of the cognate tRNA species were changed, as demonstrated by their altered reversed-phase-5 chromatograms. But, in addition, the profiles of the isoacceptors of all other tRNA species investigated, i.e. of tRNAsLeu, tRNAsSer and tRNAsArg were also altered. This means that, if there is a correlation between regulation of the level of an aminoacyl-tRNA synthetase and its cognate isoaccepting tRNAs, it is superimposed by the effect of amino acid limitation upon the concentration of all isoaccepting tRNAs. So far drastic changes in profiles of isoaccepting tRNAs have only been observed under unbalanced growth in relaxed cells or during treatment with antibiotics. Here we demonstrate that similar heavy alterations in patterns of isoaccepting tRNAs occur in a proven stringent E. coli strain growing exponentially under amino acid limitation. Thus the observed changes in the profiles of isoaccepting tRNAs during amino acid limitation signal a meaningful biological function of those newly or increasingly occurring isoaccepting tRNAs. During the growth under amino acid limitation the total acceptor activity of eight investigated tRNA species, however, stayed unchanged, except that under threonine-limited growth the total amount of tRNAIle was reduced to about half and that of tRNAGlu increased; both tRNA species of these isoacceptors are known [30,31] as spacers between ribosomal RNAs.     

Chromatographic Analyses of Isoaccepting tRNAs from Avian Myeloblastosis Virus

Avian myeloblastosis virus (AMV) 4S RNA was tested for amino acid acceptor activity for 18 of the 20 amino acids. A nonrandom distribution of viral tRNAs was found compared with tRNA from normal liver or from AMV-infected leukemic myeloblasts, confirming previous reports. Methionine and proline tRNAs were considerably enriched, whereas glutamic acid, glutamine, serine, tyrosine, and valine tRNAs were markedly depleted in AMV relative to homologous cellular tRNAs. The seven AMV tRNAs with the greatest amino acid acceptance capacities, which were in order methionine, proline, lysine, arginine, histidine, isoleucine, and threonine tRNAs, were compared with homologous tRNAs from leukemic myeloblasts and liver by reversed-phase 5 chromatography. Of the 25 isoaccepting chromatographic fractions identified, no tRNA species unique to AMV was detected. Only methionyl-tRNA showed a substantial quantitative variation in isoaccepting species compared with the host cell. Thus, viral selectivity for amino acid-specific tRNAs is not, generally, paralleled by selectivity for individual isoaccepting tRNA species. Qualitative differences in arginyl- and histidyl-tRNA isoaccepting species were discovered in virus and leukemic myeloblasts compared with liver. This indicates the existence of structural differences in these tRNA species which could be related to virus replication or expression.     

Relationships Among Deoxyribonucleic Acid, Ribonucleic Acid, and Specific Transfer Ribonucleic Acids in Escherichia coli 15T− at Various Growth Rates

The levels of macromolecules in Escherichia coli 15T(-) growing in broth, glucose, succinate, and acetate media were determined to compare relationships among deoxyribonucleic acid (DNA), ribosomal ribonucleic acid (rRNA), transfer RNA (tRNA), and protein in cells at different growth rates. DNA and protein increased in relative amounts with decreasing growth rate; relative amounts of rRNA and tRNA decreased, tRNA making up a slightly larger proportion of RNA. For several amino acid-specific tRNAs studied, acceptor capacities per unit of DNA increased with increasing growth rate. The syntheses of tRNA and rRNA are regulated by similar, yet different, mechanisms. Chromatographic examination on columns of benzoylated diethylaminoethyl-cellulose of isoaccepting tRNAs for arginine, leucine, lysine, methionine, phenylalanine, serine, and valine did not reveal differences in the isoaccepting profiles for rapidly (broth culture) and slowly growing (acetate culture) cells. Therefore, isoacceptors for individual amino acids appear to be regulated as a group. Lower efficiencies of ribosomal function in protein synthesis can be explained, in part, by a low ratio of tRNA to the number of ribosomes available and by a decreasing concentration of tRNA with decreasing growth rate. Data on the tRNAs specific for seven amino acids indicate that the decreasing concentration of tRNA is a general event rather than a severe limitation of any one tRNA or isoaccepting tRNA.     

Cluster analysis of aminoacyl-tRNAs from mouse plasmacytomas correlates chromatographic profiles with myeloma protein similarity,clonal origin of tumor lines,and the neoplastic nature of the tissues

In order to test whether tRN A populations are correlated with (determined by or adapted to) the major proteins synthesized by tumor cells, RPC-5 Chromatographie profiles of aminoacyl-tRNAs from 11 mouse plasmacytomas and from normal adult mouse liver and brain were analyzed by the use of “dissimilarity indices” drawn from all possible pairs of tissues. Cluster analysis was then performed and dendrograms constructed. Although myeloma protein synthesis is only one of many proteins being synthesized by these malignant cells, a novel nonparametric statistical analysis of these dendrograms indicates that independently arising tumors have more similar profiles if their immunoglobulin light and heavy chains are very similar than if these chains are dissimilar (P < 0·015). Even more strikingly significant was the finding that drastic changes in myeloma protein synthesis such as loss of both heavy and light chain synthesis do not result in increased dissimilarity of aminoacyl-tRNA profiles (P < 0·00001). Unlike other eukaryotic systems such as sheep reticulocytes and silk worm silk gland which have been shown to adapt their tRNA populations to changes in protein synthesis, these plasmacytomas do not appear to do so.The novel use of statistical methods, esp. cluster analysis, to examine graphic displays of data may have useful applications in comparing other Chromatographie profiles, densitometric scans, etc.     

Alterations in tRNA isoaccepting species during erythroid differentiation of the Friend leukemia cell.

The chromatographic profiles of isoaccepting tRNAs were analyzed at five time points during the 96 hr, dimethylsulfoxide induced, erythroid-like differentiation of Friend leukemia cells. Sixty-four isoaccepting species of tRNA for 16 amino acids were resolved by RPC-5 chromatography. The relative amounts of tRNAphe, tRNAile, and tRNAval species were maintained by the cells during differentiation; whereas the relative amounts of some of the isoacceptor tRNAs for the other 13 amino acids changed significantly. Fluctuations in amounts of isoacceptors occurred between 36 and 72 hr after addition of dimethysulfoxide, corresponding to globin mRNA appearance and hemoglobin synthesis, respectively. In most cases, thepredominant tRNA isoacceptors of uninduced cells were retained throughout differentiation. Notable exceptions were tRNA species for threonine, proline, and methionine. Some of the isoacceptors occurring in relatively smaller amounts were not expressed at all times. These changes possibly reflect the cell's functional adaptation of tRNA in differentiation for hemoglobin synthesis.     

Adaptation of the tRNA population of maize endosperm for zein synthesis.

Maize endosperm, 30 days after pollination is actively synthesizing zein, a storage protein containing high amounts of glutamine. leucine and alanine. Endosperm tRNAs have a higher accepting activity than embryo tRNAs for these three amino acids, but not for some other (control) amino acids. This increase in accepting activity is accompanied by a change in the distribution of the isoaccepting tRNA species corresponding to these three amino acids, but not of the isoacceptors corresponding to some other (control) amino acids. These results are in favor of the theory of functional adaptation of tRNA population.     

Adjustment of the tRNA population to the codon usage in chloroplasts.

In chloroplasts there is a correlation between the amounts of tRNAs specific for a given amino acid and the codons specifying this amino acid. Furthermore, for the amino acids coded for by more than one codon, the population of isoaccepting tRNAs is adjusted to the frequency of synonymous codons used in chloroplast protein genes. A comparison by two-dimensional gel electrophoresis of the tRNA populations extracted from chloroplasts and from chloroplast polysomes shows that all chloroplast tRNAs are involved in protein biosynthesis.     

Changes in Transfer Ribonucleic Acids Accompanying Encystment in Acanthamoeba castellanii

Transfer ribonucleic acid (tRNA) from exponentially growing cells (trophozoites) and from precysts of Acanthamoeba castellanii were examined by reversed-phase column (RPC-2) chromatography. This system gave excellent resolution of isoaccepting species of tRNA. The tRNAs for 12 amino acids were studied. A comparison of trophozoite and precyst tRNA elution profiles revealed no apparent differences in the number of isoaccepting species of alanyl-, arginyl-, asparaginyl-, glycyl-, leucyl-, lysyl-, methionyl-, phenylalanyl-, tryptophanyl-, or valyl-tRNAs. Seryl-tRNAs from trophozoites were eluted as three components, whereas precyst seryl-tRNAs were eluted as only two components. Precharged trophozoite and precyst isoleucyl-tRNAs were both eluted as single components; however, post-chromatography charging of trophozoite tRNA resulted in three components of activity for tRNA(Ile) and only one component for precyst tRNA(Ile). None of the observed changes could be attributed to differences in synthetases or to the presence of altered tRNA lacking the CCA terminus or partially degraded by nucleases. The possible significance of these observations is discussed.     

Aminoacylation of four tRNA species in lupin (Lupinus luteus) cotyledons

During germination of lupin seeds, the levels of in-vivo tRNA aminoacylation increase in different ways, depending on the species of tRNA. Column chromatography of tRNA on reverse-phase-chromatography (RPC-5) has shown the presence of 4 peaks of isoleucyl-tRNA, 5 of leucyl-tRNA, 5 of lysyl-tRNA, 2 of tyrosyl-tRNA, and 4 of valyl-tRNA. Cochromatography of periodate treated and control tRNA preparations, labeled with radioactive amino acids, indicates identical aminoacylation in vivo of isoaccepting tRNAs during plant development. One isoacceptor of isoleucine tRNA changes its elution profile after periodate treatment.Abbreviation RPC-5 reverse-phase-chromatography     

Codon Usage Bias and tRNA Abundance in Drosophila

Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development. We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the exception of Asp which had very low contribution to overall bias. Asp was also the only amino acid that did not show a clear preference for one of its synonymous codons. Synonymous codon usage in Drosophila was consistent with ``optimal' codons deduced from the isoaccepting tRNA availability. Interestingly, amino acids whose major isoaccepting tRNAs change during development did not show as strong bias as those with developmentally unchanged tRNA pools. Asp is the only amino acid for which the major isoaccepting tRNAs change between larval and adult stages. We conclude that synonymous codon usage in Drosophila is well explained by tRNA availability and is probably influenced by developmental changes in relative abundance. Received: 5 December 1996 / Accepted: 14 June 1997     

Chromatographic Analyses of Isoaccepting tRNAs from Avian Tumor Viruses

Low-molecular-weight RNA from transforming viruses (Rous sarcoma virus-Rous-associated virus 1, Schmidt-Ruppin strain of Rous sarcoma virus, and sarcoma-B(77)), from nontransforming viruses (Rous-associated virus 1 and sarcoma-NTB(77)), and from chicken liver, chicken embryo fibroblast, and Rous sarcoma virus-Rous-associated virus 1-transformed chicken embryo fibroblast was isolated and purified. To determine if there are modified, qualitatively or quantitatively different isoaccepting species of tRNA in these avian sarcoma viruses as compared with the cell of virus origin, chicken embryo fibroblast or normal chicken liver, methionyl-, arginyl-, and lysyl-tRNA (with high amino acid acceptance activity), and aspartyl- and glutamyl-tRNA from viral-trans-formed cells (with low viral amino acid acceptance activity) were co-chromatographed on reversed phase-5 chromatography columns, and elution profiles were compared. Although in each case the elution profile between a particular viral and host cell tRNA differed quantitatively, there was no qualitative difference in the profiles of corresponding tRNAs from either transforming or nontransforming viruses examined. Minor quantitative differences in the elution profiles might be a reflection of the metabolic state of the cells, since all evidence points to acceptor activity being of host rather than viral origin. Since, with the exception of selective packaging of methionyl-tRNA (IV) species by both transforming and nontransforming viruses, no selectivity was found for isoacceptor species of other tRNAs, it seems that such preferential packaging of methionyl-tRNA (IV) species has no bearing on the event of viral transformation.     

Transfer RNATyr of melanoma tissues and cells: relevance to melanin synthesis?

The tRNA present in swine melanoma tumor tissue and normal gray skin tissue were compared by aminoacylation of the unfractionated tRNA preparations. Of the seventeen amino acids studied, seven showed differences in rate of acceptance to tRNAs from normal and tumor tissues; the tRNAs of two amino acids, tyrosine and glycine, showed dramatic three fold increases in melanoma tumor. As melanin biosynthesis proceeds from tyrosine oxidation the investigations focused on the increase in tyrosine tRNA. Kinetic analysis of tyrosine aminoacylation to normal and melanoma tRNAs revealed no differences. Analysis of the isoaccepting species of tRNATyr from normal skin and melanoma tumor tissues identified three isoacceptors; tRNATyr, represented the predominant species in normal gray skin, while tRNA2Tyr predominated in melanoma tumor tissue. The tyrosine acceptances by tRNAs from three human melanoma cell lines were analyzed and found to be variable, but isoaccepting species analysis of the tRNATyr of these three cell lines still showed a correlation between the preponderance of tRNA2Tyr and extent of tyrosine acceptance. Additionally the enzymatic activity for the oxidation of tyrosine was found to be related to tyrosine acceptance and tRNA2Tyr predominance..     

The role of initiator tRNAimet in fidelity of initiation of protein synthesis

The proper arrangement of amino acids in a protein determines its proper function, which is vital for the cellular metabolism. This indicates that the process of peptide bond formation requires high fidelity. One of the most important processes for this fidelity is kinetic proofreading. As biochemical experiments suggest that kinetic proofreading plays a major role in ensuring the fidelity of protein synthesis, it is not certain whether or not a misacylated tRNA would be corrected by kinetic proofreading during the peptide bond formation. Using 2-layered ONIOM (QM/MM) computational calculations, we studied the behavior of misacylated tRNAs and compared the results with these for cognate aminoacyl-tRNAs during the process of peptide bond formation to investigate the effect of nonnative amino acids on tRNAs. The difference between the behavior of initiator tRNA(i) (met) compared to the one for the elongator tRNAs indicates that only the initiator tRNA(i) (met) specifies the amino acid side chain.     

Alterations in SVT2 cell transfer RNAs in response to cell density and serum type.

The chromatographic elution profiles of tRNA-A sn, tRNA-A sp, tRNA-H is and tRNA-T y r from SV40-transformed BALB-3T3 cells grown in fetal calf serum or cald serum-supplemented media have been examined. The relative proportions of certain of the isoaccepting species of these four tRNAs are altered in a similar fashion depending on the serum type. It is suggested that the elution profile alterations reflect the extent of modifications of a specific G residue to the minor nucleoside Q, and that this process differs between untransformed and transformed cells. In addition, cell density appears to influence the Q content of these tRNAs, though other density-dependent tRNA modifications also appear to occur.     

Aminoacyl-transfer RNA populations in mammalian cells chromatographic profiles and patterns of codon recognition.

The chromatographic profiles of 20 aminoacyl-tRNAs from rabbit liver were compared to those of rabbit reticulocytes by reverse phase chromatography and the chromatographic profiles of 20-aminoacyl-tRNAs from bovine liver were compared to those of bovine brain. The two rabbit tissues showed significant differences in the elution profiles of most aminoacyl-tRNAs, while the elution profiles of the aminoacyl-tRNAs from the bovine tissues showed fewer differences. The patterns of codon recognition of several aminoacyl-tRNAs fractionated from rabbit reticulocytes have also been compared to those fractionated from rabbit liver.     

tRNAs: Cellular barcodes for amino acids

The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl-tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis.     

Isoaccepting transfer ribonucleic acids in liver and brain of young and old BC3F1 mice

Transfer RNAs from liver and brain of young and old BC3F₁ mice were compared in regard to extent of aminoacylation and cochromatographic profiles of isoaccepting tRNA species on reversed-phase columns. Homologous synthetase preparations and optimal aminoacylation conditions were employed, having been determined for each amino acid and found to be the same for those from old and young mice. Small differences were found between tRNAs from young and old mice in the extent of acceptance for arginine and tyrosine in the liver and for aspartic acid in the brain. There were no differences observed between preparations from young and old mice in any of the cochromatographic profiles for the amino acids examined in this study, which included arginyl-, aspartyl-, glutamyl-, histidyl-, leucyl-, lysyl-, phenylalanyl-, seryl-, and tyrosyl-tRNAs from liver and arginyl-, aspartyl-, histidyl-, leucyl-, lysyl-, and seryl-tRNAs from brain. Comparisons of tRNA preparations from fetal and neonatal liver with those from adult liver did reveal both qualitative and quantitative differences. These results suggest that the postulated accumulation of errors as a result of age-related alterations in the translational mechanism does not occur in tRNA or aminoacyl-tRNA synthetases of these two tissues.