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Initiation of protein synthesis in mammalian cells with codons other than AUG and amino acids other than methionine.

Protein synthesis is initiated universally with the amino acid methionine. In Escherichia coli, studies with anticodon sequence mutants of the initiator methionine tRNA have shown that protein synthesis can be initiated with several other amino acids. In eukaryotic systems, however, a yeast initiator tRNA aminoacylated with isoleucine was found to be inactive in initiation in mammalian cell extracts. This finding raised the question of whether methionine is the only amino acid capable of initiation of protein synthesis in eukaryotes. In this work, we studied the activities, in initiation, of four different anticodon sequence mutants of human initiator tRNA in mammalian COS1 cells, using reporter genes carrying mutations in the initiation codon that are complementary to the tRNA anticodons. The mutant tRNAs used are aminoacylated with glutamine, methionine, and valine. Our results show that in the presence of the corresponding mutant initiator tRNAs, AGG and GUC can initiate protein synthesis in COS1 cells with methionine and valine, respectively. CAG initiates protein synthesis with glutamine but extremely poorly, whereas UAG could not be used to initiate protein synthesis with glutamine. We discuss the potential applications of the mutant initiator tRNA-dependent initiation of protein synthesis with codons other than AUG for studying the many interesting aspects of protein synthesis initiation in mammalian cells.

Amino Acid Sequence↗

Ribozyme expression systems.

We have succeeded in constructing an effective system for the expression of ribozymes under the control of a human tRNAVal promoter, which ensures a high level of production of ribozymes in vivo. The engineered tRNAVal-driven ribozymes, based on computer-predicted secondary structure, were relatively stable and were transported to the cytoplasm, where they could be colocalized with their target RNA. The activity of the exported ribozymes was significantly higher than that of ribozymes that remained in the nucleus. This chapter examines the methods for construction of the appropriate vector that can produce tRNA-driven ribozymes with high-level intracellular activity and for analysis of the constructs in cells.

Base Sequence↗

The RNA component of RNase P from the archaebacterium Haloferax volcanii.

RNase P, an endoribonuclease responsible for generating the mature 5' termini of tRNA precursors, is composed of both RNA and protein. It has been demonstrated that the eubacterial RNase P RNA will, under the appropriate reaction conditions, exhibit catalytic activity in vitro. Evidence has not been obtained for catalytic activity by the RNAs of eukaryotic RNase P enzymes. Using a cDNA probe prepared from RNA copurifying with RNase P activity from the archaebacterium Haloferax volcanii, we have characterized the gene encoding the RNase P RNA. The proposed transcript from this gene can assume a structure resembling the eubacterial RNase P RNA and includes many of the highly conserved sequences of these RNAs. This RNA was incapable of cleaving pre-tRNA substrates in the absence of protein under a variety of in vitro conditions. Catalytic activity was observed when this RNA was combined with the protein subunit of the Bacillus subtilis RNase P complex. Similarities among the archaebacterial, eubacterial, and eukaryotic RNase P RNA sequences and structures are discussed.

Archaea↗

A model for the aminoacyl-tRNA binding site of eukaryotic elongation factor 1 alpha.

Eukaryotic elongation factor 1 alpha (EF-1 alpha) binds all the aminoacyl-tRNAs except the initiator tRNA in a GTP-dependent manner. While the GTP binding site is delineated by the three GTP binding consensus elements, less is known about the aminoacyl-tRNA binding sites. In order to better understand this site, we have initiated cross-linking and protease mapping studies of the EF-1 alpha-GTP-aminoacyl-tRNA complex. Two different chemical cross-linking reagents, trans-diaminedichloroplatinum(II) and diepoxybutane, were used to cross-link four different aminoacyl-tRNA species to EF-1 alpha. A series of peptides were obtained, located predominantly in domains II and III. The ability of aminoacyl-tRNA to protect protease digestion sites was also monitored, and domain II was found to be protected from digestion by aminoacyl-tRNA. Last, an aminoacyl-tRNA analog with a reactive group on the aminoacyl side chain, N epsilon-bromoacetyl-Lys-tRNA, was cross-linked to EF-1 alpha. This reagent cross-liked to histidine 296 in a GTP-dependent manner and thus localizes the aminoacyl group adjacent to domain II. A model is developed for aminoacyl-tRNA binding to EF-1 alpha based on its similarity to the prokaryotic factor EF-Tu, for which an x-ray crystal structure is available.

Amino Acid Sequence↗

[A study of tRNA(adenine-1-)-methyltransferase from Thermus thermophilus HB8 with tRNA using enzymatic and spectral methods].

The contact sites of yeast tRNA1Val with tRNA(adenine-1-)-methyltransferase (EC 2.1.1.36) were studied by comparing the partial digests of free and enzyme bound tRNA. The RNAases Sa, V1, S1 and A were used for this purpose. Phosphodiester bonds on the proximal end of the acceptor stem and adjacent D- and T psi-stems, forming a continuous area, are protected by the methylase from the action of RNAases. On the contrary an enhancement of phosphodiester bond splitting of the D- and T psi-loops and of the anticodon stem is observed in the presence of methylase, which is interpreted as tertiary structure relaxation of tRNA owing to complex formation. The isotherm of ethidium bromide adsorption on free and methylase bound tRNA has shown that in enzyme shields approximately 50% of tRNA double stranded regions.

Binding Sites↗

Enzymatic alteration of the anticodon IAC of Torulopsis tRNAVal to IAU for isoleucine anticodon and aminoacylation of the variant.

By enzymatic cleavage and ligation of tRNAVa1, its anticodon sequence IAC was altered to IAU, the anticodon of tRNAI1e. Valine acceptor activity of this variant tRNAVa1 (IAU) was reduced to the extent much lower than tyrosine acceptability of the previously prepared tRNATyr (GAA) (anticodon for tRNAPhe). Isoleucine acceptor activity was undetected, contrary to tRNATyr (GAA) which accepted phenylalanine weakly. Cleavage of tRNAVa1 (IAC) between IACA37 and C38 of its anticodon loop reduced the valine acceptor activity, suggesting some contribution of the conformation of the anticodon loop to the aminoacylation reaction.

Acylation↗

[Model substrates of enzymes modifying ribonucleic acids. Synthesis of deca- and undecanucleotid-fragments of 21-member oligoribonucleotide simulating T psi C-branch of yeast valine tRNA].

Decanucleotide (Ap)6GpTpUpC and undecanucleotide GpApUpCpCp (Up)5U have been synthesised. They constitute 5'- and 3'-parts of a 21-mer which imitates T psi C-arm of yeast tRNA(Val1) and is a potential substrate for m1A-methylases and pseudouridine synthetase. The oligonucleotide blocks, synthesised enzymatically by means of ribonucleases of various substrate specificity and polynucleotide phosphorylases (TpUpC, ApUpCpC, pGpTpUpC, GpApUpCpC) or obtained by hydrolysis of poly(U) and poly(A) with Serratia marcescens endonuclease (hexauridilate and hexaadenilate), were joined by T4 RNA ligase.

Intramolecular Transferases↗

Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli.

tRNA pseudouridine 55 (psi 55) synthase, the enzyme that is specific for the conversion of U55 to psi 55 in the m5U psi CG loop in most tRNAs, has been purified from Escherichia coli and cloned. On SDS gels, a single polypeptide chain with a mass of 39.7 kDa was found. The gene is a previously described open reading frame, p35, located at 68.86 min on the E. coli chromosome between the infB and rpsO genes. The proposed name for this gene is truB. There is very little protein sequence homology between the truB gene product and the hisT (truA) product, which forms psi in the anticodon arm of tRNAs. However, there was high homology with a fragment of a Bacillus subtilis gene that may produce the analogous enzyme in that species. The cloned gene was fused to a 5'-leader coding for a (His)6 tract, and the protein was overexpressed > 400-fold in E. coli. The recombinant protein was purified to homogeneity in one step from a crude cell extract by affinity chromatography using a Ni(2+)-containing matrix. The SDS mass of the recombinant protein was 41.5 kDa, whereas that calculated from the gene was 37.3. The recombinant protein was specific for U55 in tRNA transcripts and reacted neither at other sites for psi in such transcripts nor with transcripts of 16S or 23S ribosomal RNA or subfragments. The enzyme did not require either a renatured RNA structure or Mg2+, and prior formation of m5U was not required. Stoichiometric formation of psi occurred with no requirement for an external source of energy, indicating that psi synthesis is thermodynamically favored.

Amino Acid Sequence↗

How the ribosome moves along the mRNA during protein synthesis.

The movement of a ribosome along the mRNA was assessed by the following experimental strategy. mRNAs were synthesized which contained a short coding sequence with at least four codons and a 32P label at one end and an oligo(C) sequence at the other end. When these mRNAs were fixed on the ribosome with tRNAs specific for the defined codons, the oligo(C) stretches were partially outside of the ribosome, whereas the labeled ends were inside the ribosome and thus protected. The overhanging oligo(C) regions were trimmed with the cytidyl-specific RNase CL3 identifying the nucleotides of the mRNAs, which emerged from the ribosome. An mRNA enters the ribosome at nucleotide 18 +/- 1, when counting starts at the first nucleotide of the P-site codon, and leaves the ribosome at nucleotide -21 +/- 2. The ribosome does not move at either side upon A-site occupation but does so at both sides simultaneously upon translocation. The results further indicate that most of the mRNA stretches downstream and upstream of the coding region are not required for the translocation reaction. It is therefore likely that the tRNAs are pulling the mRNA through the ribosome via codon-anticodon interactions in the course of translocation.

Amino Acid Sequence↗

RNA-DNA hybridization analyses of tRNA-Val-3b in Drosophila melanogaster.

Transfer RNA was extracted from 50-300 mg of adult flies and specifically labeled in vitro. The level of individual isoacceptors was quantitated by efficient annealing to Drosophila tRNA genes carried on recombinant DNA plasmids immobilized on nitrocellulose filters. The level of tRNAVal3b in the tRNA isolated from flies deficient in the major tRNAVal3b loci has been examined. The results show that deletion of the major tRNAVal3b loci resulted in a reduction of approximately 50% in the level of tRNAVal3b but did not produce the Minute phenotype; furthermore the effects of deficiencies at two loci were approximately additive.

Animals↗

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

Influence of the stringent control system on the transcription of ribosomal ribonucleic acid and ribosomal protein genes in Escherichia coli.

The fraction of the total ribonucleic acid (RNA) synthesis rate that is messenger RNA (mRNA) for ribosomal protein (r-protein) and ribosomal RNA (rRNA) has been estimated in valS(Ts) rel+ stringent and valS(Ts) relA1 relaxed strains of Escherichia coli during a partial inhibition of valyl-transfer RNA aminoacylation. The partial inhibition was accomplished by shifting the strains from the permissive growth temperature of 29.5 degrees C to the semipermissive temperature of 35.5 degrees C. The RNA synthesized at the elevated temperature was pulse labeled with [3H]uracil. The fraction of the total incorpoarted 3H radioactivity in r-protein mRNA or in rRNA was estimated by specific hybridization to the transducing phages gammaspc1, which carries about 15 r-protein genes and lambdailv5, which carries an rRNA transcription unit. The results clearly demonstrate that the rel gene influences the fraction of the total RNA synthesis rate that is r protein mRNA and rRNA; in the rel+ strain they are significantly increased relative to control cultures. This indicates that the expression of the genes coding for the RNA and protein component of the ribosome are most likely regulated at the level of transcription. Furthermore, it appears that the distribution of functioning RNA polymerase between rRNA genes, r-protein genes, and other types of genes is influenced by the rel gene control system; presumably this influence is mediated through the unusual nucleotide guanosine tetraphosphate.

Bacterial Proteins↗

Mutations in a nonessential viral gene permit bacteriophage T4 to form plaques on Escherichia coli valS ts relA.

During viral development bacteriophage T4 modifies the valyl-transfer RNA synthetase of its host Escherichia coli, but the function of the modification has remained elusive. A strain of Escherichia coli has now been identified which is nonpermissive for wild-type bacteriophage T4, but permissive for bacteriophage mutants impaired in the modification reaction. A comparison with other bacteria suggests that nonpermissiveness is due to synthesis of a thermolabile valyl-transfer RNA synthetase and relaxed control of RNA accumulation.

Escherichia coli↗

Synthesis of stable RNA in stringent Escherichia coli cells in the absence of charged transfer RNA.

It has been possible to demonstrate the complete absence of either charged tRNA(Glu) or charged tRNA(Val) at 42 degrees by the use of two stringent strains of E. coli, one temperature-sensitive for glutamyl-tRNA synthetase and the other temperature-sensitive for valyl-tRNA synthetase. In both strains, stable RNA synthesis ceases, and guanosine tetraphosphate accumulates upon incubation at the nonpermissive temperature. Unique among a series of antibiotics tested, only tetracycline was able to stimulate stable RNA synthesis and to cause disappearance of the guanosine nucleotide. In this regard tetracycline and the "relaxed" gene product appear to be analogous.

Amino Acyl-tRNA Synthetases↗