Isolation and some properties of methionine transfer ribonucleic acid from Escherichia coli

Regulation of methionine synthesis in Escherichia coli: Effect of metJ gene product and S-adenosylmethionine on the expression of the metF gene

The regulation of the expression of the Escherichia coli metF gene, which codes for 5,10-methylenetet-rahydrofolate reductase (EC 1.1.99.15), has been investigated by using a simplified DNA-directed in vitro system that measures the formation of the first dipeptide (fMet-Ser) of the gene product. The synthesis of fMet-Ser directed by a plasmid containing the metF gene is specifically inhibited by metJ protein (repressor protein). S-Adenosylmethionine enhances the inhibition by the metJ protein of metF gene expression. The inhibition by the metJ protein is at the level of transcription and the results suggest that S-adenosylmethionine is functioning as an allosteric effector.

Mechanism of ribosomal translocation. Translocation limits the rate of Escherichia coli elongation factor G-promoted GTP hydrolysis

The pre-steady-state kinetics of GTP hydrolysis catalysed by elongation factor G and ribosomes from Escherichia coli has been investigated by the method of quenched-flow. The GTPase activities either uncoupled from or coupled to the ribosomal translocation process were characterized under various experimental conditions. A burst of GTP hydrolysis, with a kapp value greater than 30 s-1 (20 degrees C) was observed with poly(U)-programmed vacant ribosomes, either in the presence or absence of fusidic acid. The burst was followed by a slow GTP turnover reaction, which disappears in the presence of fusidic acid. E. coli tRNAPhe, but not N-acetylphenylalanyl-tRNAPhe (N-AcPhe-tRNAPhe), stimulates the GTPase when bound in the P site. If the A site of poly(U)-programmed ribosomes, carrying tRNAPhe in the P site, is occupied by N-AcPhe-tRNAPhe, the burst of Pi discharge is replaced by a slow GTP hydrolysis. Since, under these conditions, N-AcPhe-tRNAPhe is translocated from the A to the P site, this GTP hydrolysis very probably represents a GTPase coupled to the translocation reaction.

Regulation of methionine synthesis in Escherichia coli: effect of metJ gene product and S-adenosylmethionine on the in vitro expression of the metB, metL and metJ genes

The regulation of the expression of three Escherichia coli met genes, metB, which codes for cystathionine gamma-synthetase (EC 4.2.99.9), metL, which codes for aspartokinase II-homoserine dehydrogenase II (EC 2.7.2.4-EC 1.1.1.3) and metJ, which codes for the methionine regulon aporepressor, has been studied using highly purified DNA-directed in vitro protein synthesis systems. In a system where the entire gene product is synthesized, the expression of the metB and metL genes is specifically inhibited by MetJ protein (repressor protein) and S-adenosylmethionine (AdoMet). In a simplified system that measures the formation of the first dipeptide of the gene product (fMet-Ala for the metJ gene), MetJ protein and AdoMet partially repress (approximately 40-60%) metJ gene expression. Thus, the metJ gene can be partially autoregulated by its gene product.

In vitro regulation of phage lambda cII gene expression by Escherichia coli integration host factor

The effect of Escherichia coli integration host factor (IHF) on phage lambda gene expression has been examined in a simplified DNA-directed in vitro system that measures the formation of the first dipeptide of the gene product. Plasmid pKC30cII, which contains the phage lambda genes N, cII and O, under control of the PL promoter, was used as template to study the expression of the first dipeptide of the gene products--i.e., fMet-Asp for N protein, fMet-Val for cII, and fMet-Thr for O. Purified IHF stimulates the DNA-directed synthesis of fMet-Val (cII) and fMet-Thr (O) 2-3-fold but has no effect on the synthesis of fMet-Asp (N). In this in vitro system, the stimulation by IHF of cII and O gene expression is at the level of transcription. Phage lambda repressor completely inhibits dipeptide synthesis in the presence or absence of IHF. The results are consistent with a role of IHF as a transcription antiterminator, perhaps functioning at or near the tR1 site preceding the cII gene.

Incorporation of 1,N6-ethenoadenosine into the 3' terminus of tRNA using T4 RNA ligase. 2. Preparation and ribosome interaction of fluorescent Escherichia coli tRNAMetf

A fluorescent derivative of tRNAMetf from Escherichia coli has been prepared which contains 1,N6-etheno-adenosine (epsilon A) in the place of adenosine 73, the fourth residue from the 3' end. The labeled tRNA, tRNAMetf epsilon A73, is fully active with respect to aminoacylation, formylation and formylmethionyl transfer to puromycin. The preparation procedure entails the chemical removal of four nucleotides from the 3' end of tRNAMetf, ligation of the truncated molecule with epsilon A 3',5'-bisphosphate by use of T4 RNA ligase and repair of the C-C-A end with nucleotidyl transferase. The fluorescence of fMet-tRNAMetf epsilon A73 has been exploited for studying tRNA-ribosome complexes. Upon binding the tRNA into the ribosomal P site, the fluorophor experiences a change of its molecular environment as indicated by an increased fluorescence intensity. On the other hand, iodide quenching experiments indicate that, in the complex, the fluorophor is not shielded against solvent access. The results suggest that (a) adenosine 73 is not involved in direct contacts with the ribosome and (b) the stacking of the 3'-terminal A-C-C-A sequence is changed upon binding to the ribosome.

A coupled DNA-directed in vitro system to study gene expression based on di- and tripeptide formation

In this report, a simplified coupled DNA-directed in vitro system has been described that is based on the formation of the first di- or tripeptide of the gene product. This system is gene specific and quantitative, and the assay (especially the extraction procedure) is very rapid. The fact that both transcription and translation initiation occur in this system makes it ideally suited for studies on the regulation of prokaryotic gene expression. The ideal templates are plasmids, DNA fragments or purified mRNAs that direct the synthesis of a limited number of products with different second amino acids. An essential requirement is that the initial sequence of the protein products be known, although this system could be used to determine the second amino acid in cases where there is some doubt from the DNA sequence as to where a particular protein initiates. A difficulty arises when a plasmid contains more than one gene whose protein products have the same initial dipeptide. One solution to the problem is to measure tripeptide formation if the third amino acid is different. A second procedure, if the code word for the second amino acid differs between the genes, is to use purified isoacceptor tRNA species to distinguish the products. Another important application of tripeptide synthesis is that it can be used as a measure of the amount of active mRNA present in a mixture of mRNAs. The use of a ribosomal high-salt wash instead of the purified initiation and elongation factors greatly simplifies this system and should make it suitable for routine analysis in most laboratories.

Carbodiimide modification analysis of aminoacylated yeast phenylalanine tRNA: evidence for change in the apex region

The G- and U-specific reagent, carbodiimide was used to probe the solution structure of aminoacylated yeast phenylalanine tRNA. Both quantitative and qualitative changes in modification were observed when the modification patterns of tRNA-CCA(3'OH), tRNA-CCA(3'NH2) and phe-tRNA-CCA(3'NH2) were compared. Five nucleotides were modified in all cases, D16 and G20 in the D-loop, U33 and Gm34 in the anticodon loop and U47, in the region of the extra arm. Small changes occurred in the D-loop with incorporation of the adenosine analogue manifest as new, low levels of modification of G22 (D-stem) and a loss of sensitivity to Mg+2 in modification of D16. Aminoacylation resulted in new modification of G19, modification of a residue in the T psi CG sequence, and a 2.5-fold increase in modification of G22. Taken together the results show that aminoacylation causes increased exposure of bases in the apex region of the L-shaped molecule where the D- and psi-loops are joined. The effects observed could occur as a consequence of stable or dynamic changes in conformation.

Use of different tRNASer isoacceptor species in vitro to discriminate between the expression of plasmid genes

A simplified translation system coupled to DNA transcription that involves assaying the synthesis of the first dipeptide of a gene product has been described recently [Robakis, N., Meza-Basso, L., Brot, N. & Weissbach, H. (1981) Proc. Natl. Acad. Sci. USA 78, 4261--4264]. Using this dipeptide system, we have investigated the expression of genes carried on plasmids coding for beta-lactamase, ribosomal protein L12, and the chloroplast large subunit (LS) of ribulosebisphosphate carboxylase (RbuBPCase). Although all three nascent gene products begin with the sequence fMet-Ser, the formation of fMet-Ser can be used to distinguish between the synthesis of beta-lactamase and either L12 or the LS of RbuBPCase by using different serine isoacceptor tRNA species. In beta-lactamase, the serine codon is AGU, which utilizes the serine isoacceptor species tRNASer3; in L12 and the LS of RbuBPCase, the serine codewords are UCU and UCA, respectively, both of which are recognized by the serine isoacceptor species tRNASer1. By using either pure tRNASer1 or pure tRNASer3, the expression of each gene can be quantitated. In this system, guanosine-5'-diphosphate-3'-diphosphate inhibits the expression of the beta-lactamase and L12 genes but stimulates the synthesis of the LS. In addition, the ratio of fMet-Ser/fMet-Ala (L12/L10) synthesized was about 1 as compared with the ratio of 4 that has been obtained previously in vivo or in vitro protein-synthesizing systems in which the entire gene product was measured.

Translational control of ribosomal protein L10 synthesis occurs prior to formation of first peptide bond

A simplified DNA-directed in vitro system has been developed to study the regulation of the synthesis of ribosomal protein L10 by measuring the formation of the first dipeptide, fMet-Ala. The results show that the inhibition of L10 synthesis by L10 (autoregulation) occurs at or prior to the formation of the first peptide bond.

Changes in the solution structure of yeast phenylalanine transfer ribonucleic acid associated with aminoacylation and magnesium binding

The effect of aminoacylation on the structure of yeast phenylalanine tRNA was evaluated by laser light scattering. In these experiments, the translational diffusion coefficient (D20,w) of phenylalanyl-tRNA was monitored continuously during spontaneous deacylation in a variety of solution conditions. The results reveal that significant changes can occur in the hydrodynamic volume and electric charge as a consequence of aminoacylation but that the effects are magnesium dependent. At neutral pH, 20 degrees C, and 0.1 M salt, the D20,w value increased by 18% when deacylation occurred in 2--10 mM Mg2+ concentrations while no change in diffusivity was observed for tRNA deacylating in 0.5--1.0 mM Mg2+. The Mg2+ concentration dependence of the D20,w changes behaves in highly cooperative manner. The electric charges of aminoacyl-tRNA and nonacylated tRNA in 1 and 10 mM Mg2+ were estimated from the diffusive virial coefficients. In the higher Mg2+ conditions, aminoacyl-tRNA has a charge of 15 +/- 2e- while that of the nonacylated form is 10 +/- 2e-; both acylated and nonacylated tRNA have a charge of 11 +/- 4e- in 1 mM Mg2+. Taken together, the results indicate that aminoacylation permits the binding of additional Mg2+, resulting, in turn, in the formation of a more extended conformer of lower diffusivity and greater negative charge. The results also provide a possible explanation for several contradictory results in the literature.

A study of the thermal unfolding of Escherichia coli phenylalanine transfer RNA by chemical modification at elevated temperatures

Escherichia coli tRNAPhe was modified by 3 M sodium bisulphite pH 6.0 for 24 h in the temperature range 25 degrees C (x 5 degrees C) to 55 degrees C and in the absence of added magnesium ions. The sites and extents of conversion of cytidines to uridine occurring at each temperature were determined by fingerprinting. The new sites of cytidine modification found at higher reaction temperatures were assumed to arise from breakage of secondary and tertiary structure hydrogen bonds involving cytidine residues. From these data, we conclude that hydrogen bonds within the 'complex core' of the tRNA (including the base pairs G-10 . C-25, C-11 . G-24 and C-13 . G-21 within the dihydrouridine stem and the tertiary structure base pair G-15 . C-48 melt at a lower temperature than the tertiary structure hydrogen bonds between G-19 in the dihydrouridine loop and C-56 in the TpsiC loop.

Initiation of protein synthesis by folate-sufficient and folate-deficient Streptococcus faecalis R: partial purification and properties of methionyl-transfer ribonucleic acid synthetase and methionyl-transfer ribonucleic acid formyltransferase

The initiation of protein synthesis by Streptococcus faecalis R grown in folate-free culture occurs without N-formylation or N-acylation of methionyl-tRNA(f) (Met). Methionyl-tRNA synthetase and methionyl-tRNA formyltransferase were partially purified from S. faecalis grown under normal culture conditions in the presence of folate (plus-folate); the general properties of the enzymes were determined and compared with the properties of the enzymes purified from wild-type cells grown in the absence of folate (minus-folate). S. faecalis methionyl-tRNA synthetase displays optimal activity at pH values between 7.2 and 7.8, requires Mg(2+), and has an apparent molecular weight of 106,000, as determined by gel filtration, and 127,000, as determined by sucrose density gradient centrifugation. The K(m) values of plus-folate methionyl-tRNA synthetase for each of the three substrates in the aminoacylation reaction (l-methionine, adenosine triphosphate, and tRNA) are nearly identical to the respective substrate Michaelis constants of minus-folate methionyl-tRNA synthetase. Furthermore, both plus- and minus-folate S. faecalis methionyl-tRNA synthetases catalyze, at equal rates, the aminoacylation of tRNA(f) (Met) and tRNA(m) (Met) isolated from either plus-folate or minus-folate cells. S. faecalis methionyl-tRNA formyltransferase displays optimal activity at pH values near 7.0, is stimulated by Mg(2+), and has an apparent molecular weight of approximately 29,900 when estimated by sucrose density gradient centrifugation. The K(m) value of plus-folate formyltransferase for plus-folate Met-tRNA(f) (Met) does not differ significantly from that of minus-folate formyltransferase for minus-folate Met-tRNA(f) (Met). Both enzymes can utilize either 10-formyltetrahydrofolate or 10-formyltetrahydropteroyltriglutamate as the formyl donor; the Michaelis constant for the monoglutamyl pteroyl coenzyme is slightly less than that of the triglutamyl pteroyl coenzyme for both transformylases. Tetrahydrofolate and uncharged tRNA(f) (Met) are competitive inhibitors of both plus- and minus-folate S. faecalis formyltransferase; folic acid, pteroic acid, aminopterin, and Met-tRNA(m) (Met) are not inhibitory. These results indicate that the presence or absence of folic acid in the culture medium of S. faecalis has no apparent effect on either methionyl-tRNA synthetase or methionyl-tRNA formyltransferase, the two enzymes directly involved in the formation of formylmethionyl-tRNA(f) (Met). Therefóre, the lack of N-formylation of Met-tRNA(f) (Met) in minus-folate S. faecalis is due to the absence of the formyl donor, a 10-formyl-tetrahydropteroyl derivative. Although the general properties of S. faecalis methionyl-tRNA synthetase are similar to those of other aminoacyl-tRNA synthetases, S. faecalis methionyl-tRNA formyltransferase differs from other previously described transformylases in certain kinetic parameters.

Conformation of charged and uncharged tRNA

The effect of aminoacylation on the conformation of yeast tRNA(Phe) was investigated by high-resolution (300 MHz) proton nuclear magnetic resonance (NMR) spectroscopy. Resonances in the low-field (-11 to -15 ppm) region of the spectra are due to ring NH protons of Watson-Crick base pairs, and to a very high degree of approximation (within 0.05 ppm) the low-field spectra of tRNA(Phe) and phenylalanyl-tRNA(Phe) are identical. From this observation and analysis of the low-field NMR spectra we conclude that the secondary structures of the two tRNAs are identical with respect to base-pairing schemes and interbase distances in the helical region (0.1-0.2 A). Several tertiary structural features, including conformation of the dihydro-U loop, conformation of the minor loop, relative orientations of the acceptor and the TPsiC stems, dihydro-U and anticodon stems, and probably conformation of the anticodon loop are shown to be the same in tRNA(Phe) and phenylalanyl-tRNA(Phe). Our results leave little remaining opportunity for changes in tertiary structure that would not have been observed by the NMR method.