Determination of tRNA(Phe) nucleotides contacting the subunits of Thermus thermophilus phenylalanyl-tRNA synthetase by photoaffinity crosslinking.

The nucleotides of tRNA(Phe) interacting with the subunits of Thermus thermophilus phenylalanyl-tRNA synthetase (the alpha(2)beta(2) heterotetramer) have been determined by photoaffinity crosslinking of randomly s(4)U-monosubstituted tRNA(Phe) transcripts which retain aminoacylation parameters closely similar to those of the native tRNA(Phe). The thiolated transcripts have been fractionated by affinity electrophoresis and separately crosslinked to the enzyme. Sites of crosslinking to the beta subunit have been identified at positions 33 and 39 and crosslinking sites to the alpha subunit have been localized at positions 20, 45 and 47, using alkaline hydrolysis analysis of the crosslinked proteinase K-treated tRNAs. An additional crosslink to the beta subunit, not identified in the full-length crosslinked tRNAs, has been deduced to occur at position 12, based on the analysis of an unusual (fast migrating) crosslinked product. Nucleotide s(4)U8 of native tRNA(Phe) has been shown to form a minor crosslink to the alpha subunit. Four of the seven crosslinking sites, namely nucleotides 8, 12, 20 and 39, are among those shown to be protected against cleavage by iodine in footprinting experiments; in contrast, only nucleotide 12 is among the contact sites defined in the crystal structure. The data of independent biochemical approaches strongly suggest conformational flexibility of the complex under functional conditions, thus reflecting the importance of macromolecular dynamics for the interaction.

Interaction of T. thermophilus phenylalanyl-tRNA synthetase with the 3'-terminal nucleotide of tRNAPhe.

The interaction of Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) with the 3;-terminal nucleotide of tRNAPhe has been studied by affinity labeling to solve the problem arising from X-ray crystallographic study: the binding sites of phenylalanine and the 3;-terminal nucleotide base were revealed to be identical in the crystal structures of PheRS complexed with the substrates. tRNAPhe derivatives containing a photoreactive 4-thiouridine (tRNAPhe-s4U-76) or 6-thioguanosine residue (tRNAPhe-s6G-76) in the 3;-end have been prepared using terminal tRNA nucleotidyl transferase. Kinetic measurements of aminoacylation provide evidence for a functional role of base-specific interactions of the 3;-terminal adenosine in productive interaction of tRNAPhe with the enzyme: tRNAPhe-s4U-76 cannot be aminoacylated; the replacement of A-76 with s6G results in a 370-fold reduction of catalytic efficiency of aminoacylation mainly due to decreased Vmax value. Relative cross-linking of the s6G-substituted tRNA to the alpha-subunit (69% of the total yield of the cross-linked alpha- and beta-subunits) is two times higher as compared to the cross-linking of tRNAPhe-s4U-76. The dialdehyde derivative, tRNAPhe-Aox-76, with periodate-oxidized 3;-terminal ribose is cross-linked with the same selectivity to the alpha-subunit as tRNAPhe-s6G-76. The results suggest specific binding of the 3;-terminal nucleotide of tRNAPhe by the catalytic subunit of PheRS in the absence of other substrates. Comparative analysis of the cross-linked products in the absence and in the presence of small substrates revealed ATP and aminoacyl-adenylate to effect the interaction of the tRNAPhe acceptor end with PheRS. The correct positioning of the 3;-terminal nucleotide of tRNAPhe corresponding to the structure of the productive complex with PheRS is therefore promoted only in the presence of all three substrates.

Phenylalanyl-tRNA synthetase interacts with DNA: studies on activity using deoxyribooligonucleotides.

Phenylalanyl-tRNA synthetase from Thermus thermophilus complexes with short (up to 30 nucleotide length) single-stranded DNA fragments more efficiently than with double-stranded fragments. The complexing between DNA and the protein significantly increases with deoxyribooligonucleotide longer than 20 nucleotides. Using affinity labeling, the binding site of DNA was located near the interface of the alpha- and beta-subunits. The binding sites of DNA and tRNAPhe do not overlap. Phenylalanyl-tRNA synthetase from E. coli also binds DNA.

Affinity modification of phenylalanyl-tRNA synthetase from Thermus thermophilus by tRNAPhe transcripts containing 4-thiouridine.

Photoreactive derivatives of tRNAPhe containing residues of 4-thiouridine (s4U) were synthesized by the transcription system of T7 RNA polymerase. Complete substitution of s4U for 16 uridine residues ([16s4U]-tRNAPhe) caused a 14-fold decrease in the catalytic efficiency of aminoacylation of the tRNAPhe transcript by phenylalanyl-tRNA synthetase from T. thermophilus. [1s4U]-tRNAPhe obtained by random incorporation of s4U residues with further isolation of s4U-monosubstituted RNA molecules on an affinity gel has the same kinetic parameters in aminoacylation as the tRNAPhe transcript. The s4U-containing tRNAPhe transcripts were shown to bind covalently to phenylalanyl-tRNA synthetase, and the specificity of modification was demonstrated. The modification stoichiometry determined in this work suggests that the enzyme is a functional dimer. The modification labels both alpha- and beta-subunits of the enzyme, which has an oligomeric structure of alpha2beta2, and forms "cross-linking" products of subunits upon modification with [16s4U]-tRNAPhe. The prevalence of modification of the alpha-subunit suggests that tRNA has contacts with the enzyme, which have not been deciphered previously by X-ray analysis.

Localization of the binding site for the 3'-terminal sequence of tRNAPhe in subunits of phenylalanyl-tRNA synthetase from Thermus thermophilus.

A photoreactive tRNAPhe derivative containing a 4-thiouridine residue at the 3'-end (tRNAPhe-s4U-75) was prepared by tRNA nucleotidyltransferase-mediated incorporation of s4UMP into a tRNAPhe transcript lacking the 3'-terminal dinucleotide. The resulting tRNAPhe-s4U-75 was covalently bound to phenylalanyl-tRNA synthetase from Thermus thermophilus, and all criteria of an affinity modification were met. The main products of modification displaying various electrophoretic mobilities were formed by binding tRNAPhe-s4U-75 to the beta-subunit (major) of the enzyme. These data suggest that the nucleotide found at position 75 of tRNAPhe interacts with the beta-subunit of phenylalanyl-tRNA synthetase.

A peculiarity of the reaction of tRNA aminoacylation catalyzed by phenylalanyl-tRNA synthetase from the extreme thermophile Thermus thermophilus.

It was confirmed unambiguously that the anomalously high plateau in the tRNA aminoacylation reaction catalyzed by Thermus thermophilus phenylalanyl-tRNA synthetase is a result of enzymatic synthesis of tRNA bearing two bound phenylalanyl residues (bisphenylalanyl-tRNA). The efficiency of bisphenylalanyl-tRNA formation was shown to be quite low: the second phenylalanyl residue is attached to tRNA approximately 50 times more slowly than the first one. The thermophilic synthetase can aminoacylate twice not only T. thermophilus tRNAPhe but also Escherichia coli tRNAPhe and E. coli tRNAPhe transcript, indicating that the presence of modified nucleotides is not necessary for tRNAPhe overcharging. Bisphenylalanyl-tRNA is stable in acidic solution, but it decomposes in alkaline medium yielding finally tRNA and free phenylalanine. Under these conditions phenylalanine is released from bisphenylalanyl-tRNA with almost the same rate as from monophenylalanyl-tRNA. In the presence of the enzyme the rate of bisphenylalanyl-tRNA deacylation increases. Aminoacylated tRNAPhe isolated from T. thermophilus living cells was observed to contain no detectable bisphenylalanyl-tRNA under normal growth of culture. A possible mechanism of bisphenylalanyl-tRNA synthesis is discussed.

Recognition of tRNAPhe by phenylalanyl-tRNA synthetase of Thermus thermophilus.

The tRNA(Phe) nucleotides required for recognition by phenylalanyl-tRNA synthetase of Thermus thermophilus have been determined using Escherichia coli tRNA(Phe) transcripts with various mutations. The anticodon nucleotides are shown to be the most important recognition elements. The discriminator nucleotide, A73, involved in the recognition set of yeast, E. coli and human phenylalanyl-tRNA synthetases contributes only slightly to tRNA(Phe) recognition by Th. thermophilus phenylalanyl-tRNA synthetase. Nucleotide 20 and some tertiary nucleotides, including the conserved G19.C56 base pair, are proposed to participate in stabilization of the precise tRNA conformation required for efficient aminoacylation. The role of the 3'-CCA terminus, common to all tRNAs, in the specific interaction of tRNA with phenylalanyl-tRNA synthetase is discussed.

[A comparative study of the thermal stability of phenylalanyl tRNA synthetase from Escherichia coli MRE-600 and Thermus thermophilus HB 8]. / Sravnitel'noe issledovanie termostabil'nosti fenilalanil-tRNK-sintetaz iz Escherichia coli MRE-600 i Thermus thermophilus HB 8.

The thermal stability of phenylalanyl-tRNA-synthetase (PTS) from E. coli and T.thermophilus HB 8 was studied in solution at various conditions by scanning microcalorimetry. It has been shown that the value of heating rate, concentration of the enzyme and Mg2+ ions in the solution affects the parameters of thermal denaturation of both enzymes. The higher thermal stability of PTS from T. thermophilus was observed as well as the independence of its properties upon broad variations of experimental conditions. The role of thermostability of the enzymes are discussed with respect to the biological properties of E. coli and T.thermophilus.

Phenylalanyl-tRNA synthetase from Thermus thermophilus can attach two molecules of phenylalanine to tRNA(Phe).

Phenylalanyl-tRNA synthetase from the extreme thermophilic bacterium Thermus thermophilus can incorporate more than one molecule of phenylalanine into the tRNA(Phe). It is shown that the 'hyperaminoacylated' tRNA(Phe) is the bis-2',3'-O-phenylalanyl-tRNA(Phe), and its formation is typical for the thermophilic enzyme but does not occur for E. coli phenylalanyl-tRNA synthetase under the same conditions.

Comparative study of subunits of phenylalanyl-tRNA synthetase from Escherichia coli and Thermus thermophilus.

FPLC separation of alpha- and beta-subunits of phenylalanyl-tRNA synthetases from E. coli MRE-600 and Thermus thermophilus HB8 has been carried out in the presence of urea. Native alpha-subunits of both enzymes were primarily alpha 2-dimers and tended to aggregate. Most E. coli enzyme beta-subunits were monomeric and only a small fraction was represented by beta 2-dimers. All thermophilic beta-subunits were beta 2-dimers. It was shown that monomers and all forms of homologous subunits had no catalytic activity in tRNA(Phe) aminoacylation. For the enzymes and their subunits, titration curves were obtained and isoelectric points were determined. The comparison of the relative surface charges indicated similarity of the surfaces of entire enzymes and the corresponding beta-subunits. Alpha-subunits displayed a distinctly different pH dependence of the surface charge. A spatial model of the oligomeric structure and a putative mechanism for its formation are discussed.

Diadenosine oligophosphates: peculiarities of synthesis by phenylalanyl-tRNA synthetases from E. coli MRE-600 and Thermus thermophilus HB8.

Temperature and other factors affecting synthesis of bis(5'-adenosyl) tetraphosphate (Ap4A) and bis(5'-adenosyl)triphosphate (Ap3A) catalyzed by phenylalanyl-tRNA synthetases (PheRSs) from Escherichia coli MRE-600 and Thermus thermophilus HB8 have been investigated. Those two synthetases exhibited different temperature-dependent rates of the Ap4A and Ap3A synthesis. However, with respect to the effects of such effectors of the Ap4A synthesis as Zn2+, Mg2+, tRNA and Ap4A phosphonate analogues, as well as some inhibitors of aminoacyl-tRNA synthetase, those two enzymes were apparently undistinguishable.

[A comparative study of phenylalanyl-tRNA synthetases from Escherichia coli and Thermus thermophilus by the tritium topography method]. / Sravnitel'noe issledovanie fenilalanil-tRNK-sintetaz iz Escherichia coli i Thermus thermophilus metodom tritievoi planigrafii.

A comparative study of thermostability and amino acid composition of phenylalanyl-tRNA synthetases from E. coli and Thermus thermophilus HB8 has been carried out. In the thermophilic protein the proline, leucine, phenylalanine, arginine content was considerably increased, whereas that of asparagine, isoleucine, serine, threonine and lysine was decreased as compared to the mesophilic protein. Using tritium topography, Pro, (Leu + Ile) and Gly were found to be the most accessible on the surfaces of the both enzymes. In the E. coli enzyme the threonine residues were also easy to access, while on the surface of the thermophilic enzyme arginine residues were more abundant. A quantitative assay of the surface compositions revealed the increased exposure of (Leu + Ile) residues in the thermophilic protein as well as of the charged asparagine and arginine residues. A possible relationship of the observed effects to thermostability is discussed.

[Separation and comparative characteristics of subunits of phenylalanyl-tRNA synthetase from Escherichia coli MRE-600 and Thermus thermophilus HB8]. / Razdelenie i sravnitel'naia kharakteristika sub''edinits fenilalanil-tRNK-sintetaz iz Escherichia coli MRE-600 i Thermus thermophilus HB8.

Separation of alpha- and beta-subunits of phenylalanyl-tRNA-synthetases from E. coli MRE-600 and Thermus thermophilus HB8 using FPLC has been carried out for the first time. The separated subunits of both enzymes do not possess any detectable tRNA-amino-acylation activity. It was found that in the case of the E. coli enzyme beta-subunits exist in solution mainly in the monomeric form with negligible formation of beta 2-dimers, while alpha-subunits predominantly form alpha 2-dimers over the same concentration range. In the case of Thermus thermophilus phenylalanyl-tRNA-synthetase, both alpha- and beta-subunits mainly exist in the dimeric form. The putative mechanisms of alpha-subunit aggregation and of subunit association for alpha 2 beta 2-type enzymes are discussed.

Comparative study of the phenylalanyl-tRNA synthetases from Escherichia coli and Thermus thermophlus by the tritium topography method.

A comparative study of thermostability and aminoacid composition of the phenylalanyl-tRNA synthetases from E. coli and Thermus thermophilus HB8 has been carried out. Compared with the mesophilic enzyme, a considerable increase of Pro, Leu, Phe, Arg and decrease of Asx, Ile, Ser, Thr and Lys content have been revealed in the thermophilic protein. Using tritium topography, Pro, (Leu + Ile) and Gly were found to be the most accessible on the surfaces of both the enzymes. In the E. coli enzyme, Thr residues were also easy to access while on the surface of the thermophilic enzyme there were more Arg residues. The quantitative assay of the surface compositions revealed the increased exposure of the (Leu + Ile) residues on the thermophilic protein as well as of the charged Asx and Arg residues. A possible correlation of the observed effects with thermostability is discussed.

[A study of the complex-formation of phenylalanyl-tRNA-synthetase from Escherichia coli using the tRNA-Phe method of small-angle x-ray scattering]. / Issledovanie kompleksoobrazovaniia fenilalanil-tRNK-sintetazy iz Escherichia coli s tRNK-Phe metodom malouglovogo rentgenovskogo rasseianiia.

The method of small-angle X-ray scattering was employed to analyse the equilibrium enzyme-substrate complexes in solution. A new approach of analysis of the experimental data was developed. This type of analysis provides the determination of dissociation constants and structural parameters of enzyme-substrate complexes. The radius of gyration (Rg) and dimensions of half-axis of the equivalent prolonged ellipsoid (a, b) of E. coliphenylalanyl-tRNA synthetase and its complexes with one or two tRNA(Phe) molecules have been determined. The values of these parameters speak in favour of structural rearrangements due to the interaction of the enzyme with tRNA(Phe). The thermodynamic characteristics of phenylalanyl-tRNA synthetase complexes with tRNA(Phe) testify to the negative cooperativity in binding of two tRNA molecules with the enzyme.

Application of the small-angle X-ray scattering technique for the study of equilibrium enzyme-substrate interactions of phenylalanyl-tRNA synthetase from E. coli with tRNAPhe.

The small-angle X-ray scattering technique (SAXS) is proposed for the investigation of equilibrium macromolecular interactions of the enzyme-substrate type in solution. Experimental procedures and methods of analysing the data obtained from SAXS have been elaborated. The algorithm for the data analysis allows one to determine the stoichiometric, equilibrium and structural parameters of the enzyme-substrate complexes obtained. The thermodynamic characteristics for the formation of complexes of tRNAPhe with phenylalanyl-tRNA synthetase have been determined and demonstrate negative cooperativity for binding of the two tRNAPhe molecules. The structural parameters (Rg, Rc, semi-axes) have been determined for free phenylalanyl-tRNA synthetase and tRNAPhe from E. coli MRE-600 and of enzyme complexes possessing one and two tRNAPhe molecules, indicating structural rearrangements of the enzyme in the interaction with tRNAPhe.

[Isolation and crystallization of phenylalanyl-tRNA-synthetase from Thermus thermophilus HB8]. / Vydelenie i kristallizatsiia fenilalanil-tRNK-sintetazy iz Thermus thermophilus HB8.

Method of isolation of phenylalanyl-tRNA synthetase from Thermus thermophilus HB8 is described, including chromatography on DEAE-sepharose, ammonium sulfate fractionation, hydrofobic chromatography on Toyopearl, gel filtration on ultrogel AcA-34, chromatography on phenylalanylaminohexyl-sepharose and heparine-sepharose. Yield of the purified enzyme was 10 mg from 1 kg of T. thermophilus cells. The enzyme is found to consist of two types of subunits with molecular masses 92 and 36 kDa and is likely to be a tetramer protein with molecular mass 250 kDa. Crystals of phenylalanyl-tRNA synthetase suitable for X-ray structural studies have been obtained.

Phenylalanyl-tRNA synthetase from E. coli MRE-600: analysis of the active site distribution on the enzyme subunits by affinity labelling.

Affinity labelling has been employed to localize the substrate-binding sites on the enzyme subunits of phenylalanyl-tRNA synthetase (L-phenylalanine:tRNAPhe-ligase, EC 6.1.1.20) of Escherichia coli MRE-600 (alpha 2 beta 2-type). N-Chlorambucilylphenylalanyl-tRNA, N-bromoacetylphenylalanyl-tRNA, tRNAPhe containing an azido group at the eighth position of the molecule (S4U), tRNAPhe containing azido groups at different points of the molecule, p-azidoanilidate of phenylalanine, adenosine 5'-trimethaphosphate and N-bromoacetyl-L-phenylalaninyladenylate were used in experiments. It has been shown that tRNA-binding sites are formed on heavy beta-subunits of the enzyme. Phenylalanyl-tRNA is also localized on beta-subunits, while the aminoacyl moiety of aminoacyl-tRNA is localized near the contact region of subunits. The phenylalanine-binding site is located on light alpha-subunits of the enzyme. Adenosine 5'-trimethaphosphate and the analogue of phenylalanyladenylate modify both types of enzyme subunits. In our opinion, the catalytic center of tRNA aminoacylation is formed in the contact region of subunits, and the aminoacyl moiety is transferred into tRNA (from the alpha- into beta-subunit in the region of their contact).

[Study of the possibility of identifying the structural elements of the phenylalanyl-tRNA-synthetase active center by affinity labeling]. / Issledovanie vozmozhnosti lokalizatsii strukturnykh élementov aktivnykh tsentrov fenilalanil-tRNK-sintetazy metodom affinnoi modifikatsii.

The possibility of localization of active sites structural components by affinity labelling was investigated. The modification of E. coli MRE-600 phenylalanyl-tRNA synthetase (E.C.6.1.1.20) (alpha 2 beta 2-type) by the phosphorylating analog of ATP-- [14C]adenosine-5'-trimetaphosphate results in the labelling of both heavy (beta) and light (alpha) enzyme subunits. Analysis of the peptide maps of the tryptic enzyme hydrolysate reveals a great number of peptides containing [14C]radioactivity. The decrease of covalent binding at low concentration of the analog did not abolish the plural labelling. The data permit to consider this kind of analogs as unperspective for localization of specific peptides. Modification of phenylalanyl-tRNA synthetase by tRNAPhe containing the photoreactive group (--CH2CONHC6H5N3) at eighth position of molecule (S8U) results in the labelling of only heavy beta-subunits. These data correspond to the previous results which testify to the disposition of tRNA binding sites on beta-subunits of phenylalanyl-tRNA synthetase. After hydrolysis of the modified phenylalanyl-tRNA synthetase by trypsin six peptides covalently bound with tRNAPhe were revealed. This quantity of modified peptides is higher than the number of tRNA binding sites. Hence the method of affinity labelling has definite limitations for localization of peptides of enzyme active sites.

[Purification and properties of phenylalanyl-tRNA-synthetase from Escherichia coli MRE-600]. / Ochistka i nekotorye svoistva fenilalanil-tRNK-sintetazy iz Escherichia coli MRE-600.

A preparative scale method for isolation of highly purified phenylalanyl-tRNA synthetase from E. coli MRE-600 was developed. It consists of cell destroying, nucleic acid precipitation with streptomycine sulfate, fractionation with ammonium sulfate followed by chromatography on different carriers (Sephadex G-200, DEAE-cellulose, DEAE-Sephadex A-50, and hydroxyapatite). The mode of cell destroying was found to affect the process of the further enzyme purification. The phenylalanyl-tRNA synthetase was purified 540-fold, with recovery being 20.6% and the specific activity - 540 units per mg protein. The enzyme content in the purified preparation was 80-90% judging by electrophoresis in PAAG. The molecular weights of the subunits determined by electrophoresis under denaturative conditions were found to be 102,000 +/- 4000 (beta) and 42,000 +/- 2000 (alpha). The molecular weight of the native enzyme determined by gel filtration through Sephadex G-200 and electrophoresis at varied concentrations of polyacrylamide was found to be 340,000 +/- 20,000. The Km values for tRNA, ATP and phenylalanine in the aminoacylation reaction are equal to 5.4 X 10(-7) M, 1,9 X 10(-4) M, and 3.7 X 10(-6) M, respectively.