Interaction of elongation factor Tu from Escherichia coli with aminoacyl-tRNA carrying a fluorescent reporter group on the 3' terminus

Transfer ribonucleic acids containing 2-thiocytidine in position 75 ([s2C]tRNAs) were prepared by incorporation of the corresponding cytidine analogue into 3'-shortened tRNA using ATP(CTP):tRNA nucleotidyltransferase. [s2C]tRNA was selectively alkylated with fluorescent N-iodoacetyl-N'-(5-sulfo-1-naphthyl)ethylenediamine (1,5-I-AEDANS) on the 2-thiocytidine residue. The product [AEDANS-s2C]aminoacyl-tRNA, forms a ternary complex with Escherichia coli elongation factor Tu and GTP, leading to up to 130% fluorescence enhancement of the AEDANS chromophore. From fluorescence titration experiments, equilibrium dissociation constants of 0.24 nM, 0.22 nM and 0.60 nM were determined for yeast [AEDANS-s2C]Tyr-tRNATyr, yeast Tyr-tRNATyr, and the homologous E. coli Phe-tRNAPhe, respectively, interacting with E. coli elongation factor Tu.GTP. The measurement of the association and dissociation rates of the interaction of [AEDANS-s2C]Tyr-tRNATyr with EF-Tu.GTP and the temperature dependence of the resulting dissociation constants gave values of 55 J mol-1 K-1 for delta S degrees' and -34.7 kJ mol-1 for delta H degrees' of this reaction.     

Separation of functionally distinct regions of a macromolecular substrate. Stimulation of tRNA nucleotidyltransferase by a nonreacting fragment of tRNA.

Rabbit liver tRNA nucleotidyltransferase catalyzes the incorporation of AMP and CMP into the model acceptor substrate, cytidine. The apparent Km for cytidine in this reaction is about 80 to 90 mM which is more than 10(4) greater than the Km values for the natural substrates, tRNA lacking the terminal AMP (tRNA-C-C) and tRNA lacking the terminal pCpA (tRNA-C). The Vmax values for the model reaction are only 5% and 2% of those for the reaction with the natural tRNA substrates. Addition of the tRNA fragments, tRNA lacking the terminal XpCpCpA sequence (tRNA-(X - 1)p) and tRNA lacking the terminal CpCpA (tRNA-Xp), greatly stimulates the rate of nucleotide incorporation into cytidine. In the case of CMP incorporation into cytidine, tRNA-Xp stimulates the reaction about 60-fold, to a rate similar to that of the normal reaction with tRNA-C. The tRNA fragment has no effect on the apparent Km of either cytidine or CTP, but only alters the Vmax of the reaction. Stimulation of the model reactions is maximal with tRNA fragments of specific chain lengths. These results provide direct evidence that the nonreacting regions of a substrate molecule play an important role in the catalytic efficiency of an enzyme.     

Isolation and properties of tRNA nucleotidyltransferase from wheat embryos.

From wheat embryos, tRNA nucleotidyltransferase (EC 2.7.7.25) was isolated. By chromatography on Sepharose 6B, DEAE-cellulose and affinity chromatography on tRNA-hydrazyl-Sepharose 4B, 7000-fold purification of the enzyme was achieved. The enzyme required for its activity Mg2+ or Mn2+ ion. ATP inhibited incorporation of CMP from CTP into lupin tRNA, and CTP acted as a competitive inhibitor of AMP incorporation from ATP. The regulatory role of ATP in incorporation of terminal CMP into tRNA is discussed. The incorporation of terminal CMP into tRNA deprived of terminal CCA or CA, was also studied.     

Evidence for defective transfer ribonucleic acid in polymyopathic hamsters and its inhibitory effect on protein synthesis

1. Different reaction steps involved in protein synthesis were studied in skeletal muscles from control and myopathic hamsters. 2. There was no difference between partially purified aminoacyl-tRNA synthetases from myopathic and control animals in yield or catalytic activity, as tested with exogenous deacylated tRNA. 3. However, isolated deacylated tRNA from myopathic muscle was aminoacylated by these synthetases to a lesser extent than that derived from control muscle. 4. Addition of deacylated tRNA isolated from control muscle improved the performance of pH5 enzymes from myopathic muscle in polypeptide synthesis on homologous polyribosomes; tRNA isolated from myopathic animals did not. 5. Preparation of extracts from both types of animals in the presence of the ribonuclease-absorbent bentonite led to an increased capacity of endogenous tRNA to accept amino acids in pH5 enzymes prepared from normal and abnormal tissue, but the difference between the two systems remained the same. 6. Total tRNA nucleotidyltransferase activity, tested with twice-pyrophosphorolysed rat liver tRNA, was identical in both extracts. 7. Added tRNA nucleotidyltransferase incorporated more AMP and CMP into endogenous tRNA with the pH5 enzyme from myopathic muscle than with that from control muscle. 8. Preincubation of deacylated tRNA from myopathic muscle with ATP, CTP and tRNA nucleotidyltransferase more than doubled its subsequent aminoacyl-acceptor activity, and halved the extent of the defect relative to aminoacylation of control tRNA similarly treated. Endogenous tRNA in pH5 enzyme preparations behaved likewise. 9. It is suggested that a 3'-exonuclease in myopathic muscles attacks tRNA molecules in such a way that some of them remain substrates for tRNA nucleotidyltransferase, which may incorporate into RNA not only AMP and CMP, but also GMP. 10. Cell-free protein synthesis in preparations from myopathic hamster muscles is limited by the supply of intact tRNA molecules.     

Study of the Escherichia coli tRNA nucleotidyltransferase. Specificity of the enzyme for nucleoside triphosphates

Besides the main reactions leading to the repair of tRNA molecules deprived of part or all of their 3′ terminal -pCpCpA sequence, purified E. coli tRNA nucleotidyltransferase catalyzes in vitro, under certain conditions the synthesis of sequences not found in natural tRNAs. In the absence of CTP, AMP is incorporated directly into tRNA-pX or tRNA-pXpC leading to tRNA-pXpA or tRNA-pXpCpA respectively. In the absence of ATP one extra CMP is added to tRNA-pXpCpC to form tRNA-pXpCpCpC. UMP can be incorporated instead of CMP and the sequence -pXpU and -pXpCpU formed. The incorporation of UMP cannot be followed by the incorporation of either a second UMP or an AMP. In all cases, the rate of misincorporation is lower than the rate of the synthesis of the normal sequence.The apparent K_M of the enzyme for UTP is 3.0 10⁻⁴ M. CTP inhibits competitively the incorporation of UMP into tRNA-pX with a K_i value (1.6 10⁻⁵ M) close to its apparent K_M.     

Transfer RNA pyrophosphorolysis with CTP(ATP):tRNA nucleotidyltransferase. A direct route to tRNAs modified at the 3' terminus

The pyrophosphorolysis of tRNA by yeast CTP-(ATP):tRNA nucleotidyltransferase has been studied in an effort to define the behavior of the enzyme and the experimental parameters that lead to net loss of the 3'-terminal nucleotide or to nucleotide exchange. It was found that removal of AMP from the terminus of tRNA proceeded optimally at 1.0 mM PPi; incorporation of 2'- or 3'-dAMP was also studied and shown to proceed optimally at a 6.0 mM concentration of deoxynucleoside triphosphate. CTP was shown to inhibit the pyrophosphorolysis and nucleotide exchange observed when starting from intact tRNA, but apparently not by inhibiting removal of CMP from tRNA missing the 3'-terminal adenosine moiety. The optimized conditions for nucleotide exchange were used for the preparative conversion of tRNAs to species terminating in 2'- and 3'-deoxyadenosine.     

Possible regulation by nucleosidediphosphate kinase involvement of the synthesis of tRNA 3'-terminal -pCpCpA in mammalian cells

When the cytosol of Ehrlich ascites tumor cells was fractionated by chromatofocusing in the pH range of 9 to 6, two active peaks (I and II) of tRNA nucleotidyltransferase were obtained. Fraction I was a multiple complex with a high molecular weight (M.W. greater than 300K) and fraction II comprised components derived from fraction I. Fraction II was separated into tRNA nucleotidyltransferase (M.W., ca. 46,000) and nucleosidediphosphate kinase (M.W., ca. 74,000) by subsequent Sephacryl S-200 chromatography. The two enzymes appeared to be associated loosely with each other. Using the above fraction II or a mixture of the purified tRNA nucleotidyltransferase and nucleosidediphosphate kinase, it was possible to effectively synthesize the 3'-terminal -pCpCpA of tRNA in a reaction mixture containing [3H]-CDP plus XTP or [3H]ADP plus XTP as substrate. Among the XTPs investigated, dTTP was most effective. In addition, it was found that [3H]AMP + XTP also serves as a substrate. [14C]CMP plus XTP, however, was not utilized. From the antagonism of cold CDP against [3H]CTP, and that of cold ADP and AMP against [3H]ATP with the purified tRNA nucleotidyltransferase, the affinity of CDP to the enzyme was estimated to be 1/100 of that of CTP, while the affinities of ADP and AMP to the enzyme were 3 and 30 times higher, respectively, than that of ATP, suggesting that the subsite which binds ATP also binds ADP or AMP. The tRNA nucleotidyltransferase, which had bound ADP or AMP, could not completely synthesize the 3'-terminus of tRNA.(ABSTRACT TRUNCATED AT 250 WORDS)     

The ability of an arginine to tryptophan substitution in Saccharomyces cerevisiae tRNA nucleotidyltransferase to alleviate a temperature-sensitive phenotype suggests a role for motif C in active site organization

We report that the temperature-sensitive (ts) phenotype in Saccharomyces cerevisiae associated with a variant tRNA nucleotidyltransferase containing an amino acid substitution at position 189 results from a reduced ability to incorporate AMP and CMP into tRNAs. We show that this defect can be compensated for by a second-site suppressor converting residue arginine 64 to tryptophan. The R64W substitution does not alter the structure or thermal stability of the enzyme dramatically but restores catalytic activity in vitro and suppresses the ts phenotype in vivo. R64 is found in motif A known to be involved in catalysis and nucleotide triphosphate binding while E189 lies within motif C previously thought only to connect the head and neck domains of the protein. Although mutagenesis experiments indicate that residues R64 and E189 do not interact directly, our data suggest a critical role for residue E189 in enzyme structure and function. Both R64 and E189 may contribute to the organization of the catalytic domain of the enzyme. These results, along with overexpression and deletion analyses, show that the ts phenotype of cca1-E189F does not arise from thermal instability of the variant tRNA nucleotidyltransferase but instead from the inability of a partially active enzyme to support growth only at higher temperatures.     

Absence of 3′-Terminal Residues from Transfer Ribonucleic Acid of Dormant Spores of Bacillus megaterium

Essentially all (>97%) of the transfer ribonucleic acid (tRNA) in log-phase and sporulating cells of Bacillus megaterium contains a complete 3'-cytidyl-cytidyl-adenosine terminus. However, about one-third of the tRNA in the dormant spore lacks the 3'-terminal adenosine 5'-monophosphate (AMP) residue, and some of the adjacent cytosine monophosphate residues are also missing. Examination of specific tRNAs indicated that those specific for isoleucine, leucine, and methionine are missing 30 to 40% of their terminal residue, whereas tRNAs specific for tyrosine lack 88% of the 3'-terminal AMP. Defective spore tRNA is not degraded during germination, but the missing residues are added back in the first minutes of the process. The enzyme catalyzing the addition reaction, tRNA nucleotidyltransferase, is present in the dormant spore at a level similar to that found in the vegetative cell.     

Altered specificity of transfer-ribonucleic acid nucleotidyltransferase in the presence of manganese

1. s-RNA nucleotidyltransferase incorporated CMP into phosphodiesterase-treated s-RNA more rapidly in the presence of Mg(2+) (10mm) than in the presence of Mn(2+) (2mm). UMP was incorporated more rapidly in the presence of Mn(2+), and at high ionic strength the incorporation of CMP was also more rapid in the presence of Mn(2+). 2. The capacity of phosphodiesterase-treated s-RNA for CMP, UMP and AMP was increased in the presence of Mn(2+). Terminal sequences of more than one UMP or AMP residue were synthesized, but these atypical reactions were inhibited when CTP was added. CMP was incorporated rapidly to form -pCpC terminal sequences and then more slowly as longer chains were formed, but very little CMP was incorporated into s-RNA-pCpCpA. 3. CMP was incorporated into phosphodiesterase-treated 5s RNA and ribosomal RNA to form short chains of polyC attached to the primer RNA. This reaction was inhibited by the presence of s-RNA. 4. A small Mn(2+)-dependent incorporation of CMP was also primed by poly(A).(U) and poly(C).(I).     

Cytidines in tRNAs that are required intact by ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae.

Individual species of tRNA from Escherichia coli were treated with hydrazine/3 M NaCl to modify cytidine residues. The chemically modified tRNAs were used as substrate for ATP/CTP: tRNA nucleotidyltransferases from E. coli and yeast, with [alpha-32P]ATP as cosubstrate. tRNAs that were labeled were analyzed for their content of modified cytidines. Cytidines at positions 74 and 75 were found to be required chemically intact for interaction with both enzymes. C56 was also required intact by the E. coli enzyme in all tRNAs, and by the yeast enzyme in several instances. C61 was found to be important in seven of 14 tRNAs with the E. coli enzyme but only in four of 13 tRNAs with that from yeast. Our results support a model in which nucleotidyltransferase extends from the 3' end of its tRNA substrate across the top of the stacked array of bases in the accepter- and psi-stems to the corner of the molecule where the D- and psi-loops are juxtaposed.     

Enzymatic incorporation of ATP and CTP analogues into the 3' end of tRNA

Structural analogues of adenosine 5'-triphosphate and cytidine 5'-triphosphate were investigated as substrates for ATP(CTP):tRNA nucleotidyl transferase. Eight out of 26 ATP analogues and six out of nine CTP analogues were incorporated into the 3' terminus of tRNA. In general, for the recognition of the substrates the modification of the cytidine is less critical than is the modification of adenosine. An isosteric substitution on the ribose residue is possible in both CTP and ATP. The free hydroxyls of these triphosphates can be replaced by an amino group or hydrogen atom without loss of substrate properties. Modifications of positions 1, 2, 6, and 8 on the adenine ring of ATP are not allowed whereas modification on positions 2, 4 and 5 on the cytosine ring of CTP are tolerated by the enzyme. No differences can be observed in the substrate properties of ATP(CTP):tRNA nucleotidyl transferase isolated from different sources. Methods for preparation of tRNA species, which are shortened at their 3' end by one or more nucleotides, and analytical procedures for characterisation of these modified tRNAs are described.     

Purification and characterization of a mutant tRNA nucleotidyltransferase

tRNA nucleotidyltransferase has been extensively purified from a mutant strain of Escherichia coli which displays greatly decreased AMP incorporation, but normal CMP incorporation. The defect in AMP incorporation is retained throughout the purification of the mutant protein. The mutant protein behaves identically to the wild-type protein with regard to elution position on various chromatographic columns, and both have similar molecular weights of about 50000. The defect in the mutant protein is accentuated by the use of yeast tRNA rather than E. coli tRNA-C--C as substrate, by decreased pH, by increased ionic strength and by decreased divalent cation concentration. Substitution of MN2+ for Mg2+ greatly increases the relative activity of the mutant enzyme. In all these cases, CMP incorporation by the mutant enzyme remains the same as the wild-type enzyme. The Km values of the mutant enzyme for its tRNA and triphosphate substrates are unchanged, and the mutant protein is as stable as the wild type with respect to temperature inactivation. These results strongly suggest that the mutation is in the structural gene for tRNA nucleotidyltransferase, and that the mutation probably does not affect the overall structure of the mutant protein, but only a localized region near the AMP-incorporating site.     

Amino acid acceptor activity of tRNA-C-C-C-A.

Rabbit liver tRNA nucleotidyltransferase was used to synthesize modified tRNA molecules containing an additional CMP residue at the 3′ terminus. In the first step tRNA-C-C was converted to tRNA-C-C-C by a minor activity of the purified enzyme. In the second step the lengthened molecules were converted to tRNA-C-C-C-A. AMP addition to tRNA-C-C-C occurred at about 50% the rate with tRNA-C-C. Aminoacylation studies indicated that tRNA-C-C-C-A was active for acceptance of at least 12 amino acids.     

A mutation in Escherichia coli tRNA nucleotidyltransferase that affects only AMP incorporation is in a sequence often associated with nucleotide-binding proteins

Escherichia coli strain 5C15 contains a mutation in the cca gene that decreases AMP incorporation by tRNA nucleotidyltransferase while leaving CMP incorporation unaffected. Earlier studies of the purified mutant enzyme suggested that the mutation was localized to the AMP-incorporating site. In order to analyze this mutation in more detail, the cca gene from strain 5C15 was cloned into plasmid pUC8. Analysis of tRNA nucleotidyltransferase activity in extracts of a strain transformed with this plasmid demonstrated an elevated level of CMP incorporation, but low AMP incorporation, as expected from the properties of the original mutant. Sequence analysis of the mutant cca gene revealed only a single G to A point mutation leading to a glycine to aspartic acid substitution at position 70 of the peptide chain. The amino acid change was localized to one of two Gly-X-Gly-X-X-Gly sequences present in the protein. This sequence has been identified previously near the nucleotide-binding domain of various proteins, but it has not been noted in enzymes that incorporate nucleotide residues. However, other sequences often associated with ATP-binding domains are not found in tRNA nucleotidyltransferase. The implications of these findings for our understanding of nucleotide-binding domains are discussed.     

A novel nucleolytic activity associated with rabbit liver tRNA nucleotidyltransferase

Purified preparations of rabbit liver tRNA nucleotidyltransferase contain a nucleolytic activity which removes terminal CMP residues from tRNA-C-C and tRNA-C-C-C. Other tRNA molecules, such as tRNA-C-C-A, tRNA-C-A, tRNA-C-U and tRNA-C are not substrates for this reaction. The activity exhibits a sharp optimum at about pH 10 and a divalent cation (Mg⁺⁺ or Mn⁺⁺) is required. The reaction is inhibited by ATP, CTP, pyrophosphate and potassium chloride. The relation of this activity to other reactions catalyzed by tRNA nucleotidyltransferase is discussed.     

Purines in tRNAs required for recognition by ATP/CTP:tRNA nucleotidyltransferase from rabbit liver

Recognition of tRNA by the enzyme ATP/CTP:tRNA nucleotidyltransferase from rabbit liver was studied using 12 tRNAs, previously treated with the chemical modifier diethylpyrocarbonate (DEP). Such chemically modified tRNAs were labeled with 32P by nucleotidyltransferase, using alpha-[32P]ATP as a cosubstrate. A carbethoxylated purine at position 57 in the psi-loop interfered with recognition of the tRNA in all instances. DEP-modified purines at other positions (58 in the psi-loop, 52 or 53 in the psi-stem, and 71-73 in the acceptor stem), also interfered with the interaction, but in only a few tRNAs. The mammalian enzyme was more similar to the homologous enzyme from yeast than that from bacteria, in its requirements for chemically unmodified purines. The extent of exclusion of modified bases from 32P-labeled material diminished as the concentration of enzyme increased, demonstrating that interference was not due to the inability of the chemically altered tRNA to refold into a recognizable conformation. The degree of purification of the enzyme did not affect the identity of bases that inhibited the reaction when modified.     

Schizosaccharomyces pombe contains separate CC- and A-adding tRNA nucleotidyltransferases

A specific cytidine-cytidine-adenosine (CCA) sequence is required at the 3′-terminus of all functional tRNAs. This sequence is added during tRNA maturation or repair by tRNA nucleotidyltransferase enzymes. While most eukaryotes have a single enzyme responsible for CCA addition, some bacteria have separate CC- and A-adding activities. The fungus, Schizosaccharomyces pombe, has two genes (cca1 and cca2) that are thought, based on predicted amino acid sequences, to encode tRNA nucleotidyltransferases. Here, we show that both genes together are required to complement a Saccharomyces cerevisiae strain bearing a null mutation in the single gene encoding its tRNA nucleotidyltransferase. Using enzyme assays we show further that the purified S. pombe cca1 gene product specifically adds two cytidine residues to a tRNA substrate lacking this sequence while the cca2 gene product specifically adds the terminal adenosine residue thereby completing the CCA sequence. These data indicate that S. pombe represents the first eukaryote known to have separate CC- and A-adding activities for tRNA maturation and repair. In addition, we propose that a novel structural change in a tRNA nucleotidyltransferase is responsible for defining a CC-adding enzyme.     

Preparation of Escherichia coli tRNAs terminating of modified nucleosides by the use of CTP(ATP):tRNA nucleotidyltransferase and polynucleotide phosphorylase.

Two procedures were investigated for the modification of tRNAs at the 3'-terminal nucleoside. The first involved the incubation of an enzymatically abreviated tRNA (tRNA-C-COH) with appropriate nucleoside triphosphates in the presence of CTP(ATP):tRNA nucleotidyltransferase from Escherichia coli and yeast. The E. coli enzyme did not utilize 2'- or 3'-deoxyadenosine 5'-triphosphate as substrates, but affected incorporation of the 2'- and 3'-O-methyladenosine triphosphates onto tRNA-C-Cou to the extent of 30 and 37%, respectively. Although incorporation of the deoxynucleotides could not be effected using the E. coli enzyme, yeast CTP(ATP:tRNA nucleotidyltransferase produced the desired tRNAs in yields of 45-65%. The second modification procedure involved incubation of tRNA-C-COH with (appropriately blocked) nucleoside diphosphates in the presence of polynucleotide phosphorylase. This procedure afforded the tRNAs terminating in 2'- and 3'-deoxyadenosine in yields of 4% (and the yield of the former was increased to 36% when the incubation was carried out in the presence of 20% methanol). The yields of tRNAs terminating in 2'- and 3'-O-methyladenosing produced by this procedure were 55 and 17%, respectively. Because only single isomers of most of the tRNAs terminating in 2'- and 3'-deoxy- and O-methyladenosine are aminoacylated, attempts were made to obtain the other isomericaminoacyl-tRNA by enzymatic introduction of chemically preaminoacylated nucleotides onto tRNA-C-COH. Although incubation of tRNA-C-COH with three aminoacylated nucleoside 5'-triphosphates and E. coli CTP(ATP):tRNA nucleotidyltransferase did not result in production of the desired tRNAs to a detectable extent, incubation with 2'-deoxy-3'-O-L-phenylalanyladenosine 5'-diphosphate and polynucleotide phosphorylase afforded E. coli tRNA terminating with the corresponding aminoacylated deoxynucleoside.