Mischarging in mutant tyrosine transfer RNAs

Phenylalanyl-tRNA synthetase from baker's yeast: role of 3'-terminal adenosine of tRNA-Phe in enzyme-substrate interaction studied with 3'-modified tRNA-Phe species

TRNA-Phe species from baker's yeast modified at the 3'-terminus in many cases are phenylalanylatable substrates. Out of several tRNA-Phe species possessing a modified 3'-end that cannot be phenylalanylated, only two, tRNA-Phe-C-C-2'dA and the tRNA-Phe-C-C-formycin-oxi-red, are strong competitive inhibitors for tRNA-Phe-C-C-A during phenylalanylation. In the ATP/PPi exchange, both these inhibitors reduce Vmax to about 25%; but whereas tRNA-Phe-C-C-2dA has no influence on KmATP and Km Phe during ATP/PPi exchange, tRNA-Phe-C-C-formycin-oxi-red reduces KmATP from 1430 muM, found in the absence of tRNA-Phe, to 230 muM, and Km-Phe, from 38 to 14 muM. The values found in the presence of tRNA-Phe-C-C-formycin-oxi-red during ATP/PPi exchange are identical with those determined in the phenylalanylation of tRNA-Phe-C-C-A. All other tRNA-Phe species carrying a modified 3'end that cannot be phenylalanylated exhibit a mixed competitive-noncompetitive inhibition in the phenylalanylation reaction. In the ATP/PPi exchange, they do not influence KmATP and KmPHE and only weakly, if at all, Vmax. The results show that the 3'adenosine of tRNA-Phe cannot solely be a passive acceptor for phenylalanine, but must in addition play an active role during enzyme-substrate interaction. The data can be consistently explained by the hypothesis that the 3'-adenosine of tRNA-Phe triggers a conformational change of the enzyme.

Structure and function of Escherichia coli formylmethionine transfer RNA: loss of methionine acceptor activity by modification of a specific guanosine residue in the acceptor stem of formylmethionine transfer RNA from Escherichia coli

The structural requirements of E. coli formylmethionine tRNA for aminoacylation have been examined by chemical modification of the tRNA, followed by separation of the modified molecules into active and inactive components. Photooxidation of tRNA(fMet) at 50 degrees in the presence of methylene blue results in modification of two guanosine (G) residues in the acceptor stem, at positions no. 2 and no. 71 from the 5'-phosphate terminus. Both of these modifications are present in inactive molecules, but only the G residue at position no. 2 is modified in the acceptor stem of active molecules. Loss of methionine acceptance occurs with first-order kinetics, indicating that inactivation by modification of G residue no. 71 is independent of any other modifications taking place under these conditions. The presence of a modified G residue at position no. 2 in the acceptor stem of active photooxidized molecules shows that disruption of normal base-pairing in this region is not sufficient to inactivate tRNA(fMet). These data indicate that the inactivating modification at position no. 71 is lethal due to a specific alteration in the nucleotide base, rather than simply as a result of breaking a hydrogen-bonded base pair in the acceptor stem.

Is there a discriminator site in transfer RNA?

We determined the nature of the fourth nucleotide from the 3'-end of several Escherichia coli tRNAs, and tabulated these results with the same data for all known tRNA sequences. We find a striking constancy of the fourth nucleotide in tRNAs specific for a given amino acid. Furthermore, tRNAs specific for chemically related amino acids are very likely to have the same nucleotide at the fourth position. One possible explanation for these regularities is the "discriminator" hypothesis: The code by which tRNA is recognized by its cognate aminoacyl-tRNA synthetase is logically hierarchical, with the fourth nucleotide serving as a primary "discriminator" site to subdivide the tRNAs into groups for recognition purposes. Each such group could have its own recognition code, or could be further subdivided by a secondary discriminator site. According to this hypothesis, chemically similar amino acids have the same discriminator nucleotide because they evolved from a single set of related amino acids indistinguishable to a primitive system. There are other possible explanations for the observed regularities at the fourth nucleotide. For example, it is conceivable that the position is used for a direct physical interaction with the amino acid in the charging process, and chemically similar amino acids naturally select the same nucleotide. Further experiments can be expected to clarify this question.