Active complexes derived from Escherichia coli formylmethionine tRNA which lacks the dihydrouridine-containing loop

The inhibitory effect of Alcide, an antimicrobial drug, on protein synthesis in Escherichia coli

Alcide, a broad-spectrum antimicrobial drug, has been shown to kill a wide range of common pathogenic bacteria as well as fungi, in vitro. This agent consists of Part A and Part B which contain sodium chlorite and lactic acid as the active ingredients, respectively. The mixing of these two parts immediately prior to use results in the formation of chlorine dioxide (ClO2), a potent germicidal compound. Exposure of exponentially growing E. coli cells to Alcide resulted in a rapid inhibition of growth as well as loss of viability. Alcide inhibited DNA, RNA, and protein synthesis; however, RNA and protein synthesis were affected at much lower concentrations. The accumulation of the amino acid analog amino-isobutyric acid into growing cultures of E. coli was only partially impaired by Alcide. Cell-free protein synthesis using an RNA directed system was inhibited by Alcide and this effect was lessened in the presence of mercaptoethanol. Higher concentrations of Alcide (1 mM) oxidized 25% of the methionine to methionine sulfoxide. Aminoacylation of E. coli bulk tRNA was decreased in vitro and the aminoacylation of tRNAfMet was particularly sensitive to Alcide.

Synthesis of 5' fragments of formylmethionine transfer ribonucleic acid and their reconstitution with a natural three-quarter molecule

An eicosanucleotide C--G--C--G--G--G--G--U--G--G--A--G--C--A--G--C--C--U--G--Gp corresponding to the bases 1--20 of the nascent sequence for the Escherichia coli tRNAfMet has been synthesized by the joining of the chemically synthesized oligonucleotides C--G--C--G, G--G--G--U--G--G and A--G--C--A--G--C--C--U--G--Gp using RNA ligase from T4-infected E. coli. The hexanucleotide and decanucleotide were phosphorylated with polynucleotide kinase and [gamma-32P]ATP prior to the joining reactions. The decanucleotide and eicosanucleotide were reconstituted respectively with the 3'-three-quarter molecule obtained by limited digestion with RNase T1 of the natural tRNAfMet from E. coli and the activity of the complex as a methionine acceptor was tested using purified methionyl-tRNA synthetase from E. coli. The amino acid acceptor activity of the reconstituted molecules was 11% and 84% with respect to that of the intact tRNAfMet.

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.