Accuracy of natural messenger translation: analysis of codon-anticodon recognition in a simplified cell-free system

Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch: RNA-DEPENDENT CODON SELECTION OUTSIDE THE RIBOSOME

Many amino acid-related genes in Gram-positive bacteria are regulated by the T box riboswitch. The leader RNA of genes in the T box family controls the expression of downstream genes by monitoring the aminoacylation status of the cognate tRNA. Previous studies identified a three-nucleotide codon, termed the "Specifier Sequence," in the riboswitch that corresponds to the amino acid identity of the downstream genes. Pairing of the Specifier Sequence with the anticodon of the cognate tRNA is the primary determinant of specific tRNA recognition. This interaction mimics codon-anticodon pairing in translation but occurs in the absence of the ribosome. The goal of the current study was to determine the effect of a full range of mismatches for comparison with codon recognition in translation. Mutations were individually introduced into the Specifier Sequence of the glyQS leader RNA and tRNA(Gly) anticodon to test the effect of all possible pairing combinations on tRNA binding affinity and antitermination efficiency. The functional role of the conserved purine 3' of the Specifier Sequence was also verifiedin this study. We found that substitutions at the Specifier Sequence resulted in reduced binding, the magnitude of which correlates well with the predicted stability of the RNA-RNA pairing. However, the tolerance for specific mismatches in antitermination was generally different from that during decoding, which reveals a unique tRNA recognition pattern in the T box antitermination system.

High fidelity of guanine translation in a plasmid-directed in vitro system

The extent of misreading of individual bases in the first or second codon position has been measured in vitro in a simplified plasmid-directed coupled system in which natural messenger translation is restricted to the formation of the N-terminal di- or tripeptide. Experiments were performed under conditions of competition between cognate and noncognate tRNAs in the presence of streptomycin to maximize the frequency of reading errors. A striking lack of susceptibility to mistranslation of guanine, as compared to the other 3 bases, was observed.

Differential pattern of misreading induced by streptomycin in vitro

A simplified, plasmid-directed coupled system was used to study the effect of streptomycin on the accuracy of natural messenger translation in vitro. The interaction of six different codons with their cognate tRNAs and 18 non-cognate tRNAs was analysed in the presence and absence of the antibiotic. Streptomycin appeared to modify, to a varying extent, the frequency of errors in codon-anticodon recognition. From this observation, some rules for mistranslation were inferred.

Nucleotide sequence and expression of the aceK gene coding for isocitrate dehydrogenase kinase/phosphatase in Escherichia coli

The flow of isocitrate through the glyoxylate bypass in Escherichia coli is regulated via the phosphorylation-dephosphorylation of isocitrate dehydrogenase mediated by a bifunctional enzyme: isocitrate dehydrogenase kinase/phosphatase. The aceK gene coding for this enzyme is part of the polycistronic ace operon, which also includes the aceB and aceA genes coding, respectively, for malate synthase and isocitrate lyase, the two glyoxylate bypass enzymes. The complete nucleotide sequence of a 2,214-base-pair DNA fragment containing the aceK gene and its 5' flanking region has been determined. In vivo experiments based on gene expression in a minicell system and protein fusion with beta-galactosidase, as well as in vitro assays with a plasmid-directed transcription-translation coupled system, have shown that the aceK gene extends over 1,731 nucleotides encoding a 66,528-dalton protein. The 5' flanking region presents an unusual intercistronic structural pattern consisting of two consecutive long dyad symmetries, almost identical in sequence, which can yield very stable stem-loop units. These structures are probably responsible for the drastic downshifting in expression observed in acetate-grown bacteria between the aceK gene and the aceA gene located immediately upstream in the ace operon.