Purification and characterization of AUA specific isoleucine transfer ribonucleic acid from Escherichia coli B

Multivalent translational control of transcription termination at attenuator of ilvGEDA operon of Escherichia coli K-12

The regulatory region for the ilvGEDA operon of Escherichia coli K-12 has been located and characterized. ilv leader RNA transcribed from this region is described, and the DNA sequence of the region is presented. This DNA sequence contains a transcription promoter, a region coding for a 32-amino-acid polypeptide containing multiple isoleucine, valine, and leucine codons, and a transcription termination site preceding the first structural gene. The mutually exclusive secondary structures of the leader RNA have been analyzed. On the basis of these data, a model for the multivalent attenuation of the ilvGEDA operon is proposed.

Pattern and chance in the use of the genetic code

The use of triplet code words in E. coli, phiX174, MS2, and rabbit globin was examined. A significant deficiency of purines in the third position of four fold degenerate codons was noted, although its significance is not understood. There has been no consistent selection against uracil in pyrimidine restricted codons. For many amino acids the choice between code words appears random, while for arginine, isoleucine, and probably glycine, distinct biases exist which can be explained in terms of tRNA availability.

On the possible modulating role of the isoleucine AUA-codon in bacteriophage MS2 RNA

A set of MS2 mutants were shown to have an additional silent mutation met --> ile at position 108 of the coat protein. As transitions are more frequent than transversions one would have expected an AUA codon in this position in the mutant RNAs. As the AUA codon is one of the best candidates for a modulation role in the control of translation in E. coli, the presence of this AUA in the gene for the protein made in major amounts upon viral infection would impose serious doubt on the theory of modulation. We have directly proven by minifinger-printing of mutant RNA and further analysis of the relevant spots that, in fact, the isoleucine residue at position 108 of the coat protein gene is specified by the non-rate-limiting AUU codon, in agreement with a modulation type of control of protein synthesis.

Doublet frequencies and codon weighting in the DNA of Escherichia coli and its phages

A compilation of nucleic acid sequences from E. coli and its phages has been analysed for the frequency of occurrence of nearest neighbour base doublets and codons. Several statistically significant deviations from random are found in both doublet and codon frequencies. The deviations in E. coli also appear to occur in lambda and in the coat protein gene of MS2, whereas T4 and other parts of the MS2 genome show different sequence properties. These and other findings are discussed in relation to the hypothesis that rapidity of translation of mRNAs in the E. coli system is dependent on doublet frequency and codon usage patterns.

Increased isoleucine acceptance by sulfur-deficient transfer RNA from Escherichia coli

Sulfur-deficient tRNA, isolated from Escherichia coli HfrC, rel-, met-, cys-, lambda, after cysteine starvation, was found to have an increased acceptance of isoleucine in proportion to the deficiency of 4-thiouridine. Isoleucine acceptance was not altered in the presence of other amino acids of CTP, and the higher acceptance was observed over a wide range of magnesium, isoleucine, tRNA and enzyme concentrations. The Vmax value for sulfur-deficient tRNA was more than three times greater than observed for normal tRNA. Methylated albumin kieselguhr (MAK) chromatography revealed three isoacceptor peak for normal tRNA, while sulfur-deficient tRNA was missing tRNAile, and exhibited a larger, shifted peaks for tRNA normal tRNA, while sulfur-deficient tRNA was missing tRNAille 2, and exhibited a large shifted peak for tRNAile 3 . Treatment with crude RNA sulfurtransferase both lowered the isoleucine acceptance for sulfur-deficient tRNA to that seen for normal tRNA, and restored the missing isoacceptor on MAK. The possibility that thionucleotides may play a role in the aminoacylation of tRNAile in E. coli is discussed.

Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene

Bacteriophage MS2 RNA is 3,569 nucleotides long. The nucleotide sequence has been established for the third and last gene, which codes for the replicase protein. A secondary structure model has also been proposed. Biological properties, such as ribosome binding and codon interactions can now be discussed on a molecular basis. As the sequences for the other regions of this RNA have been published already, the complete, primary chemical structure of a viral genome has now been established.

A modified uridine in the anticodon of E. coli tRNA I Tyr su + oc

The anticodon of an ochre-suppressing derivative of E. coli tRNA I Tyr, previously identified as UUA, can contain a modified uridine (U+) in the first position. The novel modified nucleotide has been identified by two-dimensional thin layer chromatography following RNase T2 digestion of anticodon-containing fragments. Up+ is found in less than stoichiometric molar yields in preparations of tRNA I Tyr su + oc. The electrophoretic mobility of Up+ is the same as Up at pH 3.5 and pH 7.5. U+ probably does not contain sulfur since it cannot be labeled with 35S in vivo incorporation experiments.

Pleiotropy of hisT mutants blocked in pseudouridine synthesis in tRNA: leucine and isoleucine-valine operons

The hisT gene codes for an enzyme responsible for the conversion of uridine to pseudouridine (Psi) in the anticodon region of many tRNA species in Salmonella typhimurium. We have previously shown that a hisT mutant has tRNA(His) which lacks pseudouridine in this region and as a consequence has an altered chromatographic behavior. We show here a similar alteration in chromatographic behavior of all tRNA(Leu) and one tRNA(Ile) species from a hisT mutant. By contrast, tRNA(Val), which contains no pseudouridine except for the one in the TPsiCG sequence, is chromatographically unaltered in a hisT mutant. The absence of pseudouridine in the anticodon region of tRNA in hisT mutants has been previously shown to cause derepression of the histidine operon. We show here that in hisT mutants the regulation of the leucine and the isoleucine and valine operons is also affected: the enzymes of these operons are refractory to repression by the branched chain amino acids. However, there is no difference between hisT and wild type in the pattern of derepression caused by isoleucine or valine limitation and only a slight difference in the enzyme levels in cells grown on minimal medium. The alteration in the regulation of branched chain amino acid operons may also explain why hisT mutants are resistant to inhibition of growth by the amino acid analogues 5,5,5-trifluoroleucine, beta-hydroxyleucine, and norleucine and by the oligopeptides glycylglycylnorleucine and norleucylnorleucine.