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J Mol Biol. 1984 Feb 25;173(2):177-209.

Transcription of a gene cluster coding for two aminoacyl-tRNA synthetases and an initiation factor in Escherichia coli.


The alpha and beta subunits of phenylalanyl-tRNA synthetase are encoded by the pheS and pheT genes, respectively. These genes are clustered closely together with the genes for threonyl-tRNA synthetase (thrS) and translation initiation factor IF3 (infC); the gene order is thrS infC pheS pheT. We have used two methods to study the transcription pattern within this cluster. The first was the in vitro transcription of DNA restriction fragments with purified RNA polymerase, followed by fractionation of the RNA products by polyacrylamide gel electrophoresis. The second method was the mapping of promoters by means of the "abortive initiation" reaction of McClure and co-workers. This procedure consists of the incubation of RNA polymerase with DNA restriction fragments plus one nucleoside monophosphate and one [alpha-32P]nucleoside triphosphate; the polymerase synthesizes dinucleotide products of known sequence at promoter sites in the DNA. We found that transcription initiated at an internal site within infC (designated P1), and at two promoter sites between infC and pheS (designated P2 and P3). Transcription terminated at two sites about 200 nucleotides apart, located just before pheS. The initiation and termination signals were arranged so as to yield a nested set of overlapping transcripts. At the P1 promoter, transcription initiated with G-C, at P2 with A-C and sometimes A-G, and at P3 with G-U. Promoter activity was also found in a 3000-base interval that includes the start of the thrS gene; eight or nine transcripts (not mapped in detail) were observed, which started with at least four different dinucleotides. All major initiation sites in the gene cluster represented purine starts, although some pyrimidine initiation was observed in trace amounts. No promoter activity was found between pheS and pheT with either of the two techniques; this observation supports the conclusion that these genes are co-transcribed. No evidence was found for any promoter between the termination sites and the beginning of the pheS gene. It is suggested that one of the terminators is an attenuation site controlling the extension of transcription into pheS and pheT. Attenuation may explain the observed regulation of phenylalanyl-tRNA synthetase by the amino acid supply.

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