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TopicPage for thrABC 5'UTR of Escherichia coli K-12

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Long 5' UTRs         

Description:

The thrABC operon, sometime referred to as the thrLABC operon, has a regulatory 5' UTR that contain a leader peptide and an attenuator (premature transcription terminator).

Details:

The ThrL leader peptide does not have a known function as a peptide product but rather serves as an indicator of charged threonine-tRNA and isoleucyl-tRNA deficiency (threonine/isoleucine starvation) by stalling at the eight Thr codons and four Ile codons in the 21 amino acid leader peptide (Freundlich, 1963; Gardner, 1979; Lynn, 1987). This stalling blocks the formation of a preemptor stem-loop that shares a stem strand with the attenuator, which in threonine/isoleucine sufficiency forms an alternative stem-loop that does not terminate transcription but does preempt the formation of the attenuator stem-loop, allowing expression of the thrABC operon and biosyntheis of threonine. The efficiency of termination at the attenuator is 90% (Lynn, 1982).

The transcription start point for the thrLABC mRNA was determined by direct RNA sequencing indicating that the 5' UTR has two closely spaced transcription start points: 5'pppA at -189 and 5'pppG at -191 relative to the ATG of thrA; only P32 gamma-labeled ATP and GTP could initiate leader transcripts in vitro; the termination points of the attenuated leader transcript was also mapped using RNase T1 digestion to -29 to -27, corresponding to U7-U9 of the trailing Us of the predicted Rho-independent transcription terminator, with the majority of the attenuated transcripts ending at -29 (Gardner, 1982). EcoGene uses the second of these starts (the A start at -189) because it is highlighted by the authors in a figure; EcoGene annotates this as initiated using promoter P1 even though it appears to be two slightly overlapping promoters. An additional transcription start was mapped to -223, 34 bp upstream of P1; the tandem P1 start sites were re-mapped as one start, a C at -190, but this is unlikely since previous work indicated that gamma-labeled CTP could not initiate P1 transcripts in vitro (Gardner, 1982; Conway, 2014). EcoGene designates the -223 promoter as P2 because it was not detected in the earlier studies. Conway et al. designates the -223 start (P2) as from the primary (P) (most upstream) promoter and the -191 start (P1) as being made from a secondary (S) promoter.


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