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BMC Mol Biol. 2010 Aug 10;11:56. doi: 10.1186/1471-2199-11-56.

A method for selecting cis-acting regulatory sequences that respond to small molecule effectors.

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1
Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia.

Abstract

BACKGROUND:

Several cis-acting regulatory sequences functioning at the level of mRNA or nascent peptide and specifically influencing transcription or translation have been described. These regulatory elements often respond to specific chemicals.

RESULTS:

We have developed a method that allows us to select cis-acting regulatory sequences that respond to diverse chemicals. The method is based on the beta-lactamase gene containing a random sequence inserted into the beginning of the ORF. Several rounds of selection are used to isolate sequences that suppress beta-lactamase expression in response to the compound under study. We have isolated sequences that respond to erythromycin, troleandomycin, chloramphenicol, meta-toluate and homoserine lactone. By introducing synonymous and non-synonymous mutations we have shown that at least in the case of erythromycin the sequences act at the peptide level. We have also tested the cross-activities of the constructs and found that in most cases the sequences respond most strongly to the compound on which they were isolated.

CONCLUSIONS:

Several selected peptides showed ligand-specific changes in amino acid frequencies, but no consensus motif could be identified. This is consistent with previous observations on natural cis-acting peptides, showing that it is often impossible to demonstrate a consensus. Applying the currently developed method on a larger scale, by selecting and comparing an extended set of sequences, might allow the sequence rules underlying the activity of cis-acting regulatory peptides to be identified.

PMID:
20698993
PMCID:
PMC2928234
DOI:
10.1186/1471-2199-11-56
[Indexed for MEDLINE]
Free PMC Article
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