PMID:12460564

Citation	Rintoul, MR, Cusa, E, Baldomà, L, Badia, J, Reitzer, L and Aguilar, J (2002) Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS.J. Mol. Biol. 324:599-610
Abstract	The allantoin regulon of Escherichia coli, formed by three operons expressed from promoters allA(P), gcl(P) and allD(P), is involved in the anaerobic utilization of allantoin as nitrogen source. The expression of these operons is under the control of the repressor AllR. The hyperinduction of one of these promoters (allD(P)) by allantoin in an AllR defective mutant suggested the action of another regulator, presumably of activator type. In this work we have identified ybbS (proposed gene name allS), divergently transcribed from allA, as the gene encoding this activator. Analysis of the expression of the three structural operons in DeltaallS mutant showed that the expression from allD(P) was abolished, suggesting that AllS is essential for the expression of the corresponding operon. In a wild-type strain expression of allS takes place mainly anaerobically and is hyperinduced when the nitrogen source limits growth. However, expression of allS is independent of regulators of the Ntr response, NtrC or Nac. Band shift experiments showed that AllR binds to DNA containing the allS-allA intergenic region and the gcl(P) promoter and its binding is abolished by glyoxylate. Both DNA fragments contain a highly conserved inverted repeat, which after site-directed mutagenesis, has been proven to be the AllR-binding site. This site displays similarity with the IclR family recognized consensus. Interaction of AllR with the single operator present in the allS-allA intergenic region prevented binding of RNA polymerase to either of the two divergent promoters. The regulator AllS interacts only with allD(P) even in the absence of allantoin. Analysis of this promoter allowed us to identify an inverted repeat as a motif for AllS binding. We propose a model for the coordinate control of the allantoin regulon by AllR and AllS.
Links	PubMed
Keywords	Allantoin; Base Sequence; Binding Sites; Chromosome Mapping; Consensus Sequence; DNA-Binding Proteins; DNA-Directed RNA Polymerases; Escherichia coli; Gene Expression Regulation, Bacterial; Models, Genetic; Molecular Sequence Data; Mutagenesis, Site-Directed; Nitrogen; Operon; Promoter Regions, Genetic; Regulon; Repressor Proteins; Sequence Alignment; Sequence Deletion; Trans-Activators; Transcription, Genetic; Transcriptional Activation
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Species	Taxon ID	Strain	Gene (if known)	OMP	Phenotype	Details	Evidence	Notes
Escherichia coli		JA178	del allS	no growth on D-xylose as carbon source when allotoin was used as a nitrogen source	Growth		Plating Assay	allS is necessary for the utilization of allantoin as a nitrogen source
Escherichia coli		JA178	del allS	abolished expression of allD	Expression	in the presence of either glyoxylate or allantoin	Other	Table 1-AllS is essential for expression from the allD promoter
Escherichia coli		JA179	del allD	abolished ability to utilize allantoin as a nitrogen source no growth on D-xylose when allantoin is used as the nitrogen source	Growth		Plating Assay
Escherichia coli		JA173	del allR	constitutive expression of allS hyper-induced expression of allS when nitrogen is limiting	Other		Other
Escherichia coli		JA178	del allS	hyper-induced expression of allS in the presence of both glyoxylate and limiting ammonia	Other		Other
Escherichia coli		JA173	del allR	constitutive expression of allS under aerobic conditions	Other		Other
Escherichia coli		LRI	glnG	no growth on D-glucose when L-arginine is used as the nitrogen source	Growth		Plating Assay
Escherichia coli		LRI	glnG	no growth on D-xylose when L-arginine is used as the nitrogen source	Growth		Plating Assay
Escherichia coli		LRI	glnG	no growth on D-glucose when gamma-aminobutyrate is used as the nitrogen source	Growth		Plating Assay
Escherichia coli		LRI	glnG	no growth on D-xylose when gamma-aminobutyrate is used as the nitrogen source	Growth		Plating Assay
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