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PMID:15520470

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Contents

Citation

Zheng, D, Constantinidou, C, Hobman, JL and Minchin, SD (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res. 32:5874-93

Abstract

The Escherichia coli cyclic AMP receptor protein (CRP) is a global regulator that controls transcription initiation from more than 100 promoters by binding to a specific DNA sequence within cognate promoters. Many genes in the CRP regulon have been predicted simply based on the presence of DNA-binding sites within gene promoters. In this study, we have exploited a newly developed technique, run-off transcription/microarray analysis (ROMA) to define CRP-regulated promoters. Using ROMA, we identified 176 operons that were activated by CRP in vitro and 16 operons that were repressed. Using positive control mutants in different regions of CRP, we were able to classify the different promoters into class I or class II/III. A total of 104 operons were predicted to contain Class II CRP-binding sites. Sequence analysis of the operons that were repressed by CRP revealed different mechanisms for CRP inhibition. In contrast, the in vivo transcriptional profiles failed to identify most CRP-dependent regulation because of the complexity of the regulatory network. Analysis of these operons supports the hypothesis that CRP is not only a regulator of genes required for catabolism of sugars other than glucose, but also regulates the expression of a large number of other genes in E.coli. ROMA has revealed 152 hitherto unknown CRP regulons.

Links

PubMed PMC528793 Online version:10.1093/nar/gkh908

Keywords

Base Sequence; Binding Sites; Cyclic AMP Receptor Protein/genetics; Cyclic AMP Receptor Protein/metabolism; Escherichia coli/genetics; Escherichia coli/metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Molecular Sequence Data; Mutation; Oligonucleotide Array Sequence Analysis; Operon; Promoter Regions, Genetic; Regulon; Transcription, Genetic

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Annotations

Gene product Qualifier GO ID GO term name Evidence Code with/from Aspect Notes Status

crp:Gene_Product(s)

GO:0006350

transcription

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc (v14.0)

complete

crp:Gene_Product(s)

GO:0016563

transcription activator activity

IEP: Inferred from Expression Pattern

F

Seeded from EcoCyc (v14.0)

complete

crp:Gene_Product(s)

GO:0016564

transcription repressor activity

IEP: Inferred from Expression Pattern

F

Seeded from EcoCyc (v14.0)

complete

crp:Gene_Product(s)

GO:0045893

positive regulation of transcription, DNA-dependent

IDA: Inferred from Direct Assay

P

replacing obsolete GO:0016563

complete

crp:Gene_Product(s)

GO:0045892

negative regulation of transcription, DNA-dependent

IDA: Inferred from Direct Assay

P

replacing obsolete GO:0016564

complete

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