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Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli

Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,¹ Departamento de Ingenieria Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62550, México,² Genencor International, Inc., Palo Alto, California 94304-1013³

Received 7 November 2003/ Accepted 22 February 2004

We report here the transcriptome analyses of highly expressed genes that are subject to catabolite repression or activation mediated by the cyclic AMP receptor protein (Crp). The results reveal that many operons encoding enzymes of central carbon metabolic pathways (e.g., Krebs cycle enzymes), as well as transporters and enzymes that initiate carbon metabolism, are subject to direct Crp-mediated catabolite repression. By contrast, few enzyme-encoding genes (direct regulation) but many ribosomal protein- and tRNA-encoding genes (indirect regulation) are subject to Crp-dependent glucose activation. Additionally, Crp mediates strong indirect catabolite repression of many cytoplasmic stress response proteins, including the major chaperone proteins, five ATP-dependent protease complexes, and several cold and heat shock proteins. These results were confirmed by (i) phenotypic analyses, (ii) real-time PCR studies, (iii) reporter gene fusion assays, and (iv) previously published reports about representative genes. The results serve to define and extend our appreciation of the Crp regulon.

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