The catabolite repressor/activator (Cra) protein of enteric bacteria

Bacteria are frequently faced with metabolic questions which, if answered appropriately, can enhance their reproductive and survival capabilities. They must decide how much of a specific nutrient they will take up and metabolize, which of the various equivalent nutrients that may be available they will select, and how they will respond to changes in relative nutrient concentrations as a function of time. They must also coordinate the acquisition of one essential class of nutrients with those of all other such classes. Thus, Escherichia coli will select glucose over lactose, will limit the rate of glucose uptake to correspond to its needs even though it possesses a greater uptake capacity, and will further restrict its carbon uptake in the absence of a required source of nitrogen, phosphorus, or sulfur. We are just now coming to appreciate the molecular details of the processes by which these regulatory interactions are achieved. In the 1970s and 1980s, the molecular details of catabolite repression in E. coli, mediated by cyclic AMP (cAMP) and its cognate receptor, the cAMP receptor protein (CRP), were elucidated (2, 26). It came to be accepted that cAMP provided the principal mechanism of catabolite repression in this enteric bacterium. As key details of the process became known, many investigators became convinced that the essence of the phenomenon had already been solved and that an understanding of this regulatory mechanism would quickly result in elucidation of other essential bacterial regulatory mechanisms. Consequently, interest, research, and funding for bacterial regulatory phenomena of this type began to subside. As early as 1978, evidence had appeared suggesting that cAMP-independent mechanisms of catabolite repression were operative in E. coli (7, 15). Similarly, experiments conducted with Bacillus subtilis and other bacteria led to the suggestion that these organisms might possess multiple cAMP-independent mechanisms of catabolite repression (8, 25). Moreover, evidence began to accumulate suggesting that the mechanisms of catabolite repression in evolutionarily divergent bacteria are not the same (17, 37, 38). These facts led to the conclusion that our knowledge of catabolite repression, based on an understanding of the cAMP-CRP-mediated regulatory process in E. coli, represented just the tip of the iceberg (35). The catabolite repressor/activator (Cra) protein of enteric bacteria was initially characterized as the fructose repressor, FruR. Mutants defective in the cra gene (previously designated fruR) exhibited a pleiotropic phenotype, being unable to grow with gluconeogenic substrates as the sole carbon source (5, 13). It became clear that the product of the cra gene controlled the transcriptional expression of numerous genes concerned with carbon and energy metabolism (4, 12, 14, 39). We summarize here the evidence suggesting that the Cra protein, a member of the LacI-GalR family, recognizes an imperfect palindromic DNA sequence to which it binds asymmetrically. If this Cra operator precedes the RNA polymerase binding site, it activates transcription of the downstream operon, but if it overlaps or follows the RNA polymerase binding site, it represses transcription. The effects of Cra on transcription are counteracted by micromolar concentrations of fructose-1-phosphate and millimolar concentrations of fructose-1,6-bisphosphate, which promote catabolite repression of Cra-activated operons and catabolite activation of Cra-repressed operons. Cra apparently controls the direction of carbon flow in E. coli and consequently influences the rates of utilization of dozens of exogenous carbon sources.