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 polym...

The Escherichia coli fructose repressor, FruR, is known to regulate expression of several genes concerned with carbon utilization. Using a previously derived consensus sequence for FruR binding, additional potential operators were identified and tested for FruR binding in DNA band migration retardation assays. Operators in the control regions of operons concerned with carbon metabolism bound FruR, while those in operons not concerned with carbon metabolism did not. In vivo assays with transcriptional lacZ fusions showed that FruR controls the expression of FruR operator-containing genes encoding key enzymes of virtually every major pathway of carbon metabolism. Moreover, a fruR null mutation altered the rates of utilization of at least 36 carbon sources. In general, oxidation rates for glycolytic substances were enhanced while those for gluconeogenic substances were depressed. Alignment of FruR operators revealed that the consensus sequence for FruR binding is the same for operons that are activated and repressed by FruR and permitted formulation of a revised FruR-binding consensus sequence. The reported observations indicate that FruR modulates the direction of carbon flow by transcriptional activation of genes encoding enzymes concerned with oxidative and gluconeogenic carbon flow and by repression of those concerned with fermentative carbon flow.

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~~We have analysed a gene cluster in the 674-769 min region of the Escherichia coli chromosome, revealed by recent systematic genome sequencing. The genes within this cluster include: (1) five genes encoding homologues of the E. coli mannose permease of the phosphotransferase system (IIB, IIB', IIC, IIC' and IID) ; (2) genes encoding a putative N-acetylgalactosamine 6-phosphate metabolic pathway including (a) a deacetylase, (b) an isomerizing deaminase, (c) a putative carbohydrate kinase, and (d) an aldolase; and (3) a transcriptional regulatory protein homologous to members of the DeoR family. Evidence is presented suggesting that the aldolase-encoding gene within this cluster is the previously designated kbe gene that encodes tagatose-1,6-bisphosphate aldolase. These proteins and a novel IIAwn-like protein encoded in the 2-01 min region are characterized with respect to their sequence similarities and phylogenetic relationships with other homologous proteins. A pathway for the metabolism of N-acetylgalactosamine biochemically similar to that for the metabolism of N-acetylglucosamine is proposed.

Gram-negative bacteria have evolved numerous systems for the export of proteins across their dual-membrane envelopes. Three of these systems (types I, III and IV) secrete proteins across both membranes in a single energy-coupled step. Four systems (Sec, Tat, MscL and Holins) secrete only across the inner membrane, and four systems [the main terminal branch (MTB), fimbrial usher porin (FUP), autotransporter (AT) and two-partner secretion families (TPS)] secrete only across the outer membrane. We have examined the genome sequences of Pseudomonas aeruginosa PAO1 and Pseudomonas fluorescens Pf0-1 for these systems. All systems except type IV were found in P. aeruginosa, and all except types III and IV were found in P. fluorescens. The numbers of each such system were variable depending on the system and species examined. Biochemical and physiological functions were assigned to these systems when possible, and the structural constituents were analyzed. Available information regarding the mechanisms of transport and energy coupling as well as physiological functions is summarized. This report serves to identify and characterize protein secretion systems in two divergent pseudomonads, one an opportunistic human pathogen, the other a plant symbiont.