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The fructose repressor (FruR) affects carbon flux through the central metabolic pathways of Escherichia coli . In this study, l -tryptophan production in Escherichia coli FB-04 was improved by knocking out the fruR gene, thereby inactivating FruR. This fruR knockout strain, E. coli FB-04( ΔfruR ), not only exhibited higher growth efficiency, it also showed substantially improved l -tryptophan production. l -tryptophan production by E. coli FB-04( ΔfruR ) and l -tryptophan yield per glucose were increased by 62.5% and 52.4%, respectively, compared with the parent E. coli FB-04. Metabolomics analysis showed that the fruR knockout significantly enhances metabolic flow through glycolysis, the pentose phosphate pathway and the TCA cycle, increasing levels of critical precursors and substrates for l -tryptophan biosynthesis. These results indicate that fruR deletion should enhance l -tryptophan production and improve the efficiency of carbon source utilization independent of genetic background. [ABSTRACT FROM AUTHOR]

Abstract: In Corynebacterium glutamicum, the transcriptional regulators of acetate metabolism RamA (encoded by cg2831) and RamB (encoded by cg0444) play an important role in expression control of genes involved in acetate and ethanol metabolism. Both regulators were speculated to have broader significance in expression control of further genes in the central metabolism of C. glutamicum. Here we investigated the RamA and RamB regulons by genome-wide transcriptome analysis with special emphasis on genes encoding enzymes of the central carbon metabolism. When compared to the parental wild-type, 253 genes and 81 genes showed different mRNA levels in defined RamA- and RamB-deficient C. glutamicum strains, respectively. Among these were genes involved in sugar uptake, glycolysis, gluconeogenesis, acetate, l-lactate or ethanol metabolism. The direct interaction of RamA and RamB proteins with the respective promoter/operator fragments was demonstrated in vitro by electrophoretic mobility shift assays. Taken together, we present evidence for an important role of RamA and RamB in global gene expression control in C. glutamicum. [Copyright &y& Elsevier]

Abstract: Corynebacterium glutamicum is an industrially important producer of amino acids and an emerging model system for the Corynebacterineae. The glxR gene of C. glutamicum ATCC 13032 encodes a DNA binding transcription factor of the Crp-Fnr protein family. Available data indicated a prominent role of GlxR in the transcriptional regulatory network of C. glutamicum. We have used recently published whole-genome annotations of several corynebacteria to derive further evidence for GlxR-mediated transcriptional regulation from a comparative genomics approach. A bioinformatic strategy detected 22 genes belonging to a proposed GlxR core regulon in corynebacteria. Binding of purified GlxR protein to 40-mer oligonucleotides representing predicted GlxR binding sites in the upstream region of core genes from C. glutamicum ATCC 13032 was verified in vitro by electrophoretic mobility shift assays. Based on current data, a reliable genome-scale prediction of GlxR binding sites was performed, indicating that about 14% of the annotated C. glutamicum genes might be under direct transcriptional control by GlxR. Integration of GlxR-mediated regulatory interactions with the data stored in CoryneRegNet enabled the reconstruction of a refined transcriptional regulatory network model for C. glutamicum. This network model exhibited a hierarchical and modular structure and is characterized by the presence of master regulators in each functional module, with GlxR serving as the dominating regulatory hub. [Copyright &y& Elsevier]

Abstract: The glxR (cg0350) gene of Corynebacterium glutamicum ATCC 13032 encodes a DNA-binding trancription regulator of the CRP/FNR protein family. Five genomic DNA regions known to be bound by GlxR provided the seed information for DNA binding site discovery by expectation maximization and Gibbs sampling approaches. The detection of additional motifs in the genome sequence of C. glutamicum was performed with a position weight matrix and a profile hidden Markov model, both deduced from the initial motif discovery. A combined iterative search for GlxR binding sites revealed 201 potential operator sequences. The interaction of purified GlxR protein with 51 selected binding sites was demonstrated in vitro by performing electrophoretic mobility shift assays with double-stranded 40-mer oligonucleotides. Considering potential operon structures and the genomic organization of C. glutamicum, the expression of 53 transcription units comprising 96 genes may be controlled directly by GlxR. The DNA binding site of GlxR is apparently specified by the consensus sequence TGTGANNTANNTCACA. Integration of the data into the transcriptional regulatory network model of C. glutamicum revealed a high connectivity of the deduced regulatory interactions and suggested that GlxR controls at least (i) sugar uptake, glycolysis, and gluconeogenesis, (ii) acetate, lactate, gluconate, and ethanol metabolism, (iii) aromatic compound degradation, (iv) aerobic and anaerobic respiration, (v) glutamate uptake and nitrogen assimilation, (vi) fatty acid biosynthesis, (vii) deoxyribonucleotide biosynthesis, (viii) the cellular stress response, and (ix) resuscitation. [Copyright &y& Elsevier]