The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator.

The glxR (cg0350) gene of Corynebacterium glutamicum ATCC 13032 encodes a DNA-binding transcription 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.