Genome-Wide Analysis of the Role of Global Transcriptional Regulator GntR1 in Corynebacterium glutamicum

Abstract

bThe transcriptional regulator GntR1 downregulates the genes for gluconate catabolism and pentose phosphate pathway in Corynebacterium glutamicum. Gluconate lowers the DNA binding affinity of GntR1, which is probably the mechanism of gluconate-dependent induction of these genes. In addition, GntR1 positively regulates ptsG, a gene encoding a major glucose transporter, and pck, a gene encoding phosphoenolpyruvate carboxykinase. Here, we searched for the new target of GntR1 on a genome-wide scale by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis. This analysis identified 56 in vivo GntR1 binding sites, of which 7 sites were previously reported. The newly identified GntR1 sites include the upstream regions of carbon metabolism genes such as pyk, maeB, gapB, and icd, encoding pyruvate kinase, malic enzyme, glyceraldehyde 3-phosphate dehydrogenase B, and isocitrate dehydrogenase, respectively. Binding of GntR1 to the promoter region of these genes was confirmed by electrophoretic mobility shift assay. The activity of the icd, gapB, and maeB promoters was reduced by the mutation at the GntR1 binding site, in contrast to the pyk promoter activity, which was increased, indicating that GntR1 is a transcriptional activator of icd, gapB, and maeB and is a repressor of pyk. Thus, it is likely that GntR1 stimulates glucose uptake by inducing the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) gene while repressing pyk to increase PEP availability in the absence of gluconate. Repression of zwf and gnd may reduce the NADPH supply, which may be compensated by the induction of maeB and icd. Upregulation of icd, gapB, and maeB and downregulation of pyk by GntR1 probably support gluconeogenesis.

Enhanced Glucose Consumption and Organic Acid Production by Engineered Corynebacterium glutamicum Based on Analysis of a pfkB1 Deletion Mutant

“…A DNA microarray assay for transcriptome analysis was conducted on the Agilent eArray platform (Agilent Technologies, Palo Alto, CA) as described previously (31,58). RNA was extracted from the cells during aerobic cultivation on A medium with glucose or fructose in the early exponential phase (at 4 h) and in late exponential/stationary phases (at 12 h).…”

“…SugR-driven repression is relieved when the bacteria are cultivated with sugars such as glucose or fructose because sugar metabolite intermediates, sugar phosphates, are potent effectors to inhibit SugR function (21,22,25,26). In addition, RamA, RamB (27), GlxR (28,29), GntR1, and GntR2 (30,31) are known as transcriptional regulators of multiple genes involved in carbon metabolism.…”

Recent advances in the metabolic engineering of Corynebacterium glutamicum for the production of lactate and succinate from renewable resources

“…Optimizing the redox state through simple genetic engineering could further improve succinate production under anaerobic conditions. Another expectation for improving process productivity derives from recently revealed research on the global regulators governing the expression of genes involved in sugar uptake, glycolysis, the pentose phosphate pathway, and the TCA cycle [64,68,76]. On l-isoleucine production, overexpression of the gene encoding the global regulator Lrp (which regulates the expression of several operons involved in the metabolism of branched-chain amino acid) was shown to increase the productivity [87].…”

Characterization of MocR, a GntR-like transcriptional regulator, in Bradyrhizobium japonicum: its impact on motility, biofilm formation, and soybean nodulation

“…The GntR superfamily is further divided into subfamilies such as AraR, DevA, FadR, HutC, MocR, PlmA, and YrA according to the secondary structure prediction based on their amino acid sequences. GntR-like regulators have been found to control many fundamental cellular processes such as carbon metabolism, motility, development, antibiotic production, and virulence (Haine et al, 2005;Hillerich and Westpheling, 2006;Jaques and McCarter, 2006;Hoskisson and Rigali, 2009;Tanaka et al, 2014). Additionally, they can act as activators or repressors of gene expression in other parts of the genome.…”