Insights into the regulatory mechanisms and application prospects of the transcription factor Cra

Abstract

Cra (catabolite repressor/activator) is a global transcription factor (TF) that plays a pleiotropic role in controlling the transcription of several genes involved in carbon utilization and energy metabolism. Multiple studies have investigated the regulatory mechanism of Cra and its rational use for metabolic regulation, but due to the complexity of its regulation, there remain challenges in the efficient use of Cra. Here, the structure, mechanism of action, and regulatory function of Cra in carbon and nitrogen flow are reviewed. In addition, this paper highlights the application of Cra in metabolic engineering, including the promotion of metabolite biosynthesis, the regulation of stress tolerance and virulence, the use of a Cra-based biosensor, and its coupling with other transcription factors. Finally, the prospects of Cra-related regulatory strategies are discussed. This review provides guidance for the rational design and construction of Cra-based metabolic regulation systems.

Keywords: carbon metabolism; metabolic regulation; transcription factor Cra.

Fig 1

Schematic of the structure of Cra. (A) Structural domains of Cra. (B) Structure of NTD (PDB ID: 1UXD). (C) Structure of CTD (PDB ID: 7DOB). The α-helices are colored blue; the β-sheets are colored red, and the loops are colored purple.

Fig 2

Metabolic regulatory network of Cra. The genes shown in red are activated by Cra, the genes shown in blue are repressed by Cra, and the genes shown in purple are both activated and repressed by Cra. Key genes for enzymes: Phosphocarrier protein HPr ptsH, PTS enzyme I ptsI, Enzyme IIAGlc crr, Glucokinase glk, Glucose-6-phosphate dehydrogenase zwf, Mannose-specific PTS enzyme IIAB component manX, Mannose-specific PTS enzyme IIC component manY, Mannose-specific PTS enzyme IID component manZ, Mannitol-specific PTS enzyme IICBA component mtlA, Mannitol-1-phosphate 5-dehydrogenase mtlD, Fructose PTS system EIIBC or EIIC component fruA, fructose PTS system EIIA component fruB, 1-phosphofructokinase fruK, 6-phosphofructokinase 1 pfkA, Fructose-1,6-bisphosphatase fbp, Fructose-bisphosphate aldolase class II fbaA, Fructose-bisphosphate aldolase class I fbaB, Triose-phosphate isomerase tpiA, Glyceraldehyde-3-phosphate dehydrogenase A gapA, Phosphoglycerate kinase pgk, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmM, Enolase eno, Pyruvate kinase 1 pykF, Phosphoenolpyruvate synthetase ppsA, Pyruvate dehydrogenase E1 component aceE, Pyruvate dehydrogenase E2 component aceF, Lipoamide dehydrogenase lpd, Phosphoenolpyruvate carboxylase ppc, Phosphoenolpyruvate carboxykinase pck, Aconitase acnB, Isocitrate lyase aceA, Malate synthase aceB, Isocitrate dehydrogenase icd, Phosphogluconate dehydratase edd, KHG/KDPG aldolase eda. Metabolic intermediates: Glucose 6-phosphate G6P, Fructose 6-phosphate F6P, 1,6-fructose diphosphate FBP, glyceraldehyde-3 phosphate G3P, 1,3-disphosphoglycerate 1,3-DPG, 3-phosphoglycerate 3 PG, 2-phosphoglycerate 2 PG, Phosphoenolpyruvate PEP, Pyruvate PYR, Acetyl-CoA AcCoA, Citrate CIT, Isocitrate ISOCIT, α-Ketoglutaric acid α-KG, Succinyl coenzyme A SUCCoA, Succinate SUC, Fumarate FUM, Malate MAL, Oxaloacetate OAA, 6-phosphogluconolactonase 6 PGL, 6-phosphogluconate 6 PG, Ribulose 5-phosphate RU5P, and 2-keto-3-deoxy-6-phosphogluconic acid KDPG.