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

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.

Synthetic redesign of Escherichia coli W for faster metabolism of sugarcane molasses

BACKGROUND

Sugarcane molasses, rich in sucrose, glucose, and fructose, offers a promising carbon source for industrial fermentation due to its abundance and low cost. However, challenges arise from the simultaneous utilization of multiple sugars and carbon catabolite repression (CCR). Despite its nutritional content, sucrose metabolism in Escherichia coli, except for W strain, remains poorly understood, hindering its use in microbial fermentation. In this study, E. coli W was engineered to enhance sugar consumption rates and overcome CCR. This was achieved through the integration of a synthetically designed csc operon and the optimization of glucose and fructose co-utilization pathways. These advancements facilitate efficient utilization of sugarcane molasses for the production of 3-hydroxypropionic acid (3-HP), contributing to sustainable biochemical production processes.

RESULTS

In this study, we addressed challenges associated with sugar metabolism in E. coli W, focusing on enhancing sucrose consumption and improving glucose-fructose co-utilization. Through targeted engineering of the sucrose utilization system, we achieved accelerated sucrose consumption rates by modulating the expression of the csc operon components, cscB, cscK, cscA, and cscR. Our findings revealed that monocistronic expression of the csc genes with the deletion of cscR, led to optimal sucrose utilization without significant growth burden. Furthermore, we successfully alleviated fructose catabolite repression by modulating the binding dynamics of FruR with the fructose PTS regulon, enabling near-equivalent co-utilization of glucose and fructose. To validate the industrial applicability of our engineered strain, we pursued 3-HP production from sugarcane molasses. By integrating heterologous genes and optimizing metabolic pathways, we achieved improvements in 3-HP titers compared to previous studies. Additionally, glyceraldehyde-3-phosphate dehydrogenase (gapA) repression aids in carbon flux redistribution, enhancing molasses conversion to 3-HP.

CONCLUSIONS

Despite limitations in sucrose metabolism, the redesigned E. coli W strain, adept at utilizing sugarcane molasses, is a valuable asset for industrial fermentation. Its synthetic csc operon enhances sucrose consumption, while mitigating CCR improves glucose-fructose co-utilization. These enhancements, coupled with repression of gapA, aim to efficiently convert sugarcane molasses into 3-HP, addressing limitations in sucrose and fructose metabolism for industrial applications.

Techno-economical valorization of sugarcane bagasse for efficiently producing optically pure D-(-)-lactate approaching the theoretical maximum yield in low-cost salt medium by metabolically engineered Klebsiella oxytoca

Sugarcane bagasse (SCB) was utilized for efficiently producing optically pure D-(-)-lactate by Klebsiella oxytoca KIS004-91T strain. Cellulase (15 U/g NaOH-treated SCB) sufficiently liberated high sugars with saccharifications of 79.8 % cellulose and 52.5 % hemicellulose. For separated hydrolysis and fermentation, D-(-)-lactate was produced at 53.5 ± 2.1 g/L (0.98 ± 0.01 g/g sugar utilized or 0.71 ± 0.01 g/g total sugars) while D-(-)-lactate at 47.2 ± 1.8 g/L (0.78 ± 0.03 g/g sugar used or 0.69 ± 0.01 g/g total sugars) was obtained under simultaneous saccharification and fermentation (SSF). D-(-)-lactate at 99.9 ± 0.9 g/L (0.97 ± 0.01 g/g sugar utilized or 0.78 ± 0.01 g/g total sugars) was improved via fed-batch SSF. Based on mass balance, raw SCB of 7 kg is required to produce 1 kg D-(-)-lactate. Unlike others, D-(-)-lactate production was performed in low-cost salt medium without requirements of rich nutrients. Costs regarding medium, purification, and waste disposal may be reduced. This unlocks economic capability of SCB bioconversion or agricultural and agro-industrial wastes into high valuable D-(-)-lactate.

Cra and cAMP Receptor Protein Have Opposing Roles in the Regulation of fruB in Vibrio cholerae

Vibrio cholerae is the causative agent of cholera disease. While current treatments of care are accessible, we still lack an understanding of the molecular mechanisms that allow V. cholerae to survive in both aquatic reservoirs and the human small intestine, where pathogenesis occurs.

The Gram-negative bacterium Vibrio cholerae adapts to changes in the environment by selectively producing the necessary machinery to take up and metabolize available carbohydrates. The import of fructose by the fructose-specific phosphoenolpyruvate (PEP) phosphotransferase system (PTS) is of particular interest because of its putative connection to cholera pathogenesis and persistence. Here, we describe the expression and regulation of fruB, which encodes an EIIA-FPr fusion protein as part of the fructose-specific PTS in V. cholerae. Using a series of transcriptional reporter fusions and additional biochemical and genetic assays, we identified Cra (catabolite repressor/activator) and cAMP receptor protein (CRP) as regulators of fruB expression and determined that this regulation is dependent upon the presence or absence of PTS sugars. Cra functions as a repressor, downregulating fruB expression in the absence of fructose when components of PTS^Fru are not needed. CRP functions as an activator of fruB expression. We also report that Cra and CRP can affect fruB expression independently; however, CRP can modulate cra expression in the presence of fructose and glucose. Evidence from this work provides the foundation for continued investigations into PTS^Fru and its relationship to the V. cholerae life cycle.

IMPORTANCEVibrio cholerae is the causative agent of cholera disease. While current treatments of care are accessible, we still lack an understanding of the molecular mechanisms that allow V. cholerae to survive in both aquatic reservoirs and the human small intestine, where pathogenesis occurs. Central to V. cholerae’s survival is its ability to use available carbon sources. Here, we investigate the regulation of fruB, which encodes a protein central to the import and metabolism of fructose. We show that fruB expression is controlled by the transcriptional regulators Cra and CRP. This work contributes toward a clearer understanding of how carbon source availability impacts the physiology and, potentially, the persistence of the pathogen.

Vibrio cholerae FruR facilitates binding of RNA polymerase to the fru promoter in the presence of fructose 1-phosphate

In most bacteria, efficient use of carbohydrates is primarily mediated by the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS), which concomitantly phosphorylates the substrates during import. Therefore, transcription of the PTS-encoding genes is precisely regulated by transcriptional regulators, depending on the availability of the substrate. Fructose is transported mainly through the fructose-specific PTS (PTS^Fru) and simultaneously converted into fructose 1-phosphate (F1P). In Gammaproteobacteria such as Escherichia coli and Pseudomonas putida, transcription of the fru operon encoding two PTS^Fru components, FruA and FruB, and the 1-phosphofructokinase FruK is repressed by FruR in the absence of the inducer F1P. Here, we show that, contrary to the case in other Gammaproteobacteria, FruR acts as a transcriptional activator of the fru operon and is indispensable for the growth of Vibrio cholerae on fructose. Several lines of evidence suggest that binding of the FruR-F1P complex to an operator which is located between the –35 and –10 promoter elements changes the DNA structure to facilitate RNA polymerase binding to the promoter. We discuss the mechanism by which the highly conserved FruR regulates the expression of its target operon encoding the highly conserved PTS^Fru and FruK in a completely opposite direction among closely related families of bacteria.

Metabolic Engineering and Fermentation Process Strategies for L-Tryptophan Production by Escherichia coli

L-tryptophan is an essential aromatic amino acid that has been widely used in medicine, food, and animal feed. Microbial biosynthesis of L-tryptophan through metabolic engineering approaches represents a sustainable, cost-effective, and environmentally friendly route compared to chemical synthesis. In particular, metabolic pathway engineering allows enhanced product titers by inactivating/blocking the competing pathways, increasing the intracellular level of essential precursors, and overexpressing rate-limiting enzymatic steps. Based on the route of the L-tryptophan biosynthesis pathway, this review presents a systematic and detailed summary of the contemporary metabolic engineering approaches employed for L-tryptophan production. In addition to the engineering of the L-tryptophan biosynthesis pathway, the metabolic engineering modification of carbon source uptake, by-product formation, key regulatory factors, and the polyhydroxybutyrate biosynthesis pathway in L-tryptophan biosynthesis are discussed. Moreover, fermentation bioprocess optimization strategies used for L-tryptophan overproduction are also delineated. Towards the end, the review is wrapped up with the concluding remarks, and future strategies are outlined for the development of a high L-tryptophan production strain.

In silico model-guided identification of transcriptional regulator targets for efficient strain design

BACKGROUND

Cellular metabolism is tightly regulated by hard-wired multiple layers of biological processes to achieve robust and homeostatic states given the limited resources. As a result, even the most intuitive enzyme-centric metabolic engineering endeavours through the up-/down-regulation of multiple genes in biochemical pathways often deliver insignificant improvements in the product yield. In this regard, targeted engineering of transcriptional regulators (TRs) that control several metabolic functions in modular patterns is an interesting strategy. However, only a handful of in silico model-added techniques are available for identifying the TR manipulation candidates, thus limiting its strain design application.

RESULTS

We developed hierarchical-Beneficial Regulatory Targeting (h-BeReTa) which employs a genome-scale metabolic model and transcriptional regulatory network (TRN) to identify the relevant TR targets suitable for strain improvement. We then applied this method to industrially relevant metabolites and cell factory hosts, Escherichia coli and Corynebacterium glutamicum. h-BeReTa suggested several promising TR targets, many of which have been validated through literature evidences. h-BeReTa considers the hierarchy of TRs in the TRN and also accounts for alternative metabolic pathways which may divert flux away from the product while identifying suitable metabolic fluxes, thereby performing superior in terms of global TR target identification.

CONCLUSIONS

In silico model-guided strain design framework, h-BeReTa, was presented for identifying transcriptional regulator targets. Its efficacy and applicability to microbial cell factories were successfully demonstrated via case studies involving two cell factory hosts, as such suggesting several intuitive targets for overproducing various value-added compounds.

Microbial Cell Factories à la Carte: Elimination of Global Regulators Cra and ArcA Generates Metabolic Backgrounds Suitable for the Synthesis of Bioproducts in Escherichia coli

Manipulation of global regulators is one of the strategies used for the construction of bacterial strains suitable for the synthesis of bioproducts. However, the pleiotropic effects of these regulators can vary under different conditions and are often strain dependent. This study analyzed the effects of ArcA, CreC, Cra, and Rob using single deletion mutants of the well-characterized and completely sequenced Escherichia coli strain BW25113. Comparison of the effects of each regulator on the synthesis of major extracellular metabolites, tolerance to several compounds, and synthesis of native and nonnative bioproducts under different growth conditions allowed the discrimination of the particular phenotypes that can be attributed to the individual mutants and singled out Cra and ArcA as the regulators with the most important effects on bacterial metabolism. These data were used to identify the most suitable backgrounds for the synthesis of the reduced bioproducts succinate and 1,3-propanediol (1,3-PDO). The Δcra mutant was further modified to enhance succinate synthesis by the addition of enzymes that increase NADH and CO₂ availability, achieving an 80% increase compared to the parental strain. Production of 1,3-PDO in the ΔarcA mutant was optimized by overexpression of PhaP, which increased more than twice the amount of the diol compared to the wild type in a semidefined medium using glycerol, resulting in 24 g · liter^-1 of 1,3-PDO after 48 h, with a volumetric productivity of 0.5 g · liter^-1 h^-1 IMPORTANCE Although the effects of many global regulators, especially ArcA and Cra, have been studied in Escherichia coli, the metabolic changes caused by the absence of global regulators have been observed to differ between strains. This scenario complicates the identification of the individual effects of the regulators, which is essential for the design of metabolic engineering strategies. The genome of Escherichia coli BW25113 has been completely sequenced and does not contain additional mutations that could mask or interfere with the effects of the global regulator mutations. The uniform genetic background of the Keio collection mutants enabled the characterization of the physiological consequences of altered carbon and redox fluxes caused by each global regulator deletion, eliminating possible strain-dependent results. As a proof of concept, Δcra and ΔarcA mutants were subjected to further manipulations to obtain large amounts of succinate and 1,3-PDO, demonstrating that the metabolic backgrounds of the mutants were suitable for the synthesis of bioproducts.

Proteomic changes in EHEC O157:H7 under catechin intervention

Catechin exhibits antimicrobial activity against various microorganisms, such as EHEC O157:H7. This study reports the bactericidal effect of catechin on EHEC O157:H7 in simulated human gastrointestinal environment and the underlying antibacterial mechanism. Bacteriostasis test results showed that the minimum bactericidal concentration of catechin for EHEC O157:H7 was 5 g/L. The bactericidal effect of catechin in the gastrointestinal juice became more significant with increased culture time, and catechin exhibited a synergistic effect with bile salt in inhibiting EHEC O157:H7. Changes in the profile of protein expression in EHEC O157:H7 in response to catechin intervention were investigated. Two-dimensional electrophoresis identified 34 proteins with significantly altered expression. A total of 2 and 12 proteins were upregulated and downregulated, respectively. However, 20 proteins disappeared. No new protein was expressed compared with the control. Hence, catechin intervention resulted in diverse changes in the expression of proteins associated with cell structure and genetic information processing. Catechin could cause the disappearance of certain proteins or the destruction of certain peptides. These processes lead to the inhibition of EHEC O157: H7 cells.

A single metabolite production by Escherichia coli BW25113 and its pflA.cra mutant cultivated under microaerobic conditions using glycerol or glucose as a carbon source

Abundant, low prices and a highly reduced nature make glycerol to be an ideal feedstock for the production of reduced biochemicals and biofuels. Escherichia coli has been paid much attention as the platform of microbial cell factories due to its high growth rate (giving higher metabolite production rate) and the capability of utilizing a wide range of carbon sources. However, one of the drawbacks of using E. coli as a platform is its mixed metabolite formation under anaerobic conditions. In the present study, it was shown that ethanol could be exclusively produced from glycerol by the wild type E. coli, while d-lactic acid could be exclusively produced from glucose by pflA.cra mutant, where the glucose uptake rate could be increased by this mutant as compared to the wild type strain. It was also shown that the growth rate is significantly reduced in pflA.cra mutant for the case of using glycerol as a carbon source due to redox imbalance. The metabolic regulation mechanisms behind the fermentation characteristic were clarified to some extent.

Modulating the direction of carbon flow in Escherichia coli to improve l-tryptophan production by inactivating the global regulator FruR

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.