Genome-wide survey and crystallographic analysis suggests a role for both horizontal gene transfer and duplication in pantothenate biosynthesis pathways

Implication of Molecular Constraints Facilitating the Functional Evolution of Pseudomonas aeruginosa KPR2 into a Versatile α-Keto-Acid Reductase

Theoretical concepts linking the structure, function, and evolution of a protein, while often intuitive, necessitate validation through investigations in real-world systems. Our study empirically explores the evolutionary implications of multiple gene copies in an organism by shedding light on the structure-function modulations observed in Pseudomonas aeruginosa's second copy of ketopantoate reductase (PaKPR2). We demonstrated with two apo structures that the typical active site cleft of the protein transforms into a two-sided pocket where a molecular gate made up of two residues controls the substrate entry site, resulting in its inactivity toward the natural substrate ketopantoate. Strikingly, this structural modification made the protein active against several important α-keto-acid substrates with varied efficiency. Structural constraints at the binding site for this altered functional trait were analyzed with two binary complexes that show the conserved residue microenvironment faces restricted movements due to domain closure. Finally, its mechanistic highlights gathered from a ternary complex structure help in delineating the molecular perspectives behind its kinetic cooperativity toward these broad range of substrates. Detailed structural characteristics of the protein presented here also identified four key amino acid residues responsible for its versatile α-keto-acid reductase activity, which can be further modified to improve its functional properties through protein engineering.

Microbial production of vitamin B5: current status and prospects

Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.

Metabolic Engineering of Saccharomyces cerevisiae for Vitamin B5 Production

Vitamin B5, also called d-pantothenic acid, is an essential vitamin in the human body and is widely used in pharmaceuticals, nutritional supplements, food, and cosmetics. However, few studies have investigated the microbial production of d-pantothenic acid, especially in Saccharomyces cerevisiae. By employing a systematic optimization strategy, we screened seven key genes in d-pantothenic acid biosynthesis from diverse species, including bacteria, yeast, fungi, algae, plants, animals, etc., and constructed an efficient heterologous d-pantothenic acid pathway in S. cerevisiae. By adjusting the copy number of the pathway modules, knocking out the endogenous bypass gene, balancing NADPH utilization, and regulating the GAL inducible system, a high-yield d-pantothenic acid-producing strain, DPA171, which can regulate gene expression using glucose, was constructed. By optimizing fed-batch fermentation, DPA171 produced 4.1 g/L d-pantothenic acid, which is the highest titer in S. cerevisiae to date. This study provides guidance for the development of vitamin B5 microbial cell factories.

Hot spot-based engineering of ketopantoate hydroxymethyltransferase for the improvement of D-pantothenic acid production in Escherichia coli

D-Pantothenic acid (D-PA) is an essential vitamin with wide applications. However, the biotechnological production of D-PA is still not competitive with the chemical synthesis in terms of production cost. Ketopantoate hydroxymethyltransferase is a crucial enzyme in the D-PA synthetic pathway in Escherichia coli encoded by the panB gene. Here a hot spots study was applied to a ketopantoate hydroxymethyltransferase from Corynebacterium glutamicum (CgKPHMT) to relieve the product inhibitory effect and thus improve the D-PA production. Compared with the wild type, the double-site variant CgKPHMT-K25A/E189S showed 1.8 times higher enzyme activity and 2.1 times higher catalytic efficiency, 1.88 and 3.32 times higher inhibitory constant of α-ketoisovalerate and D-PA, respectively. The D-PA yield using E. coli W3110 adopted the double-site variant was 41.17 g·L^-1 within 48 h, a 9.80 g·L^-1 increase. Structural analysis of K25A/E189S revealed the expansion of the entry channel and the change of the electric charge from negative to uncharged due to the substitution from glutamic acid to serine at site 189. Our study emphasized the positive roles of ketopantoate hydroxymethyltransferase in D-PA production and paved the way by analyzing critical enzymes in the synthetic pathway of E. coli to increase the D-PA yield.

Crystallographic and biophysical analyses of Pseudomonas aeruginosa ketopantoate reductase: Implications of ligand induced conformational changes in cofactor recognition

Ketopantoate reductases (KPRs) catalyse NADPH-dependent reduction of ketopantoate to pantoate, the rate-limiting step of pantothenate biosynthetic pathway. In our recent study, we showed KPRs are under dynamic evolutionary selection and highlighted the possible role of ordered substrate binding kinetics for cofactor selection. To further delineate this at molecular level, here, we perform X-ray crystallographic and biophysical analyses of KPR in presence of non-canonical cofactor NAD⁺. In our structure, NAD⁺ was found to be highly dynamic in catalytic pocket of KPR, which could attain stable conformation only in presence of ketopantoate. Further, isothermal calorimetric (ITC) titrations showed that affinity of KPR for ketopantoate is higher in presence of NADP⁺ than in presence of NAD⁺ and lowest in absence of redox cofactors. In sum, our results clearly depict two modes of redox cofactor selections in KPRs, firstly by specific salt bridge interactions with unique phosphate moiety of NADP⁺ and secondly via ordered sequential heterotrophic cooperative binding of substrate ketopantoate.

Moringa oleifera polysaccharides regulates caecal microbiota and small intestinal metabolic profile in C57BL/6 mice

This study investigated the effects of Moringa oleifera polysaccharides (MOP) on the serum indexes, small intestinal morphology, small intestinal metabolic profile, and caecal microbiota of mice. A new type of polysaccharides with 104,031 Da molecular weight and triple helix structure was isolated from M. oleifera leaves for in vivo experiment. Forty male SPF C57BL/6 mice aged 4 weeks were average divided into four groups randomly according to the MOP gavaged daily (0, 20, 40 and 60 mg/kg body weight MOP). After a 7-day preliminary trial period and a 28-day official trial period, the mice were slaughtered. Results showed that MOP reduced glucose, total cholesterol, and malondialdehyde. It also improved superoxide dismutase and catalase in serum (P < 0.05). For small intestinal morphology, MOP improved the villi length and crypt depth in both ileum and jejunum (P < 0.05); the ratio of villi length to crypt depth in jejunum increased (P < 0.05). MOP could cause the increase of beneficial bacteria and the decrease of harmful bacteria in caecum, further affecting the function of microbiota. In addition, MOP regulated 114 metabolites enriched in the pathway related to the synthesis and metabolism of micromolecules. In sum, MOP exerted positive effects on the serum indexes and intestinal health of mice.

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery.

Coenzyme A thioester-mediated carbon chain elongation as a paintbrush to draw colorful chemical compounds

The biosynthesis of various useful chemicals from simple substrates using industrial microorganisms is becoming increasingly crucial to address the challenge of dwindling non-renewable resources. As the most common intermediate substrates in organisms, Coenzyme A (CoA) thioesters play a central role in the carbon chain elongation process of their products. As a result, numerous of chemicals can be synthesized by the iterative addition of various CoA thioester extender units at a given CoA thioester primer backbone. However, these elongation reactions and the product yields are still restricted due to the low enzymatic performance and supply of CoA thioesters. This review highlights the current protein and metabolic engineering strategies used to enhance the diversity and product yield by coupling different primers, extender units, enzymes, and termination pathways, in an attempt to provide a road map for producing a more diverse range of industrial chemicals.