Metabolic recycling of storage lipids promotes squalene biosynthesis in yeast.

BACKGROUND: Metabolic rewiring in microbes is an economical and sustainable strategy for synthesizing valuable natural terpenes. Terpenes are the largest class of nature-derived specialized metabolites, and many have valuable pharmaceutical or biological activity. Squalene, a medicinal terpene, is used as a vaccine adjuvant to improve the efficacy of vaccines, including pandemic coronavirus disease 2019 (COVID-19) vaccines, and plays diverse biological roles as an antioxidant and anticancer agent. However, metabolic rewiring interferes with inherent metabolic pathways, often in a way that impairs the cellular growth and fitness of the microbial host. In particular, as the key starting molecule for producing various compounds including squalene, acetyl-CoA is involved in numerous biological processes with tight regulation to maintain metabolic homeostasis, which limits redirection of metabolic fluxes toward desired products. RESULTS: In this study, focusing on the recycling of surplus metabolic energy stored in lipid droplets, we show that the metabolic recycling of the surplus energy to acetyl-CoA can increase squalene production in yeast, concomitant with minimizing the metabolic interferences in inherent pathways. Moreover, by integrating multiple copies of the rate-limiting enzyme and implementing N-degron-dependent protein degradation to downregulate the competing pathway, we systematically rewired the metabolic flux toward squalene, enabling remarkable squalene production (1024.88 mg/L in a shake flask). Ultimately, further optimization of the fed-batch fermentation process enabled remarkable squalene production of 6.53 g/L. CONCLUSIONS: Our demonstration of squalene production via engineered yeast suggests that plant- or animal-based supplies of medicinal squalene can potentially be complemented or replaced by industrial fermentation. This approach will also provide a universal strategy for the more stable and sustainable production of high-value terpenes.

Effective Cryopreservation of a Bioluminescent Auxotrophic Escherichia coli-Based Amino Acid Array to Enable Long-Term Ready-to-Use Applications.

Amino acid arrays comprising bioluminescent amino acid auxotrophic Escherichia coli are effective systems to quantitatively determine multiple amino acids. However, there is a need to develop a method for convenient long-term preservation of the array to enable its practical applications. Here, we reported a potential strategy to efficiently maintain cell viability within the portable array. The method involves immobilization of cells within agarose gel supplemented with an appropriate cryoprotectant in individual wells of a 96-well plate, followed by storage under freezing conditions. Six cryoprotectants, namely dimethyl sulfoxide, glycerol, ethylene glycol, polyethylene glycol, sucrose, and trehalose, were tested in the methionine (Met) auxotroph-based array. Carbohydrate-type cryoprotectants (glycerol, sucrose, and trehalose) efficiently preserved the linearity of determination of Met concentration. In particular, the array with 5% trehalose exhibited the best performance. The Met array with 5% trehalose could determine Met concentration with high linearity (R2 value = approximately 0.99) even after storage at -20 °C for up to 3 months. The clinical utilities of the Met and Leu array, preserved at -20 °C for 3 months, were also verified by successfully quantifying Met and Leu in spiked blood serum samples for the diagnosis of the corresponding metabolic diseases. This long-term preservation protocol enables the development of a ready-to-use bioluminescent E. coli-based amino acid array to quantify multiple amino acids and can replace the currently used laborious analytical methods.

Tailoring the Saccharomyces cerevisiae endoplasmic reticulum for functional assembly of terpene synthesis pathway.

The endoplasmic reticulum (ER) is a dynamic organelle that synthesizes and folds proteins. An imbalance between the ER protein synthesis load and its folding capacity triggers the unfolded protein response, thereby restoring normal ER functions via size adjustment. Inspired by such inherent genetic programming events, we engineered Saccharomyces cerevisiae to expand the ER by overexpressing a key ER size regulatory factor, INO2. ER space expansion enhanced ER protein synthesis and folding capacity, and relieved metabolic constraints imposed by the limited enzyme abundance. Harnessing the yeast ER for metabolic engineering, we ultimately increased the production of squalene and cytochrome P450-mediated protopanaxadiol by 71-fold and 8-fold, compared to their respective control strains without overexpression of INO2. Furthermore, genome-wide transcriptome analysis of the ER-expanded strain revealed that the significant improvement in terpene production was associated with global rewiring of the metabolic network. Therefore, the yeast ER can be engineered as a specialized compartment for enhancing terpene production, representing new possibilities for the high-level production of other value-added chemicals.

Co3O4/Au Hybrid Nanostructures as Efficient Peroxidase Mimics for Colorimetric Biosensing.

Nanomaterials with enzyme-like characteristics (nanozymes) have emerged as potential replacements for natural enzymes due to their potential to overcome several critical limitations of natural enzymes, including low stability as well as high costs in preparation and purification. Herein, we have developed hybrid nanostructures that incorporate cobalt oxide nanoparticles (Co3O4 NPs) and gold nanoclusters (AuNCs) through electrostatic attraction induced by simple incubation in an aqueous buffer for 2 hours. Owing to the synergistic effect of Co3O4 NPs and AuNCs, the constructed Co3O4/Au hybrid nanostructures yielded highly enhanced peroxidase-like activity and enabled rapid catalytic oxidation of a chromogenic substrate, 3,3',5,5'-tetramethylbenzidine (TMB), producing a blue colored solution depending on the amount of H2O2. Moreover, we observed catalytic activity of the Co3O4/Au hybrid over a broad pH range, especially at physiologically relevant pH in the range of 5.0-7.4, which is advantageous for applications in biological systems. Using the hybrid as peroxidase mimic, we successfully determined the level of target H2O2 or glucose by coupling with glucose oxidase with excellent specificity and sensitivity. Based on this study, we expect that Co3O4/Au hybrid nanostructures can serve as potent peroxidase mimics for the detection of clinically important target molecules.

Rerouting of NADPH synthetic pathways for increased protopanaxadiol production in Saccharomyces cerevisiae.

Ginseng (Panax ginseng) and its bioactive components, ginsenosides, are popular medicinal herbal products, exhibiting various pharmacological effects. Despite their advocated use for medication, the long cultivation periods of ginseng roots and their low ginsenoside content prevent mass production of this compound. Yeast Saccharomyces cerevisiae was engineered for production of protopanaxadiol (PPD), a type of aglycone characterizing ginsenoside. PPD-producing yeast cell factory was further engineered by obtaining a balance between enzyme expressions and altering cofactor availability. Different combinations of promoters (PGPD, PCCW12, and PADH2) were utilized to construct the PPD biosynthetic pathway. Rerouting the redox metabolism to improve NADPH availability in the engineered S. cerevisiae also increased PPD production. Combining these approaches resulted in more than an 11-fold increase in PPD titer over the initially constructed strain. The series of metabolic engineering strategies of this study provides a feasible approach for the microbial production of PPD and development of microbial platforms producing other industrially-relevant terpenoids.

Improving the efficiency of homologous recombination by chemical and biological approaches in Yarrowia lipolytica.

Gene targeting is a challenge in Yarrowia lipolytica (Y. lipolytica) where non-homologous end-joining (NHEJ) is predominant over homologous recombination (HR). To improve the frequency and efficiency of HR in Y. lipolytica, the ku70 gene responsible for a double stand break (DSB) repair in the NHEJ pathway was disrupted, and the cell cycle was synchronized to the S-phase with hydroxyurea, respectively. Consequently, the HR frequency was over 46% with very short homology regions (50 bp): the pex10 gene was accurately deleted at a frequency of 60% and the ß-carotene biosynthetic genes were integrated at the correct locus at an average frequency of 53%. For repeated use, the URA3 marker gene was also excised and deleted at a frequency of 100% by HR between the 100 bp homology regions flanking the URA3 gene. It was shown that appropriate combination of these chemical and biological approaches was very effective to promote HR and construct genetically modified Y. lipolytica strains for biotechnological applications.

Hydroxyproline-containing collagen peptide derived from the skin of the Alaska pollack inhibits HIV-1 infection.

The human immunodeficiency virus (HIV) is a lentivirus that results in acquired immunodeficiency syndrome (AIDS). HIV treatment involving chemical therapeutic agents has improved the quality of life of HIV/AIDS patients. The present study demonstrates that a hydroxyproline-containing marine collagen peptide (APHCP) derived from Alaska pollack inhibits HIV­1 infection in the MT-4 human T cell­line. APHCP inhibited HIV-1IIIB-induced cell lysis, syncytia formation, reverse transcriptase activity and viral p24 production at non­cytotoxic concentrations; however, APHCP did not inhibit HIV­2ROD infection in MT­4 cells. This suggests that the anti­HIV activity of APHCP is specific to HIV­1. In addition, substitution of hydroxyproline residues in APHCP with prolines impaired its anti­HIV­1 activity, suggesting that the hydroxyl group of hydroxyprolines is required for the anti­HIV­1 activity of APHCP. These results suggested that the marine peptide APHCP may be a novel drug candidate in the development of next­generation therapeutic agents for the treatment of HIV/AIDS.