A teaching protocol demonstrating the use of EasyClone and CRISPR/Cas9 for metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica

Biomimetic Approach to Diverse Coral Diterpenes from a Biosynthetic Scaffold

Thousands of coral terpenes originate from simple scaffolds that undergo oxidative tailoring. While corals are excellent sources of drug leads, the challenge of supplying structurally complex drug leads from marine organisms has sometimes slowed their development. Making this even more challenging, in comparison to other organisms, such as plants and microbes, for which the terpene literature is substantial, very little is known about how the unique coral terpenes are biosynthesized and elaborated in nature. In this study, we used a semisynthetic strategy to produce at gram scale in yeast the eunicellane scaffold that underlies >200 coral compounds. Synthetic oxidation reactions were explored, generating key scaffolds that reflect three of the four structural classes derived from eunicellane and enabling the first asymmetric syntheses of the natural products solenopodin C and klysimplexin Q. Biomimetic methods and detailed mechanistic studies of synthetic reactions shed light on potential enzymological reactivity, including the role of epoxide rearrangement in eunicellane biosynthesis.

Metabolic Engineering of Yarrowia lipolytica for Terpenoid Production: Tools and Strategies

Terpenoids are a diverse group of compounds with isoprene units as basic building blocks. They are widely used in the food, feed, pharmaceutical, and cosmetic industries due to their diverse biological functions such as antioxidant, anticancer, and immune enhancement. With an increase in understanding the biosynthetic pathways of terpenoids and advances in synthetic biology techniques, microbial cell factories have been built for the heterologous production of terpenoids, with the oleaginous yeast Yarrowia lipolytica emerging as an outstanding chassis. In this paper, recent progress in the development of Y. lipolytica cell factories for terpenoid production with a focus on the advances in novel synbio tools and metabolic engineering strategies toward enhanced terpenoid biosynthesis is reviewed.

Expanding the neutral sites for integrated gene expression in Saccharomyces cerevisiae

Construction of efficient microbial cell factories always requires assembling biosynthetic pathways and rewiring cellular metabolism with overexpression of multiple genes. Genomic integration is considered to be helpful for stable gene expression in compared with the episomal plasmids. However, the limited availability of suitable loci hinders the extensive metabolic engineering. We here characterized 30 neutral sites in Saccharomyces cerevisiae genome that did not affect cellular fitness by using expression cassettes of green fluorescent protein (eGFP) and fatty acyl-CoA reductase (MaFAR1) with the aid of efficient CRISPR-Cas9 technique. We found that integration of gene expression cassettes to different genome loci resulted a varied GFP signal and fatty alcohol production, which showed that genomic loci could be used for tuning gene expression. The characterized set of neutral sites should be helpful for extensively metabolic engineering of S. cerevisiae for chemical production and other purposes.

Modulation of the cell wall protein Ecm33p in yeast Saccharomyces cerevisiae improves the production of small metabolites

The cell wall is a dynamic organelle that determines the shape and provides the cell with mechanical strength. This study investigated whether modulation of cell wall composition can influence the production or secretion of small metabolites by yeast cell factories. We deleted and upregulated several cell wall-related genes KRE2, CWP1, CWP2, ECM33, PUN1, and LAS21 in yeast Saccharomyces cerevisiae engineered for p-coumaric acid or β-carotene production. Deletions of las21∆ and ecm33∆ impaired the yeast growth on medium with cell wall stressors, calcofluor white, and caffeine. Both overexpression and deletion of ECM33 significantly improved the specific yield of p-coumaric acid and β-carotene. We observed no change in secretion in any cell wall altered mutants, suggesting the cell wall is not a limiting factor for small molecule secretion at the current production levels. We evaluated the cell wall morphology of the ECM33 mutant strains using transmission electron microscopy. The ecm33∆ mutants had an increased chitin deposition and a less structured cell wall, while the opposite was observed in ECM33-overexpressing strains. Our results point at the cell wall-related gene ECM33 as a potential target for improving production in engineered yeast cell factories.

Intelligent host engineering for metabolic flux optimisation in biotechnology

Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N. Optimising the expression levels of P proteins that materially affect host performance, each of which might also take 20 (logarithmically spaced) values, implies a similar search space of 20P. In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent. In practice, however, they have different means for avoiding the inevitable difficulties of implementation. The spare capacity exhibited in metabolic networks implies that host engineering may admit substantial increases in flux to targets of interest. Thus, we rehearse the relevant issues for those wishing to understand and exploit those modern genome-wide host engineering tools and thinking that have been designed and developed to optimise fluxes towards desirable products in biotechnological processes, with a focus on microbial systems. The aim throughput is 'making such biology predictable'. Strategies have been aimed at both transcription and translation, especially for regulatory processes that can affect multiple targets. However, because there is a limit on how much protein a cell can produce, increasing kcat in selected targets may be a better strategy than increasing protein expression levels for optimal host engineering.

Metabolic engineering of Saccharomyces cerevisiae for production of β-carotene from hydrophobic substrates

β-Carotene is a yellow–orange–red pigment used in food, cosmetics and pharmacy. There is no commercial yeast-based process for β-carotene manufacturing. In this work, we engineered the baker's yeast Saccharomyces cerevisiae by expression of lipases and carotenogenic genes to enable the production of β-carotene on hydrophobic substrates. First, the extracellular lipase (LIP2) and two cell-bound lipases (LIP7 and LIP8) from oleaginous yeast Yarrowia lipolytica were expressed either individually or in combination in S. cerevisiae. The engineered strains could grow on olive oil and triolein as the sole carbon source. The strain expressing all three lipases had ∼40% lipid content per dry weight. Next, we integrated the genes encoding β-carotene biosynthetic pathway, crtI, crtYB and crtE from Xanthophyllomyces dendrorhous. The resulting engineered strain bearing the lipases and carotenogenic genes reached a titer of 477.9 mg/L β-carotene in yeast peptone dextrose (YPD) medium supplemented with 1% (v/v) olive oil, which was 12-fold higher than an analogous strain without lipases. The highest β-carotene content of 46.5 mg/g DCW was obtained in yeast nitrogen base (YNB) medium supplemented with 1% (v/v) olive oil. The study demonstrates the potential of applying lipases and hydrophobic substrate supplementation for the production of carotenoids in S. cerevisiae.