Metabolic engineering of Saccharomyces cerevisiae for linalool production

Recent developments in enzymatic and microbial biosynthesis of flavor and fragrance molecules

Flavors and fragrances are an important class of specialty chemicals for which interest in biomanufacturing has risen during recent years. These naturally occurring compounds are often amenable to biosynthesis using purified enzyme catalysts or metabolically engineered microbial cells in fermentation processes. In this review, we provide a brief overview of the categories of molecules that have received the greatest interest, both academically and industrially, by examining scholarly publications as well as patent literature. Overall, we seek to highlight innovations in the key reaction steps and microbial hosts used in flavor and fragrance manufacturing.

Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of -carotene

β-Carotene is one kind of the most important carotenoids. The major functions of β-carotene include the antioxidant and anti-cardiovascular properties, which make it a growing market. Recently, the use of metabolic engineering to construct microbial cell factories to synthesize β-carotene has become the latest model for its industrial production. Among these cell factories, yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica have attracted the most attention because of the: security, mature genetic manipulation tools, high flux toward carotenoids using the native mevalonate pathway and robustness for large-scale fermentation. In this review, the latest strategies for β-carotene biosynthesis, including protein engineering, promoters engineering and morphological engineering are summarized in detail. Finally, perspectives for future engineering approaches are proposed to improve β-carotene production.

Two-Phase Fermentation Systems for Microbial Production of Plant-Derived Terpenes

Microbial cell factories, renowned for their economic and environmental benefits, have emerged as a key trend in academic and industrial areas, particularly in the fermentation of natural compounds. Among these, plant-derived terpenes stand out as a significant class of bioactive natural products. The large-scale production of such terpenes, exemplified by artemisinic acid-a crucial precursor to artemisinin-is now feasible through microbial cell factories. In the fermentation of terpenes, two-phase fermentation technology has been widely applied due to its unique advantages. It facilitates in situ product extraction or adsorption, effectively mitigating the detrimental impact of product accumulation on microbial cells, thereby significantly bolstering the efficiency of microbial production of plant-derived terpenes. This paper reviews the latest developments in two-phase fermentation system applications, focusing on microbial fermentation of plant-derived terpenes. It also discusses the mechanisms influencing microbial biosynthesis of terpenes. Moreover, we introduce some new two-phase fermentation techniques, currently unexplored in terpene fermentation, with the aim of providing more thoughts and explorations on the future applications of two-phase fermentation technology. Lastly, we discuss several challenges in the industrial application of two-phase fermentation systems, especially in downstream processing.

Application of Metabolite-Responsive Biosensors for Plant Natural Products Biosynthesis

Plant natural products (PNPs) have shown various pharmaceutical activities, possessing great potential in global markets. Microbial cell factories (MCFs) provide an economical and sustainable alternative for the synthesis of valuable PNPs compared with traditional approaches. However, the heterologous synthetic pathways always lack native regulatory systems, bringing extra burden to PNPs production. To overcome the challenges, biosensors have been exploited and engineered as powerful tools for establishing artificial regulatory networks to control enzyme expression in response to environments. Here, we reviewed the recent progress involved in the application of biosensors that are responsive to PNPs and their precursors. Specifically, the key roles these biosensors played in PNP synthesis pathways, including isoprenoids, flavonoids, stilbenoids and alkaloids, were discussed in detail.

Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis

The optimization of cellular functions often requires the balancing of gene expression, but the physical construction and screening of alternative designs are costly and time-consuming. Here, we construct a strain of Saccharomyces cerevisiae that contains a "sensor array" containing bacterial regulators that respond to four small-molecule inducers (vanillic acid, xylose, aTc, IPTG). Four promoters can be independently controlled with low background and a 40- to 5000-fold dynamic range. These systems can be used to study the impact of changing the level and timing of gene expression without requiring the construction of multiple strains. We apply this approach to the optimization of a four-gene heterologous pathway to the terpene linalool, which is a flavor and precursor to energetic materials. Using this approach, we identify bottlenecks in the metabolic pathway. This work can aid the rapid automated strain development of yeasts for the bio-manufacturing of diverse products, including chemicals, materials, fuels, and food ingredients.

Multi-Level Optimization and Strategies in Microbial Biotransformation of Nature Products

Continuously growing demand for natural products with pharmacological activities has promoted the development of microbial transformation techniques, thereby facilitating the efficient production of natural products and the mining of new active compounds. Furthermore, due to the shortcomings and defects of microbial transformation, it is an important scientific issue of social and economic value to improve and optimize microbial transformation technology in increasing the yield and activity of transformed products. In this review, the aspects regarding the optimization of fermentation and the cross-disciplinary strategy, leading to the microbial transformation of increased levels of the high-efficiency process from natural products of a plant or microbial origin, were discussed. Additionally, due to the increasing craving for targeted and efficient methods for detecting transformed metabolites, analytical methods based on multiomics were also discussed. Such strategies can be well exploited and applied to the production of more efficient and more natural products from microbial resources.

Solvent-free dehydration, cyclization, and hydrogenation of linalool with a dual heterogeneous catalyst system to generate a high-performance sustainable aviation fuel

The development of efficient catalytic methods for the synthesis of bio-based, full-performance jet fuels is critical for limiting the impacts of climate change while enabling a thriving modern society. To help address this need, here, linalool, a terpene alcohol that can be produced via fermentation of biomass sugars, was dehydrated, cyclized, and hydrogenated in a one-pot reaction under moderate reaction conditions. This sequence produced a biosynthetic fuel mixture primarily composed of 1-methyl-4-isopropylcyclohexane (p-menthane) and 2,6-dimethyloctane (DMO). The reaction was promoted by a catalyst composed of commercial Amberlyst-15, H⁺ form, and 10% Pd/C. Two other terpenoid substrates (1,8-cineole and 1,4-cineole) were subjected to the same conditions and excellent conversion to high purity p-menthane was observed. The fuel mixture derived from linalool exhibits a 1.7% higher gravimetric heat of combustion and 66% lower kinematic viscosity at -20 °C compared to the limits for conventional jet fuel. These properties suggest that isomerized hydrogenated linalool (IHL) can be blended with conventional jet fuel or synthetic paraffinic kerosenes to deliver high-performance sustainable aviation fuels for commercial and military applications.

A comparative evaluation of chemical composition and antimicrobial activities of essential oils extracted from different chemotypes of Cinnamomum camphora (L.) Presl

The purpose of this study is to determine the chemical composition of the essential oils of Cinnamomum camphora (L.) Presl leaves (CCPL) from 5 different habitats in China by GC-MS, and to evaluate their antimicrobial activities against 3 foodborne pathogens, using a paper disc diffusion method. A total of 30 compounds were identified with a predominance of oxygenated monoterpenes, including linalool (42.65%-96.47%), eucalyptol (39.07%-55.35%) and camphor (26.08%) as well as monoterpene hydrocarbons such as sabinene (6.18%-12.93%) and α-terpineol (8.19%-13.81%). Through cluster analysis, CCPL from 5 different habitats can be well divided into 2 categories. Combining with principal component analysis, the habitats can be better correlated with the chemical constituents of the essential oils. The antimicrobial activities of 5 extracted essential oils against 2 gram-negative bacteria and one gram-positive bacteria were assessed. It showed that the essential oil extracted from the CCPL harvested in Jinxi had the strongest antibacterial property. The results of this study provided basis for resource identification of CCPL and quality difference identification of essential oils. Research on the antibacterial properties of several pathogenic strains has proved its application value as a natural food preservative.

Metabolic Perturbation and Synthetic Biology Strategies for Plant Terpenoid Production-An Updated Overview

Terpenoids represent one of the high-value groups of specialized metabolites with vast structural diversity. They exhibit versatile human benefits and have been successfully exploited in several sectors of day-to-day life applications, including cosmetics, foods, and pharmaceuticals. Historically, the potential use of terpenoids is challenging, and highly hampered by their bioavailability in their natural sources. Significant progress has been made in recent years to overcome such challenges by advancing the heterologous production platforms of hosts and metabolic engineering technologies. Herein, we summarize the latest developments associated with analytical platforms, metabolic engineering, and synthetic biology, with a focus on two terpenoid classes: monoterpenoids and sesquiterpenoids. Accumulated data showed that subcellular localization of both the precursor pool and the introduced enzymes were the crucial factors for increasing the production of targeted terpenoids in plants. We believe this timely review provides a glimpse of current state-of-the-art techniques/methodologies related to terpenoid engineering that would facilitate further improvements in terpenoids research.

The beauty of biocatalysis: sustainable synthesis of ingredients in cosmetics

Covering: 2015 up to July 2021The market for cosmetics is consumer driven and the desire for green, sustainable and natural ingredients is increasing. The use of isolated enzymes and whole-cell organisms to synthesise these products is congruent with these values, especially when combined with the use of renewable, recyclable or waste feedstocks. The literature of biocatalysis for the synthesis of ingredients in cosmetics in the past five years is herein reviewed.

Increased Accumulation of Squalene in Engineered Yarrowia lipolytica through Deletion of PEX10 and URE2

Squalene is a triterpenoid serving as an ingredient of various products in the food, cosmetic, pharmaceutical industries. The oleaginous yeast Yarrowia lipolytica offers enormous potential as a microbial chassis for the production of terpenoids, such as carotenoid, limonene, linalool, and farnesene, as the yeast provides ample storage space for hydrophobic products. Here, we present a metabolic design that allows the enhanced accumulation of squalene in Y. lipolytica. First, we improved squalene accumulation in Y. lipolytica by overexpressing the genes (ERG and HMG) coding for the mevalonate pathway enzymes. Second, we increased the production of lipid where squalene is accumulated by overexpressing DGA1 (encoding diacylglycerol acyltransferase) and deleting PEX10 (for peroxisomal membrane E3 ubiquitin ligase). Third, we deleted URE2 (coding for a transcriptional regulator in charge of nitrogen catabolite repression [NCR]) to induce lipid accumulation regardless of the carbon-to-nitrogen ratio in culture media. The resulting engineered Y. lipolytica exhibited a 115-fold higher squalene content (22.0 mg/g dry cell weight) than the parental strain. These results suggest that the biological function of Ure2p in Y. lipolytica is similar to that in Saccharomyces cerevisiae, and its deletion can be utilized to enhance the production of hydrophobic target products in oleaginous yeast strains. IMPORTANCE This study demonstrated a novel strategy for increasing squalene production in Y. lipolytica. URE2, a bifunctional protein that is involved in both nitrogen catabolite repression and oxidative stress response, was identified and demonstrated correlation to squalene production. The data suggest that double deletion of PEX10 and URE2 can serve as a positive synergistic effect to help yeast cells in boosting squalene production. This discovery can be combined with other strategies to engineer cell factories to efficiently produce terpenoid in the future.

Isopentenol Utilization Pathway for the Production of Linalool in Escherichia coli Using an Improved Bacterial Linalool/Nerolidol Synthase

Linalool is a monoterpenoid used as a fragrance ingredient, and is a promising source for alternative fuels. Synthetic biology offers attractive alternative production methods compared to extraction from natural sources and chemical synthesis. Linalool/nerolidol synthase (bLinS) from Streptomyces clavuligerus is a bifunctional enzyme, producing linalool as well as the sesquiterpenoid nerolidol when expressed in engineered Escherichia coli harbouring a precursor terpenoid pathway such as the mevalonate (MVA) pathway. Here we identified two residues important for substrate selection by bLinS, L72 and V214, where the introduction of bulkier residues results in variants with reduced nerolidol formation. Terpenoid production using canonical precursor pathways is usually limited by numerous and highly regulated enzymatic steps. Here we compared the canonical MVA pathway to the non-canonical isopentenol utilization (IU) pathway to produce linalool using the optimised bLinS variant. The IU pathway uses isoprenol and prenol to produce linalool in only five steps. Adjusting substrate, plasmid system, inducer concentration, and cell strain directs the flux towards monoterpenoids. Our integrated approach, combining enzyme engineering with flux control using the artificial IU pathway, resulted in high purity production of the commercially attractive monoterpenoid linalool, and will guide future efforts towards efficient optimisation of terpenoid production in engineered microbes.

Synthetic Protein Scaffolds for Improving R-(-)-Linalool Production in Escherichia coli

R-(-)-Linalool is widely used in the pharmaceutical, agrochemical, and fragrance industries; however, its applications are limited owing to low yield and high cost of production. To improve the production efficiency of R-(-)-linalool in Escherichia coli, three enzymes [E. coli-derived isopentenyl diphosphate isomerase, Abies grandis-derived geranyl diphosphate synthase, and Streptomyces clavuligerus-derived (3R)-linalool synthases] were physically colocalized to synthetic complexes using synthetic protein scaffolds of GTPase-binding domain, Src homology 3, and PSD95/DlgA/Zo-1. R-(-)-Linalool was produced at the highest concentration in the strain IGL114 containing a scaffold ratio of 1:1:4. By further optimizing the inducer, temperature, and glycerol concentration, the production titer of R-(-)-linalool in the shake flask was increased by approximately 10 times compared with that of the scaffold-free control and was 2.78 times the previously reported yield. The production in the fermenter was about 1.5 times the previous highest production. In general, the final strain accumulated 277.8 and 1523.2 mg/L R-(-)-linalool under the conditions of shake-flask and fed-batch fermentation, respectively. This study provides a foundation for the assembly of bacterial intracellular protein scaffolds.

Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals

The long road from emerging biotechnologies to commercial “green” biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessing approach, whereby microorganisms convert lignocellulose waste into advanced fuels and other chemicals. As lignocellulose is a highly complex network of polymers, enzymatic degradation or “saccharification” requires a range of cellulolytic enzymes acting synergistically to release the abundant sugars contained within. Complications arise from the need for extracellular localisation of cellulolytic enzymes, whether they be free or cell-associated. This review highlights the current progress in the consolidated bioprocessing approach, whereby microbial chassis are engineered to grow on lignocellulose as sole carbon sources whilst generating commercially useful chemicals. Future perspectives in the emerging biofoundry approach with bacterial hosts are discussed, where solutions to existing bottlenecks could potentially be overcome though the application of high throughput and iterative Design-Build-Test-Learn methodologies. These rapid automated pathway building infrastructures could be adapted for addressing the challenges of increasing cellulolytic capabilities of microorganisms to commercially viable levels.

New Trends in the Use of Volatile Compounds in Food Packaging

In the last years, many of the research studies in the packaging industry have been focused on food active packaging in order to develop new materials capable of retaining the active agent in the polymeric matrix and controlling its release into food, which is not easy in many cases due to the high volatility of the chemical compounds, as well as their ease of diffusion within polymeric matrices. This review presents a complete revision of the studies that have been carried out on the incorporation of volatile compounds to food packaging applications. We provide an overview of the type of volatile compounds used in active food packaging and the most recent trends in the strategies used to incorporate them into different polymeric matrices. Moreover, a thorough discussion regarding the main factors affecting the retention capacity and controlled release of volatile compounds from active food packaging is presented.

Bornyl Diphosphate Synthase From Cinnamomum burmanni and Its Application for (+)-Borneol Biosynthesis in Yeast

(+)-Borneol is a desirable monoterpenoid with effective anti-inflammatory and analgesic effects that is known as soft gold. (+)-bornyl diphosphate synthase is the key enzyme in the (+)-borneol biosynthesis pathway. Despite several reported (+)-bornyl diphosphate synthase genes, relatively low (+)-borneol production hinders the attempts to synthesize it using microbial fermentation. Here, we identified the highly specific (+)-bornyl diphosphate synthase CbTPS1 from Cinnamomum burmanni. An in vitro assay showed that (+)-borneol was the main product of CbTPS1 (88.70% of the total products), and the K _m value was 5.11 ± 1.70 μM with a k _cat value of 0.01 s^-1. Further, we reconstituted the (+)-borneol biosynthetic pathway in Saccharomyces cerevisiae. After tailored truncation and adding Kozak sequences, the (+)-borneol yield was improved by 96.33-fold to 2.89 mg⋅L^-1 compared with the initial strain in shake flasks. This work is the first reported attempt to produce (+)-borneol by microbial fermentation. It lays a foundation for further pathway reconstruction and metabolic engineering production of this valuable natural monoterpenoid.

Combinatorial Modulation of Linalool Synthase and Farnesyl Diphosphate Synthase for Linalool Overproduction in Saccharomyces cerevisiae

Linalool, as a fragrant monoterpene, is an important feedstock for food, pharmaceuticals, and cosmetics industries. Although our previous study had significantly increased linalool production by the directed evolution of linalool synthase and overexpression of the whole mevalonate pathway genes, the engineered yeast strain suffered from dramatically reduced biomass. Herein, a stress-free linalool-producing yeast cell factory was constructed by the combinational regulation of linalool synthase and farnesyl diphosphate synthase instead of multienzyme overexpression. First, the expression level of linalool synthase was successfully enhanced by introducing a N-terminal SKIK tag, which improved linalool production by 3.3-fold. Subsequently, the modular assembly of linalool synthase and dominant negative farnesyl diphosphate synthase via short peptide tags efficiently converted geranyl pyrophosphate to linalool. Additional downregulation of the native farnesyl diphosphate synthase led to the highest reported linalool production (80.9 mg/L) in yeast. This combinatorial modulation strategy may also be applied to the production of other high-value monoterpenes.

Efficient Biosynthesis of R-(-)-Linalool through Adjusting the Expression Strategy and Increasing GPP Supply in Escherichia coli

R-(-)-linalool is widely used in pharmaceutical, agrochemical, and fragrance industries. However, plant extraction furnishes only limited and unstable R-(-)-linalool yields that do not satisfy market demand. Therefore, a sustainable yet efficient and productive method is urgently needed. To induce the R-(-)-linalool biosynthesis pathway in Escherichia coli, we expressed several heterologous (3R)-linalool synthases (LISs) and then chose a suitable LIS from Streptomyces clavuligerus (bLIS) for further study. The bLIS expression was markedly elevated by using optimized ribosomal binding sites and protein fusion tags. To increase the geranyl diphosphate content, we tested various alterations in prenyltransferases and their mutants. The final strain accumulated 100.1 and 1027.3 mg L^-1 R-(-)-linalool under shake flask and fed-batch fermentation conditions, respectively. The latter is the highest reported R-(-)-linalool yield to date. This work could lay theoretical and empirical foundations for engineering terpenoid pathways and optimizing other metabolic pathways.

Bioactivity, phytochemical profile and pro-healthy properties of Actinidia arguta: A review

Hardy kiwi (Actinidia arguta) is a climbing, perennial and dioecious vine from Actinidiaceae family, native from Asia and valued as ornamental and traditional medicine. In the last decade, the growing interest as fruit-bearing plant encourage the expanding cultivation of A. arguta mainly to fruits production, particularly in Europe and North America. A. arguta plants have an extensive range ofbioactive compoundsthat can be obtained from different botanical structures, such as fruits, leaves, flowers and stems. These bioactive molecules, with well-recognized health-promoting properties, include phenolic compounds, minerals, carbohydrates or even volatile substances, with a great potential to be used in several formulations of food products. Phytochemical studies on this plant reported hypoglycemic effects as well as antioxidant and anti-inflammatory activities, among others. The traditional uses ofA. arguta have been experimentally proved byin vitroandin vivostudies, in which its bioactivities were associated to its phytochemical composition. This review aims to assess and summarize the phytochemical and healthy properties ofthe different botanical parts of A. arguta, describing their bioactive composition and exploring it potential functional properties on foodstuffs.

Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts

Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.

The Potential Production of the Bioactive Compound Pinene Using Whey Permeate

Pinene is a secondary plant metabolite that has functional properties as a flavor additive as well as potential cognitive health benefits. Although pinene is present in low concentrations in several plants, it is possible to engineer microorganisms to produce pinene. However, feedstock cost is currently limiting the industrial scale-up of microbial pinene production. One potential solution is to leverage waste streams such as whey permeate as an alternative to expensive feedstocks. Whey permeate is a sterile-filtered dairy effluent that contains 4.5% weight/weight lactose, and it must be processed or disposed of due its high biochemical oxygen demand, often at significant cost to the producer. Approximately 180 million m3 of whey is produced annually in the U.S., and only half of this quantity receives additional processing for the recovery of lactose. Given that organisms such as recombinant Escherichia coli grow on untreated whey permeate, there is an opportunity for dairy producers to microbially produce pinene and reduce the biological oxygen demand of whey permeate via microbial lactose consumption. The process would convert a waste stream into a valuable coproduct. This review examines the current approaches for microbial pinene production, and the suitability of whey permeate as a medium for microbial pinene production.

Organism Engineering for the Bioproduction of the Triaminotrinitrobenzene (TATB) Precursor Phloroglucinol (PG)

Organism engineering requires the selection of an appropriate chassis, editing its genome, combining traits from different source species, and controlling genes with synthetic circuits. When a strain is needed for a new target objective, for example, to produce a chemical-of-need, the best strains, genes, techniques, software, and expertise may be distributed across laboratories. Here, we report a project where we were assigned phloroglucinol (PG) as a target, and then combined unique capabilities across the United States Army, Navy, and Air Force service laboratories with the shared goal of designing an organism to produce this molecule. In addition to the laboratory strain Escherichia coli, organisms were screened from soil and seawater. Putative PG-producing enzymes were mined from a strain bank of bacteria isolated from aircraft and fuel depots. The best enzyme was introduced into the ocean strain Marinobacter atlanticus CP1 with its genome edited to redirect carbon flux from natural fatty acid ester (FAE) production. PG production was also attempted in Bacillus subtilis and Clostridium acetobutylicum. A genetic circuit was constructed in E. coli that responds to PG accumulation, which was then ported to an in vitro paper-based system that could serve as a platform for future low-cost strain screening or for in-field sensing. Collectively, these efforts show how distributed biotechnology laboratories with domain-specific expertise can be marshalled to quickly provide a solution for a targeted organism engineering project, and highlights data and material sharing protocols needed to accelerate future efforts.

High-level production of linalool by engineered Saccharomyces cerevisiae harboring dual mevalonate pathways in mitochondria and cytoplasm

Linalool, a valuable monoterpene alcohol, is widely used in cosmetics and flavoring ingredients. However, its scalable production by microbial fermentation is not yet achieved. In this work, considerable increase in linalool production was obtained in Saccharomyces cerevisiae by dual metabolic engineering of the mevalonic acid (MVA) pathway in both mitochondria and cytoplasm. A farnesyl pyrophosphate synthase mutant ERG20^F96W/N127W and a linalool synthase from Cinnamomum osmophloeum (CoLIS) were introduced and meanwhile the endogenous ERG20 was down-regulated to prevent the competitive loss of precursor. In addition, overexpression of the proteins of CoLIS and ERG20^F96W/N127W and another copy of the same enzymes CoLIS/ERG20^F96W/N127W with mitochondrial localization signal (MLS) were carried out to further pull the flux to linalool. Finally, a maximum linalool titer of 23.45 mg/L was obtained in a batch fermentation with sucrose as carbon source. This combinatorial engineering strategy may provide hints for biosynthesis of other monoterpenes.

Alpha-Terpineol production from an engineered Saccharomyces cerevisiae cell factory

Background

Alpha-Terpineol (α-Terpineol), a C₁₀ monoterpenoid alcohol, is widely used in the cosmetic and pharmaceutical industries. Construction Saccharomyces cerevisiae cell factories for producing monoterpenes offers a promising means to substitute chemical synthesis or phytoextraction.

Results

α-Terpineol was produced by expressing the truncated α-Terpineol synthase (tVvTS) from Vitis vinifera in S. cerevisiae. The α-Terpineol titer was increased to 0.83 mg/L with overexpression of the rate-limiting genes tHMG1, IDI1 and ERG20^F96W-N127W. A GSGSGSGSGS linker was applied to fuse ERG20^F96W-N127W with tVvTS, and expressing the fusion protein increased the α-Terpineol production by 2.87-fold to 2.39 mg/L when compared with the parental strain. In addition, we found that farnesyl diphosphate (FPP) accumulation by down-regulation of ERG9 expression and deletion of LPP1 and DPP1 did not improve α-Terpineol production. Therefore, ERG9 was overexpressed and the α-Terpineol titer was further increased to 3.32 mg/L. The best α-Terpineol producing strain LCB08 was then used for batch and fed-batch fermentation in a 5 L bioreactor, and the production of α-Terpineol was ultimately improved to 21.88 mg/L.

Conclusions

An efficient α-Terpineol production cell factory was constructed by engineering the S. cerevisiae mevalonate pathway, and the metabolic engineering strategies could also be applied to produce other valuable monoterpene compounds in yeast.

Characterization of two Vitis vinifera carotenoid cleavage dioxygenases by heterologous expression in Saccharomyces cerevisiae

Norisoprenoids are produced from carotenoids under oxidative degradation mediated by carotenoid cleavage dioxygenases (CCDs) and contribute to floral and fruity notes in grape berries and wine. The diversity of CCD substrates and products has been demonstrated by in vitro recombinant proteins extracted from Escherichia coli expressing CCD genes and of in vivo proteins in an E. coli system co-expressing genes for carotenoid synthesis and cleavage. In the current study, VvCCD1 and VvCCD4b were isolated from the cDNA library of Vitis vinifera L. cv. Cabernet Sauvignon and then transformed into carotenoid-accumulating recombinant Saccharomyces cerevisiae strains. The expression of the target genes was monitored during the yeast growth period, and the accumulation of carotenoids and norisoprenoids in the recombinant strains was measured. The results indicated that both of the VvCCDs cleaved β-carotene at the 7, 8 (7', 8') position into β-cyclocitral for the first time. Additionally, the two enzymes also degraded β-carotene at the 9, 10 (9', 10') position to generate β-ionone and cleaved lycopene at the 5, 6 (5', 6') position into 6-methyl-5-hepten-2-one. These findings suggested that the VvCCDs may possess more cleavage characteristics under the eukaryotic expression system in S. cerevisiae than the prokaryotic system in E. coli, which could better explain the biochemical functions of VvCCDs in grape berries.

Potential Natural Food Preservatives and Their Sustainable Production in Yeast: Terpenoids and Polyphenols

Terpenoids and polyphenols are high-valued plant secondary metabolites. Their high antimicrobial activities demonstrate their huge potential as natural preservatives in the food industry. With the rapid development of metabolic engineering, it has become possible to realize large-scale production of non-native terpenoids and polyphenols by using the generally recognized as safe (GRAS) strain, Saccharomyces cerevisiae, as a cell factory. This review will summarize the major terpenoid and polyphenol compounds with high antimicrobial properties, describe their native metabolic pathways as well as antimicrobial mechanisms, and highlight current progress on their heterologous biosynthesis in S. cerevisiae. Current challenges and perspectives for the sustainable production of terpenoid and polyphenol as natural food preservatives via S. cerevisiae will also be discussed.

Optimization of linalool-loaded solid lipid nanoparticles using experimental factorial design and long-term stability studies with a new centrifugal sedimentation method

Linalool (C₁₀H₁₈O), also known as 3, 7-dimethyl-1, 6-octadien-3-ol, is the most common acyclic monoterpene tertiary alcohol present in essential oils of several aromatic plant species. Previous studies indicate that linalool is a valuable compound with a wide range of therapeutic properties. The promising therapeutic effects of linalool are however limited by its poor water solubility and volatility. Recently, the encapsulation of linalool in drug delivery systems, such as solid lipid nanoparticles (SLN) and nanostructured lipid carriers (NLC) has demonstrated to overcome linalool physicochemical limitations_. The present study aimed the production and optimization of linalool encapsulation in SLN applying the experimental full factorial design. The estimation of the long-term stability of the produced linalool-loaded SLN was carried out using a new centrifugal sedimentation method, LUMiSizer®. SLN dispersions were produced by the hot high pressure homogenization (HPH) method. The influence of the independent variables, surfactant and lipid concentrations on linalool-loaded SLN particle size, polydispersity index (PI) and zeta potential (ZP) was evaluated by a 2² factorial design composed of 2 variables which were set at 2-levels each. For each of the three dependent variables, analysis of the variance (ANOVA) was performed using a 95% confidence interval. The concentration of surfactant, as well as, the interaction between the different concentrations of lipid and surfactant, hada statistically significant effect on the particle size and PI. Experimental factorial design has been successfully employed to develop an optimal SLN dispersion, requiring a minimum of performed experiments. Based on the obtained results, the optimal linalool-loaded SLN dispersion was composed of 1% (w/v) linalool 2% (w/v) of solid lipid and 5% (w/v) of surfactant. Furthermore, the stability analysis revealed that the produced linalool-loaded SLN dispersions have limited storage stability which can be easily overcome through the assembly of a polymeric coating on the SLN surface. LUMiSizer® has been successfully used in the kinetic analysis of linalool-SLN during accelerated storage time.

Heterologous Production of Flavour and Aroma Compounds in Saccharomyces cerevisiae

Over the last two decades, rapid progress in the field of synthetic biology has opened several avenues for the heterologous de novo production of complex biological compounds, such as biofuels, pharmaceuticals, and food additives in microbial hosts. This minireview addresses the usage of the yeast Saccharomyces cerevisiae as a microbial cell factory for the production of flavour and aroma compounds, thereby providing a path towards a sustainable and efficient means of producing what are normally rare, and often expensive plant-derived chemicals.

Overproduction of isoprenoids by Saccharomyces cerevisiae in a synthetic grape juice medium in the absence of plant genes

The objective of this work is to demonstrate if the hexaprenyl pyrophosphate synthetase Coq1p might be involved in monoterpenes synthesis in Saccharomyces cerevisiae, although its currently known function in yeast is to catalyze the first step in ubiquinone biosynthesis. However, in a BY4743 laboratory strain, the presence of an empty plasmid in a chemically defined grape juice medium results in a statistically significant increase of linalool, (E)-nerolidol and (E,E)-farnesol. When COQ1 is overexpressed from a plasmid, the levels of the volatile isoprenoids are further increased. Furthermore, overexpression of COQ1 in the same genetic context but with a mutated farnesyl pyrophosphate synthetase (erg20 mutation K197E), results in statistically significant higher levels of linalool (above 750 μg/L), geraniol, α-terpineol, and the sesquiterpenes, farnesol and nerolidol (total concentration of volatile isoprenoids surpasses 1300 μg/L). We show that the levels of monoterpenes and sesquiterpenes that S. cerevisiae can produce, in the absence of plant genes, depend on the composition of the medium and the genetic context. To the best of our knowledge, this is the highest level of linalool produced by S. cerevisiae up to now. Further research will be needed for understanding how COQ1 and the medium composition might interact to increase flavor complexity of fermented beverages.

Engineering Saccharomyces cerevisiae for the production of the valuable monoterpene ester geranyl acetate

Background

Geranyl acetate is widely used in the fragrance and cosmetic industries, and thus has great economic value. However, plants naturally produce a mixture of hundreds of esters, and geranyl acetate is usually only present in trace amounts, which makes its economical extraction from plant sources practically impossible. As an ideal host for heterologous production of fragrance compound, the Saccharomyces cerevisiae has never been engineered to produce the esters, such as geranyl acetate.

Results

In this study, a heterologous geranyl acetate synthesis pathway was constructed in S. cerevisiae for the first time, and a titer of 0.63 mg/L geranyl acetate was achieved. By expressing an Erg20 mutant to divert carbon flux from FPP to GPP, the geranyl acetate production increased to 2.64 mg/L. However, the expression of heterologous GPP had limited effect. The highest production of 13.27 mg/L geranyl acetate was achieved by additional integration and expression of tHMG1, IDI1 and MAF1. Furthermore, through optimizing fermentation conditions, the geranyl acetate titer increased to 22.49 mg/L.

Conclusions

We constructed a monoterpene ester producing cell factory in S. cerevisiae for the first time, and demonstrated the great potential of this system for the heterologous production of a large group of economically important fragrance compounds.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0930-y) contains supplementary material, which is available to authorized users.

Multidimensional heuristic process for high-yield production of astaxanthin and fragrance molecules in Escherichia coli

Optimization of metabolic pathways consisting of large number of genes is challenging. Multivariate modular methods (MMMs) are currently available solutions, in which reduced regulatory complexities are achieved by grouping multiple genes into modules. However, these methods work well for balancing the inter-modules but not intra-modules. In addition, application of MMMs to the 15-step heterologous route of astaxanthin biosynthesis has met with limited success. Here, we expand the solution space of MMMs and develop a multidimensional heuristic process (MHP). MHP can simultaneously balance different modules by varying promoter strength and coordinating intra-module activities by using ribosome binding sites (RBSs) and enzyme variants. Consequently, MHP increases enantiopure 3S,3′S-astaxanthin production to 184 mg l⁻¹ day⁻¹ or 320 mg l⁻¹. Similarly, MHP improves the yields of nerolidol and linalool. MHP may be useful for optimizing other complex biochemical pathways.

Achieving high titer yield and productivity of target chemicals in industrial organism depends on multidimensional pathway optimization. Here, the authors use a refined modular method called multidimensional heuristic process to improve production of astaxanthin, nerolidol and linalool in E. coli.

P450s controlling metabolic bifurcations in plant terpene specialized metabolism

ABSTRACT

Catalyzing stereo- and regio-specific oxidation of inert hydrocarbon backbones, and a range of more exotic reactions inherently difficult in formal chemical synthesis, cytochromes P450 (P450s) offer outstanding potential for biotechnological engineering. Plants and their dazzling diversity of specialized metabolites have emerged as rich repository for functional P450s with the advances of deep transcriptomics and genome wide discovery. P450s are of outstanding interest for understanding chemical diversification throughout evolution, for gaining mechanistic insights through the study of their structure-function relationship, and for exploitation in Synthetic Biology. In this review, we highlight recent developments and examples in the discovery of plant P450s involved in the biosynthesis of industrially relevant monoterpenoids, sesquiterpenoids, diterpenoids and triterpenoids, throughout 2016 and early 2017. Examples were selected to illustrate the spectrum of value from commodity chemicals, flavor and fragrance compounds to pharmacologically active terpenoids. We focus on a recently emerging theme, where P450s control metabolic bifurcations and chemical diversity of the final product profile, either within a pathway, or through neo-functionalization in related species. The implications may inform approaches for rational assembly of recombinant pathways, biotechnological production of high value terpenoids and generation of novel chemical entities.

Enhancing linalool production by engineering oleaginous yeast Yarrowia lipolytica

In this study, stepwise increases in linalool production were obtained by combining metabolic engineering and process optimization of an unconventional oleaginous yeast Yarrowia lipolytica. The linalool synthetic pathway was successfully constructed by heterologously expressing a codon-optimized linalool synthase gene from Actinidia arguta in Y. lipolytica. To enhance linalool productivity, key genes involved in the mevalonate pathway were overexpressed in different combinations. Moreover, the overexpression of mutant ERG20^F88W-N119W gene resulted in further linalool production. A maximum linalool titre of 6.96±0.29mg/L was achieved in shake flasks, which was the highest level ever reported in yeasts.

Production of jet fuel precursor monoterpenoids from engineered Escherichia coli

Monoterpenes (C₁₀ isoprenoids) are the main components of essential oils and are possible precursors for many commodity chemicals and high energy density fuels. Monoterpenes are synthesized from geranyl diphosphate (GPP), which is also the precursor for the biosynthesis of farnesyl diphosphate (FPP). FPP biosynthesis diverts the carbon flux from monoterpene production to C₁₅ products and quinone biosynthesis. In this study, we tested a chromosomal mutation of Escherichia coli's native FPP synthase (IspA) to improve GPP availability for the production of monoterpenes using a heterologous mevalonate pathway. Monoterpene production at high levels required not only optimization of GPP production but also a basal level of FPP to maintain growth. The optimized strains produced two jet fuel precursor monoterpenoids 1,8-cineole and linalool at the titer of 653 mg/L and 505 mg/L, respectively, in batch cultures with 1% glucose. The engineered strains developed in this work provide useful resources for the production of high-value monoterpenes. Biotechnol. Bioeng. 2017;114: 1703-1712. © 2017 Wiley Periodicals, Inc.

Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies

BACKGROUND

Transcriptional reprogramming is a fundamental process of living cells in order to adapt to environmental and endogenous cues. In order to allow flexible and timely control over gene expression without the interference of native gene expression machinery, a large number of studies have focused on developing synthetic biology tools for orthogonal control of transcription. Most recently, the nuclease-deficient Cas9 (dCas9) has emerged as a flexible tool for controlling activation and repression of target genes, by the simple RNA-guided positioning of dCas9 in the vicinity of the target gene transcription start site.

RESULTS

In this study we compared two different systems of dCas9-mediated transcriptional reprogramming, and applied them to genes controlling two biosynthetic pathways for biobased production of isoprenoids and triacylglycerols (TAGs) in baker's yeast Saccharomyces cerevisiae. By testing 101 guide-RNA (gRNA) structures on a total of 14 different yeast promoters, we identified the best-performing combinations based on reporter assays. Though a larger number of gRNA-promoter combinations do not perturb gene expression, some gRNAs support expression perturbations up to ~threefold. The best-performing gRNAs were used for single and multiplex reprogramming strategies for redirecting flux related to isoprenoid production and optimization of TAG profiles. From these studies, we identified both constitutive and inducible multiplex reprogramming strategies enabling significant changes in isoprenoid production and increases in TAG.

CONCLUSION

Taken together, we show similar performance for a constitutive and an inducible dCas9 approach, and identify multiplex gRNA designs that can significantly perturb isoprenoid production and TAG profiles in yeast without editing the genomic context of the target genes. We also identify a large number of gRNA positions in 14 native yeast target pomoters that do not affect expression, suggesting the need for further optimization of gRNA design tools and dCas9 engineering.

Road to the future of systems biotechnology: CRISPR-Cas-mediated metabolic engineering for recombinant protein production

The rising potential for CRISPR-Cas-mediated genome editing has revolutionized our strategies in basic and practical bioengineering research. It provides a predictable and precise method for genome modification in a robust and reproducible fashion. Emergence of systems biotechnology and synthetic biology approaches coupled with CRISPR-Cas technology could change the future of cell factories to possess some new features which have not been found naturally. We have discussed the possibility and versatile potentials of CRISPR-Cas technology for metabolic engineering of a recombinant host for heterologous protein production. We describe the mechanisms involved in this metabolic engineering approach and present the diverse features of its application in biotechnology and protein production.

A 'Plug and Play' Platform for the Production of Diverse Monoterpene Hydrocarbon Scaffolds in Escherichia coli

The terpenoids constitute one of the largest and most diverse classes of natural compounds with applications as pharmaceuticals, flavorings and fragrances, pesticides and biofuels. Synthetic biology is ideally placed to create new routes to this chemical diversity and facilitation of new compound discovery. The C10 monoterpenoids display a huge structural diversity produced from a single substrate, geranyl diphosphate, by a family of monoterpene cyclases and synthases (mTC/S). Here we employ a library of mTC/S in a single ‘plug and play’ platform system for the production of over 30 different monoterpenoids in Escherichia coli by fermentation on glucose. These products include several compounds never before produced in engineered microbes demonstrating the power of this approach to rapidly create routes to structural diversity.