Integrating Enzyme and Metabolic Engineering Tools for Enhanced α-Ionone Production

Recent Advancements in the Biomanufacturing of Crocetin and Crocins: Key Enzymes and Metabolic Engineering

Crocetin and crocins are high-value apocarotenoids recognized for their role as food colorants as well as for their numerous industrial and therapeutic applications. Biotechnological platforms have the potential to replace traditional plant-based extraction of these compounds with a more sustainable approach. This review first introduced the catalytic characteristics of key enzymes involved in the biosynthetic pathway of crocetin and crocins, including carotenoid cleavage dioxygenases, aldehyde dehydrogenases, and uridine diphosphate glycosyltransferases. Next, we highlighted advanced metabolic engineering strategies aimed at enhancing crocetin and crocin production, such as increasing the pool of precursors and cofactors, protein mining and engineering, tuning protein expression, biosensor, genomic integration, and process optimization. Finally, the paper proposed potential strategies and tools associated with further boosting the heterologous production of crocetin and crocins to meet commercial-scale demands.

Protein engineering of an oxidative cleavage-free pathway for crocetin-dialdehyde production in Escherichia coli

The growing depletion of petroleum resources and the increasing demand for sustainable alternatives have spurred advancements in microorganism-based biofactories. Among high-value compounds, carotenoids are widely sought after in pharmaceuticals, cosmetics, and nutrition, making them prime candidates for microbial production. In this study, we engineered an efficient biosynthetic pathway in Escherichia coli for the production of the C20-carotenoid crocetin-dialdehyde. By bypassing traditional oxidative cleavage reactions mediated by carotenoid cleavage dioxygenases (CCDs), our approach reduces the enzymatic complexity of the pathway. Using the crystal structure of a CrtMLIKE enzyme identified in this study, we developed a mutant enzyme capable of condensing two C10-geranyl pyrophosphate molecules to form C20-phytoene. This intermediate was then desaturated and oxidized by CrtN and CrtP to produce crocetin-dialdehyde, achieving a yield of 1.13 mg/L. By reducing enzyme requirements from six to three and eliminating the need for CCDs, this pathway alleviates metabolic stress on the host and enhances the scalability of production for industrial applications. Overall, our research presents a streamlined and innovative approach to carotenoid biosynthesis, advancing sustainable production methods for short-chain carotenoids.

Reshaping Phosphatase Substrate Preference for Controlled Biosynthesis Using a "Design-Build-Test-Learn" Framework

Biosynthesis is the application of enzymes in microbial cell factories and has emerged as a promising alternative to chemical synthesis. However, natural enzymes with limited catalytic performance often need to be engineered to meet specific needs through a time-consuming trial-and-error process. This study presents a quantum mechanics (QM)-incorporated design-build-test-learn (DBTL) framework to rationally design phosphatase BT4131, an enzyme with an ambiguous substrate spectrum involved in N-acetylglucosamine (GlcNAc) biosynthesis. First, mutant M1 (L129Q) is designed using force field-based methods, resulting in a 1.4-fold increase in substrate preference (kcat/Km) toward GlcNAc-6-phosphate (GlcNAc6P). QM calculations indicate that the shift in substrate preference is caused by a 13.59 kcal mol-1 reduction in activation energy. Furthermore, an iterative computer-aided design is conducted to stabilize the transition state. As a result, mutant M4 (I49Q/L129Q/G172L) with a 9.5-fold increase in kcat-GlcNAc6P/Km-GlcNAc6P and a 59% decrease in kcat-Glc6P/Km-Glc6P is highly desirable compared to the wild type in the GlcNAc-producing chassis. The GlcNAc titer increases to 217.3 g L-1 with a yield of 0.597 g (g glucose)-1 in a 50-L bioreactor, representing the highest reported level. Collectively, this DBTL framework provides an easy yet fascinating approach to the rational design of enzymes for industrially viable biocatalysts.

Combining enzyme and metabolic engineering for microbial supply of therapeutic phytochemicals

The history of pharmacology is deeply intertwined with plant-derived compounds, which continue to be crucial in drug development. However, their complex structures and limited availability in plants challenge drug discovery, optimization, development, and industrial production via chemical synthesis or natural extraction. This review delves into the integration of metabolic and enzyme engineering to leverage micro-organisms as platforms for the sustainable and reliable production of therapeutic phytochemicals. We argue that engineered microbes can serve a triple role in this paradigm: facilitating pathway discovery, acting as cell factories for scalable manufacturing, and functioning as platforms for chemical derivatization. Analyzing recent progress and outlining future directions, the review highlights microbial biotechnology's transformative potential in expanding plant-derived human therapeutics' discovery and supply chains.

De Novo Synthesis of Dihydro-β-ionone through Metabolic Engineering and Bacterium-Yeast Coculture

Dihydro-β-ionone is a common type of ionone used in the flavor and fragrance industries because of its characteristic scent. The production of flavors in microbial cell factories offers a sustainable and environmentally friendly approach to accessing them, independent of extraction from natural sources. However, the native pathway of dihydro-β-ionone remains unclear, hindering heterologous biosynthesis in microbial hosts. Herein, we devised a microbial platform for de novo syntheses of dihydro-β-ionone from a simple carbon source with glycerol. The complete dihydro-β-ionone pathway was reconstructed in Escherichia coli with multiple metabolic engineering strategies to generate a strain capable of producing 8 mg/L of dihydro-β-ionone, although this was accompanied by a surplus precursor β-ionone in culture. To overcome this issue, Saccharomyces cerevisiae was identified as having a conversion rate for transforming β-ionone to dihydro-β-ionone that was higher than that of E. coli via whole-cell catalysis. Consequently, the titer of dihydro-β-ionone was increased using the E. coli-S. cerevisiae coculture to 27 mg/L. Our study offers an efficient platform for biobased dihydro-β-ionone production and extends coculture engineering to overproducing target molecules in extended metabolic pathways.

Carotenoid Cleavage Dioxygenase 1 and Its Application for the Production of C13-Apocarotenoids in Microbial Cell Factories: A Review

C13-apocarotenoids are naturally derived from the C9-C10 (C9'-C10') double-bond cleavage of carotenoids by carotenoid cleavage dioxygenases (CCDs). As high-value flavors and fragrances in the food and cosmetic industries, the sustainable production of C13-apocarotenoids is emerging in microbial cell factories by the carotenoid cleavage dioxygenase 1 (CCD1) subfamily. However, the commercialization of microbial-based C13-apocarotenoids is still limited by the poor performance of CCD1, which severely constrains its conversion efficiency from precursor carotenoids. This review focuses on the classification of CCDs and their cleavage modes for carotenoids to generate corresponding apocarotenoids. We then emphatically discuss the advances for C13-apocarotenoid biosynthesis in microbial cell factories with various strategies, including optimization of CCD1 expression, improvement of CCD1's catalytic activity and substrate specificity, strengthening of substrate channeling, and development of oleaginous microbial hosts, which have been verified to increase the conversion rate from carotenoids. Lastly, the current challenges and future directions will be discussed to enhance CCDs' application for C13-apocarotenoids biomanufacturing.

Total enzymatic synthesis of cis-α-irone from a simple carbon source

Metabolic engineering has become an attractive method for the efficient production of natural products. However, one important pre-requisite is to establish the biosynthetic pathways. Many commercially interesting molecules cannot be biosynthesized as their native biochemical pathways are not fully elucidated. Cis-α-irone, a top-end perfumery molecule, is an example. Retrobiosynthetic pathway design by employing promiscuous enzymes provides an alternative solution to this challenge. In this work, we design a synthetic pathway to produce cis-α-irone with a promiscuous methyltransferase (pMT). Using structure-guided enzyme engineering strategies, we improve pMT activity and specificity towards cis-α-irone by >10,000-fold and >1000-fold, respectively. By incorporating the optimized methyltransferase into our engineered microbial cells, ~86 mg l-1 cis-α-irone is produced from glucose in a 5 l bioreactor. Our work illustrates that integrated retrobiosynthetic pathway design and enzyme engineering can offer opportunities to expand the scope of natural molecules that can be biosynthesized.

Mediating oxidative stress enhances α-ionone biosynthesis and strain robustness during process scaling up

BACKGROUND

α-Ionone is highly valued in cosmetics and perfumery with a global usage of 100-1000 tons per year. Metabolic engineering by microbial fermentation offers a promising way to produce natural (R)-α-ionone in a cost-effective manner. Apart from optimizing the metabolic pathways, the approach is also highly dependent on generating a robust strain which retains productivity during the scale-up process. To our knowledge, no study has investigated strain robustness while increasing α-ionone yield.

RESULTS

Built on our previous work, here, we further increased α-ionone yield to 11.4 mg/L/OD in 1 mL tubes by overexpressing the bottleneck dioxygenase CCD1 and re-engineering the pathway, which is  > 65% enhancement as compared to our previously best strain. However, the yield decreased greatly to 2.4 mg/L/OD when tested in 10 mL flasks. Further investigation uncovered an unexpected inhibition that excessive overexpression of CCD1 was accompanied with increased hydrogen peroxide (H₂O₂) production. Excessive H₂O₂ broke down lycopene, the precursor to α-ionone, leading to the decrease in α-ionone production in flasks. This proved that expressing too much CCD1 can lead to reduced production of α-ionone, despite CCD1 being the rate-limiting enzyme. Overexpressing the alkyl hydroperoxide reductase (ahpC/F) partially solved this issue and improved α-ionone yield to 5.0 mg/L/OD in flasks by reducing oxidative stress from H₂O₂. The strain exhibited improved robustness and produced  ~ 700 mg/L in 5L bioreactors, the highest titer reported in the literature.

CONCLUSION

Our study provides an insight on the importance of mediating the oxidative stress to improve strain robustness and microbial production of α-ionone during scaling up. This new strategy may be inspiring to the biosynthesis of other high-value apocarotenoids such as retinol and crocin, in which oxygenases are also involved.

Enhancing fluxes through the mevalonate pathway in Saccharomyces cerevisiae by engineering the HMGR and β-alanine metabolism

Mevalonate (MVA) pathway is the core for terpene and sterol biosynthesis, whose metabolic flux influences the synthesis efficiency of such compounds. Saccharomyces cerevisiae is an attractive chassis for the native active MVA pathway. Here, the truncated form of Enterococcus faecalis MvaE with only 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) activity was found to be the most effective enzyme for MVA pathway flux using squalene as the metabolic marker, resulting in 431-fold and 9-fold increases of squalene content in haploid and industrial yeast strains respectively. Furthermore, a positive correlation between MVA metabolic flux and β-alanine metabolic activity was found based on a metabolomic analysis. An industrial strain SQ3-4 with high MVA metabolic flux was constructed by combined engineering HMGR activity, NADPH regeneration, cytosolic acetyl-CoA supply and β-alanine metabolism. The strain was further evaluated as the chassis for terpenoids production. Strain SQ3-4-CPS generated from expressing β-caryophyllene synthase in SQ3-4 produced 11.86 ± 0.09 mg l-1 β-caryophyllene, while strain SQ3-5 resulted from down-regulation of ERG1 in SQ3-4 produced 408.88 ± 0.09 mg l-1 squalene in shake flask cultivations. Strain SQ3-5 produced 4.94 g l-1 squalene in fed-batch fermentation in cane molasses medium, indicating the promising potential for cost-effective production of squalene.

One-pot synthesis of dihydro-β-ionone from carotenoids using carotenoid cleavage dioxygenase and enoate reductase

Dihydro-β-ionone is a characteristic aroma compound of Osmanthus fragrans and is widely applied in the flavor & fragrance industry. However, the main focus is on chemical synthesis due to the metabolic pathways of dihydro-β-ionone is still unclear. Here, we explored the one-pot synthesis system for dihydro-β-ionone production using carotenoid cleavage dioxygenase (CCD) and enoate reductase. After screening the CCD enzyme, PhCCD1 from the Petunia hybrid was identified as the suitable enzyme for the first step of dihydro-β-ionone synthesis due to the high enzyme activity for carotenoid. The PhCCD1 was expressed in Escherichia coli and further characterized. The optimal activity of PhCCD1 was observed at pH 6.8 and 45 °C. The enzyme was stable over the pH range of 6.0-8.0 and had good thermal stability below 40 °C. Then, we optimized the coupled reaction conditions for dihydro-β-ionone production by PhCCD1 and enoate reductase AaDBR1 from Artemisia annua. Furthermore, we introduced the NADPH regeneration system with a 1.5-fold enhancement for dihydro-β-ionone production. Collectively, approximately 13.34 mg/L dihydro-β-ionone was obtained by the one-pot biosystem with a corresponding molar conversion of 85.8%. For the first time, we successfully designed and constructed a new synthesis pathway for dihydro-β-ionone production in vitro. The coupled catalysis reported herein illustrates the feasibility of producing dihydro-β-ionone from carotenoids and guides further engineering in the food industry.

Engineered EryF hydroxylase improving heterologous polyketide erythronolide B production in Escherichia coli

In the last two decades, the production of complex polyketides such as erythromycin and its precursor 6-deoxyerythronolide B (6-dEB) was demonstrated feasible in Escherichia coli. Although the heterologous production of polyketide skeleton 6-dEB has reached 210 mg l^-1 in E. coli, the yield of its post-modification products erythromycins remains to be improved. Cytochrome P450EryF catalyses the C6 hydroxylation of 6-dEB to form erythronolide B (EB), which is the initial rate-limiting modification in a multi-step pathway to convert 6-dEB into erythromycin. Here, we engineered hydroxylase EryF to improve the production of heterologous polyketide EB in E. coli. By comparative analysis of various versions of P450EryFs, we confirmed the optimal SaEryF for the biosynthesis of EB. Further mutation of SaEryF based on the crystal structure of SaEryF and homology modelling of AcEryF and AeEryF afforded the enhancement of EB production. The designed mutant of SaEryF, I379V, achieved the yield of 131 mg l^-1 EB, which was fourfold to that produced by wild-type SaEryF. Moreover, the combined mutagenesis of multiple residues led to further boost the EB concentration by another 41%, which laid the foundation for efficient heterologous biosynthesis of erythromycin or other complex polyketides.

Metabolic engineering of Escherichia coli BL21 strain using simplified CRISPR-Cas9 and asymmetric homology arms recombineering

BACKGROUND

The recent CRISPR-Cas coupled with λ recombinase mediated genome recombineering has become a common laboratory practice to modify bacterial genomes. It requires supplying a template DNA with homology arms for precise genome editing. However, generation of homology arms is a time-consuming, costly and inefficient process that is often overlooked.

RESULTS

In this study, we first optimized a CRISPR-Cas genome engineering protocol in the Escherichia coli (E. coli) BL21 strain and successfully deleted 10 kb of DNA from the genome in one round of editing. To further simplify the protocol, asymmetric homology arms were produced by PCR in a single step with two primers and then purified using a desalting column. Unlike conventional homology arms that are prepared through overlapping PCR, cloning into a plasmid or annealing synthetic DNA fragments, our method significantly both shortened the time taken and reduced the cost of homology arm preparation. To test the robustness of the optimized workflow, we successfully deleted 26 / 27 genes across the BL21 genome. Noteworthy, gRNA design is important for the CRISPR-Cas system and a general heuristic gRNA design has been proposed in this study. To apply our established protocol, we targeted 16 genes and iteratively deleted 7 genes from BL21 genome. The resulting strain increased lycopene yield by ~ threefold.

CONCLUSIONS

Our work has optimized the homology arms design for gene deletion in BL21. The protocol efficiently edited BL21 to improve lycopene production. The same workflow is applicable to any E. coli strain in which genome engineering would be useful to further increase metabolite production.

Overexpression and Characterization of a Novel Plant Carotenoid Cleavage Dioxygenase 1 from Morus notabilis

Synthesis of β-ionone in microbial cell factories is limited by the efficiency of carotenoid cleavage dioxygenases (CCDs). To obtain genes responsible for specific cleavage of carotenoids generating β-ionone, a novel carotenoid cleavage dioxygenase 1 from Morus notabilis was cloned and overexpressed in Escherichia coli. The MnCCD1 protein was able to cleave a variety of carotenoids at the positions 9, 10 (9', 10') to produce β-ionone, 3-hydroxy-4-oxo-β-ionone, 3-hydroxy-β-ionone, and 3-hydroxy-α-ionone in vitro. MnCCD1 could also cleave lycopene and β-carotene at the 9, 10 (9', 10') bind bond to produce pseudoionone and β-ionone, respectively, in E. coli accumulating carotenoids. The enzyme activity of MnCCD1 was reached 2.98 U/mL at optimized conditions (temperature 28 °C, IPTG 0.1 mM, induction time 24 h). The biochemical characterization of MnCCD1 revealed the optimal activities were at pH 8.4 and 35 °C. The addition of 10 % ethanol could increase enzyme activity at above 15 %. However, an obvious decline was observed on enzyme activity as the concentration of Fe²⁺ increased (0-1 mM). The V_max for β-apo-8'-carotenal was 72.5 U/mg, while the K_m was 0.83 mM. The results provide a foundation for developing the application of carotenoid cleavage dioxygenases as biocatalysis and synthetic biology platforms to produce volatile aroma components from carotenoids.

Cloning and Characterization of a Novel Carotenoid Cleavage Dioxygenase 1 from Helianthus annuus

Natural β-ionone, a high-value flavoring agent, has been widely applied in the food, cosmetics, and perfume industry. However, attempts to overproduce β-ionone in microorganisms have been limited by the efficiency of carotenoid cleavage dioxygenases (CCDs), which catalyzes β-carotene in the biosynthesis pathway. In order to obtain CCD genes responsible for the specific cleavage of carotenoids generating β-ionone, a novel carotenoid cleavage dioxygenase 1 from Helianthus annuus was cloned and overexpressed in Escherichia coli BL21(DE3). The recombinant CCD was able to cleave a variety of carotenoids at the 9, 10 (9', 10') sites to produce C13 products in vitro, including β-ionone, pseudoionone, 3-hydroxy-4-oxo-β-ionone, 3-hydroxy-β-ionone, and 3-hydroxy-α-ionone, which vary depending on the carotenoid substrates. In comparison with lycopene and zeaxanthin, HaCCD1 also showed the high specificity for β-carotene to cleave the 9, 10 (9', 10') double bond to produce β-ionone in E. coli accumulating carotenoids. Finally, the expression of HaCCD1 in E. coli was optimized, and biochemical characterizations were further clarified. The optimal activity of HaCCD1 was at pH 8.8 and 50 °C. The V_max for β-apo-8'-carotenal was 10.14 U/mg, while the K_m was 0.32 mM. Collectively, our study provides a valuable enzyme for the synthesis of natural β-ionone by biotransformation and synthetic biology platform.

CsCCD2 Access Tunnel Design for a Broader Substrate Profile in Crocetin Production

Crocetin, a high-value apocarotenoid in saffron, is widely applied to the fields of food and medicine. However, the existing method of obtaining crocetin through large-scale cultivation is far from meeting the market demand. Microbial synthesis of crocetin is a potential alternative to traditional resources, and it is found that carotenoid cleavage dioxygenase (CCD) is the critical enzyme to synthesize crocetin. So, in this study, we used "hybrid-tunnel" engineering to obtain variants of Crocus sativus-derived CsCCD2, essential for zeaxanthin conversion into crocetin, with a broader substrate specificity and higher catalytic efficiency. Variants including S323A, with a lower charge bias and a larger tunnel size than the wild-type, showed a 5-fold higher crocetin titer in yeast-based fermentations. S323A could also convert the β-carotene substrate to crocetin dialdehyde and exhibited a 12.83-fold greater catalytic efficiency (k_cat/K_m) toward zeaxanthin than the wild-type in vitro. This strategy enabled the production of 107 mg/L crocetin in 5 L fed-batch fermentation, higher than that previously reported. Our findings demonstrate that engineering access tunnels to expand the substrate profile by in silico protein design represents a viable strategy to refine the catalytic properties of enzymes across a range of applications.

Biotechnological applications of S-adenosyl-methionine-dependent methyltransferases for natural products biosynthesis and diversification

In the biosynthesis of natural products, methylation is a common and essential transformation to alter molecules' bioavailability and bioactivity. The main methylation reaction is performed by S-adenosylmethionine (SAM)-dependent methyltransferases (MTs). With advancements in genomic and chemical profiling technologies, novel MTs have been discovered to accept complex substrates and synthesize industrially valuable natural products. However, to achieve a high yield of small molecules in microbial hosts, many methyltransferase activities have been reported to be insufficient. Moreover, inadequate co-factor supplies and feedback inhibition of the by-product, S-adenosylhomocysteine (SAH), further limit MTs' activities. Here, we review recent advances in SAM-dependent MTs to produce and diversify natural products. First, we surveyed recently identified novel methyltransferases in natural product biosynthesis. Second, we summarized enzyme engineering strategies to improve methyltransferase activity, with a particular focus on high-throughput assay design and application. Finally, we reviewed innovations in co-factor regeneration and diversification, both in vitro and in vivo. Noteworthily, many MTs are able to accept multiple structurally similar substrates. Such promiscuous methyltransferases are versatile and can be tailored to design de novo pathways to produce molecules whose biosynthetic pathway is unknown or non-existent in nature, thus broadening the scope of biosynthesized functional molecules.

Regulation of carotenoid degradation and production of apocarotenoids in natural and engineered organisms

Carotenoids are important precursors of a wide range of apocarotenoids with their functions including: hormones, pigments, retinoids, volatiles, and signals, which can be used in the food, flavors, fragrances, cosmetics, and pharmaceutical industries. This article focuses on the formation of these multifaceted apocarotenoids and their diverse biological roles in all living systems. Carotenoid degradation pathways include: enzymatic oxidation by specific carotenoid cleavage oxygenases (CCOs) or nonspecific enzymes such as lipoxygenases and peroxidases and non-enzymatic oxidation by reactive oxygen species. Recent advances in the regulation of carotenoid cleavage genes and the biotechnological production of multiple apocarotenoids are also covered. It is suggested that different developmental stages and environmental stresses can influence both the expression of carotenoid cleavage genes and the formation of apocarotenoids at multiple levels of regulation including: transcriptional, transcription factors, posttranscriptional, posttranslational, and epigenetic modification. Regarding the biotechnological production of apocarotenoids especially: crocins, retinoids, and ionones, enzymatic biocatalysis and metabolically engineered microorganisms have been a promising alternative route. New substrates, carotenoid cleavage enzymes, biosynthetic pathways for apocarotenoids, and new biological functions of apocarotenoids will be discussed with the improvement of our understanding of apocarotenoid biology, biochemistry, function, and formation from different organisms.

Engineering Saccharomyces cerevisiae for the Overproduction of β-Ionone and Its Precursor β-Carotene

β-ionone is a commercially attractive industrial fragrance produced naturally from the cleavage of the pigment β-carotene in plants. While the production of this ionone is typically performed using chemical synthesis, environmentally friendly and consumer-oriented biotechnological production is gaining increasing attention. A convenient cell factory to address this demand is the yeast Saccharomyces cerevisiae. However, current β-ionone titers and yields are insufficient for commercial bioproduction. In this work, we optimized S. cerevisiae for the accumulation of high amounts of β-carotene and its subsequent conversion to β-ionone. For this task, we integrated systematically the heterologous carotenogenic genes (CrtE, CrtYB and CrtI) from Xanthophyllomyces dendrorhous using markerless genome editing CRISPR/Cas9 technology; and evaluated the transcriptional unit architecture (bidirectional or tandem), integration site, and impact of gene dosage, first on β-carotene accumulation, and later, on β-ionone production. A single-copy insertion of the carotenogenic genes in high expression loci of the wild-type yeast CEN.Pk2 strain yielded 4 mg/gDCW of total carotenoids, regardless of the transcriptional unit architecture employed. Subsequent fine-tuning of the carotenogenic gene expression enabled reaching 16 mg/gDCW of total carotenoids, which was further increased to 32 mg/gDCW by alleviating the known pathway bottleneck catalyzed by the hydroxymethylglutaryl-CoA reductase (HMGR1). The latter yield represents the highest total carotenoid concentration reported to date in S. cerevisiae for a constitutive expression system. For β-ionone synthesis, single and multiple copies of the carotene cleavage dioxygenase 1 (CCD1) gene from Petunia hybrida (PhCCD1) fused with a membrane destination peptide were expressed in the highest β-carotene-producing strains, reaching up to 33 mg/L of β-ionone in the culture medium after 72-h cultivation in shake flasks. Finally, interrogation of a contextualized genome-scale metabolic model of the producer strains pointed to PhCCD1 unspecific cleavage activity as a potentially limiting factor reducing β-ionone production. Overall, the results of this work constitute a step toward the industrial production of this ionone and, more broadly, they demonstrate that biotechnological production of apocarotenoids is technically feasible.

Metabolic Engineering Strategies for Sustainable Terpenoid Flavor and Fragrance Synthesis

Terpenoids derived from plant material are widely applied in the flavor and fragrance industry. Traditional extraction methods are unsustainable, but microbial synthesis offers a promising solution to attain efficient production of natural-identical terpenoids. Overproduction of terpenoids in microbes requires careful balancing of the synthesis pathway constituents within the constraints of host cell metabolism. Advances in metabolic engineering have greatly facilitated overcoming the challenges of achieving high titers, rates, and yields (TRYs). The review summarizes recent development in the molecular biology toolbox to achieve high TRYs for terpenoid biosynthesis, mainly in the two industrial platform microorganisms: Escherichia coli and Saccharomyces cerevisiae. The biosynthetic pathways, including alternative pathway designs, are briefly introduced, followed by recently developed methodologies used for pathway, genome, and strain optimization. Integrated applications of these tools are important to achieve high "TRYs" of terpenoid production and pave the way for translating laboratory research into successful commercial manufacturing.

Modular engineering for microbial production of carotenoids

There is an increasing demand for carotenoids due to their applications in the food, flavor, pharmaceutical and feed industries, however, the extraction and synthesis of these compounds can be expensive and technically challenging. Microbial production of carotenoids provides an attractive alternative to the negative environmental impacts and cost of chemical synthesis or direct extraction from plants. Metabolic engineering and synthetic biology approaches have been widely utilized to reconstruct and optimize pathways for carotenoid overproduction in microorganisms. This review summarizes the current advances in microbial engineering for carotenoid production and divides the carotenoid biosynthesis building blocks into four distinct metabolic modules: 1) central carbon metabolism, 2) cofactor metabolism, 3) isoprene supplement metabolism and 4) carotenoid biosynthesis. These four modules focus on redirecting carbon flux and optimizing cofactor supplements for isoprene precursors needed for carotenoid synthesis. Future perspectives are also discussed to provide insights into microbial engineering principles for overproduction of carotenoids.

Application of Stable Isotope Tracing to Elucidate Metabolic Dynamics During Yarrowia lipolytica α-Ionone Fermentation

Targeted metabolite analysis in combination with ¹³C-tracing is a convenient strategy to determine pathway activity in biological systems; however, metabolite analysis is limited by challenges in separating and detecting pathway intermediates with current chromatographic methods. Here, a hydrophilic interaction chromatography tandem mass spectrometry approach was developed for improved metabolite separation, isotopologue analysis, and quantification. The physiological responses of a Yarrowia lipolytica strain engineered to produce ∼400 mg/L α-ionone and temporal changes in metabolism were quantified (e.g., mevalonate secretion, then uptake) indicating bottleneck shifts in the engineered pathway over the course of fermentation. Dynamic labeling results indicated limited tricarboxylic acid cycle label incorporation and, combined with a measurable ATP shortage during the high ionone production phase, suggested that electron transport and oxidative phosphorylation may limit energy supply and strain performance. The results provide insights into terpenoid pathway metabolic dynamics of non-model yeasts and offer guidelines for sensor development and modular engineering.

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A HILIC method is demonstrated for efficient separation of 57 cellular metabolites

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Production of α-ionone was ∼400 mg/L in bench-top bioreactors

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Engineered Y. lipolytica secreted then consumed mevalonate during fermentation

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Oxidative phosphorylation may limit performance in high-cell-density fermentations

Bioflavour Conference 2018-Biotechnology for Flavors, Fragrances, and Functional Ingredients

The "Bioflavour 2018-Biotechnology of Flavors, Fragrances, and Functional Ingredients" conference was held from September 18th to 21st, 2018 at the DECHEMA house in Frankfurt, Germany. The conference attracted more than 190 participants from over 25 countries, with about 40% share from industry. Particular sessions of Bioflavour 2018 focused on "flavor perception and biotechnology", "microbial cell factories", "novel pathways, enzymes, and biocatalysts", "technological and regulatory aspects of flavor and fragrance biotechnology", "advanced analytics and novel compounds", "plant biosynthesis and plant enzymes", "modern biotechnology in the world of wine", "receptors, flavors, and bioactives", and "bioprocess development and downstream processing". At Bioflavour 2018, both cutting-edge science from renowned academic research groups and current innovation from this modern biotechnology industry were presented and discussed. This special issue highlights a selection of 12 manuscripts from oral presentations and poster contributions.