Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production

Engineering the L-tryptophan metabolism for efficient de novo biosynthesis of tryptophol in Saccharomyces cerevisiae

Tryptophol (IET) is a metabolite derived from L-tryptophan that can be isolated from plants, bacteria, and fungi and has a wide range of biological activities in living systems. Despite the fact that IET biosynthesis pathways exist naturally in living organisms, industrial-scale production of IET and its derivatives is solely based on environmentally unfriendly chemical conversion. With diminishing petroleum reserves and a significant increase in global demand in all major commercial segments, it becomes essential to develop new technologies to produce chemicals from renewable resources and under mild conditions, such as microbial fermentation. Here we characterized and engineered the less-studied L-tryptophan pathway and IET biosynthesis in the baker's yeast Saccharomyces cerevisiae, with the goal of investigating microbial fermentation as an alternative/green strategy to produce IET. In detail, we divided the aromatic amino acids (AAAs) metabolism related to IET synthesis into the shikimate pathway, the L-tryptophan pathway, the competing L-tyrosine/L-phenylalanine pathways, and the Ehrlich pathway based on a modular engineering concept. Through stepwise engineering of these modules, we obtained a yeast mutant capable of producing IET up to 1.04 g/L through fed-batch fermentation, a ~ 650-fold improvement over the wild-type strain. Besides, our engineering process also revealed many insights about the regulation of AAAs metabolism in S. cerevisiae. Finally, during our engineering process, we also discovered yeast mutants that accumulate anthranilate and L-tryptophan, both of which are precursors of various valuable secondary metabolites from fungi and plants. These strains could be developed to the chassis for natural product biosynthesis upon introducing heterologous pathways.

Advances in Engineering Nucleotide Sugar Metabolism for Natural Product Glycosylation in Saccharomyces cerevisiae

Glycosylation is a ubiquitous modification present across all of biology, affecting many things such as physicochemical properties, cellular recognition, subcellular localization, and immunogenicity. Nucleotide sugars are important precursors needed to study glycosylation and produce glycosylated products. Saccharomyces cerevisiae is a potentially powerful platform for producing glycosylated biomolecules, but it lacks nucleotide sugar diversity. Nucleotide sugar metabolism is complex, and understanding how to engineer it will be necessary to both access and study heterologous glycosylations found across biology. This review overviews the potential challenges with engineering nucleotide sugar metabolism in yeast from the salvage pathways that convert free sugars to their associated UDP-sugars to de novo synthesis where nucleotide sugars are interconverted through a complex metabolic network with governing feedback mechanisms. Finally, recent examples of engineering complex glycosylation of small molecules in S. cerevisiae are explored and assessed.

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.

Revealing the Mechanism of Aroma Production Driven by High Salt Stress in Trichomonascus ciferrii WLW

Douchi is a Chinese traditional fermented food with a unique flavor. Methyl anthranilate (MA) plays an important role in formation of this flavor. However, the complicated relationship between the MA formation and the metabolic mechanism of the key functional microorganisms remains unclear. Here, we elucidated the response mechanism of aroma production driven by high salt stress in Trichomonascus ciferrii WLW (T. ciferrii WLW), which originates from the douchi fermentation process. The highest production of MA was obtained in a 10% NaCl environment. The enhanced expression of the key enzyme genes of the pentose phosphate pathway and shikimic acid pathway directed carbon flow toward aromatic amino acid synthesis and helped sustain an increased expression of metK to synthesize a large amount of the methyl donor S-adenosylmethionine, which promoted methyl anthranilate yield. This provides a theoretical basis for in-depth research on the applications of the flavor formation mechanisms of fermented foods.

Precision fermentation for improving the quality, flavor, safety, and sustainability of foods

Precision fermentation involves the rewiring of metabolic pathways in generally recognized as safe microorganisms, fermentation scale-up, and downstream processing to produce food ingredients from abundant and inexpensive substrates. Using precise genome editing of food-fermenting microorganisms, precision fermentation can also produce fermented foods with more desirable properties. These genetic tools allow for the manipulation of flavors and nutritional content in fermented foods, the economic production of functional food ingredients, and the sustainable production of otherwise-costly macronutrients. By introducing the metabolic designs, genetic modifications, and resulting products of engineered microorganisms developed through academic and industrial research, this review aims to provide insights into the potentials and challenges of precision fermentation for the economic, safe, and sustainable production of foods.

Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals

In the twenty first century, biotechnology offers great opportunities and solutions to climate change mitigation, energy and food security and resource efficiency. The use of metabolic engineering to modify microorganisms for producing industrially significant chemicals is developing and becoming a trend. As a famous, generally recognized as a safe (GRAS) model microorganism, Saccharomyces cerevisiae is widely used due to its excellent operational convenience and high fermentation efficiency. This review summarizes recent advancements in the field of using metabolic engineering strategies to construct engineered S. cerevisiae over the past ten years. Five different types of compounds are classified by their metabolites, and the modified metabolic pathways and strategies are summarized and discussed independently. This review may provide guidance for future metabolic engineering efforts toward such compounds and analogues. Additionally, the limitations of S. cerevisiae as a cell factory and its future trends are comprehensively discussed.

Comparative putative metabolites profiling of Tachypleus gigas and Carcinoscorpius rotundicauda hemocytes stimulated with lipopolysaccharide

Horseshoe crabs are among the most studied invertebrates due to their unique, innate immune system and biological processes. The metabolomics study was conducted on lipopolysaccharide (LPS)-stimulated and non-stimulated hemocytes isolated from the Malaysian Tachypleus gigas and Carcinoscorpius rotundicauda. LC-TOF-MS, multivariate analyses, principal component analysis (PCA), and partial least squares-discriminant analysis (PLS-DA) were included in this study to profile the metabolites. A total of 37 metabolites were identified to be differentially abundant and were selected based on VIP > 1. However, of the 37 putative metabolites, only 23 were found to be significant with ANOVA at p < 0.05. The metabolites were identified using several databases, and the literature review of the metabolites was reported in the manuscript. Thus, this study has provided further insights into the putative metabolites' presence in the hemocytes of horseshoe crabs that are stimulated and non-stimulated with LPS and their abundance in each species. Several putative metabolites showed they have medicinal values from previous studies.

A comprehensive review and comparison of L-tryptophan biosynthesis in Saccharomyces cerevisiae and Escherichia coli

L-tryptophan and its derivatives are widely used in the chemical, pharmaceutical, food, and feed industries. Microbial fermentation is the most commonly used method to produce L-tryptophan, which calls for an effective cell factory. The mechanism of L-tryptophan biosynthesis in Escherichia coli, the widely used producer of L-tryptophan, is well understood. Saccharomyces cerevisiae also plays a significant role in the industrial production of biochemicals. Because of its robustness and safety, S. cerevisiae is favored for producing pharmaceuticals and food-grade biochemicals. However, the biosynthesis of L-tryptophan in S. cerevisiae has been rarely summarized. The synthetic pathways and engineering strategies of L-tryptophan in E. coli and S. cerevisiae have been reviewed and compared in this review. Furthermore, the information presented in this review pertains to the existing understanding of how L-tryptophan affects S. cerevisiae's stress fitness, which could aid in developing a novel plan to produce more resilient industrial yeast and E. coli cell factories.

Spontaneously established syntrophic yeast communities improve bioproduction

Nutritional codependence (syntrophy) has underexplored potential to improve biotechnological processes by using cooperating cell types. So far, design of yeast syntrophic communities has required extensive genetic manipulation, as the co-inoculation of most eukaryotic microbial auxotrophs does not result in cooperative growth. Here we employ high-throughput phenotypic screening to systematically test pairwise combinations of auxotrophic Saccharomyces cerevisiae deletion mutants. Although most coculture pairs do not enter syntrophic growth, we identify 49 pairs that spontaneously form syntrophic, synergistic communities. We characterized the stability and growth dynamics of nine cocultures and demonstrated that a pair of tryptophan auxotrophs grow by exchanging a pathway intermediate rather than end products. We then introduced a malonic semialdehyde biosynthesis pathway split between different pairs of auxotrophs, which resulted in increased production. Our results report the spontaneous formation of stable syntrophy in S. cerevisiae auxotrophs and illustrate the biotechnological potential of dividing labor in a cooperating intraspecies community.

Production and sensory analysis of grape flavoured beer by co-fermentation of an industrial and a genetically modified laboratory yeast strain

The so-called "craft beer revolution" has increased the demand for new styles of beers, often with new ingredients like flavour extracts. In recent years, synthetic biology has realized the production of a plethora of plant secondary metabolites in microbial hosts, which could provide an alternative source for these compounds. In this study, we selected a in situ flavour production approach for grape flavour addition. We used an O-methyl anthranilate (OmANT) producing laboratory Saccharomyces cerevisiae strain in co-fermentations with an industrial beer yeast strain WLP644. The laboratory strain provided an ease of genetic manipulation and the desirable properties of the WLP644 strain were not modified in this approach. In shake flasks, a 10:90 ratio of the yeasts produced grape flavoured beer with the yeast produced flavour compound in a range normally used for flavoured beverages. Hopped and unhopped beers were analysed by VTT's trained sensory panel and with olfactory GC-MS. OmANT was successfully detected from the beers as a floral odour and flavour. Moreover, no off-flavours were detected and aroma profiles outside the grape flavour were rather similar. These results indicate that the co-fermentation principle is a suitable approach to change the flavour profiles of beers with a simple yeast strain drop-in approach.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00217-023-04274-1.

Engineered Escherichia coli cell factory for anthranilate over-production

Anthranilate is a key platform chemical in high demand for synthesizing food ingredients, dyes, perfumes, crop protection compounds, pharmaceuticals, and plastics. Microbial-based anthranilate production strategies have been developed to overcome the unstable and expensive supply of anthranilate via chemical synthesis from non-renewable resources. Despite the reports of anthranilate biosynthesis in several engineered cells, the anthranilate production yield is still unsatisfactory. This study designed an Escherichia coli cell factory and optimized the fed-batch culture process to achieve a high titer of anthranilate production. Using the previously constructed shikimate-overproducing E. coli strain, two genes (aroK and aroL) were complemented, and the trpD responsible for transferring the phosphoribosyl group to anthranilate was disrupted to facilitate anthranilate accumulation. The genes with negative effects on anthranilate biosynthesis, including pheA, tyrA, pabA, ubiC, entC, and trpR, were disrupted. In contrast, several shikimate biosynthetic pathway genes, including aroE and tktA, were overexpressed to maximize glucose uptake and the intermediate flux. The rationally designed anthranilate-overproducing E. coli strain grown in an optimized medium produced approximately 4 g/L of anthranilate in 7-L fed-batch fermentation. Overall, rational cell factory design and culture process optimization for microbial-based anthranilate production will play a key role in complementing traditional chemical-based anthranilate production processes.

Anthranilic Acid Accumulation in Saccharomyces cerevisiae Induced by Expression of a Nonribosomal Peptide Synthetase Gene from Paecilomyces cinnamomeus BCC 9616

Heterologous expression of nrps33, a nonribosomal peptide synthetase gene, from Paecilomyces cinnamomeus BCC 9616 in Saccharomyces cerevisiae unexpectedly resulted in the accumulation of anthranilic acid, an intermediate in tryptophan biosynthesis. Based on transcriptomic and real-time quantitative polymerase chain reaction (RT-qPCR) results, expression of nrps33 affected the transcription of tryptophan biosynthesis genes especially TRP1 which is also the selectable auxotrophic marker for the expression vector used in this work. The product of nrps33 could inhibit the activity of Trp4 involved in the conversion of anthranilate to N-(5'-phosphoribosyl)anthranilate and therefore caused the accumulation of anthranilic acid. This accumulation could in turn result in down-regulation of downstream tryptophan biosynthesis genes. Anthranilic acid is typically produced by chemical synthesis and has been used as a substrate for synthesising bioactive compounds including commercial drugs; our results could provide a new biological platform for production of this compound.

Designing Microbial Cell Factories for the Production of Chemicals

The sustainable production of chemicals from renewable, nonedible biomass has emerged as an essential alternative to address pressing environmental issues arising from our heavy dependence on fossil resources. Microbial cell factories are engineered microorganisms harboring biosynthetic pathways streamlined to produce chemicals of interests from renewable carbon sources. The biosynthetic pathways for the production of chemicals can be defined into three categories with reference to the microbial host selected for engineering: native-existing pathways, nonnative-existing pathways, and nonnative-created pathways. Recent trends in leveraging native-existing pathways, discovering nonnative-existing pathways, and designing de novo pathways (as nonnative-created pathways) are discussed in this Perspective. We highlight key approaches and successful case studies that exemplify these concepts. Once these pathways are designed and constructed in the microbial cell factory, systems metabolic engineering strategies can be used to improve the performance of the strain to meet industrial production standards. In the second part of the Perspective, current trends in design tools and strategies for systems metabolic engineering are discussed with an eye toward the future. Finally, we survey current and future challenges that need to be addressed to advance microbial cell factories for the sustainable production of chemicals.

Dynamic flux regulation for high-titer anthranilate production by plasmid-free, conditionally-auxotrophic strains of Pseudomonas putida

Anthranilate, an intermediate of the shikimate pathway, is a high-value aromatic compound widely used as a precursor in the production of dyes, fragrances, plastics and pharmaceuticals. Traditional strategies adopted for microbial anthranilate production rely on the implementation of auxotrophic strains-which requires aromatic amino acids or complex additives to be supplemented in the culture medium, negatively impacting production costs. In this work, we engineered the soil bacterium Pseudomonas putida for high-titer, glucose-dependent anthranilate production by repurposing elements of the Esa quorum sensing (QS) system of Pantoea stewartii. The P_esaS promoter mediated a self-regulated transcriptional response that effectively knocked-down the expression of the trpDC genes. Next, we harnessed the synthetic QS elements to engineer a growth-to-anthranilate production switch. The resulting plasmid-free P. putida strain produced the target compound at 3.8 ± 0.3 mM in shaken-flask cultures after 72 h-a titer >2-fold higher than anthranilate levels reported thus far. Our results highlight the value of dynamic flux regulation for the production of intermediate metabolites within highly-regulated routes (such as the shikimate pathway), thereby circumventing the need of expensive additives.

De Novo Biosynthesis and Whole-Cell Catalytic Production of 2-Acetamidophenol in Escherichia coli

2-Acetamidophenol (AAP) is an aromatic product with promising activities in agricultural applications and medical research. At present, AAP is synthesized by chemical methods from nonrenewable fossil fuel resources, which cause environmental pollution and the reaction conditions are harsh. In this study, we constructed the artificial biosynthetic pathway of AAP with five different expressed proteins in Escherichia coli for the first time. By introducing the hydrogen peroxide degrading enzyme catalase and improving cell tolerance to toxic intermediates or products, the yield of AAP reached 33.54 mg/L using shaking-flask culture. The best-engineered strain could produce 568.57 mg/L AAP by fed-batch fermentation from glucose and precursor (2-aminophenol, 2-AP) addition. Furthermore, a one-pot whole-cell cascade biocatalytic pathway to AAP and analogues was developed and optimized. This method can efficiently produce 1.8 g/L AAP using the methyl anthranilate hydrolysis product as the substrate. This study provides not only the de novo artificial biosynthetic pathway of AAP in E. coli but also a promising sustainable and efficient strategy to enable the synthesis of AAP on a gram scale.

Current Promising Therapeutic Targets for Aspergillosis Treatment

Aspergillosis is a fungal disease caused by different species of Aspergillus. They live in soil,dust and decomposed material. Number of Aspergillus species found till now is about 300 and more are still to be identified. Only few Aspergillus species can cause human disease and the most common species for human infection is Aspergillus fumigatus, which is a ubiquitous airborne saprophytic fungus. Severity of the disease ranges from an allergic response to life-threatening generalized infection. They grow optimally at 37°C and can grow upto 50°C. The fungal conidia are being constantly inhaled by humans and animals everyday normally gets eliminated by innate immune mechanism. Due to increasing number of immunocompromised patients, severe and fatal Aspergillosis cases have augmented. Currently, available antifungal drug for the treatment of Aspergillosis act on these three molecular target are 14 alpha demethylase for Azoles, ergosterol for Polyene and β-1,3-glucan synthase for Echinocandin. These antifungal drug show high resistance problem and toxicity. So, it is high time to develop new drugs for treatment with reduced toxicity and drug resistant problem. Synthesis of essential amino acid is absent in human as they obtain it from their diet but fungi synthesis these amino acid. Thus, enzymes in this pathway acts as novel drug target. This article summarizes promising drug targets presents in different metabolic pathway of Aspergillus genome and discusses their molecular functions in detail. This review also list down the inhibitors of these novel target. We present a comprehensive review that will pave way for discovery and development of novel antifungals against these drug targets for Aspergillosis treatment.