Synthesis of chemicals by metabolic engineering of microbes

Systems Metabolic Engineering of Clostridium tyrobutyricum for 1,3-Propanediol Production From Crude Glycerol

Clostridium tyrobutyricum has emerged as a non-pathogenic microbial cell factory capable of anaerobic production of various value-added products, such as butyrate, butanol, and butyl butyrate. This study reports the first systematic engineering of C. tyrobutyricum for the heterologous production of 1,3-propanediol (1,3-PDO) from industrial by-product crude glycerol. Initially, the glycerol reductive pathway for 1,3-PDO production was constructed, and the unique glycerol oxidation pathway in C. tyrobutyricum was elucidated. Subsequently, the glycerol metabolism and 1,3-PDO synthesis pathways were enhanced. Furthermore, the intracellular reducing power supply and the fermentation process were optimized to improve 1,3-PDO production. Consequently, 54.06 g/L 1,3-PDO with a yield of 0.64 mol/mol and a productivity of 1.13 g/L·h was obtained using crude glycerol and fish meal. The strategies described herein could facilitate the engineering of C. tyrobutyricum as a robust host for synthesizing valuable chemicals.

O-methylation modifications in the biosynthetic pathway of dibenzocyclooctadiene lignans

Schisandra chinensis, a well-known traditional Chinese herb used for hepatitis treatment, contains dibenzocyclooctadiene lignans as its primary active compounds, which undergo extensive multi-site O-methylation. However, O-methyltransferases (OMT) involved in this process have not been previously reported. This study employed transcriptomic analysis of S. chinensis treated with methyl jasmonate, alongside expression profiling, phylogenetic analysis, and heterologous expression to characterize the functional roles of OMTs. The study identified 4 OMTs: SchiOMT4, SchiOMT12, SchiOMT16, and SchiOMT22, which catalyze C-3 O-methylation of caffeic acid and Caffeyl aldehyde to form ferulic acid and coniferyl aldehyde. Additionally, SchiOMT12 and SchiOMT16 methylated gomisin L2 at C-3, while SchiOMT16 also O-methylation schisanhenol at C-14 and performed sequential O-methylation at C-3 and C-12 of gomisin J. Molecular docking further clarified the regioselectivity of SchiOMT16 and SchiOMT12, elucidating the differences in their catalytic activities. This study is the first to identify methyltransferases involved in the subsequent modifications of dibenzocyclooctadiene lignans, underscoring the broad substrate range, selective O-methylation, and regulatory importance of OMTs in their biosynthesis.

Direct 3D Mass Spectrometry Imaging Analysis of Environmental Microorganisms

Assessing the spatial distribution of microorganisms' metabolites in growth medium remains a challenge. Here, we present the first use of the newly developed LARAPPI/CI-MSI 3D (laser ablation remote atmospheric pressure photoionization/chemical ionization mass spectrometry imaging) method for direct three-dimensional (3D) mass spectrometry imaging of bacterial and fungal metabolites in solid culture media. Two-dimensional (2D) MSI was also performed, and it indicated the presence of metabolites belonging to, and including, amino acids and their derivatives, dipeptides, organic acids, fatty acids, sugars and sugar derivatives, benzene derivatives, and indoles. Distribution at a selected depth within the culture medium with the estimation of concentration across all dimensions of 16 metabolites was visualized using LARAPPI/CI-MSI 3D. The imaging results were correlated with the results of ultra-high-performance liquid chromatography-ultra-high-resolution mass spectrometry (UHPLC-UHRMS). A total of 351-393 chemical compounds, depending on the tested microorganism, were identified, while 242-262 were recognized in the HMDB database in MetaboAnalyst (v 6.0). The LARAPPI/CI-MSI 3D method enables the rapid screening of the biotechnological potential of environmental strains, facilitating the discovery of industrially valuable biomolecules.

Assessment of Anticancer and Antimicrobial Potential of Bioactive Metabolites and Optimization of Culture Conditions of Pseudomonas aurantiaca PB-St2 for High Yields

The following study aimed to characterize the biological potential of the purified compounds of Pseudomonas aurantiaca PB-St2. Optimization of temperature and incubation time of 32oC and 72 h yielded the highest crude extract weight and optical density of bacterial culture. HPLC analysis of the crude metabolite extract (purified using gravitational column chromatography) showed three fractions named as PC1, PC2, and PC3. HPLC-purified fractions were subjected to LC-MS/MS analysis and the data was compared using reference library. Fraction PC1 was identified as mupirocin, PC2 as phenazine-1-carboxylic acid (PCA), and PC3 as the mixture of three compounds including pyoluteorin, PCA and 2-hydroxyphenazine (2-OH-phz). Fungicidal potential of the purified compounds was assessed against phytopathogens including Fusarium equiseti, Fusarium incarnatum, Alternaria alternata, and Colletotrichum falcatum. Fraction PC3 showed the highest fungicidal activity of ~89%, whereas, the least antifungal activity (~27%) was noted for mupirocin. Antibacterial activity of the purified compounds against Gram-positive pathogen Bacillus cereus, and Gram-negative pathogens Pseudomonas aeruginosa, Salmonella enterica, and Klebsiella oxytoca was also assessed. Fraction PC3 demonstrated the highest antibacterial activity against B. cereus and P. aeruginosa showing 1.8 cm, and 0.9 cm zones of inhibition, respectively. Against K. oxytoca and S. enterica, the antibacterial activity of PB-St2 crude extract was slightly higher than the fraction PC3. The fraction PC3 also demonstrated the highest IC50 against HepG-2 and SF767 cancer cell lines at 25 μg and 20 μg concentrations, respectively. The multifaceted attributes of P. aurantiaca PB-St2 make it an ideal candidate for agricultural and pharmacological applications.

Bacterial metabolomics: current applications for human welfare and future aspects

An imbalanced microbiome is linked to several diseases, such as cancer, inflammatory bowel disease, obesity, and even neurological disorders. Bacteria and their by-products are used for various industrial and clinical purposes. The metabolites under discussion were chosen based on their biological impacts on host and gut microbiota interactions as established by metabolome research. The separation of bacterial metabolites by using statistics and machine learning analysis creates new opportunities for applications of bacteria and their metabolites in the environmental and medical sciences. Thus, the metabolite production strategies, methodologies, and importance of bacterial metabolites for human well-being are discussed in this review.

Towards microbial consortia in fermented foods for metabolic engineering and synthetic biology

The fermented foods microbiota, whose community structures evolve through a succession of different microbial groups, play a central role in fermented food production. The texture and flavor, functions, shelf-life and safety, are largely determined by the interactions among bacteria and yeast within these communities. Although much indispensable work has described the microbial composition and succession in various fermentation foods, yet the specific microbial interactions involved are not well understood. Here, we review the current mechanisms of microbial interactions (amensalism, competition, commensalism, and mutualism) existed in the fermented foods. We also examine the function of these interactions. In addition, we provide our perspectives on the future development of functional and novel fermented foods by combining the new starter cultures with the native microbial consortia and applications of these stable and robust microbial consortia for metabolic engineering and synthetic biology.

Volatilome of the maize phytopathogenic fungus Fusarium verticillioides: potential applications in diagnosis and biocontrol

BACKGROUND

Fusarium verticillioides is a maize fungal phytopathogen and a producer of volatile organic compounds (VOCs) and fumonisin B1 (FB1). Our aim was to study the volatilome, conidial production, ergosterol and FB1 biosynthesis in maize cultures over a 30-day incubation period (5, 10, 15, 20, 25, 30 days post inoculation [DPI]). The effect of pure VOCs on the same parameters was then evaluated to study their potential role as biocontrol agents.

RESULTS

In total, 91 VOCs were detected, with volatile profiles being more similar between 5 and 10 DPI compared with 15, 20, 25 and 30 DPI. Ergosterol content increased steadily with incubation time, and three growth stages were identified: a lag phase (0 to 15 DPI), an exponential phase (15 to 20 DPI) and a stationary phase (20 to 30 DPI). The maximum concentration of FB1 was detected at 25 (0.030 μg FB1/μg ergosterol) and 30 DPI (0.037 μg FB1/μg ergosterol), whereas conidial production showed a maximum value at 15 DPI (4.3 ± 0.2 × 105 conidia/μg ergosterol). Regarding pure VOCs, minimal inhibitory concentration values ranged from 0.3 mm for 4-hexen-3-one to 7.4 mm for 2-undecanone. Pure VOCs reduced radial growth, conidial production and ergosterol and FB1 biosynthesis.

CONCLUSIONS

The marked resemblance between VOC profiles at 5 and 10 DPI suggests that they could act as early indicators of fungal contamination, particularly 4-ethylguaiacol, 4-ethyl-2-methoxyanisole, heptanol and heptyl acetate. On the other hand, their role as inhibitors of fungal growth and FB1 biosynthesis prove their great potential as safer alternatives to control phytopathogenic fungi. © 2024 Society of Chemical Industry.

Biotechnological applications of purine and pyrimidine deaminases

Deaminases, ubiquitous enzymes found in all living organisms from bacteria to humans, serve diverse and crucial functions. Notably, purine and pyrimidine deaminases, while biologically essential for regulating nucleotide pools, exhibit exceptional versatility in biotechnology. This review systematically consolidates current knowledge on deaminases, showcasing their potential uses and relevance in the field of biotechnology. Thus, their transformative impact on pharmaceutical manufacturing is highlighted as catalysts for the synthesis of nucleic acid derivatives. Additionally, the role of deaminases in food bioprocessing and production is also explored, particularly in purine content reduction and caffeine production, showcasing their versatility in this field. The review also delves into most promising biomedical applications including deaminase-based GDEPT and genome and transcriptome editing by deaminase-based systems. All in all, illustrated with practical examples, we underscore the role of purine and pyrimidine deaminases in advancing sustainable and efficient biotechnological practices. Finally, the review highlights future challenges and prospects in deaminase-based biotechnological processes, encompassing both industrial and medical perspectives.

Overview of resveratrol properties, applications, and advances in microbial precision fermentation

Resveratrol is an antioxidant abundant in plants like grapes and peanuts and has garnered significant attention for its potential therapeutic applications. This review explores its chemical attributes, stability, and solubility, influencing its diverse applications and bioavailability. Resveratrol's multifaceted therapeutic roles encompass: antioxidant, cardioprotective, anti-inflammatory, neuroprotective, anti-aging, and anticancer properties. While traditionally studied in preclinical settings, a surge in clinical trials underscores resveratrol's promise for human health. Over 250 recent clinical trials investigate its effects alone and in combination with other compounds. Commercially utilized in food, cosmetics, supplements, and pharmaceuticals, the resveratrol market is expanding, driven by microbial fermentation. Microbes offer advantages over plant extraction and chemical synthesis, providing cost-effective, pure, and sustainable production. Microbial biosynthesis can be attained from carbon sources, such as glucose or xylose, among others, which can be obtained from renewable resources or agro-industrial wastes. While Saccharomyces cerevisiae has been the most used host, non-conventional yeasts like Yarrowia lipolytica and bacteria like Escherichia coli have also demonstrated potential. Genetic modifications such as increasing acetyl-CoA/malonyl-CoA pools, boosting the shikimate pathway, or multi-copy expression of pathway genes, allied to the optimization of fermentation strategies have been promising in increasing titers. Microbial biosynthesis of resveratrol aligns with the shift toward sustainable and renewable bio-based compounds, exemplifying a circular bioeconomy. Concluding, microbial fermentation presents a promising avenue for efficient resveratrol production, driven by genetic engineering, pathway optimization, and fermentation strategies. These advances hold the key to unlocking the potential of resveratrol for diverse therapeutic applications, contributing to a greener and sustainable future.

Rational and Semirational Approaches for Engineering Salicylate Production in Escherichia coli

Salicylate plays a pivotal role as a pharmaceutical intermediate in drugs, such as aspirin and lamivudine. The low catalytic efficiency of key enzymes and the inherent toxicity of salicylates to cells pose significant challenges to large-scale microbial production. In this study, we introduced the salicylate synthase Irp9 into an l-phenylalanine-producing Escherichia coli, constructing the shortest salicylate biosynthetic pathway. Subsequent protein engineering increased the catalytic efficiency of Irp9 by 33.5%. Furthermore, by integrating adaptive evolution with transcriptome analysis, we elucidated the crucial mechanism of efflux proteins in salicylate tolerance. The elucidation of this mechanism guided us in the targeted modification of these transport proteins, achieving a reported maximum level of 3.72 g/L of salicylate in a shake flask. This study highlights the importance of efflux proteins for enhancing the productivity of microbial cell factories in salicylate production, which also holds potential for application in the green synthesis of other phenolic acids.

De Novo Synthesis of Resveratrol from Sucrose by Metabolically Engineered Yarrowia lipolytica

Resveratrol, a phenylpropanoid compound, exhibits diverse pharmacological properties, making it a valuable candidate for health and disease management. However, the demand for resveratrol exceeds the capacity of plant extraction methods, necessitating alternative production strategies. Microbial synthesis offers several advantages over plant-based approaches and presents a promising alternative. Yarrowia lipolytica stands out among microbial hosts due to its safe nature, abundant acetyl-CoA and malonyl-CoA availability, and robust pentose phosphate pathway. This study aimed to engineer Y. lipolytica for resveratrol production. The resveratrol biosynthetic pathway was integrated into Y. lipolytica by adding genes encoding tyrosine ammonia lyase from Rhodotorula glutinis, 4-coumarate CoA ligase from Nicotiana tabacum, and stilbene synthase from Vitis vinifera. This resulted in the production of 14.3 mg/L resveratrol. A combination of endogenous and exogenous malonyl-CoA biosynthetic modules was introduced to enhance malonyl-CoA availability. This included genes encoding acetyl-CoA carboxylase 2 from Arabidopsis thaliana, malonyl-CoA synthase, and a malonate transporter protein from Bradyrhizobium diazoefficiens. These strategies increased resveratrol production to 51.8 mg/L. The further optimization of fermentation conditions and the utilization of sucrose as an effective carbon source in YP media enhanced the resveratrol concentration to 141 mg/L in flask fermentation. By combining these strategies, we achieved a titer of 400 mg/L resveratrol in a controlled fed-batch bioreactor. These findings demonstrate the efficacy of Y. lipolytica as a platform for the de novo production of resveratrol and highlight the importance of metabolic engineering, enhancing malonyl-CoA availability, and media optimization for improved resveratrol production.

Evaluation of stress tolerance and design of alternative culture media for the production of fermentation starter cultures in cacao

Ecuador is one of the world's leading producers of cacao beans, and Nacional x Trinitario cacao represents one of the most distinctive varieties due to its flavor and aroma characteristics. This study aimed to evaluate the effect of the starter culture isolated from microbial diversity during the spontaneous fermentation of Nacional x Trinitario cacao. A total of 249 microbial isolates were obtained from spontaneous culture, with Lactiplantibacillus (45 %), Saccharomyces (17 %), and Acetobacter (2 %) being the most relevant genera for fermentation. Tolerance tests were conducted to select microorganisms for the starter culture. Lactiplantibacillus plantarum exhibited the highest tolerance at pH 5 and 6 % ethanol and tolerated concentrations up to 15 % for glucose and fructose. Acetobacter pasteurianus grew at pH 2 and 6 % ethanol, tolerating high sugar concentrations of up to 15 % for glucose and 30 % for fructose, with growth observed in concentrations up to 5 % for lactic and acetic acid. Subsequently, a laboratory-scale fermentation was conducted with the formulated starter culture (SC) comprising S. cerevisiae, L. plantarum, and A. pasteurianus, which exhibited high tolerance to various stress conditions. The fermentation increased alcoholic compounds, including citrusy, fruity aromas, and floral notes such as 2-heptanol and phenylethyl alcohol, respectively 1.6-fold and 5.6-fold compared to the control. Moreover, the abundance of ketones 2-heptanone and 2-nonanone increased significantly, providing sweet green herbs and fruity woody aromas. Cacao fermented with this SC significantly enhanced the favorable aroma-producing metabolites characteristic of Fine-aroma cacao. These findings underscore the potential of tailored fermentation strategies to improve cacao product quality and sensory attributes, emphasizing the importance of ongoing research in optimizing fermentation processes for the cacao industry.

Dynamic regulation and cofactor engineering of escherichia coli to enhance production of glycolate from corn stover hydrolysate

Glycolic acid is widely employed in chemical cleaning, the production of polyglycolic acid-lactic acid, and polyglycolic acid. Currently, the bottleneck of glycolate biosynthesis lies on the imbalance of metabolic flux and the deficiency of NADPH. In this study, a dynamic regulation system was developed and optimized to enhance the metabolic flux from glucose to glycolate. Additionally, the knockout of transhydrogenase (sthA), along with the overexpression of pyridine nucleotide transhydrogenase (pntAB) and the implementation of the Entner-Doudoroff pathway, were performed to further increase the production of the NADPH, thereby increasing the titer of glycolate to 5.6 g/L. To produce glycolate from corn stover hydrolysate, carbon catabolite repression was alleviated and glucose utilization was accelerated. The final strain, E. coli Mgly10-245, is inducer-free, achieving a glycolate titer of 46.1 g/L using corn stover hydrolysate (77.1 % of theoretical yield). These findings will contribute to the advancement of industrial glycolate production.

Intermediate product control in cascade reaction for one-pot production of ε-caprolactone by Escherichia coli

ε-Caprolactone is an important non-toxic compound for polymer synthesis like polycaprolactone which has been widely used in drug delivery and degradable plastics. To meet the demand for a green economy, a bi-enzymatic cascade, consisting of an alcohol dehydrogenase (ADH) and a cyclohexanone monooxygenase (CHMO), was designed and introduced into Escherichia coli to synthesize ε-caprolactone from cyclohexanol with a self-sufficient NADPH-cofactor regeneration system. To further improve the catalytic efficiency, a carbonyl group-dependent colorimetric method using inexpensive 2,4-dinitrophenylhydrazine (DNPH) was developed for assay of cyclohexanone, an intermediate production of cascade reaction. It can be used to screen mutant strains with high catalytic efficiency from high-throughput library by detecting the absorbance value in microtiter plates (MTP) instead of gas chromatography (GC) analysis. Moreover, an RBS combinatorial library was constructed for balancing the expression of ADH and CHMO from two independent transcriptional units. After the high-throughput screening based on intermediate product control, an optimal variant with higher substrate tolerance and long-term stability was obtained from RBS combinatorial library. Through a fed-batch process, ε-caprolactone production reached 148.2 mM after 70 h of reaction under the optimized conditions, which was the highest yield achieved to date.

FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization

Overproduction of desired native or nonnative biochemical(s) in (micro)organisms can be achieved through metabolic engineering. Appropriate rewiring of cell metabolism is performed by making rational changes such as insertion, up-/down-regulation and knockout of genes and consequently metabolic reactions. Finding appropriate targets (including proper sets of reactions to be knocked out) for metabolic engineering to design optimal production strains has been the goal of a number of computational algorithms. We developed FastKnock, an efficient next-generation algorithm for identifying all possible knockout strategies (with a predefined maximum number of reaction deletions) for the growth-coupled overproduction of biochemical(s) of interest. We achieve this by developing a special depth-first traversal algorithm that allows us to prune the search space significantly. This leads to a drastic reduction in execution time. We evaluate the performance of the FastKnock algorithm using various Escherichia coli genome-scale metabolic models in different conditions (minimal and rich mediums) for the overproduction of a number of desired metabolites. FastKnock efficiently prunes the search space to less than 0.2% for quadruple- and 0.02% for quintuple-reaction knockouts. Compared to the classic approaches such as OptKnock and the state-of-the-art techniques such as MCSEnumerator methods, FastKnock found many more beneficial and important practical solutions. The availability of all the solutions provides the opportunity to further characterize, rank and select the most appropriate intervention strategy based on any desired evaluation index. Our implementation of the FastKnock method in Python is publicly available at https://github.com/leilahsn/FastKnock .

FastKnock: An efficient next-generation approach to identify all knockout strategies for strain optimization

Overproduction of desired native or nonnative biochemical(s) in (micro)organisms can be achieved through metabolic engineering. Appropriate rewiring of cell metabolism is performed making rational changes such as insertion, up-/down-regulation and knockout of genes and consequently metabolic reactions. Finding appropriate targets (including proper sets of reactions to be knocked out) for metabolic engineering to design optimal production strains has been the goal of a number of computational algorithms. We developed FastKnock, an efficient next-generation algorithm for identifying all possible knockout strategies for the growth-coupled overproduction of biochemical(s) of interest. We achieve this by developing a special depth-first traversal algorithm that allows us to prune the search space significantly. This leads to a drastic reduction in execution time. We evaluate the performance of the FastKnock algorithm using three Escherichia coli genome-scale metabolic models in different conditions (minimal and rich mediums) for the overproduction of a number of desired metabolites. FastKnock efficiently prunes the search space to less than 0.2% for quadruple and 0.02% for quintuple-reaction knockouts. Compared to the classic approaches such as OptKnock and the state-of-the-art techniques such as MCSEnumerator methods, FastKnock found many more useful and important practical solutions. The availability of all the solutions provides the opportunity to further characterize and select the most appropriate intervention strategy based on any desired evaluation index. Our implementation of the FastKnock method in Python is publicly available at https://github.com/leilahsn/FastKnock.

Promoting cell growth for bio-chemicals production via boosting the synthesis of L/D-alanine and D-alanyl-D-alanine in Bacillus licheniformis

Metabolic engineering is a substantial approach for escalating the production of biochemical products. Cell biomass is lowered by system constraints and toxication carried on by the aggregation of metabolites that serve as inhibitors of product synthesis. In order to increase the production of biochemical products, it is important to trace the relationship between alanine metabolism and biomass. According to our investigation, the appropriate concentration of additional L/D-alanine (0.1 g/L) raised the cell biomass (OD₆₀₀) in Bacillus licheniformis in contrast to the control strain. Remarkably, it was also determined that high levels of intracellular L/D-alanine and D-alanyl-D-alanine were induced by the overexpression of the ald, dal, and ddl genes to accelerate cell proliferation. Our findings clearly revealed that 0.2 g/L of L-alanine and D-alanine substantially elevated the titer of poly-γ-glutamic acid (γ-PGA) by 14.89% and 6.19%, correspondingly. And the levels of γ-PGA titer were hastened by the overexpression of the ald, dal, and ddl genes by 19.72%, 15.91%, and 16.64%, respectively. Furthermore, overexpression of ald, dal, and ddl genes decreased the by-products (acetoin, 2,3-butanediol, acetic acid and lactic acid) formation by about 14.10%, 8.77%, and 8.84% for augmenting the γ-PGA production. Our results also demonstrated that overexpression of ald gene amplified the production of lichenysin, pulcherrimin and nattokinase by about 18.71%, 19.82% and 21.49%, respectively. This work delineated the importance of the L/D-alanine and D-alanyl-D-alanine synthesis to the cell growth and the high production of bio-products, and provided an effective strategy for producing bio-products.

Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways

Platform chemicals and polymer precursors can be produced via enzymatic pathways starting from lignocellulosic waste materials. The hemicellulose fraction of lignocellulose contains aldopentose sugars, such as D-xylose and L-arabinose, which can be enzymatically converted into various biobased products by microbial non-phosphorylated oxidative pathways. The Weimberg and Dahms pathways convert pentose sugars into α-ketoglutarate, or pyruvate and glycolaldehyde, respectively, which then serve as precursors for further conversion into a wide range of industrial products. In this review, we summarize the known three-dimensional structures of the enzymes involved in oxidative non-phosphorylative pathways of pentose catabolism. Key structural features and reaction mechanisms of a diverse set of enzymes responsible for the catalytic steps in the reactions are analysed and discussed.

High-yield production of protopanaxadiol from sugarcane molasses by metabolically engineered Saccharomyces cerevisiae

Background

Ginsenosides are Panax plant-derived triterpenoid with wide applications in cardiovascular protection and immunity-boosting. However, the saponins content of Panax plants is fairly low, making it time-consuming and unsustainable by direct extraction. Protopanaxadiol (PPD) is a common precursor of dammarane-type saponins, and its sufficient supply is necessary for the efficient synthesis of ginsenoside.

Results

In this study, a combinational strategy was used for the construction of an efficient yeast cell factory for PPD production. Firstly, a PPD-producing strain was successfully constructed by modular engineering in Saccharomyces cerevisiae BY4742 at the multi-copy sites. Then, the INO2 gene, encoding a transcriptional activator of the phospholipid biosynthesis, was fine-tuned to promote the endoplasmic reticulum (ER) proliferation and improve the catalytic efficiency of ER-localized enzymes. To increase the metabolic flux of PPD, dynamic control, based on a carbon-source regulated promoter P_HXT1, was introduced to repress the competition of sterols. Furthermore, the global transcription factor UPC2-1 was introduced to sterol homeostasis and up-regulate the MVA pathway, and the resulting strain BY-V achieved a PPD production of 78.13 ± 0.38 mg/g DCW (563.60 ± 1.65 mg/L). Finally, sugarcane molasses was used as an inexpensive substrate for the first time in PPD synthesis. The PPD titers reached 1.55 ± 0.02 and 15.88 ± 0.65 g/L in shake flasks and a 5-L bioreactor, respectively. To the best of our knowledge, these results were new records on PPD production.

Conclusion

The high-level of PPD production in this study and the successful comprehensive utilization of low-cost carbon source -sugarcane molassesindicate that the constructed yeast cell factory is an excellent candidate strain for the production of high-value-added PPD and its derivativeswith great industrial potential.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01949-4.

Design of stable and self-regulated microbial consortia for chemical synthesis

Microbial coculture engineering has emerged as a promising strategy for biomanufacturing. Stability and self-regulation pose a significant challenge for the generation of intrinsically robust cocultures for large-scale applications. Here, we introduce the use of multi-metabolite cross-feeding (MMCF) to establish a close correlation between the strains and the design rules for selecting the appropriate metabolic branches. This leads to an intrinicially stable two-strain coculture where the population composition and the product titer are insensitive to the initial inoculation ratios. With an intermediate-responsive biosensor, the population of the microbial coculture is autonomously balanced to minimize intermediate accumulation. This static-dynamic strategy is extendable to three-strain cocultures, as demonstrated with de novo biosynthesis of silybin/isosilybin. This strategy is generally applicable, paving the way to the industrial application of microbial cocultures.

Stability and tunability are two desirable properties of microbial consortia-based bioproduction. Here, the authors integrate a caffeate-responsive biosensor into two and three strains coculture system to achieve autonomous regulation of strain ratios for coniferol and silybin/isosiltbin production, respectively.

Enhancing the degradation of Aflatoxin B1 by co-cultivation of two fungi strains with the improved production of detoxifying enzymes

After the co-culture of Aspergillus niger and Pleurotus ostreatus, the obtained extracellular crude enzymes solution was employed to aflatoxin B₁ (AFB₁) degradation. The maximum AFB₁ degradation with co-culture reached 93.4%, which increased by 65.9% and 37.6%, respectively, compared with those of the mono-culture of Pleurotus ostreatus and Aspergillus niger. The molecular weight of the key detoxifying enzymes isolated by ultrafiltration was 58 and 63 kDa by SDS-PAGE analysis. The purified detoxifying enzymes had a high detoxification effect on AFB₁ with the degradation rate of 94.7%. It was found that the co-culture of Pleurotus ostreatus and Aspergillus niger promoted the production of 58 and 63 kDa detoxifying enzymes to enhance the AFB₁ degradation. The chemical structure of major degradation products of AFB₁ by the mixed cultures were preliminarily identified by LC-Triple TOF MS. Two pathways of AFB₁ degradation were inferred with the high potential of fungal co-cultivations for AFB₁ detoxification applications.

CRISPR-based metabolic engineering in non-model microorganisms

Non-model microorganisms possess unique and versatile metabolic characteristics, offering great opportunities as cell factories for biosynthesis of target products. However, lack of efficient genetic tools for pathway engineering represents a big challenge to unlock the full production potential of these microbes. Over the past years, CRISPR systems have been extensively developed and applied to domesticate non-model microorganisms. In this paper, we summarize the current significant advances in designing and constructing CRISPR-mediated genetic modification systems in non-model microorganisms, such as bacteria, fungi and cyanobacteria. We particularly put emphasis on reviewing some successful implementations in metabolic pathway engineering via CRISPR-based genome editing tools. Moreover, the current barriers and future perspectives on improving the editing efficiency of CRISPR systems in non-model microorganisms are also discussed.

Integration of GWAS, metabolomics, and sensorial analyses to reveal novel metabolic pathways involved in cocoa fruity aroma GWAS of fruity aroma in Theobroma cacao

Nacional is a variety of cocoa tree known for its "Arriba" aroma characterised mainly by fruity, floral, and spicy aromatic notes. In this study, the genetic basis of the fruity aroma of modern Nacional cocoa was investigated. GWAS studies have been conducted on biochemical and sensorial fruity traits and allowed to identify a large number of association zones. These areas are linked to both the volatile compounds known to provide fruity flavours and present in the beans before and after roasting, and to the fruity notes detected by sensorial analysis. Five main metabolic pathways were identified as involved in the fruity traits of the Nacional population: the protein degradation pathway, the sugar degradation pathway, the fatty acid degradation pathway, the monoterpene pathway, and the L-phenylalanine pathway. Candidate genes involved in the biosynthetic pathways of volatile compounds identified in association areas were detected for a large number of associations.

Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19

The present global COVID-19 pandemic caused by the noble pleomorphic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a vulnerable situation in the global healthcare and economy. In this pandemic situation, researchers all around the world are trying their level best to find suitable therapeutics from various sources to combat against the SARS-CoV-2. To date, numerous bioactive compounds from different sources have been tested to control many viral diseases. However, microbial metabolites are advantageous for drug development over metabolites from other sources. We herein retrieved and reviewed literatures from PubMed, Scopus and Google relevant to antiviral microbial metabolites by searching with the keywords "antiviral microbial metabolites," "microbial metabolite against virus," "microorganism with antiviral activity," "antiviral medicine from microbial metabolite," "antiviral bacterial metabolites," "antiviral fungal metabolites," "antiviral metabolites from microscopic algae' and so on. For the same purpose, the keywords "microbial metabolites against COVID-19 and SARS-CoV-2" and "plant metabolites against COVID-19 and SARS-CoV-2" were used. Only the full text literatures available in English and pertinent to the topic have been included and those which are not available as full text in English and pertinent to antiviral or anti-SARS-CoV-2 activity were excluded. In this review, we have accumulated microbial metabolites that can be used as antiviral agents against a broad range of viruses including SARS-CoV-2. Based on this concept, we have included 330 antiviral microbial metabolites so far available to date in the data bases and were previously isolated from fungi, bacteria and microalgae. The microbial source, chemical nature, targeted viruses, mechanism of actions and IC50/EC50 values of these metabolites are discussed although mechanisms of actions of many of them are not yet elucidated. Among these antiviral microbial metabolites, some compounds might be very potential against many other viruses including coronaviruses. However, these potential microbial metabolites need further research to be developed as effective antiviral drugs. This paper may provide the scientific community with the possible secret of microbial metabolites that could be an effective source of novel antiviral drugs to fight against many viruses including SARS-CoV-2 as well as the future viral pandemics.

Metabolic engineering for the production of butanol, a potential advanced biofuel, from renewable resources

Butanol is an important chemical and potential fuel. For more than 100 years, acetone-butanol-ethanol (ABE) fermentation of Clostridium strains has been the most successful process for biological butanol production. In recent years, other microbes have been engineered to produce butanol as well, among which Escherichia coli was the best one. Considering the crude oil price fluctuation, minimizing the cost of butanol production is of highest priority for its industrial application. Therefore, using cheaper feedstocks instead of pure sugars is an important project. In this review, we summarized butanol production from different renewable resources, such as industrial and food waste, lignocellulosic biomass, syngas and other renewable resources. This review will present the current progress in this field and provide insights for further engineering efforts on renewable butanol production.

Medium supplementation and thorough optimization to induce carboxymethyl cellulase production by Trichoderma reesei under solid state fermentation of nettle biomass

In the present study, the production of cellulase by Trichoderma reesei under solid-state fermentation of nettle biomass was promoted through supplementation of the culture media using carbonaceous additives and comprehensive optimization of the cultivation via the Taguchi method. CMCase activities about 5.5-6.1 U/gds were obtained by fermentation of the autoclave-pretreated biomass, among various chemical and physical pretreatments. Then, several additives including Tween 80, betaine, carboxymethyl cellulose, and lactose were individually or in combination added to the culture media to induce the enzyme production. The results proved that such additives could act as either inducers or inhibitors. Furthermore, CMCase activity surprisingly increased to 14.0 U/gds by supplementing the fermentation medium with the optimal mixture of additives including 0.08 mg/gds Tween 80, 0.4 mg/gds betaine, and 0.2 mg/gds carboxymethyl cellulose. Factor screening according to Plackett-Burman design confirmed that the levels of Urea and MgSO₄ among basal medium constituents as well as pH of the medium were significantly affected CMCase production. By optimizing the levels of these factors, CMCase activity of 18.8 U/gds was obtained, which was noticeably higher than that of fermentation of the raw nettle. The applied procedure can be promisingly used to convert the nettle biomass into valuable products.

Co-Cultivation of Two Bacillus Strains for Improved Cell Growth and Enzyme Production to Enhance the Degradation of Aflatoxin B1

Bacillus sp. H16v8 and Bacillus sp. HGD9229 were identified as Aflatoxin B₁ (AFB₁) degrader in nutrient broth after a 12 h incubation at 37 °C. The degradation efficiency of the two-strain supernatant on 100 μg/L AFB₁ was higher than the bacterial cells and cell lysate. Moreover, degradations of AFB₁ were strongly affected by the metal ions in which Cu²⁺ stimulated the degradation and Zn²⁺ inhibited the degradation. The extracellular detoxifying enzymes produced by co-cultivation of two strains were isolated and purified by ultrafiltration. The molecular weight range of the detoxifying enzymes was 20-25 kDa by SDS-PAGE. The co-culture of two strains improved the total cell growth with the enhancement of the total protein content and detoxifying enzyme production. The degradation efficiency of the supernatant from mixed cultures increased by 87.7% and 55.3% compared to Bacillus sp. H16v8 and HGD9229, individually. Moreover, after the degradation of AFB₁, the four products of the lower toxicity were identified by LC-Triple TOF-MS with the two proposed hypothetical degradation pathways.

Resveratrol Production in Yeast Hosts: Current Status and Perspectives

Resveratrol is a plant secondary metabolite known for its therapeutic applications as an antioxidant, anti-cancer, anti-inflammatory, anti-aging, cardio-protective, and neuroprotective agent. Topical formulas of resveratrol are also used for skin disease management and in cosmetic industries. Due to its importance, high resveratrol production is urgently required. Since the last decade, intensive efforts have been devoted to obtaining resveratrol from microorganisms by pathway and metabolic engineering. Yeasts were proven to be excellent host candidates for resveratrol production. In addition to the similar intracellular compartments between yeasts and plants, yeasts exhibit the ability to express genes coding for plant-derived enzymes and to perform post-translational modification. Therefore, this review summarizes the attempts to use yeasts as a platform for resveratrol synthesis as the next promising route in producing high titers of resveratrol from genetically engineered strains.

Electrospun nanofibers enhance trehalose synthesis by regulating gene expression for Micrococcus luteus fermentation

In this study, mesoporous polyacrylonitrile (PAN)/thermoplastic polyurethane (TPU) blended nanofibers were prepared to immobilize Micrococcus luteus for enhancing the conversion of trehalose. The images of SEM showed the cells were adsorbed on the surface and pores due to the unique pore structure. The results of contact angle, Zeta potential and water holding ratio exhibited the good hydrophilicity and stability of PAN/TPU-P2. Besides, it was indicated that the biomass and immobilization efficiency were increased to 0.633 g/L and 0.153 g/g, respectively. It was the most noteworthy that the trehalose yield could reach 23.46 g/L, which was 71.62 % higher than that of the control in the multi-batch fermentation. Moreover, the reactive oxygen species (ROS) level was decreased to 12.8 % while the enzyme concentration was increased to 11.176 mg/mL. Meanwhile, it was also found that PAN/TPU-P2 immobilization substantially increased the expression of target gene MtreY by 3.500 times. In other words, the mechanism by which immobilized cells increased trehalose yield was that PAN/TPU-P regulated gene expression of MtreY. Therefore, this research provided theoretical foundation for the metabolic regulation of sufficient trehalose production by immobilized cells.

Development of antisense RNA-mediated quantifiable inhibition for metabolic regulation

Trans-regulating elements such as noncoding RNAs are crucial in modifying cells, and has shown broad application in synthetic biology, metabolic engineering and RNA therapies. Although effective, titration of the regulatory levels of such elements is less explored. Encouraged by the need of fine-tuning cellular functions, we studied key parameters of the antisense RNA design including oligonucleotide length, targeting region and relative dosage to achieve differentiated inhibition. We determined a 30-nucleotide configuration that renders efficient and robust inhibition. We found that by targeting the core RBS region proportionally, quantifiable inhibition levels can be rationally obtained. A mathematic model was established accordingly with refined energy terms and successfully validated by depicting the inhibition levels for genomic targets. Additionally, we applied this fine-tuning approach for 4-hydroxycoumarin biosynthesis by simultaneous and quantifiable knockdown of multiple targets, resulting in a 3.58-fold increase in titer of the engineered strain comparing to that of the non-regulated. We believe the developed tool is broadly compatible and provides an extra layer of control in modifying living systems.

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Achieved quantifiable asRNA inhibition by varying core RBS coverage.

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Developed and validated a mathematical model for quantifiable inhibition.

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Improved 4-hydroxycoumarin biosynthesis by 3.58 folds with multiplexed inhibition.

Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics

Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.

Piceatannol Inhibits P. acnes-Induced Keratinocyte Proliferation and Migration by Downregulating Oxidative Stress and the Inflammatory Response

The Cutibacterium acnes (also called Propionibacterium acnes, P. acnes)-induced proliferation and migration of keratinocytes contribute to acne vulgaris (AV), which is a common inflammatory skin disease that causes physical and psychological impairments. Piceatannol (3, 5, 3', 4'-tetrahydroxy-trans-stilbene, PCT) is naturally present in many human diets and plays antioxidant and anti-inflammatory roles that inhibit cell proliferation and migration. We aimed to analyse the functions and underlying mechanisms of PCT in P. acnes-stimulated keratinocytes. First, PCT showed no toxicity against the normal human keratinocyte cell line HaCaT but inhibited P. acnes-induced HaCaT cell proliferation. Next, PCT promoted the nuclear translocation and target gene transcription of the antioxidant transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2), thereafter decreasing intracellular reactive oxygen species (ROS) levels. In addition, PCT inhibited the nuclear translocation of p65 [a subunit of nuclear factor kappa B (NF-κB)] and the secretion of pro-inflammatory cytokines, including interleukin-6 (IL-6), tumour necrosis factor-α (TNF-α) and interleukin-8 (IL-8). Finally, a transfection assay showed that PCT inhibited P. acnes-induced HaCaT cell proliferation and migration by activating the antioxidant Nrf2 pathway and inhibiting the inflammatory NF-κB pathway. Our data suggested that PCT alleviated P. acnes-induced HaCaT cell proliferation and migration through its antioxidant and anti-inflammatory roles, suggesting the potential of PCT to treat AV.

Bioactive molecules from protists: Perspectives in biotechnology

For hundreds of years, mankind has benefited from the natural metabolic processes of microorganisms to obtain basic products such as fermented foods and alcoholic beverages. More recently, microorganisms have been exploited for the production of antibiotics, vitamins and enzymes to be used in medicine and chemical industries. Additionally, several modern drugs, including those for cancer therapy, are natural products or their derivatives. Protists are a still underexplored source of natural products potentially of interest for biotechnological and biomedical applications. This paper focuses on some examples of bioactive molecules from protists and associated bacteria and their possible use in biotechnology.

Light-powered Escherichia coli cell division for chemical production

Cell division can perturb the metabolic performance of industrial microbes. The C period of cell division starts from the initiation to the termination of DNA replication, whereas the D period is the bacterial division process. Here, we first shorten the C and D periods of E. coli by controlling the expression of the ribonucleotide reductase NrdAB and division proteins FtsZA through blue light and near-infrared light activation, respectively. It increases the specific surface area to 3.7 μm⁻¹ and acetoin titer to 67.2 g·L⁻¹. Next, we prolong the C and D periods of E. coli by regulating the expression of the ribonucleotide reductase NrdA and division protein inhibitor SulA through blue light activation-repression and near-infrared (NIR) light activation, respectively. It improves the cell volume to 52.6 μm³ and poly(lactate-co-3-hydroxybutyrate) titer to 14.31 g·L⁻¹. Thus, the optogenetic-based cell division regulation strategy can improve the efficiency of microbial cell factories.

Manipulation of genes controlling microbial shapes can affect bio-production. Here, the authors employ an optogenetic method to realize dynamic morphological engineering of E. coli replication and division and show the increased production of acetoin and poly(lactate-co-3-hydroxybutyrate).

An overview of the bacterial SsrA system modulating intracellular protein levels and activities

In bacteria, the truncated forms of mRNAs, which usually lack a stop codon, are occasionally generated by premature termination of gene transcription and/or endo- or exonucleolytic cleavage events. Ribosomes proceeding on these molecules stall at the 3' end of the chain and are rescued by a widely distributed mechanism known as trans-translation, which includes two essential elements, ssrA RNA (a special RNA) and SmpB (a small protein). Through this mechanism, the polypeptides translated from truncated mRNAs are marked by a short peptide, known as SsrA tag, at their C-termini and directed to the specific endogenous proteases for C-terminal proteolysis. Based on the deep understanding of the SsrA tagging and degradation mechanisms, recently a series of SsrA-based genetic tools have been developed for gene regulation on the level of post-translation. They are successfully applied for controllable regulation of biological circuits in bacteria. In the present article, we systematically summarize the history, structural characteristics, and functional mechanisms of the SsrA tagging and degrading machineries, as well as their technical uses and limitations.Key Points• SsrA system plays an important role in ribosome rescue in bacteria.• SsrA-based genetic tools are useful for controlling protein levels and activities.

Bioprocess Optimization for the Production of Aromatic Compounds With Metabolically Engineered Hosts: Recent Developments and Future Challenges

The most common route to produce aromatic chemicals - organic compounds containing at least one benzene ring in their structure - is chemical synthesis. These processes, usually starting from an extracted fossil oil molecule such as benzene, toluene, or xylene, are highly environmentally unfriendly due to the use of non-renewable raw materials, high energy consumption and the usual production of toxic by-products. An alternative way to produce aromatic compounds is extraction from plants. These extractions typically have a low yield and a high purification cost. This motivates the search for alternative platforms to produce aromatic compounds through low-cost and environmentally friendly processes. Microorganisms are able to synthesize aromatic amino acids through the shikimate pathway. The construction of microbial cell factories able to produce the desired molecule from renewable feedstock becomes a promising alternative. This review article focuses on the recent advances in microbial production of aromatic products, with a special emphasis on metabolic engineering strategies, as well as bioprocess optimization. The recent combination of these two techniques has resulted in the development of several alternative processes to produce phenylpropanoids, aromatic alcohols, phenolic aldehydes, and others. Chemical species that were unavailable for human consumption due to the high cost and/or high environmental impact of their production, have now become accessible.

Stimulus response-based fine-tuning of polyhydroxyalkanoate pathway in Halomonas

Optimization of intracellular biosynthesis process involving regulation of multiple gene expressions is dependent on the efficient and accurate expression of each expression unit independently. However, challenges of analyzing intermediate products seriously hinder the application of high throughput assays. This study aimed to develop an engineering approach for unsterile production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) or (P3HB4HB) by recombinant Halomonas bluephagenesis (H. bluephagenesis) constructed via coupling the design of GFP-mediated transcriptional mapping and high-resolution control of gene expressions (HRCGE), which consists of two inducible systems with high- and low-dynamic ranges employed to search the exquisite transcription level of each expression module in the presence of γ-butyrolactone, the intermediate for 4-hydroxybutyrate (4HB) synthesis. It has been successful to generate a recombinant H. bluephagenesis, namely TD68-194, able to produce over 36 g/L P3HB4HB consisting of 16 mol% 4HB during a 7-L lab-scale fed-batch growth process, of which cell dry weight and PHA content reached up to 48.22 g/L and 74.67%, respectively, in 36 h cultivation. HRCGE has been found useful for metabolic pathway construction.

Tailoring of microbes for the production of high value plant-derived compounds: From pathway engineering to fermentative production

Plant natural products have been an attracting platform for the isolation of various active drugs and other bioactives. However large-scale extraction of these compounds is affected by the difficulty in mass cultivation of these plants and absence of strategies for successful extraction. Even though, synthesis by chemical method is an alternative method; it is less efficient as their chemical structure is highly complex which involve enantio-selectivity. Thus an alternate bio-system for heterologous production of plant natural products using microbes has emerged. Advent of various omics, synthetic and metabolic engineering strategies revolutionised the field of heterologous plant metabolite production. In this context, various engineering methods taken to synthesise plant natural products are described with an additional focus to fermentation strategies.

Developing a pyruvate-driven metabolic scenario for growth-coupled microbial production

Microbial-based chemical synthesis serves as a promising approach for sustainable production of industrially important products. However, limited production performance caused by metabolic burden or genetic variations poses one of the major challenges in achieving an economically viable biomanufacturing process. To address this issue, one superior strategy is to couple the product synthesis with cellular growth, which renders production obligatory for cell survival. Here we create a pyruvate-driven metabolic scenario in engineered Escherichia coli for growth-coupled bioproduction, with which we demonstrate its application in boosting production of anthranilate and its derivatives. Deletion of a minimal set of endogenous pyruvate-releasing pathways engenders anthranilate synthesis as the salvage route for pyruvate generation to support cell growth, concomitant with simultaneous anthranilate production. Further introduction of native and non-native downstream pathways affords production enhancement of two anthranilate-derived high-value products including L-tryptophan and cis, cis-muconic acid from different carbon sources. The work reported here presents a new growth-coupled strategy with demonstrated feasibility for promoting microbial production.