Maximizing the Efficiency of Vanillin Production by Biocatalyst Enhancement and Process Optimization

Efficient synthesis of vanillylamine through bioamination of lignin-derived vanillin by recombinant E. coli containing ω-transaminase from Caulobacter sp. D5 in dimethyl sulfoxide-water

Lignin is a plentiful and readily accessible renewable resource. Vanillylamine is a crucial raw material used to synthesize pharmaceuticals and high-value furan compounds that can be acquired by aminating lignin-derived vanillin (Van). However, effectually achieving the biocatalytic synthesis of vanillylamine has remained challenging. In this study, a dimethyl sulfoxide (DMSO)-H2O (1:9, vol/vol) bioreaction medium was constructed, and a recombinant E. coli ATA1012 carrying ω-transaminase from Caulobacter sp. D5 was used as the ω-transaminase biocatalyst to acquire the effectual biocatalytic synthesis of vanillylamine. Under optimized bioreaction conditions (37 ℃ and pH 7.5) by supplementary of isopropylamine (IPA) (Van/IPA = 1:5, mol/mol), 80-100 mM Van could be effectually converted by ATA1012 whole cells in DMSO-H2O (1:9, vol/vol) within 12 h, yielding 91.2 %-95.4 % vanillylamine, with >99 % selectivity. An efficient amination process was developed using ATA1012 with superior transaminase catalytic activity and substrate tolerance to effectively convert Van to vanillylamine in a DMSO-H2O medium.

Optimizing bio-vanillin synthesis from ferulic acid via Pediococcus acidilactici: A systematic approach to process enhancement and yield maximization

The use of lignocellulosic biomass to create natural flavor has drawn attention from researchers. A key flavoring ingredient that is frequently utilized in the food industry is vanillin. In this present study, Pediococcus acidilactici PA VIT effectively involved in the production of bio-vanillin by using Ferulic acid as an intermediate with a yield of 11.43 µg/mL. The bio-vanillin produced by Pediococcus acidilactici PA VIT was examined using FTIR, XRD, HPLC, and SEM techniques. These characterizations exhibited a unique fingerprinting signature like that of standard vanillin. Additionally, the one variable at a time method, placket Burmann method, and response surface approach, were employed to optimize bio-vanillin. Based on the central composite rotary design, the most important process factors were determined such as agitation speed, substrate concentration, and inoculum size. After optimization, bio-vanillin was found to have tenfold increase, with a maximum yield of 376.4 µg/mL obtained using the response surface approach. The kinetic study was performed to analyze rate of reaction and effect of metal ions in the production of bio-vanillin showing Km of 10.25, and Vmax of 1250 were required for the reaction. The metal ions that enhance the yield of bio-vanillin are Ca2+, k+, and Mg2+ and the metal ions that affects the yield of bio-vanillin are Pb+ and Cr+ were identified from the effect of metal ions in the bio-vanillin production.

Construction of a Novel Vanillin-Induced Autoregulating Bidirectional Transport System in a Vanillin-Producing E. coli Cell Factory

Vanillin is one of the world's most extensively used flavoring agents with high application value. However, the yield of vanillin biosynthesis remains limited due to the low efficiency of substrate uptake and the inhibitory effect on cell growth caused by vanillin. Here, we screened high-efficiency ferulic acid importer TodX and vanillin exporters PP_0178 and PP_0179 by overexpressing genes encoding candidate transporters in a vanillin-producing engineered Escherichia coli strain VA and further constructed an autoregulatory bidirectional transport system by coexpressing TodX and PP_0178/PP_0179 with a vanillin self-inducible promoter ADH7. Compared with strain VA, strain VA-TodX-PP_0179 can efficiently transport ferulic acid across the cell membrane and convert it to vanillin, which significantly increases the substrate utilization rate efficiency (14.86%) and vanillin titer (51.07%). This study demonstrated that the autoregulatory bidirectional transport system significantly enhances the substrate uptake efficiency while alleviating the vanillin toxicity issue, providing a promising viable route for vanillin biosynthesis.

A comprehensive review of eclectic approaches to the biological synthesis of vanillin and their application towards the food sector

Vanillin, a highly regarded flavor compound, has earned widespread recognition for its natural and aromatic qualities, piquing substantial interest in the scientific community. This comprehensive review delves deeply into the intricate world of vanillin synthesis, encompassing a wide spectrum of methodologies, including enzymatic, microbial, and immobilized systems. This investigation provides a thorough analysis of the precursors of vanillin and also offers a comprehensive overview of its transformation through these diverse processes, making it an invaluable resource for researchers and enthusiasts alike. The elucidation of different substrates such as ferulic acid, eugenol, veratraldehyde, vanillic acid, glucovanillin, and C6-C3 phenylpropanoids adds a layer of depth and insight to the understanding of vanillin synthesis. Moreover, this comprehensive review explores the multifaceted applications of vanillin within the food industry. While commonly known as a flavoring agent, vanillin transcends this role by finding extensive use in food preservation and food packaging. The review meticulously examines the remarkable preservative properties of vanillin, providing a profound understanding of its crucial role in the culinary and food science sectors, thus making it an indispensable reference for professionals and researchers in these domains.

Graphical abstract

Biotransformation of maize bran-derived ferulic acid to vanillin using an adapted strain of Amycolatopsis sp. ATCC 39116

Maize bran, an agro-processing waste residue, is a good source of ferulic acid that can be further valorized for vanillin production. However, extraction of ferulic acid from natural sources has been challenging due to low concentrations and intensive extraction procedures. In the present work, ferulic acid streams (purities ranging from 5% to 75%) extracted from maize bran using thermochemical methods were evaluated for biotransformation to vanillin, employing Amycolatopsis sp. as a whole-cell biocatalyst. Initial adaptation studies were critical in improving ferulic acid assimilation and its conversion to vanillin by 65% and 56%, respectively by the fourth adaptation cycle. The effect of cell's physiological states and vanillic acid supplementation on vanillin production was studied using standard ferulic acid as a substrate in an effort to achieve further improvement in vanillin yield. In the presence of vanillic acid, 18 h cultured cells using 2 g/L of standard and isolated ferulic acid produced vanillin concentrations of up to 0.71 and 0.48 g/L, respectively. Furthermore, intermediates involved in the ferulic acid catabolic pathway and their interrelations were studied using GC-MS analysis. Results indicated that two different routes were involved in the catabolism of standard ferulic acid, and similar metabolic routes were observed for an isolated ferulic acid stream. These findings effectively evaluated isolated ferulic acid for sustainable vanillin production while reducing agro-industrial waste pollution.

Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production

Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.

The Scent of Change: Sustainable Fragrances Through Industrial Biotechnology

Current environmental and safety considerations urge innovation to address the need for sustainable high-value chemicals that are embraced by consumers. This review discusses the concept of sustainable fragrances, as high-value, everyday and everywhere chemicals. Current and emerging technologies represent an opportunity to produce fragrances in an environmentally and socially responsible way. Biotechnology, including fermentation, biocatalysis, and genetic engineering, has the potential to reduce the environmental footprint of fragrance production while maintaining quality and consistency. Computational and in silico methods, including machine learning (ML), are also likely to augment the capabilities of sustainable fragrance production. Continued innovation and collaboration will be crucial to the future of sustainable fragrances, with a focus on developing novel sustainable ingredients, as well as ethical sourcing practices.

Microbial Secondary Metabolites via Fermentation Approaches for Dietary Supplementation Formulations

Food supplementation formulations refer to products that are designed to provide additional nutrients to the diet. Vitamins, dietary fibers, minerals and other functional compounds (such as antioxidants) are concentrated in dietary supplements. Specific amounts of dietary compounds are given to the body through food supplements, and these include as well so-called non-essential compounds such as secondary plant bioactive components or microbial natural products in addition to nutrients in the narrower sense. A significant social challenge represents how to moderately use the natural resources in light of the growing world population. In terms of economic production of (especially natural) bioactive molecules, ways of white biotechnology production with various microorganisms have recently been intensively explored. In the current review other relevant dietary supplements and natural substances (e.g., vitamins, amino acids, antioxidants) used in production of dietary supplements formulations and their microbial natural production via fermentative biotechnological approaches are briefly reviewed. Biotechnology plays a crucial role in optimizing fermentation conditions to maximize the yield and quality of the target compounds. Advantages of microbial production include the ability to use renewable feedstocks, high production yields, and the potential for cost-effective large-scale production. Additionally, it can be more environmentally friendly compared to chemical synthesis, as it reduces the reliance on petrochemicals and minimizes waste generation. Educating consumers about the benefits, safety, and production methods of microbial products in general is crucial. Providing clear and accurate information about the science behind microbial production can help address any concerns or misconceptions consumers may have.

Bio-Based Valorization of Lignin-Derived Phenolic Compounds: A Review

Lignins are the most abundant biopolymers that consist of aromatic units. Lignins are obtained by fractionation of lignocellulose in the form of "technical lignins". The depolymerization (conversion) of lignin and the treatment of depolymerized lignin are challenging processes due to the complexity and resistance of lignins. Progress toward mild work-up of lignins has been discussed in numerous reviews. The next step in the valorization of lignin is the conversion of lignin-based monomers, which are limited in number, into a wider range of bulk and fine chemicals. These reactions may need chemicals, catalysts, solvents, or energy from fossil resources. This is counterintuitive to green, sustainable chemistry. Therefore, in this review, we focus on biocatalyzed reactions of lignin monomers, e.g., vanillin, vanillic acid, syringaldehyde, guaiacols, (iso)eugenol, ferulic acid, p-coumaric acid, and alkylphenols. For each monomer, its production from lignin or lignocellulose is summarized, and, mainly, its biotransformations that provide useful chemicals are discussed. The technological maturity of these processes is characterized based on, e.g., scale, volumetric productivities, or isolated yields. The biocatalyzed reactions are compared with their chemically catalyzed counterparts if the latter are available.

Combining genetic engineering and bioprocess concepts for improved phenylpropanoid production

The group of natural aromatic compounds known as phenylpropanoids has diverse applications, but current methods of production which are largely based on synthesis from petrochemicals or extraction from agricultural biomass are unsustainable. Bioprocessing is a promising alternative, but improvements in production titers and rates are required to make this method profitable. Here the recent advances in genetic engineering and bioprocess concepts for the production of phenylpropanoids are presented for the purpose of identifying successful strategies, including adaptive laboratory evolution, enzyme engineering, in-situ product removal, and biocatalysis. The pros and cons of bacterial and yeast hosts for phenylpropanoid production are discussed, also in the context of different phenylpropanoid targets and bioprocess concepts. Finally, some broad recommendations are made regarding targets for continued improvement and areas requiring specific attention from researchers to further improve production titers and rates.

Optimization of the growth conditions through response surface methodology and metabolomics for maximizing the auxin production by Pantoea agglomerans C1

Introduction

The fermentative production of auxin/indole 3-acetate (IAA) using selected Pantoea agglomerans strains can be a promising approach to developing novel plant biostimulants for agriculture use.

Methods

By integrating metabolomics and fermentation technologies, this study aimed to define the optimal culture conditions to obtain auxin/IAA-enriched plant postbiotics using P. agglomerans strain C1. Metabolomics analysis allowed us to demonstrate that the production of a selected.

Results and discussion

Array of compounds with plant growth-promoting- (IAA and hypoxanthine) and biocontrol activity (NS-5, cyclohexanone, homo-L-arginine, methyl hexadecenoic acid, and indole-3-carbinol) can be stimulated by cultivating this strain on minimal saline medium amended with sucrose as a carbon source. We applied a three-level-two-factor central composite design (CCD) based response surface methodology (RSM) to explore the impact of the independent variables (rotation speed and medium liquid-to-flask volume ratio) on the production of IAA and IAA precursors. The ANOVA component of the CCD indicated that all the process-independent variables investigated significantly impacted the auxin/IAA production by P. agglomerans strain C1. The optimum values of variables were a rotation speed of 180 rpm and a medium liquid-to-flask volume ratio of 1:10. Using the CCD-RSM method, we obtained a maximum indole auxin production of 208.3 ± 0.4  mg IAA_equ/L, which was a 40% increase compared to the growth conditions used in previous studies. Targeted metabolomics allowed us to demonstrate that the IAA product selectivity and the accumulation of the IAA precursor indole-3-pyruvic acid were significantly affected by the increase in the rotation speed and the aeration efficiency.

Process optimization of vanillin production by conversion of ferulic acid by Bacillus megaterium

BACKGROUND

Vanillin is an important flavoring and aromatic ingredient found mainly in the pods of the tropical plant vanilla and is widely used in the food industry. Attempts have been made to produce vanillin from ferulic acid esters in agricultural residues of wheat bran.

RESULTS

The results showed that a strain with high tolerance to the substrate ferulic acid was isolated and screened from soil and identified as belonging to the genus Bacillus (Bacillus megaterium). The concentration of vanillin produced by this strain was 0.048 g L^-1 , and the molar conversion of vanillin was 12.25%. The production of vanillin was optimized by orthogonal experiments. Beef pastes 6.0 g L^-1 , soybean meal 5.0 g L^-1 , magnesium sulfate heptahydrate 1.0 g L^-1 , iron(II) sulfate heptahydrate 1.0 g L^-1 , calcium chloride 1.0 g L^-1 , dipotassium hydrogen phosphate trihydrate 1.0 g L^-1 ; fermentation culture conditions were pH 7.0, inoculum level 5%, loading volume 20%, ferulic acid 1.0 g L^-1 , fermentation culture temperature 35 °C. The concentration of vanillin obtained was 0.218 g L^-1 . Finally, transcriptomic analysis of the strain samples before and after the optimization of the fermentation conditions was carried out to study the effect of the optimization of the fermentation conditions on the concentration of vanillin produced by the strain.

CONCLUSION

This study provides a theoretical basis for further improving the yield of vanillin and gradually realizing efficient industrial production. © 2022 Society of Chemical Industry.

Engineering plant family TPS into cyanobacterial host for terpenoids production

Terpenoids are synthesized naturally by plants as secondary metabolites, and are diverse and complex in structure with multiple applications in bioenergy, food, cosmetics, and medicine. This makes the production of terpenoids such as isoprene, β-phellandrene, farnesene, amorphadiene, and squalene valuable, owing to which their industrial demand cannot be fulfilled exclusively by plant sources. They are synthesized via the Methylerythritol phosphate pathway (MEP) and the Mevalonate pathway (MVA), both existing in plants. The advent of genetic engineering and the latest accomplishments in synthetic biology and metabolic engineering allow microbial synthesis of terpenoids. Cyanobacteria manifest to be the promising hosts for this, utilizing sunlight and CO₂. Cyanobacteria possess MEP pathway to generate precursors for terpenoid synthesis. The terpenoid synthesis can be amplified by overexpressing the MEP pathway and engineering MVA pathway genes. According to the desired terpenoid, terpene synthases unique to the plant kingdom must be incorporated in cyanobacteria. Engineering an organism to be used as a cell factory comes with drawbacks such as hampered cell growth and disturbance in metabolic flux. This review set forth a comparison between MEP and MVA pathways, strategies to overexpress these pathways with their challenges.

Engineering a Feruloyl-Coenzyme A Synthase for Bioconversion of Phenylpropanoid Acids into High-Value Aromatic Aldehydes

Aromatic aldehydes find extensive applications in food, perfume, pharmaceutical, and chemical industries. However, a limited natural enzyme selectivity has become the bottleneck of bioconversion of aromatic aldehydes from natural phenylpropanoid acids. Here, based on the original structure of feruloyl-coenzyme A (CoA) synthetase (FCS) from Streptomyces sp. V-1, we engineered five substrate-binding domains to match specific phenylpropanoid acids. FcsCIA^E407A/K483L, FcsMA^{E407R/I481R/K483R}, FcsHA^{E407K/I481K/K483I}, FcsCA^{E407R/I481R/K483T}, and FcsFA^{E407R/I481K/K483R} showed 9.96-, 10.58-, 4.25-, 6.49-, and 8.71-fold enhanced catalytic efficiency for degrading CoA thioesters of cinnamic acid, 4-methoxycinnamic acid, 4-hydroxycinnamic acid, caffeic acid, and ferulic acid, respectively. Molecular dynamics simulation illustrated that novel substrate-binding domains formed strong interaction forces with substrates' methoxy/hydroxyl group and provided hydrophobic/alkaline catalytic surfaces. Five recombinant E. coli with FCS mutants were constructed with the maximum benzaldehyde, p-anisaldehyde, p-hydroxybenzaldehyde, protocatechualdehyde, and vanillin productivity of 6.2 ± 0.3, 5.1 ± 0.23, 4.1 ± 0.25, 7.1 ± 0.3, and 8.7 ± 0.2 mM/h, respectively. Hence, our study provided novel and efficient enzymes for the bioconversion of phenylpropanoid acids into aromatic aldehydes.

High-throughput colorimetric assays optimized for detection of ketones and aldehydes produced by microbial cell factories

Randomized strain and pathway engineering are critical to improving microbial cell factory performance, calling for the development of high‐throughput screening and selection systems. To facilitate this effort, we have developed two 96‐well plate format colorimetric assays for reliable quantification of various ketones and aldehydes from culture supernatants, based on either a vanillin‐acetone reaction or the 2,4‐dinitrophenylhydrazine (2,4‐DNPH) reagent. The vanillin‐acetone assay enabled accurate and selective measurement of acetone titers up to 2 g l⁻¹ in a minimal culture medium. The 2,4‐DNPH‐based assay can be used for a wide range of aldehydes and ketones, shown here through the optimization of conditions for 15 different compounds. Both assays were implemented to improve acetone production from different substrates by an engineered Escherichia coli strain. The fast and user‐friendly colorimetric assays proposed here open the potential for iterative rounds of (automated) strain and pathway engineering and screening, facilitating the efforts towards further boosting production titers of industrially relevant ketones and aldehydes.

Biotechnological production of specialty aromatic and aromatic-derivative compounds

Aromatic compounds are an important class of chemicals with different industrial applications. They are usually produced by chemical synthesis from petroleum-derived feedstocks, such as toluene, xylene and benzene. However, we are now facing threats from the excessive use of fossil fuels causing environmental problems such as global warming. Furthermore, fossil resources are not infinite, and will ultimately be depleted. To cope with these problems, the sustainable production of aromatic chemicals from renewable non-food biomass is urgent. With this in mind, the search for alternative methodologies to produce aromatic compounds using low-cost and environmentally friendly processes is becoming more and more important. Microorganisms are able to produce aromatic and aromatic-derivative compounds from sugar-based carbon sources. Metabolic engineering strategies as well as bioprocess optimization enable the development of microbial cell factories capable of efficiently producing aromatic compounds. This review presents current breakthroughs in microbial production of specialty aromatic and aromatic-derivative products, providing an overview on the general strategies and methodologies applied to build microbial cell factories for the production of these compounds. We present and describe some of the current challenges and gaps that must be overcome in order to render the biotechnological production of specialty aromatic and aromatic-derivative attractive and economically feasible at industrial scale.

Deciphering the metabolic distribution of vanillin in Rhodococcus opacus during lignin valorization

Vanillin bioconversion is important for the biological lignin valorization. In this study, the obscure vanillin metabolic distribution in Rhodoccous opacus PD630 was deciphered by combining the strategies of intermediate detection, putative gene prediction, and target gene verification. The results suggest that approximately 10% (mol/mol) of consumed vanillin is converted to vanillic acid for further metabolism, and a large amount is converted to dead-end vanillyl alcohol in R. opacus PD630. Subsequently, five vanillin reductases were identified in R. opacus PD630, among which Pd630_LPD03722 product exhibited the greatest activity. With the detected metabolic distributions of vanillin, the conversion of vanillin to muconic acid was facilitated by deleting domestic vanillin reductase genes and introducing vanillin dehydrogenase from Sphingobium sp. SYK-6. Ultimately, the muconic acid yield from vanillin increased to 97.83% (mol/mol) from the initial 10% (mol/mol). Moreover, this study demonstrated the existence of vanillin reductases in Escherichia coli, Bacillus subtilis, and Corynebacterium glutamicum.

Biosynthesis of vanillin by different microorganisms: a review

Vanillin is a popular flavoring agent widely used around the world. Vanillin is generated by natural extraction, chemical synthesis, or tissue culture technology, but these production methods no longer meet the increasing worldwide demand for vanillin. Accordingly, a biotechnological approach may provide an effective replacement route to obtaining vanillin. Processes for environmentally friendly production of vanillin in microorganisms from different carbon sources, such as eugenol, isoeugenol, lignin, ferulic acid, sugars, and waste residues, with high productivity and yield have been developed. However, challenges remain for optimizing the vanillin biosynthesis process and further improving production titer and yield. In this review, successful and applicable strategies for increasing vanillin titer and yield in different microorganisms are summarized. Additionally, perspectives for further optimizing the production of vanillin are discussed.

Developing efficient vanillin biosynthesis system by regulating feruloyl-CoA synthetase and enoyl-CoA hydratase enzymes

Vanillin is one of the most commonly used natural-occurring flavors in the world. This study successfully constructed an efficient whole-cell catalytic system for vanillin biosynthesis from ferulic acid by regulating feruloyl-CoA synthetase (FCS) and enoyl-CoA hydratase (ECH). First, we constructed an efficient cell-free catalytic system with FCS-Str (fcs from Streptomyces sp. V-1) and ECH-Str (ech from Streptomyces sp. V-1) combination at 1:1. The efficient cell-free catalytic system provided necessary strategies for optimizing the whole-cell catalytic system. Then, we constructed the recombinant Escherichia coli by heterologously expressing the fcs-Str and ech-Str combination. Moreover, E. coli JM109 was a better recombinant Escherichia coli than E. coli BL21 with higher vanillin production. Finally, we first adjusted the ratio of FCS and ECH in E. coli JM109 to 1:1 using two copies of fcs-Str. For higher vanillin production, we further optimized the induction conditions of E. coli JM109 to increase the amount of FCS and ECH. The optimized E. coli JM109-FE-F constructed in this study has the highest vanillin synthesis rate of converting 20 mM ferulic acid to 15 mM vanillin in 6 h among all of the E. coli catalytic systems. Our study made a significant contribution to the construction of the vanillin biosynthesis system and provided a valuable strategy for increasing vanillin production. KEY POINTS: • The efficient cell-free vanillin biosynthesis system was constructed by FCS-Str and ECH-Str combination at 1:1. • Escherichia coli JM109 was determined as a better recombinant Escherichia coli than E. coli BL21 with higher vanillin production. • Escherichia coli JM109-FE-F with two copies of fcs-Str and one copy of ech-Str has the highest catalytic efficiency for vanillin production.

Improving the Intensity of Integrated Expression for Microbial Production

Chromosomal integration of exogenous genes is preferred for industrially related fermentation, as plasmid-mediated fermentation leads to extra metabolic burden and genetic instability. Moreover, with the development and advancement of genome engineering and gene editing technologies, inserting genes into chromosomes has become more convenient; integration expression is extensively utilized in microorganisms for industrial bioproduction and expected to become the trend of recombinant protein expression. However, in actual research and application, it is important to enhance the expression of heterologous genes at the host genome level. Herein, we summarized the basic principles and characteristics of genomic integration; furthermore, we highlighted strategies to improve the expression of chromosomal integration of genes and pathways in host strains from three aspects, including chassis cell optimization, regulation of expression elements in gene expression cassettes, optimization of gene dose level and integration sites on chromosomes. Moreover, we reviewed and summarized the relevant studies on the application of integrated expression in the exploration of gene function and the various types of industrial microorganism production. Consequently, this review would serve as a reference for the better application of integrated expression.

One-pot microbial bioconversion of wheat bran ferulic acid to biovanillin

Due to growing consumer preference towards natural ingredients in food products, the production of flavors by microbial biotransformation of agrowastes provides an eco-friendly, cost-effective and sustainable pathway for biovanillin production. In the present study, biovanillin was produced by microbial biotransformation of ferulic acid (FA) using Streptomyces sp. ssr-198. The strain was able to grow in glucose medium supplemented with 1 g/L FA and produce 20.91 ± 1.11 mg/L vanillin within 96 h, along with 5.78 ± 0.13 mg/L vanillic acid in 144 h. Estimation of enzymes involved in FA degradation detected maximum feruloyl-CoA synthetase activity (1.21 ± 0.03 U/mg protein) at 96 h and maximum vanillin dehydrogenase activity (0.31 ± 0.008 U/mg protein) at 168 h, with small amounts of ferulic acid esterase activity (0.13 ± 0.002 U/mg protein) in the fermentation medium. Further, the glucose deficient production medium supplemented with 3 g/L of ferulic acid when inoculated with Streptomyces sp. ssr-198 (6% wet weight) produced maximum vanillin (685 ± 20.11 mg/L) within 72 h at 37 °C under agitation (150 rpm) and declined thereafter. Furthermore, in a one-pot experiment, wherein crude ferulic acid esterase (700 IU/g of substrate) from Enterococcus lactis SR1 was added into 10% w/v wheat bran (natural source of ferulic acid) based medium and was inoculated with 1% w/v of Streptomyces sp. ssr-198 resulted in maximum vanillin production (1.02 ± 0.02 mg/g of substrate) within 60 h of incubation. The study provides an insight into synergistic effect of using FAE of E. lactis SR1 and Streptomyces sp. ssr-198 for bioproduction of biovanillin using agro residues.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03006-0.

Ferulic acid production by metabolically engineered Escherichia coli

Ferulic acid (p-hydroxy-3-methoxycinnamic acid, FA) is a natural active substance present in plant cell walls, with antioxidant, anticancer, antithrombotic and other properties; it is widely used in medicine, food, and cosmetics. Production of FA by eco-friendly bioprocess is of great potential. In this study, FA was biosynthesized by metabolically engineered Escherichia coli. As the first step, the genes tal (encoding tyrosine ammonia-lyase, RsTAL) from Rhodobacter sphaeroides, sam5 (encoding p-coumarate 3-hydroxylase, SeSAM5) from Saccharothrix espanaensis and comt (encoding Caffeic acid O-methytransferase, TaCM) from Triticum aestivum were cloned in an operon on the pET plasmid backbone, E. coli strain containing this construction was proved to produce FA from L-tyrosine successfully, and confirmed the function of TaCM as caffeic acid O-methytransferase. Fermentation result revealed JM109(DE3) as a more suitable host cell for FA production than BL21(DE3). After that the genes expression strength of FA pathway were optimized by tuning of promoter strength (T7 promoter or T5 promoter) and copy number (pBR322 or p15A), and the combination p15a-T5 works best. To further improve FA production, E. coli native pntAB, encoding pyridine nucleotide transhydrogenase, was selected from five NADPH regeneration genes to supplement redox cofactor NADPH for converting p-coumaric acid into caffeic acid in FA biosynthesis process. Sequentially, to further convert caffeic acid into FA, a non-native methionine kinase (MetK from Streptomyces spectabilis) was also overexpressed. Based on the flask fermentation data which show that the engineered E. coli strain produced 212 mg/L of FA with 11.8 mg/L caffeic acid residue, it could be concluded that it is the highest yield of FA achieved by E. coli K-12 strains reported to the best of our knowledge.

Microbial synthesis of vanillin from waste poly(ethylene terephthalate)

Poly(ethylene terephthalate) (PET) is an abundant and extremely useful material, with widespread applications across society. However, there is an urgent need to develop technologies to valorise post-consumer PET waste to tackle plastic pollution and move towards a circular economy. Whilst PET degradation and recycling technologies have been reported, examples focus on repurposing the resultant monomers to produce more PET or other second-generation materials. Herein, we report a novel pathway in engineered Escherichia coli for the direct upcycling of PET derived monomer terephthalic acid into the value-added small molecule vanillin, a flavour compound ubiquitous in the food and cosmetic industries, and an important bulk chemical. After process optimisation, 79% conversion to vanillin from TA was achieved, a 157-fold improvement over our initial conditions. Parameters such as temperature, cell permeabilisation and in situ product removal were key to maximising vanillin titres. Finally, we demonstrate the conversion of post-consumer PET from a plastic bottle into vanillin by coupling the pathway with enzyme-catalysed PET hydrolysis. This work demonstrates the first biological upcycling of post-consumer plastic waste into vanillin using an engineered microorganism.

Antifungal Activity against Botryosphaeriaceae Fungi of the Hydro-Methanolic Extract of Silybum marianum Capitula Conjugated with Stevioside

Silybum marianum (L.) Gaertn, viz. milk thistle, has been the focus of research efforts in the past few years, albeit almost exclusively restricted to the medicinal properties of its fruits (achenes). Given that other milk thistle plant organs and tissues have been scarcely investigated for the presence of bioactive compounds, in this study, we present a phytochemical analysis of the extracts of S. marianum capitula during the flowering phenological stage (stage 67). Gas chromatography–mass spectroscopy results evidenced the presence of high contents of coniferyl alcohol (47.4%), and secondarily of ferulic acid ester, opening a new valorization strategy of this plant based on the former high-added-value component. Moreover, the application of the hydro-methanolic extracts as an antifungal agent has been also explored. Specifically, their activity against three fungal species responsible for the so-called Botryosphaeria dieback of grapevine (Neofusicoccum parvum, Dothiorella viticola and Diplodia seriata) has been assayed both in vitro and in vivo. From the mycelial growth inhibition assays, the best results (EC₉₀ values of 303, 366, and 355 μg·mL⁻¹ for N. parvum, D. viticola, and D. seriata, respectively) were not obtained for the hydroalcoholic extract alone, but after its conjugation with stevioside, which resulted in a strong synergistic behavior. Greenhouse experiments confirmed the efficacy of the conjugated complexes, pointing to the potential of the combination of milk thistle extracts with stevioside as a promising plant protection product in organic Viticulture.

Whole-Cell Biosensors Aid Exploration of Vanillin Transmembrane Transport

Transcriptional regulatory protein (TRP)-based whole-cell biosensors are widely used nowadays. Here, they were demonstrated to have great potential application in screening cell efflux and influx pumps for small molecules. First, a vanillin whole-cell biosensor was developed by altering the specificity of a TRP, VanR, and strains with improved vanillin productions that were selected from a random genome mutagenesis library by using this biosensor as a high-throughput screening tool. A high intracellular vanillin concentration was found to accumulate due to the inactivation of the AcrA protein, indicating the involvement of this protein in vanillin efflux. Then, the application of this biosensor was extended to explore efflux and influx pumps, combined with directed genome evolution. Elevated intracellular vanillin levels resulting from efflux pump inactivation or influx pump overexpression could be rapidly detected by the whole-cell biosensor, markedly facilitating the identification of genome targets related to small-molecule transmembrane transport, which is of great importance in metabolic engineering.

Synthetic Biology towards Engineering Microbial Lignin Biotransformation

Lignin is the second most abundant biopolymer on earth and is a major source of aromatic compounds; however, it is vastly underutilized owing to its heterogeneous and recalcitrant nature. Microorganisms have evolved efficient mechanisms that overcome these challenges to depolymerize lignin and funnel complex mixtures of lignin-derived monomers to central metabolites. This review summarizes recent synthetic biology efforts to enhance lignin depolymerization and aromatic catabolism in bacterial and fungal hosts for the production of both natural and novel bioproducts. We also highlight difficulties in engineering complex phenotypes and discuss the outlook for the future of lignin biological valorization.

Lichen-associated bacteria transform antibacterial usnic acid to products of lower antibiotic activity

Lichens are specific symbiotic organisms harboring various microorganisms in addition to the two classic partners (algae or cyanobacterium and fungus). Although lichens produce many antibiotic compounds such as (+)-usnic acid, their associated microorganisms possess the ability to colonize an environment where antibiosis exists. Here, we have studied the behavior of several lichen-associated bacterial strains in the presence of (+)-usnic acid, a known antibiotic lichen compound. The effect of this compound was firstly evaluated on the growth and metabolism of three bacteria, thus showing its ability to inhibit Gram-positive bacteria. This inhibition was not thwarted with the usnic acid producer strain Streptomyces cyaneofuscatus. The biotransformation of this lichen metabolite was also studied. An ethanolamine derivative of (+)-usnic acid with low antibiotic activity was highlighted with chemical profiling, using HPLC-UV combined with low resolution mass spectrometry. These findings highlight the way in which some strains develop resistance mechanisms. A methylated derivative of (+)-usnic acid was annotated using the molecular networking method, thus showing the interest of this computer-based approach in biotransformation studies.

Bio-synthesis of food additives and colorants-a growing trend in future food

Food additives and colorants are extensively used in the food industry to improve food quality and safety during processing, storage and packing. Sourcing of these molecules is predominately through three means: extraction from natural sources, chemical synthesis, and bio-production, with the first two being the most utilized. However, growing demands for sustainability, safety and "natural" products have renewed interest in using bio-based production methods. Likewise, the move to more cultured foods and meat alternatives requires the production of new additives and colorants. The production of bio-based food additives and colorants is an interdisciplinary research endeavor and represents a growing trend in future food. To highlight the potential of microbial hosts for food additive and colorant production, we focus on current advances for example molecules based on their utilization stage and bio-production yield as follows: (I) approved and industrially produced with high titers; (II) approved and produced with decent titers (in the g/L range), but requiring further engineering to reduce production costs; (III) approved and produced with very early stage titers (in the mg/L range); and (IV) new/potential candidates that have not been approved but can be sourced through microbes. Promising approaches, as well as current challenges and future directions will also be thoroughly discussed for the bioproduction of these food additives and colorants.

Multi-Faceted Systems Biology Approaches Present a Cellular Landscape of Phenolic Compound Inhibition in Saccharomyces cerevisiae

Synthetic biology has played a major role in engineering microbial cell factories to convert plant biomass (lignocellulose) to fuels and bioproducts by fermentation. However, the final product yield is limited by inhibition of microbial growth and fermentation by toxic phenolic compounds generated during lignocellulosic pre-treatment and hydrolysis. Advances in the development of systems biology technologies (genomics, transcriptomics, proteomics, metabolomics) have rapidly resulted in large datasets which are necessary to obtain a holistic understanding of complex biological processes underlying phenolic compound toxicity. Here, we review and compare different systems biology tools that have been utilized to identify molecular mechanisms that modulate phenolic compound toxicity in Saccharomyces cerevisiae. By focusing on and comparing functional genomics and transcriptomics approaches we identify common mechanisms potentially underlying phenolic toxicity. Additionally, we discuss possible ways by which integration of data obtained across multiple unbiased approaches can result in new avenues to develop yeast strains with a significant improvement in tolerance to phenolic fermentation inhibitors.

Metabolites Secreted by a Plant-Growth-Promoting Pantoea agglomerans Strain Improved Rooting of Pyrus communis L. cv Dar Gazi Cuttings

Strains belonging to Pantoea agglomerans species are known for their ability to produce metabolites that can act in synergy with auxins to induce the adventitious root (AR) formation. The latter is critically important in the agamic propagation of several woody species, including pear (Pyrus communis L.), playing a considerable role in the commercial nursery farms including those using micropropagation techniques. When grown on a medium amended with tryptophan, the plant-growth-promoting (PGP) strain P. agglomerans C1 produces a cocktail of auxin and auxin-like molecules that can be utilized as biostimulants to improve the rooting of vegetable (Solanum lycopersicum L.) and woody crop species (Prunus rootstock GF/677 and hazelnut). In this study, we evaluated the morphological and molecular responses induced by strain C1 exometabolites in microcuttings of P. communis L. cv Dar Gazi and the potential benefits arising from their application. Results showed that exometabolites by P. agglomerans C1 induced a direct and earlier emergence of roots from stem tissues and determined modifications of root morphological parameters and root architecture compared to plants treated with the synthetic hormone indole-3-butyric acid (IBA). Transcription analysis revealed differences in the temporal expression pattern of ARF17 gene when IBA and C1 exometabolites were used alone, while together they also determined changes in the expression pattern of other key auxin-regulated plant genes. These results suggest that the phenotypic and molecular changes triggered by P. agglomerans C1 are dependent on different stimulatory and inhibitory effects that auxin-like molecules and other metabolites secreted by this strain have on the gene regulatory network of the plant. This evidence supports the hypothesis that the strategies used to harness the metabolic potential of PGP bacteria are key factors in obtaining novel biostimulants for sustainable agriculture. Our results demonstrate that metabolites secreted by strain C1 can be successfully used to increase the efficiency of micropropagation of pear through tissue culture techniques.

A Genetic and Metabolomic Perspective on the Production of Indole-3-Acetic Acid by Pantoea agglomerans and Use of Their Metabolites as Biostimulants in Plant Nurseries

The species Pantoea agglomerans includes strains that are agronomically relevant for their growth-promoting or biocontrol traits. Molecular analysis demonstrated that the IPDC pathway involved in the conversion of tryptophan (Trp) to indole-3-acetic acid (IAA) is highly conserved among P. agglomerans strains at both gene and protein levels. Results also indicated that the promoter region controlling the inducible expression of ipdC gene differs from the model system Enterobacter cloacae, which is in accordance with the observation that P. agglomerans accumulates higher levels of IAA when cells are collected in the exponential phase of growth. To assess the potential applications of these microorganisms for IAA production, P. agglomerans C1, an efficient auxin-producer strain, was cultivated in 5 L fermenter so as to evaluate the effect of the medium formulation, the physiological state of the cells, and the induction timing on the volumetric productivity. Results demonstrated that higher IAA levels were obtained by using a saline medium amended with yeast extract and saccharose and by providing Trp, which acts both as a precursor and an inducer, to a culture in the exponential phase of growth. Untargeted metabolomic analysis revealed a significant effect of the carbon source on the exometabolome profile relative to IAA-related compounds and other plant bioactive signaling molecules. The IAA-enriched metabolites secreted in the culture medium by P. agglomerans C1 were used as plant biostimulants to run a series of trials at a large-scale nursery farm. Tests were carried out with in vitro and ex vitro systems following the regular protocols used for large-scale plant tree agamic propagation. Results obtained with 4,540 microcuttings of Prunus rootstock GF/677 and 1,080 plantlets of Corylus avellana L. showed that metabolites from strain C1 improved percentage of rooted-explant, number of adventitious root formation, plant survival, and quality of plant as vigor, with an increase in the leaf area between 17.5 and 42.7% compared to IBA-K (indole-3-butyric acid potassium salt)-treated plants.

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.