Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries

Genetic Engineering Approaches for the Microbial Production of Vanillin

Vanilla flavour is widely used in various industries and is the most broadly used flavouring agent in the food industry. The demand for this flavour is, therefore, extremely high, yet vanilla bean extracts can only meet about 1% of the overall demand. Vanillin, the main constituent of vanilla flavour, can easily be obtained through chemical synthesis. Nonetheless, consumer demands for natural products and environmentally friendly industrial processes drive the development of biotechnological approaches for its production. Some microorganisms can naturally produce vanillin when fed with various substrates, including eugenol, isoeugenol, and ferulic acid. The characterisation of the genes and enzymes involved in these bioconversion pathways, as well as progress in the understanding of vanillin biosynthesis in Vanilla orchids, allowed the development of genetic engineering and synthetic biology approaches to increase vanillin production in naturally vanillin-producing microorganisms, or to implement novel vanillin biosynthetic pathways in microbial chassis. This review summarises and discusses these genetic engineering and synthetic biology approaches for the microbial production of vanillin.

Bacterial valorization of lignin for the sustainable production of value-added bioproducts

As the most abundant aromatic biopolymer in the biosphere, lignin represents a promising alternative feedstock for the industrial production of various value-added bioproducts with enhanced economical value. However, the large-scale implementation of lignin valorization remains challenging because of the heterogeneity and irregular structure of lignin. General fragmentation and depolymerization processes often yield various products, but these approaches necessitate tedious purification steps to isolate target products. Moreover, microbial biocatalytic processes, especially bacterial-based systems with high metabolic activity, can depolymerize and further utilize lignin in an eco-friendly way. Considering that wild bacterial strains have evolved several metabolic pathways and enzymatic systems for lignin degradation, substantial efforts have been made to exploit their potential for lignin valorization. This review summarizes recent advances in lignin valorization for the production of value-added bioproducts based on bacterial systems. Additionally, the remaining challenges and available strategies for lignin biodegradation processes and future trends of bacterial lignin valorization are discussed.

Microbial Upcycling of Depolymerized Lignin into Value-Added Chemicals

Lignin is one of the most widespread organic compounds found on earth, boasting a wealth of aromatic molecules. The use of lignin feedstock for biochemical productions is of great importance for achieving "carbon neutrality." In recent years, a strategy for lignin valorization known as the "bio-funnel" has been proposed as a means to generate a variety of commercially valuable chemicals from lignin-derived compounds. The implementation of biocatalysis and metabolic engineering techniques has substantially advanced the biotransformation of depolymerized lignin into chemicals and materials within the supply chain. In this review, we present an overview of the latest advancements in microbial upcycling of depolymerized lignin into value-added chemicals. Besides, the review provides insights into the problems facing current biological lignin valorization while proposing further research directions to improve these technologies for the extensive accomplishment of the lignin upcycling.

Lignin Modification for Enhanced Performance of Polymer Composites

The biopolymer lignin, which is heterogeneous and abundant, is usually present in plant cell walls and gives them rigidity and strength. As a byproduct of the wood, paper, and pulp manufacturing industry, lignin ranks as the second most prevalent biopolymer worldwide, following cellulose. This review paper explores the extraction, modification, and prospective applications of lignin in various industries, including the enhancement of thermosetting and thermoplastic polymers, biomedical applications such as vanillin production, fuel development, carbon fiber composites, and the creation of nanomaterials for food packaging and drug delivery. The structural characteristics of lignin remain undefined due to its origin, separation, and fragmentation processes. This comprehensive overview encompasses state-of-the-art techniques, potential applications, diverse extraction methods, chemical modifications, carbon fiber utilization, and the extraction of vanillin. Moreover, the review focuses on the utilization of lignin-modified polymer blends across multiple manufacturing sectors, providing insights into the advantages and limitations of this innovative approach for the development of environmentally friendly materials.

Biosensor-guided discovery and engineering of metabolic enzymes

A variety of chemicals have been produced through metabolic engineering approaches, and enhancing biosynthesis performance can be achieved by using enzymes with high catalytic efficiency. Accordingly, a number of efforts have been made to discover enzymes in nature for various applications. In addition, enzyme engineering approaches have been attempted to suit specific industrial purposes. However, a significant challenge in enzyme discovery and engineering is the efficient screening of enzymes with the desired phenotype from extensive enzyme libraries. To overcome this bottleneck, genetically encoded biosensors have been developed to specifically detect target molecules produced by enzyme activity at the intracellular level. Especially, the biosensors facilitate high-throughput screening (HTS) of targeted enzymes, expanding enzyme discovery and engineering strategies with advances in systems and synthetic biology. This review examines biosensor-guided HTS systems and highlights studies that have utilized these tools to discover enzymes in diverse areas and engineer enzymes to enhance their properties, such as catalytic efficiency, specificity, and stability.

Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion

Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.

Strategies for improving the production of bio-based vanillin

Vanillin (4-hydroxy-3-methoxybenzaldehyde) is one of the most popular flavors with wide applications in food, fragrance, and pharmaceutical industries. However, the high cost and limited yield of plant extraction failed to meet the vast market demand of natural vanillin. Vanillin biotechnology has emerged as a sustainable and cost-effective alternative to supply vanillin. In this review, we explored recent advances in vanillin biosynthesis and highlighted the potential of vanillin biotechnology. In particular, we addressed key challenges in using microorganisms and provided promising approaches for improving vanillin production with a special focus on chassis development, pathway construction and process optimization. Future directions of vanillin biosynthesis using inexpensive precursors are also thoroughly discussed.

An insight into omics analysis and metabolic pathway engineering of lignin-degrading enzymes for enhanced lignin valorization

Lignin, a highly heterogeneous polymer of lignocellulosic biomass, is intricately associated with cellulose and hemicellulose, responsible for its strength and rigidity. Lignin decomposition is carried out through certain enzymes derived from microorganisms to promote the hydrolysis of lignin. Analyzing multi-omics data helps to emphasize the probable value of fungal-produced enzymes to degrade the lignocellulosic material, which provides them an advantage in their ecological niches. This review focuses on lignin biodegrading microorganisms and associated ligninolytic enzymes, including lignin peroxidase, manganese peroxidase, versatile peroxidase, laccase, and dye-decolorizing peroxidase. Further, enzymatic catalysis, lignin biodegradation mechanisms, vital factors responsible for lignin modification and degradation, and the design and selection of practical metabolic pathways are also discussed. Highlights were made on metabolic pathway engineering, different aspects of omics analyses, and its scope and applications to ligninase enzymes. Finally, the advantages and essential steps of successfully applying metabolic engineering and its path forward have been addressed.

A Review on the Utilization of Lignin as a Fermentation Substrate to Produce Lignin-Modifying Enzymes and Other Value-Added Products

The lignocellulosic biomass is comprised of three major components: cellulose, hemicellulose, and lignin. Among these three, cellulose and hemicellulose were already used for the generation of simple sugars and subsequent value-added products. However, lignin is the least applied material in this regard because of its complex and highly variable nature. Regardless, lignin is the most abundant material, and it can be used to produce value-added products such as lignin-modifying enzymes (LMEs), polyhydroxyalkanoates (PHAs), microbial lipids, vanillin, muconic acid, and many others. This review explores the potential of lignin as the microbial substrate to produce such products. A special focus was given to the different types of lignin and how each one can be used in different microbial and biochemical pathways to produce intermediate products, which can then be used as the value-added products or base to make other products. This review paper will summarize the effectiveness of lignin as a microbial substrate to produce value-added products through microbial fermentations. First, basic structures of lignin along with its types and chemistry are discussed. The subsequent sections highlight LMEs and how such enzymes can enhance the value of lignin by microbial degradation. A major focus was also given to the value-added products that can be produced from lignin.

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.

A model-driven approach towards rational microbial bioprocess optimization

Due to sustainability concerns, bio-based production capitalizing on microbes as cell factories is in demand to synthesize valuable products. Nevertheless, the nonhomogenous variations of the extracellular environment in bioprocesses often challenge the biomass growth and the bioproduction yield. To enable a more rational bioprocess optimization, we have established a model-driven approach that systematically integrates experiments with modeling, executed from flask to bioreactor scale, and using ferulic acid to vanillin bioconversion as a case study. The impacts of mass transfer and aeration on the biomass growth and bioproduction performances were examined using minimal small-scale experiments. An integrated model coupling the cell factory kinetics with the three-dimensional computational hydrodynamics of bioreactor was developed to better capture the spatiotemporal distributions of bioproduction. Full-factorial predictions were then performed to identify the desired operating conditions. A bioconversion yield of 94% was achieved, which is one of the highest for recombinant Escherichia coli using ferulic acid as the precursor.

Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods

Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.

Bacterial enzymes for lignin depolymerisation: new biocatalysts for generation of renewable chemicals from biomass

The conversion of polymeric lignin from plant biomass into renewable chemicals is an important unsolved problem in the biorefinery concept. This article summarises recent developments in the discovery of bacterial enzymes for lignin degradation, our current understanding of their molecular mechanism of action, and their use to convert lignin or lignocellulose into aromatic chemicals. The review also discusses the recent developments in screening of metagenomic libraries for new biocatalysts, and the use of protein engineering to enhance lignin degradation activity.

Biotransformation of lignin: Mechanisms, applications and future work

As one of the most abundant polymers in biosphere, lignin has attracted extensive attention as a kind of promising feedstock for biofuel and bio-based products. However, the utilization of lignin presents various challenges in that its complex composition and structure and high resistance to degradation. Lignin conversion through biological platform harnesses the catalytic power of microorganisms to decompose complex lignin molecules and obtain value-added products through biosynthesis. Given the heterogeneity of lignin, various microbial metabolic pathways are involved in lignin bioconversion processes, which has been characterized in extensive research work. With different types of lignin substrates (e.g., model compounds, technical lignin, and lignocellulosic biomass), several bacterial and fungal species have been proved to own lignin-degrading abilities and accumulate microbial products (e.g., lipid and polyhydroxyalkanoates), while the lignin conversion efficiencies are still relatively low. Genetic and metabolic strategies have been developed to enhance lignin biodegradation by reprogramming microbial metabolism, and diverse products, such as vanillin and dicarboxylic acids were also produced from lignin. This article aims at presenting a comprehensive review on lignin bioconversion including lignin degradation mechanisms, metabolic pathways, and applications for the production of value-added bioproducts. Advanced techniques on genetic and metabolic engineering are also covered in the recent development of biological platforms for lignin utilization. To conclude this article, the existing challenges for efficient lignin bioprocessing are analyzed and possible directions for future work are proposed.

Genetically encoded biosensors for lignocellulose valorization

Modern society is hugely dependent on finite oil reserves for the supply of fuels and chemicals. Moving our dependence away from these unsustainable oil-based feedstocks to renewable ones is, therefore, a critical factor towards the development of a low carbon bioeconomy. Lignin derived from biomass feedstocks offers great potential as a renewable source of aromatic compounds if methods for its effective valorization can be developed. Synthetic biology and metabolic engineering offer the potential to synergistically enable the development of cell factories with novel biosynthetic routes to valuable chemicals from these sustainable sources. Pathway design and optimization is, however, a major bottleneck due to the lack of high-throughput methods capable of screening large libraries of genetic variants and the metabolic burden associated with bioproduction. Genetically encoded biosensors can provide a solution by transducing the target metabolite concentration into detectable signals to provide high-throughput phenotypic read-outs and allow dynamic pathway regulation. The development and application of biosensors in the discovery and engineering of efficient biocatalytic processes for the degradation, conversion, and valorization of lignin are paving the way towards a sustainable and economically viable biorefinery.

Development of a Vanillate Biosensor for the Vanillin Biosynthesis Pathway in E. coli

The engineered de novo vanillin biosynthesis pathway constructed in Escherichia coli is industrially relevant but limited by the reaction catalyzed by catechol O-methyltransferase, which is intended to catalyze the conversion of protocatechuate to vanillate. To identify alternative O-methyltransferases, we constructed a vanillate sensor based on the Caulobacter crescentus VanR-VanO system. Using an E. coli promoter library, we achieved greater than 14-fold dynamic range in our best rationally constructed sensor. We found that this construct and an evolved variant demonstrate remarkable substrate selectivity, exhibiting no detectable response to the regioisomer byproduct isovanillate and minimal response to structurally similar pathway intermediates. We then harnessed the evolved biosensor to conduct rapid bioprospecting of natural catechol O-methyltransferases and identified three previously uncharacterized but active O-methyltransferases. Collectively, these efforts enrich our knowledge of how biosensing can aid metabolic engineering and constitute the foundation for future improvements in vanillin pathway productivity.

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli

Background

Acrylic acid (AA) is a widely used commodity chemical derived from non-renewable fossil fuel sources. Alternative microbial-based production methodologies are being developed with the aim of providing “green” acrylic acid. These initiatives will benefit from component sensing tools that facilitate rapid and easy detection of in vivo AA production.

Results

We developed a novel transcriptional sensor facilitating in vivo detection of acrylic acid (AA). RNAseq analysis of Escherichia coli exposed to sub-lethal doses of acrylic acid identified a selectively responsive promoter (P_yhcN) that was cloned upstream of the eGFP gene. In the presence of AA, eGFP expression in E. coli cells harbouring the sensing construct was readily observable by fluorescence read-out. Low concentrations of AA (500 μM) could be detected whilst the closely related lactic and 3-hydroxy propionic acids failed to activate the sensor. We further used the developed AA-biosensor for in vivo FACS-based screening and identification of amidase mutants with improved catalytic properties for deamination of acrylamide to acrylic acid.

Conclusions

The transcriptional AA sensor developed in this study will benefit strain, enzyme and pathway engineering initiatives targeting the efficient formation of bio-acrylic acid.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1185-y) contains supplementary material, which is available to authorized users.

Cell-based biosensors: Recent trends, challenges and future perspectives

Existing at the interface of biology and electronics, living cells have been in use as biorecognition elements (bioreceptors) in biosensors since the early 1970s. They are an interesting choice of bioreceptors as they allow flexibility in determining the sensing strategy, are cheaper than purified enzymes and antibodies and make the fabrication relatively simple and cost-effective. And with advances in the field of synthetic biology, microfluidics and lithography, many exciting developments have been made in the design of cell-based biosensors in the last about five years. 3D cell culture systems integrated with electrodes are now providing new insights into disease pathogenesis and physiology, while cardiomyocyte-integrated microelectrode array (MEA) technology is set to be standardized for the assessment of drug-induced cardiac toxicity. From cell microarrays for high-throughput applications to plasmonic devices for anti-microbial susceptibility testing and advent of microbial fuel cell biosensors, cell-based biosensors have evolved from being mere tools for detection of specific analytes to multi-parametric devices for real time monitoring and assessment. However, despite these advancements, challenges such as regeneration and storage life, heterogeneity in cell populations, high interference and high costs due to accessory instrumentation need to be addressed before the full potential of cell-based biosensors can be realized at a larger scale. This review summarizes results of the studies that have been conducted in the last five years toward the fabrication of cell-based biosensors for different applications with a comprehensive discussion on the challenges, future trends, and potential inputs needed for improving them.

Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products

Lignin is the most abundant aromatic substrate on Earth and its valorization technologies are still under developed. Depolymerization and fragmentation are the predominant preparatory strategies for valorization of lignin to chemicals and fuels. However, due to the structural heterogeneity of lignin, depolymerization and fragmentation typically result in diverse product species, which require extensive separation and purification procedures to obtain target products. For lignin valorization, bacterial-based systems have attracted increasing attention because of their diverse metabolisms, which can be used to funnel multiple lignin-based compounds into specific target products. Here, recent advances in lignin valorization using bacteria are critically reviewed, including lignin-degrading bacteria that are able to degrade lignin and use lignin-associated aromatics, various associated metabolic pathways, and application of bacterial cultures for lignin valorization. This review will provide insight into the recent breakthroughs and future trends of lignin valorization based on bacterial systems.