Recent advances in metabolic engineering of purple non‑sulfur photosynthetic bacteria for enhanced biohydrogen production.

Advanced Strategies for Production of Natural Products in Yeast.

Advances in metabolic engineering of cyanobacteria for production of biofuels

Cocoa butter is extracted from cocoa beans, and it is mainly used as the raw material for the production of chocolate and cosmetics. Increased demands and insufficient cocoa plants led to a shortage of cocoa butter supply, and there is therefore much interesting in finding an alternative cocoa butter supply. However, the most valuable component of cocoa butter is rarely available in other vegetable oils. Saccharomyces cerevisiae is an important industrial host for production of chemicals, enzyme and pharmaceuticals. Advances in synthetical biology and metabolic engineering had enabled high-level of triacylglycerols (TAG) production in yeast, which provided possible solutions for cocoa butter equivalents (CBEs) production. Diverse engineering strategies focused on the fatty acid-producing pathway had been applied in S. cerevisiae, and the key enzymes determining the TAG structure were considered as the main engineering targets. Recent development in phytomics and multi-omics technologies provided clues to identify potential targeted enzymes, which are responsible for CBE production. In this review, we have summarized recent progress in identification of the key plant enzymes for CBE production, and discussed recent and future metabolic engineering and synthetic biology strategies for increased CBE production in S. cerevisiae.

Metabolic engineering of Corynebacterium glutamicum: Unlocking its potential as a key cell factory platform for organic acid production

The fermentative production of platform chemicals in biorefineries is a sustainable alternative to current petroleum‐refining processes. Industrial microorganisms, such as Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum, have been engineered as microbial cell factories that are able to utilize biomass for the production of value‐added platform chemicals and polymers. Compared to E. coli and S. cerevisiae, C. glutamicum displays weak carbon catabolite repression and can co‐utilize mixed sugars as carbon sources, without any significant growth retardation. Pathways for the utilization of alternative carbon sources, such as d‐xylose and l‐arabinose from lignocellulosic biomass, lactose and galactose from whey, glycerol from biodiesel, and methanol from natural gas refineries, have been evaluated for chemical production. However, the application of C. glutamicum in biorefineries is limited because it does not secrete hydrolases for the efficient utilization of cellulose, xylan, and starch from lignocellulosic and starch biomass. To solve the limitation, C. glutamicum has been engineered for the consolidated bioprocessing of biomass by the heterologous expression of amylolytic and cellulolytic enzymes. Recently, C. glutamicum has been extensively engineered for polyamide monomer production owing to its ability to produce l‐lysine and l‐glutamate. This review summarizes recent advances in the development of C. glutamicum strains that can utilize renewable biomass resources for the production of industrially important chemicals. It highlights recent progress in metabolic engineering for the production of polyamide monomers. © 2018 Society of Chemical Industry and John Wiley & Sons, Ltd

Preface

Next-Generation Plant Metabolic Engineering, Inspired by an Ancient Chinese Irrigation System

Metabolic engineering has evolved exponentially due to rapid progress in the development of omics (proteomics, lipidomics and glycomics) technology and synthetic biology toolsets. Particularly, omics technologies, synthetic biology and metabolic engineering are interdependent in terms of principles of technology and their biological applications. In this article, we showcase synthetic biology toolsets currently used for the metabolic engineering of microbes and focus on some of the recent advances in the field. Specifically we have elaborated on recent progress in metabolic engineering, the associated synthetic biology toolsets, microbiome metabolic engineering (MME) and the potential industrial metabolic engineering applications. As a case study for the industrial application of metabolic engineering, we have reviewed the use of synthetic biology toolsets to bioengineer microbes and re-engineer their metabolic pathways for customised industrial applications. Some of the examples included in this article are as follows: (a) metabolic engineering of cyanobacteria, (b) metabolic engineering of Bacillus subtilis and (c) metabolic engineering in synthetic yeast for industrial applications. As a future perspective, this chapter presents a case for the broader use of synthetic biology toolsets across metabolic engineering applications.

The extremely thermophilic cellulolytic bacterium, Caldicellulosiruptor bescii (C. bescii), degrades plant biomass at high temperature without any pretreatments and can serve as a strategic platform for industrial applications. C. bescii can utilize various carbohydrates, and its high growth temperature offers benefits such as reduced risk of phage infection and contamination, increased solubility of plant biomass polysaccharides, and the potential to distill volatile products directly from fermentation broths. Therefore, it has become an interest of research and has been metabolically engineered to produce desired bioproducts. The metabolic engineering of C. bescii, however, faces potential bottlenecks in bio-based chemical productions. Genome-scale metabolic modeling (GEM) is a common approach used to examine potential bottlenecks that may be encountered in metabolic engineering for optimizing the production of certain substances. In this work, we reconstructed the GEM for C. bescii based on its genome and other related information from reliable sources (e.g., peer-reviewed literature). The model utilizes subsystems-based genome annotation, targeted reconstruction of carbohydrate utilization pathways, and biochemical and physiological based experimental validations. Specifically, carbohydrate transport and utilization pathways involving 160 genes and their corresponding functions were incorporated, representing the utilization of C5/C6 monosaccharides, disaccharides, and polysaccharides such as cellulose and xylan. To illustrate its utility, the model predicted that optimal production from biomass-based sugars of the model product, ethanol, was driven by adenosine triphosphate (ATP) production, redox balancing, and proton translocation, mediated through the interplay of an ATP synthase, a membrane-bound hydrogenase, a bifurcating hydrogenase and a bifurcating NAD- and NADP-dependent oxidoreductase. Also, it revealed that ATP is a limiting factor for producing another valuable chemical, 2,3-Butanediol (2,3-BDO), via metabolic engineered C. bescii. These mechanistic insights guided the design and optimization of new engineering strategies for product optimization, which were subsequently tested in the C. bescii model, showing a near two-fold increase in ethanol yields. Overall, the C. bescii model provides a useful platform for investigating the potential redox controls that mediate the carbon and energy flows in metabolism and sets the stage for future design of engineering strategies aiming at optimizing the production of ethanol and other bio-based chemicals.

Fucoxanthin, a bioactive carotenoid derived from algae, has attracted considerable attention for its applications in health, cosmetics, and nutrition. Advances in metabolic engineering, such as the overexpression of pathway-specific enzymes and enhancement of precursor availability, have shown promising results in improving production efficiency. However, despite its high value, the biosynthetic pathway of fucoxanthin remains only partially elucidated, posing significant challenges for metabolic engineering efforts. Recent studies have identified previously unknown enzymes and regulatory elements within the pathway, providing opportunities for further productivity enhancements through targeted metabolic modifications. Additionally, adaptive evolution, mutagenesis-driven strain development, and optimized cultivation conditions have demonstrated significant potential to boost fucoxanthin yields. This review consolidates the latest insights into the biosynthetic pathway of fucoxanthin and highlights metabolic engineering strategies aimed at enhancing the production of fucoxanthin and related carotenoids, offering approaches to design high-yielding strains. Furthermore, recent advancements in random mutagenesis and cultivation technology are discussed. By integrating these developments, more economically viable and environmentally sustainable fucoxanthin production systems can be achieved.Key Points• Insights into fucoxanthin biosynthesis enable targeted metabolic engineering.• ALE and cultivation strategies complement metabolic engineering efforts.• Balanced push–pull-block strategies improve fucoxanthin production efficiency.

Bacterial glycobiotechnology: A biosynthetic route for the production of biopharmaceutical glycans

Towards a super H 2 producer: Improvements in photofermentative biohydrogen production by genetic manipulations

Advances in metabolic engineering of yeasts for the production of fatty acid-derived hydrocarbon fuels

Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned out to be a global hot topic. Ethanol is by far the leading yeast output amongst a broad spectrum of bio-based industries. Thus, as a well-known platform microorganism and native ethanol producer, baker’s yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol production processes. We delve into the current state of the field and show that metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies. We also discuss potential future directions that involve recent advancements in directed genome evolution, including CRISPR-Cas9 technology.

Isoflavonoids are well-known plant secondary metabolites that have gained importance in recent time due to their multiple nutraceutical and pharmaceutical applications. In plants, isoflavonoids play a role in plant defense and can confer the host plant a competitive advantage to survive and flourish under environmental challenges. In animals, isoflavonoids have been found to interact with multiple signaling pathways and have demonstrated estrogenic, antioxidant and anti-oncologic activities in vivo. The activity of isoflavonoids in the estrogen pathways is such that the class has also been collectively called phytoestrogens. Over 2,400 isoflavonoids, predominantly from legumes, have been identified so far. The biosynthetic pathways of several key isoflavonoids have been established, and the genes and regulatory components involved in the biosynthesis have been characterized. The biosynthesis and accumulation of isoflavonoids in plants are regulated by multiple complex environmental and genetic factors and interactions. Due to this complexity of secondary metabolism regulation, the export and engineering of isoflavonoid biosynthetic pathways into non-endogenous plants are difficult, and instead, the microorganisms Saccharomyces cerevisiae and Escherichia coli have been adapted and engineered for heterologous isoflavonoid synthesis. However, the current ex-planta production approaches have been limited due to slow enzyme kinetics and traditionally laborious genetic engineering methods and require further optimization and development to address the required titers, reaction rates and yield for commercial application. With recent progress in metabolic engineering and the availability of advanced synthetic biology tools, it is envisaged that highly efficient heterologous hosts will soon be engineered to fulfill the growing market demand.