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Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO2 to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO2 emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO2 to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO2. Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO2. Cupriavidus necator has a wide metabolic range and naturally creates a biopolymer, poly[(R)-3 hydroxybutyrate] (PHB). Using metabolic engineering techniques, carbon flux can be directed away from PHB synthesis toward the generation of biofuels and bioproducts.Researchers demonstrated the production of many biofuel products using C. necator, including methyl ketones, isoprenoids and terpenes, isobutanol, alkanes and alkenes, and a wide variety of commodity chemicals from CO2.Growth of C. necator and bioproduct production using electrolysis was recently demonstrated, including the use of an artificial leaf system.While genetic engineering of C. necator remains a laborious process, synthetic biology tools for this organism are being expanded with new technologies that will allow for large alterations to its genome.

ObjectivesTo produce flavonol and flavone 6-C-glucosides by bioconversion using recombinant Escherichia coli expressing a C-glucosyltransferase from wasabi (WjGT1).ResultsEscherichia coli expressing WjGT1 (Ec-WjGT1) converted flavones (apigenin and luteolin) and flavonols (quercetin and kaempferol) into their 6-C-glucosides in M9 minimal media supplemented with glucose, and released these products into the culture media. Ec-WjGT1 system also converts a flavanone (naringenin) into its C-glucoside at a conversion rate of 60% in 6 h. For scale-up production, apigenin, kaempferol, and quercetin were sequentially fed into the Ec-WjGT1 system at concentrations of 20–50 µM every 15–60 min, and the system was then able to produce isovitexin, kaempferol 6-C-glucoside, and quercetin 6-C-glucoside at an 89–99% conversion rate.ConclusionsThe Ec-WjGT1 system quickly and easily produces flavone and flavonol 6-C-glucosides at high conversion rates when using sequential administration to avoid precipitation of substrates.

The tricarboxylic acid (TCA) cycle has been used for decades in the microbial production of chemicals such as citrate, L-glutamate, and succinate. Maximizing yield is key for cost-competitive production. However, for most TCA cycle products, the maximum pathway yield is lower than the theoretical maximum yield (YE). For succinate, this was solved by creating two pathways to the product, using both branches of the TCA cycle, connected by the glyoxylate shunt (GS). A similar solution cannot be applied directly for production of compounds from the oxidative branch of the TCA cycle because irreversible reactions are involved. Here, we describe how this can be overcome and what the impact is on the yield. The TCA cycle is a source of industrially important chemicals. Current pathway yields of chemicals from the TCA cycle are below their theoretical maximum (YE). YE becomes achievable by combining the oxidative and reductive part of the TCA cycle. Metabolic engineering is required to reverse some of the thermodynamically unfeasible steps.

PET hydrolase (PETase), which hydrolyzes polyethylene terephthalate (PET) into soluble building blocks, provides an attractive avenue for the bioconversion of plastics. Here we present the structures of a novel PETase from the PET-consuming microbe Ideonella sakaiensis in complex with substrate and product analogs. Through structural analyses, mutagenesis, and activity measurements, a substrate-binding mode is proposed, and several features critical for catalysis are elucidated. Poly-ethylene terephthalate (PET) is a widely used plastic which accumulates in the environment with detrimental consequences. Here the authors report crystal structures of a PET-hydrolyzing enzyme from the microbe Ideonella sakaiensis bound to substrate and product analogs, and suggest a catalytic mechanism for its PET-degrading activity.

Biogas produced by anaerobic digestion is an important renewable energy carrier. Nevertheless, the high CO2 content in biogas limits its utilization to mainly heat and electricity generation. Upgrading biogas into biomethane broadens its potential as a vehicle fuel or substitute for natural gas. CO2-to-CH4 bioconversion represents one cutting-edge solution for biogas upgrading. In situ bioconversion can capture endogenous CO2 directly from the biogas reactor, is easy to operate, and provides an infrastructure for renewable electricity storage. Despite these advantages, several challenges need to be addressed to move in situ upgrading technologies closer to applications at scale. This opinion article reviews the state of the art of this technology and identifies some obstacles and opportunities of biological in-situ upgrading technologies for future development. Upgrading biogas into biomethane broadens its applications and increases the value of biogas. Among these, in situ CO2-to-CH4 bioconversion can capture endogenous CO2 directly from the biogas reactor, is easy to operate, and provides infrastructure for renewable electricity storage.Although promising, several intrinsic challenges need to be addressed to move in situ upgrading technologies closer to scaled-up application.In situ CO2-to-CH4 bioconversion powered by renewable electricity could integrate multidisciplinary approaches including wind or solar energy technology, P2G technology, anaerobic digestion technology, and biogas upgrading technology.Bioelectrochemical systems are a potential technology for biogas upgrading and storing discontinuous wind/solar energy. However, their operating mechanism and scale-up feasibilities need to be further explored.

Dietary polyphenols are components of many foods such as tea, fruit, and vegetables and are associated with several beneficial health effects although, sofar, largely based on epidemiological studies. The intact forms of complex dietary polyphenols have limited bioavailability, with low circulating levels in plasma. A major part of the polyphenols persists in the colon, where the resident microbiota produce metabolites that can undergo further metabolism upon entering systemic circulation. Unraveling the complex metabolic fate of polyphenols in this human superorganism requires joint deployment of in vitro and humanized mouse models and human intervention trials. Within these systems, the variation in diversity and functionality of the colonic microbiota can increasingly be captured by rapidly developing microbiomics and metabolomics technologies. Furthermore, metabolomics is coming to grips with the large biological variation superimposed on relatively subtle effects of dietary interventions. In particular when metabolomics is deployed in conjunction with a longitudinal study design, quantitative nutrikinetic signatures can be obtained. These signatures can be used to define nutritional phenotypes with different kinetic characteristics for the bioconversion capacity for polyphenols. Bottom-up as well as top-down approaches need to be pursued to link gut microbial diversity to functionality in nutritional phenotypes and, ultimately, to bioactivity of polyphenols. This approach will pave the way for personalization of nutrition based on gut microbial functionality of individuals or populations.

Functional production of soluble methane monooxygenase (sMMO) in Escherichia coli, supported by chaperonins and maturases, and the first methane (CH4)-to-methanol conversion by a truncated mini-sMMO variant represent major advances toward synthetic methanotrophy in industrial hosts.Natural CH4-oxidizing enzymes [sMMO, particulate methane monooxygenase (pMMO), methyl-coenzyme M reductase (MCR)] and synthetic de novo monooxygenases (mini-sMMO) are engineered as complementary biocatalysts for CH4 oxidation in synthetic methanotrophy.Miniaturized, online-monitored CH4 fermentation platforms enable systematic optimization of gas transfer, pressure control, and safety management, enhancing process scale-up.Fully synthetic methylotrophy has been achieved in model organisms, confirming the feasibility of complete synthetic one-carbon (C1) assimilation as an alternative to natural pathways. Development of methylotrophic biosensor strains in traditional hosts provides a powerful tool for growth-coupled engineering, while also offering a genetically tractable framework for integrating CH4 oxidation modules.The convergence of synthetic methylotrophy, engineered CH4-oxidizing enzymes, and gas bioprocess technologies establishes a blueprint for scalable, circular, and carbon-neutral CH4-to-chemical conversion. Methane (CH4) represents an abundant source of carbon and energy with significant potential for sustainable biotechnological processes. For efficient bioconversion of CH4 into value-added products, synthetic methanotrophy has emerged as a promising strategy, enabling the rational design of engineered microbial systems. In this review, we highlight recent advances in CH4-based bioprocesses, covering the metabolic design of synthetic methanotrophs and optimization of bioreactor systems adapted for gas fermentation. A comparative analysis of key CH4-converting enzymes is provided, with particular emphasis on soluble methane monooxygenase and its heterologous production in industrial chassis. Recent progress in modular one-carbon (C1)-pathway engineering accelerates enzyme optimization and highlights synthetic methylotrophy as a prerequisite for robust synthetic methanotrophy. Collectively, these advances establish a foundation for scalable, efficient, and sustainable CH4-based biotechnological processes. Methane (CH4) represents an abundant source of carbon and energy with significant potential for sustainable biotechnological processes. For efficient bioconversion of CH4 into value-added products, synthetic methanotrophy has emerged as a promising strategy, enabling the rational design of engineered microbial systems. In this review, we highlight recent advances in CH4-based bioprocesses, covering the metabolic design of synthetic methanotrophs and optimization of bioreactor systems adapted for gas fermentation. A comparative analysis of key CH4-converting enzymes is provided, with particular emphasis on soluble methane monooxygenase and its heterologous production in industrial chassis. Recent progress in modular one-carbon (C1)-pathway engineering accelerates enzyme optimization and highlights synthetic methylotrophy as a prerequisite for robust synthetic methanotrophy. Collectively, these advances establish a foundation for scalable, efficient, and sustainable CH4-based biotechnological processes.

There is a growing awareness that lignocellulose will be a major raw material for production of both fuel and chemicals in the coming decades--most likely through various fermentation routes. Considerable attention has been given to the problem of finding efficient means of separating the major constituents in lignocellulose (i.e., lignin, hemicellulose, and cellulose) and to efficiently hydrolyze the carbohydrate parts into sugars. In these processes, by-products will inevitably form to some extent, and these will have to be dealt with in the ensuing microbial processes. One group of compounds in this category is the furaldehydes. 2-Furaldehyde (furfural) and substituted 2-furaldehydes--most importantly 5-hydroxymethyl-2-furaldehyde--are the dominant inhibitory compounds found in lignocellulosic hydrolyzates. The furaldehydes are known to have biological effects and act as inhibitors in fermentation processes. The effects of these compounds will therefore have to be considered in the design of biotechnological processes using lignocellulose. In this short review, we take a look at known metabolic effects, as well as strategies to overcome problems in biotechnological applications caused by furaldehydes.

Lignin, the largest renewable aromatic resource, is a promising alternative feedstock for the sustainable production of various chemicals, fuels, and materials. Despite this potential, lignin is characterized by heterogeneous and macromolecular structures that must be addressed. In this review, we present biological lignin conversion routes (BLCRs) that offer opportunities for overcoming these challenges, making lignin valorization feasible. Funneling heterogeneous aromatics via a ‘biological funnel’ offers a high-specificity bioconversion route for aromatic platform chemicals. The inherent aromaticity of lignin drives atom-economic functionalization routes toward aromatic natural product generation. By harnessing the ligninolytic capacities of specific microbial systems, powerful aromatic ring-opening routes can be developed to generate various value-added products. Thus, BLCRs hold the promise to make lignin valorization feasible and enable a lignocellulose-based bioeconomy. Biological lignin conversion routes (BLCRs) overcome the heterogeneous structures of lignin by harnessing the inherent capacity of ligninolytic microbes, opening the way to value-added products.Lignin depolymerization provides bioavailable aromatic derivatives suitable for downstream bioconversion.Atom-economic conversion routes are backbones in taping into the inherent aromaticity value of lignin to promote the microbial synthesis of valuable products.The scientific and technical evolution of synthetic biology enable the construction of microbial cell factories to improve lignin bioconversion.Lignin bioconversion would enable the economic viability of biorefineries and contribute to a sustainable lignocellulose-based bioeconomy.

Burkholderia, a bacterial genus comprising more than 120 species, is typically reported to inhabit soil and water environments. These Gram-negative bacteria harbor a variety of aromatic catabolic pathways and are thus potential organisms for bioremediation of sites contaminated with aromatic pollutants. However, there are still substantial gaps in our knowledge of these catabolic processes that must be filled before these pathways and organisms can be harnessed for biotechnological applications. This review presents recent discoveries on the catabolism of monoaromatic and polycyclic aromatic hydrocarbons, as well as of heterocyclic compounds, by a diversity of Burkholderia strains. We also present a perspective on the beneficial features of Burkholderia spp. and future directions for their potential utilization in the bioremediation and bioconversion of aromatic compounds. Burkholderia is a versatile genus that can tolerate and degrade a variety of aromatic compounds (monoaromatic, polycyclic aromatic, and heterocyclic). It is therefore an increasingly promising host for bioremediation and bioconversion applications.Despite the positive features of Burkholderia in degrading aromatic compounds and promoting plant growth, this genus remains understudied compared with other aromatic catabolizing bacteria.Modern systems biology tools (such as multi-omic analyses) and metabolic engineering are currently being applied to elucidate catabolic pathways in Burkholderia.Degradation studies in the presence of cosubstrates confirm the importance of considering the environmental conditions to reach better conclusions regarding bioremediation efficiency.