Fuelling the future: microbial engineering for the production of sustainable biofuels

Progress on production of malic acid and succinic acid by industrially-important engineered microorganisms

Organic acids are widely used as additives in the food, pharmaceutical, chemical, and plastic industries. Currently, the industrial production methods of organic acids mainly include plant extraction and chemical synthesis. The latter mainly uses petroleum-based compounds as raw materials to synthesize organic acids through a series of chemical reactions. All of these methods have problems such as environmental pollution, high cost, and unsustainability. By contrast, microbial fermentation can effectively utilize a variety of carbon sources. Due to its low production cost, environmental friendliness, and high product purity, microbial fermentation has received increasing attention in recent years. However, the low yield and long fermentation cycle of microbial fermentation limits its industrial application. With the development of genomics, transcriptomics, and other omics technologies, the metabolic pathways of various strains producing organic acids have gradually been elucidated. Based on this, new technologies such as synthetic biology and high-throughput screening have also been extensively studied. This review summarizes the latest research progress in improving organic acid biosynthesis through metabolic engineering, focusing on L-malic acid (L-MA) and succinic acid (SA). Finally, we also discuss the challenges and future prospects of this field. This review has important reference value in the fields of food, pharmaceuticals, and chemicals, providing a theoretical basis for the study of organic acid biosynthesis.

Engineering a Photoautotrophic Microbial Coculture toward Enhanced Biohydrogen Production

The application of synthetic phototrophic microbial consortia holds promise for sustainable bioenergy production. Nevertheless, strategies for the efficient construction and regulation of such consortia remain challenging. Applying tools of genetic engineering, this study successfully constructed a synthetic community of phototrophs using Rhodopseudomonas palustris (R. palustris) and an engineered strain of Synechocystis sp PCC6803 for acetate production (Synechocystis_acs), enabling the production of biohydrogen and fatty acids during nitrogen and carbon dioxide fixation. Elemental balance confirmed carbon capture and nitrogen fixation into the consortium. The strategy of circadian illumination effectively limited oxygen levels in the system, ensuring the activity of the nitrogenase in R. palustris, despite oxygenic photosynthesis happening in Synechocystis. When infrared light was introduced into the circadian illumination, the production of H2 (9.70 μmol mg-1) and fatty acids (especially C16 and C18) was significantly enhanced. Proteomic analysis indicated acetate exchange and light-dependent regulation of metabolic activities. Infrared illumination significantly stimulated the expression of proteins coding for nitrogen fixation, carbohydrate metabolism, and transporters in R. palustris, while constant white light led to the most upregulation of photosynthesis-related proteins in Synechocystis_acs. This study demonstrated the successful construction and light regulation of a phototrophic community, enabling H2 and fatty acid production through carbon and nitrogen fixation.

Engineering cellular redox homeostasis to optimize ethanol production in xylose-fermenting Saccharomyces cerevisiae strains

The transition from fossil fuels dependency to embracing renewable alternatives is pivotal for mitigating greenhouse gas emissions, with biorefineries playing a central role at the forefront of this transition. As a sustainable alternative, lignocellulosic feedstocks hold great promise for biofuels and biochemicals production. However, the effective utilization of complex sugars, such as xylose, remains a significant hurdle. To address this challenge, yeasts can be engineered as microbial platforms to convert the complex sugars derived from biomass. The efficient use of xylose by XR-XDH strains still poses a significant challenge due to redox imbalance limitations, leading to the accumulation of undesirable by-products. In this study, we focused on engineering the industrial S. cerevisiae strain PE-2, known for its robustness, and compared different strategies to balance cellular redox homeostasis, guided by a genome-scale metabolic model. Flux balance analysis guided the selection of four approaches: i. decoupling NADPH regeneration from CO2 production; ii. altering XDH cofactor affinity; iii. shifting XR cofactor preference; iv. incorporating alternate phosphoketolase and acetic acid conversion pathways. A comparative time-course targeted metabolic profile was conducted to assess the redox status of xylose-fermenting cells under anaerobic conditions. The main limitations of xylose-fermenting strains were tested and the replacement of xylose reductase with a NADH-preferred XR in the LVY142 strain proved to be the most effective strategy, resulting in an increase in ethanol yield and productivity, coupled with a reduction in by-products. Comparative analysis of various genetic approaches provided valuable insights into the complexities of redox engineering, highlighting the need for tailored strategies in yeast metabolic engineering for efficient biofuels and biochemicals production from lignocellulosic feedstocks.

Protein engineering of an oxidative cleavage-free pathway for crocetin-dialdehyde production in Escherichia coli

The growing depletion of petroleum resources and the increasing demand for sustainable alternatives have spurred advancements in microorganism-based biofactories. Among high-value compounds, carotenoids are widely sought after in pharmaceuticals, cosmetics, and nutrition, making them prime candidates for microbial production. In this study, we engineered an efficient biosynthetic pathway in Escherichia coli for the production of the C20-carotenoid crocetin-dialdehyde. By bypassing traditional oxidative cleavage reactions mediated by carotenoid cleavage dioxygenases (CCDs), our approach reduces the enzymatic complexity of the pathway. Using the crystal structure of a CrtMLIKE enzyme identified in this study, we developed a mutant enzyme capable of condensing two C10-geranyl pyrophosphate molecules to form C20-phytoene. This intermediate was then desaturated and oxidized by CrtN and CrtP to produce crocetin-dialdehyde, achieving a yield of 1.13 mg/L. By reducing enzyme requirements from six to three and eliminating the need for CCDs, this pathway alleviates metabolic stress on the host and enhances the scalability of production for industrial applications. Overall, our research presents a streamlined and innovative approach to carotenoid biosynthesis, advancing sustainable production methods for short-chain carotenoids.

Optimal resource allocation in micro-organisms under periodic nutrient fluctuations

Although microorganisms often live in dynamic environments, most studies, both experimental and theoretical, are carried out under static conditions. In this work, we investigate the issue of optimal resource allocation in bacteria growing in periodic environments. We consider a dynamic model describing the microbial metabolism under varying conditions, involving a control variable quantifying the protein precursors allocation. Our objective is to determine the optimal strategies maximizing the long-term growth of cells under a piecewise-constant periodic environment. Firstly, we perform a theoretical analysis of the resulting optimal control problem (OCP), based on the application the Pontryagin's Maximum Principle (PMP). We determine that the structure of the optimal control must be bang-bang, with possibly some singular arcs corresponding to optimal equilibria of the system. If the control presents singular arcs, then these can only be reached and left through chattering arcs. We also use a direct optimization method, implemented in the BOCOP software, to solve the studied OCP. Our study reveals that the optimal solution over a large time horizon is related to the one over a single period of the varying environment with periodic constraints. Moreover, we observe that the maximal average growth rate attainable under periodic conditions can be higher than the one under a constant environment. We further extend our analysis to conduct a qualitative comparison between the predictions from our model and some recent biological experiments on E. coli. This analysis particularly highlights the mechanisms of action of the ppGpp signaling molecule, thus providing relevant explanations of the experimental observations. In conclusion, our study corroborates previous research indicating that this molecule plays a crucial role in the regulation of resource allocation of protein precursors in E. coli.

Creating a Genetic Toolbox for the Carbon-Fixing, Nitrogen-Fixing and Dehalogenating Bacterium Xanthobacter autotrophicus

Xanthobacter autotrophicus is a metabolically flexible microorganism with two key features: (1) The organism has adapted to grow on a wide variety of carbon sources including CO2, methanol, formate, propylene, haloalkanes and haloacids; and (2) X. autotrophicus was the first chemoautotroph identified that could also simultaneously fix N2, meaning the organism can utilize CO2, N2, and H2 for growth. This metabolic flexibility has enabled use of X. autotrophicus for gas fixation, the creation of fertilizers and foods from gases, and the dehalogenation of environmental contaminants. Despite the wide variety of applications that have already been demonstrated for this organism, there are few genetic tools available to explore and exploit its metabolism. Here, we report a genetic toolbox for use in X. autotrophicus. We first identified suitable origins of replication and quantified their copy number, and identified antibiotic resistance cassettes that could be used as selectable markers. We then tested several constitutive and inducible promoters and terminators and quantified their promoter strengths and termination efficiencies. Finally, we demonstrated that gene expression tools remain effective under both autotrophic and dehalogenative metabolic conditions to show that these tools can be used in the environments that make X. autotrophicus unique. Our extensive characterization of these tools in X. autotrophicus will enable genetic and metabolic engineering to optimize production of fertilizers and foods from gases, and enable bioremediation of halogenated environmental contaminants.

Ogataea polymorpha as a next-generation chassis for industrial biotechnology

Ogataea (Hansenula) polymorpha is a nonconventional yeast with some unique characteristics, including fast growth, thermostability, and broad substrate spectrum. Other than common applications for protein production, O. polymorpha is attracting interest for chemical and protein production from methanol; a promising feedstock for the next-generation biomanufacturing due to its abundant sources and excellent characteristics. Benefiting from the development of synthetic biology, it has been engineered to produce value-added chemicals by extensively rewiring cellular metabolism. This Review discusses recently developed synthetic biology tools of O. polymorpha. The advances of chemicals production and systems biology were reviewed comprehensively. Finally, we look ahead to the developments of biomanufacturing in O. polymorpha to make an overall understanding of this chassis for academia and industry.

Shifting redox reaction equilibria on demand using an orthogonal redox cofactor

Nature's two redox cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), are held at different reduction potentials, driving catabolism and anabolism in opposite directions. In biomanufacturing, there is a need to flexibly control redox reaction direction decoupled from catabolism and anabolism. We established nicotinamide mononucleotide (NMN+) as a noncanonical cofactor orthogonal to NAD(P)+. Here we present the development of Nox Ortho, a reduced NMN+ (NMNH)-specific oxidase, that completes the toolkit to modulate NMNH:NMN+ ratio together with an NMN+-specific glucose dehydrogenase (GDH Ortho). The design principle discovered from Nox Ortho engineering and modeling is facilely translated onto six different enzymes to create NMN(H)-orthogonal biocatalysts with a consistent ~103-106-fold cofactor specificity switch from NAD(P)+ to NMN+. We assemble these enzymes to produce stereo-pure 2,3-butanediol in cell-free systems and in Escherichia coli, enabled by NMN(H)'s distinct redox ratio firmly set by its designated driving forces, decoupled from both NAD(H) and NADP(H).

Assessing global carbon sequestration and bioenergy potential from microalgae cultivation on marginal lands leveraging machine learning

This comprehensive study unveils the vast global potential of microalgae as a sustainable bioenergy source, focusing on the utilization of marginal lands and employing advanced machine learning techniques to predict biomass productivity. By identifying approximately 7.37 million square kilometers of marginal lands suitable for microalgae cultivation, this research uncovers the extensive potential of these underutilized areas, particularly within equatorial and low-latitude regions, for microalgae bioenergy development. This approach mitigates the competition for food resources and conserves freshwater supplies. Utilizing cutting-edge machine learning algorithms based on robust datasets from global microalgae cultivation experiments spanning 1994 to 2017, this study integrates essential environmental variables to map out a detailed projection of potential yields across a variety of landscapes. The analysis further delineates the bioenergy and carbon sequestration potential across two effective cultivation methods: Photobioreactors (PBRs), and Open Ponds, with PBRs showcasing exceptional productivity, with a global average daily biomass productivity of 142.81mgL-1d-1, followed by Open Ponds at 122.57mgL-1d-1. Projections based on optimal PBR conditions suggest an annual yield of 99.54 gigatons of microalgae biomass. This yield can be transformed into 64.70 gigatons of biodiesel, equivalent to 58.68 gigatons of traditional diesel, while sequestering 182.16 gigatons of CO2, equating to approximately 4.5 times the global CO2 emissions projected for 2023. Notably, Australia leads in microalgae biomass production, with an annual output of 16.19 gigatons, followed by significant contributions from Kazakhstan, Sudan, Brazil, the United States, and China, showcasing the diverse global potential for microalgae bioenergy across varying ecological and geographical landscapes. Through this rigorous investigation, the study emphasizes the strategic importance of microalgae cultivation in achieving sustainable energy solutions and mitigating climate change, while also acknowledging the scalability challenges and the necessity for significant economic and energy investments.

Expanding chemistry through in vitro and in vivo biocatalysis

Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.

A chimeric membrane enzyme and an engineered whole-cell biocatalyst for efficient 1-alkene production

Bioproduction of 1-alkenes from naturally abundant free fatty acids offers a promising avenue toward the next generation of hydrocarbon-based biofuels and green commodity chemicals. UndB is the only known membrane-bound 1-alkene-producing enzyme, with great potential for 1-alkene bioproduction, but the enzyme exhibits limited turnovers, thus restricting its widespread usage. Here, we explore the molecular basis of the limitation of UndB activity and substantially improve its catalytic power. We establish that the enzyme undergoes peroxide-mediated rapid inactivation during catalysis. To counteract this inactivation, we engineered a chimeric membrane enzyme by conjugating UndB with catalase that protected UndB against peroxide and enhanced its number of turnovers tremendously. Notably, our chimeric enzyme is the only example of a membrane enzyme successfully engineered with catalase. We subsequently constructed a whole-cell biocatalytic system and achieved remarkable efficiencies (up to 95%) in the biotransformation of a wide range of fatty acids (both aliphatic and aromatic) into corresponding 1-alkenes with numerous biotechnological applications.

Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis

BACKGROUND

Computational mining of useful enzymes and biosynthesis pathways is a powerful strategy for metabolic engineering. Through systematic exploration of all conceivable combinations of enzyme reactions, including both known compounds and those inferred from the chemical structures of established reactions, we can uncover previously undiscovered enzymatic processes. The application of the novel alternative pathways enables us to improve microbial bioproduction by bypassing or reinforcing metabolic bottlenecks. Benzylisoquinoline alkaloids (BIAs) are a diverse group of plant-derived compounds with important pharmaceutical properties. BIA biosynthesis has developed into a prime example of metabolic engineering and microbial bioproduction. The early bottleneck of BIA production in Escherichia coli consists of 3,4-dihydroxyphenylacetaldehyde (DHPAA) production and conversion to tetrahydropapaveroline (THP). Previous studies have selected monoamine oxidase (MAO) and DHPAA synthase (DHPAAS) to produce DHPAA from dopamine and oxygen; however, both of these enzymes produce toxic hydrogen peroxide as a byproduct.

RESULTS

In the current study, in silico pathway design is applied to relieve the bottleneck of DHPAA production in the synthetic BIA pathway. Specifically, the cytochrome P450 enzyme, tyrosine N-monooxygenase (CYP79), is identified to bypass the established MAO- and DHPAAS-mediated pathways in an alternative arylacetaldoxime route to DHPAA with a peroxide-independent mechanism. The application of this pathway is proposed to result in less formation of toxic byproducts, leading to improved production of reticuline (up to 60 mg/L at the flask scale) when compared with that from the conventional MAO pathway.

CONCLUSIONS

This study showed improved reticuline production using the bypass pathway predicted by the M-path computational platform. Reticuline production in E. coli exceeded that of the conventional MAO-mediated pathway. The study provides a clear example of the integration of pathway mining and enzyme design in creating artificial metabolic pathways and suggests further potential applications of this strategy in metabolic engineering.

Local Ordering, Distortion, and Redox Activity in (La0.75Sr0.25)(Mn0.25Fe0.25Co0.25Al0.25)O3 Investigated by a Computational Workflow for Compositionally Complex Perovskite Oxides

Mixing multiple cations can result in a significant configurational entropy, offer a new compositional space with vast tunability, and introduce new computational challenges. For applications such as the two-step solar thermochemical hydrogen (STCH) generation techniques, we demonstrate that using density functional theory (DFT) combined with Metropolis Monte Carlo method (DFT-MC) can efficiently sample the possible cation configurations in compositionally complex perovskite oxide (CCPO) materials, with (La0.75Sr0.25)(Mn0.25Fe0.25Co0.25Al0.25)O3 as an example. In the presence of oxygen vacancies (VO), DFT-MC simulations reveal a significant increase of the local site preference of the cations (short-range ordering), compared to a more random mixing without VO. Co is found to be the redox-active element and the VO is the preferentially generated next to Co due to the stretched Co-O bonds. A clear definition of the vacancy formation energy (Evf) is proposed for CCPO in an ensemble of structures evolved in parallel from independent DFT-MC paths. By combining the distribution of Evf with VO interactions into a statistical model, the oxygen nonstoichiometry (δ), under the STCH thermal reduction and oxidation conditions, is predicted and compared with the experiments. Similar to the experiments, the predicted δ can be used to extract the enthalpy and entropy of reduction using the van't Hoff method, providing direct comparisons with the experimental results. This procedure provides a full predictive workflow for using DFT-MC to obtain possible local ordering or fully random structures, understand the redox activity of each element, and predict the thermodynamic properties of CCPOs, for computational screening and design of these CCPO materials at STCH conditions.

Perspectives on Genetically Engineered Microorganisms and Their Regulation in the United States

Genetically engineered microorganisms (GEMs) represent a new paradigm in our ability to address the needs of a growing, changing world. GEMs are being used in agriculture, food production and additives, manufacturing, commodity and noncommodity products, environmental remediation, etc., with even more applications in the pipeline. Along with modern advances in genome-manipulating technologies, new manufacturing processes, markets, and attitudes are driving a boom in more products that contain or are derived from GEMs. Consequentially, researchers and developers are poised to interact with biotechnology regulatory policies that have been in effect for decades, but which are out of pace with rapidly changing scientific advances and knowledge. In the United States, biotechnology is regulated by multiple agencies with overlapping responsibilities. This poses a challenge for both developers and regulators to simultaneously allow new innovation and products into the market while also ensuring their safety and efficacy for the public and environment. This article attempts to highlight the various factors that interact between regulatory policy and development of GEMs in the United States, with perspectives from both regulators and developers. We present insights from a 2022 workshop hosted at the University of California, Berkeley that convened regulators from U.S. regulatory agencies and industry developers of various GEMs and GEM-derived products. We highlight several new biotechnologies and applications that are driving innovation in this space, and how regulatory agencies evaluate and assess these products according to current policies. Additionally, we describe recent updates to regulations that incorporate new technology and knowledge and how they can adapt further to effectively continue regulating for the future.

Engineering a solar formic acid/pentose (SFAP) pathway in Escherichia coli for lactic acid production

Microbial CO2 fixation into lactic acid (LA) is an important approach for low-carbon biomanufacturing. Engineering microbes to utilize CO2 and sugar as co-substrates can create efficient pathways through input of moderate reducing power to drive CO2 fixation into product. However, to achieve complete conservation of organic carbon, how to engineer the CO2-fixing modules compatible with native central metabolism and merge the processes for improving bioproduction of LA is a big challenge. In this study, we designed and constructed a solar formic acid/pentose (SFAP) pathway in Escherichia coli, which enabled CO2 fixation merging into sugar catabolism to produce LA. In the SFAP pathway, adequate reducing equivalents from formate oxidation drive glucose metabolism shifting from glycolysis to the pentose phosphate pathway. The Rubisco-based CO2 fixation and sequential reduction of C3 intermediates are conducted to produce LA stoichiometrically. CO2 fixation theoretically can bring a 20% increase of LA production compared with sole glucose feedstock. This SFAP pathway in the integration of photoelectrochemical cell and an engineered Escherichia coli opens an efficient way for fixing CO2 into value-added bioproducts.

Parageobacillus thermoglucosidasius as an emerging thermophilic cell factory

Parageobacillus thermoglucosidasius is a thermophilic and facultatively anaerobic microbe, which is emerging as one of the most promising thermophilic model organisms for metabolic engineering. The use of thermophilic microorganisms for industrial bioprocesses provides the advantages of increased reaction rates and reduced cooling costs for bioreactors compared to their mesophilic counterparts. Moreover, it enables starch or lignocellulose degradation and fermentation to occur at the same temperature in a Simultaneous Saccharification and Fermentation (SSF) or Consolidated Bioprocessing (CBP) approach. Its natural hemicellulolytic capabilities and its ability to convert CO to metabolic energy make P. thermoglucosidasius a potentially attractive host for bio-based processes. It can effectively degrade hemicellulose due to a number of hydrolytic enzymes, carbohydrate transporters, and regulatory elements coded from a genomic cluster named Hemicellulose Utilization (HUS) locus. The growing availability of effective genetic engineering tools in P. thermoglucosidasius further starts to open up its potential as a versatile thermophilic cell factory. A number of strain engineering examples showcasing the potential of P. thermoglucosidasius as a microbial chassis for the production of bulk and fine chemicals are presented along with current research bottlenecks. Ultimately, this review provides a holistic overview of the distinct metabolic characteristics of P. thermoglucosidasius and discusses research focused on expanding the native metabolic boundaries for the development of industrially relevant strains.

A US perspective on closing the carbon cycle to defossilize difficult-to-electrify segments of our economy

Electrification to reduce or eliminate greenhouse gas emissions is essential to mitigate climate change. However, a substantial portion of our manufacturing and transportation infrastructure will be difficult to electrify and/or will continue to use carbon as a key component, including areas in aviation, heavy-duty and marine transportation, and the chemical industry. In this Roadmap, we explore how multidisciplinary approaches will enable us to close the carbon cycle and create a circular economy by defossilizing these difficult-to-electrify areas and those that will continue to need carbon. We discuss two approaches for this: developing carbon alternatives and improving our ability to reuse carbon, enabled by separations. Furthermore, we posit that co-design and use-driven fundamental science are essential to reach aggressive greenhouse gas reduction targets.

The Sustainable Approach of Process Intensification in Biorefinery Through Reactive Extraction Coupled with Regeneration for Recovery of Protocatechuic Acid

In the current scenario, where environmental degradation, global climate change, and the depletion of petroleum feedstock pose significant challenges, the chemical industry seeks sustainable alternatives for manufacturing chemicals, fuels, and bioplastics. Biorefining processes that integrate biomass conversion and microbial fermentation have emerged as preferred approaches to create value-added compounds. However, commercializing biorefinery products is hindered by dilute concentrations of final products and the demand for high purity goods. To address these challenges, effective separation and recovery procedures are essential to minimize costs and equipment size. This article proposes a biorefinery route for the production of protocatechuic acid (PCA) by focusing on in situ PCA separation and purification from fermentation broth. PCA is a significant phenolic molecule with numerous applications in the pharmaceutical sector for its anti-inflammatory, antiapoptotic, and antioxidant properties, as well as in the food, polymer, and other chemical industries. The chemical approach is predominantly used to produce PCA due to the cost-prohibitive nature of natural extraction techniques. Reactive extraction, a promising technique known for its enhanced extraction efficiency, is identified as a viable strategy for recovering carboxylic acids compared to conventional methods. The extraction of PCA has been explored using various solvents, including natural and conventional solvents, such as aminic and organophosphorous extractants, as well as the potential utilization of ionic liquids as green solvents. Additionally, back extraction techniques like temperature swing and diluent composition swing can be employed for reactive extraction product recovery, facilitating the regeneration of the extractant from the organic phase. By addressing the challenges associated with PCA production and usage, particularly through reactive extraction, this proposed biorefinery route aims to contribute to a more sustainable and environmentally friendly chemical industry. The incorporation of PCA in the biorefinery process allows for the utilization of this valuable compound with diverse industrial applications, thus providing an additional incentive for the development and optimization of efficient separation techniques.

Simultaneous glucose and xylose utilization by an Escherichia coli catabolite repression mutant

As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation of the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutant of the gene encoding the cyclic AMP receptor protein, crp*, has been shown to disable CCR and improve the co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site-specific crp* chromosomal mutant in E. coli BL21 star (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomics further showed that glucose was routed to the C5 carbon utilization pathways to support both de novo nucleotide synthesis and energy production in the crp* mutant strain. Metabolite analyses further show that overflow metabolism contributes to the slower growth in the crp* mutant. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.IMPORTANCEAs the need for renewable biofuel and biochemical production processes continues to grow, there is an associated need for microbial technology capable of utilizing cheap, widely available, and renewable carbon substrates. This work details the construction and characterization of the first B-lineage Escherichia coli strain with mutated cyclic AMP receptor protein, Crp*, which deregulates the carbon catabolite repression (CCR) system and enables the co-utilization of multiple sugar sources in the growth medium. In this study, we focus our analysis on glucose and xylose utilization as these two sugars are the primary components in lignocellulosic biomass hydrolysate, a promising renewable carbon feedstock for industrial bioprocesses. This strain is valuable to the field as it enables the use of mixed sugar sources in traditional fed-batch based approaches, whereas the wild-type carbon catabolite repression system leads to biphasic growth and possible buildup of non-preferential sugars, reducing process efficiency at scale.

Functional production and biochemical investigation of an integral membrane enzyme for olefin biosynthesis

Integral membrane enzymes play essential roles in a plethora of biochemical processes. The fatty acid desaturases (FADS)-like superfamily is an important group of integral membrane enzymes that catalyze a wide array of reactions, including hydroxylation, desaturation, and cyclization; however, due to the membrane-bound nature, the majority of these enzymes have remained poorly understood. UndB is a member of the FADS-like superfamily, which catalyzes fatty acid decarboxylation, a chemically challenging reaction at the membrane interface. UndB reaction produces terminal olefins that are prominent biofuel candidates and building blocks of polymers with widespread industrial applications. Despite the great importance of UndB for several biotechnological applications, the enzyme has eluded comprehensive investigation. Here, we report details of the expression, solubilization, and purification of several constructs of UndB to achieve the optimally functional enzyme. We gained important insights into the biochemical, biophysical, and catalytic properties of UndB, including the thermal stability and factors influencing the enzyme activity. Additionally, we established the ability and kinetics of UndB to produce dienes by performing di-decarboxylation of diacids. We found that the reaction proceeds by forming a mono-carboxylic acid intermediate. Our findings shed light on the unexplored biochemical properties of the UndB and extend opportunities for its rigorous mechanistic and structural characterization.

Biosynthesis mechanisms of medium-chain carboxylic acids and alcohols in anaerobic microalgae fermentation regulated by pH conditions

Valorization of microalgae into high-value products and drop-in chemicals can reduce our dependence on non-renewable fossil fuels in an environmentally sustainable way. Among the valuable products, medium-chain carboxylic acids (MCCAs) and alcohols are attractive building blocks as fuel precursors. However, the biosynthetic mechanisms of MCCAs and alcohols in anaerobic microalgae fermentation and the regulating role of pH on the microbial structure and metabolism interaction among different functional groups have never been documented. In this work, we systematically investigated the roles of pH (5, 7, and 10) on the production of MCCAs and alcohols in anaerobic microalgae fermentation. The gene-centric and genome-centric metagenomes were employed to uncover the dynamics and metabolic network of the key players in the microbial communities. The results indicated that the pH significantly changed the product spectrum. The maximum production rate of alcohol was obtained at pH 5, while pH 7 was more beneficial for MCCA production. Metagenomic analysis reveals that this differential performance under different pH is attributed to the transformation of microbial guild and metabolism regulated by pH. The composition of various functional groups for MCCA and alcohol production also varies at different pH levels. Finally, a metabolic network was proposed to reveal the microbial interactions at different pH levels and thus provide insights into bioconversion of microalgae to high-value biofuels.IMPORTANCECarboxylate platforms encompass a biosynthesis process involving a mixed and undefined culture, enabling the conversion of microalgae, rich in carbohydrates and protein, into valuable fuels and mitigating the risks associated with algae blooms. However, there is little known about the effects of pH on the metabolic pathways of chain elongation and alcohol production in anaerobic microalgae fermentation. Moreover, convoluted and interdependent microbial interactions encumber efforts to characterize how organics and electrons flow among microbiome members. In this work, we compared metabolic differences among three different pH levels (5, 7, and 10) in anaerobic microalgae fermentation. In addition, genome-centric metagenomic analysis was conducted to reveal the microbial interaction for medium-chain carboxylic acid and alcohol production.

Engineering a Novel Acetyl-CoA Pathway for Efficient Biosynthesis of Acetyl-CoA-Derived Compounds

Acetyl-CoA is an essential central metabolite in living organisms and a key precursor for various value-added products as well. However, the intracellular availability of acetyl-CoA limits the efficient production of these target products due to complex and strict regulation. Here, we proposed a new acetyl-CoA pathway, relying on two enzymes, threonine aldolase and acetaldehyde dehydrogenase (acetylating), which can convert one l-threonine into one acetyl-CoA, one glycine, and generate one NADH, without carbon loss. Introducing the acetyl-CoA pathway could increase the intracellular concentration of acetyl-CoA by 8.6-fold compared with the wild-type strain. To develop a cost-competitive and genetically stable acetyl-CoA platform strain, the new acetyl-CoA pathway, driven by the constitutive strong promoter, was integrated into the chromosome of Escherichia coli. We demonstrated the practical application of this new acetyl-CoA pathway by high titer production of β-alanine, mevalonate, and N-acetylglucosamine. At the same time, this pathway achieved a high-yield production of glycine, a value-added commodity chemical for the synthesis of glyphosate and thiamphenicol. This work shows the potential of this new acetyl-CoA pathway for the industrial production of acetyl-CoA-derived compounds.

Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli

One-carbon (C1) substrates, such as methanol or formate, are attractive feedstocks for circular bioeconomy. These substrates are typically converted into formaldehyde, serving as the entry point into metabolism. Here, we design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, leveraging a promiscuous dihydroxyacetone phosphate dependent aldolase as key enzyme. In silico modeling reveals that the cycle is highly energy-efficient, holding the potential for high bioproduct yields. Dissecting the EuMP into four modules, we use a stepwise strategy to demonstrate in vivo feasibility of the modules in E. coli sensor strains with sarcosine as formaldehyde source. From adaptive laboratory evolution for module integration, we identify key mutations enabling the accommodation of the EuMP reactions with endogenous metabolism. Overall, our study demonstrates the proof-of-concept for a highly efficient, new-to-nature formaldehyde assimilation pathway, opening a way for the development of a methylotrophic platform for a C1-fueled bioeconomy in the future.

Automated Platform for the Plasmid Construction Process

There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J5 DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.

Thermal Sensitivity of the Enzymatic Activity of β-Glucosidase: Simulations Lend Mechanistic Insights into Experimental Observations

A crucial prerequisite for industrial applications of enzymes is the maintenance of specific activity across wide thermal ranges. β-Glucosidase (EC 3.2.1.21) is an essential enzyme for converting cellulose in biomass to glucose. While the reaction mechanisms of β-glucosidases from various thermal ranges (hyperthermophilic, thermophilic, and mesophilic) are similar, the factors underlying their thermal sensitivity remain obscure. The work presented here aims to unravel the molecular mechanisms underlying the thermal sensitivity of the enzymatic activity of the β-glucosidase BglB from the bacterium Paenibacillus polymyxa. Experiments reveal a maximum enzymatic activity at 315 K, with a marked decrease in the activity below and above this temperature. Employing in silico simulations, we identified the crucial role of the active site tunnel residues in the thermal sensitivity. Specific tunnel residues were identified via energetic decomposition and protein-substrate hydrogen bond analyses. The experimentally observed trends in specific activity with temperature coincide with variations in overall binding free energy changes, showcasing a predominantly electrostatic effect that is consistent with enhanced catalytic pocket-substrate hydrogen bonding (HB) at Topt. The entropic advantage owing to the HB substate reorganization was found to facilitate better substrate binding at 315 K. This study elicits molecular-level insights into the associative mechanisms between thermally enabled fluctuations and enzymatic activity. Crucial differences emerge between molecular mechanisms involving the actual substrate (cellobiose) and a commonly employed chemical analogue. We posit that leveraging the role of fluctuations may reveal unexpected insights into enzyme behavior and offer novel paradigms for enzyme engineering.

Carbon dioxide reduction to high-value chemicals in microbial electrosynthesis system: Biological conversion and regulation strategies

Large emissions of atmospheric carbon dioxide (CO2) are causing climatic and environmental problems. It is crucial to capture and utilize the excess CO2 through diverse methods, among which the microbial electrosynthesis (MES) system has become an attractive and promising technology to mitigate greenhouse effects while reducing CO2 to high-value chemicals. However, the biological conversion and metabolic pathways through microbial catalysis have not been clearly elucidated. This review first introduces the main acetogenic bacteria for CO2 reduction and extracellular electron transfer mechanisms in MES. It then intensively analyzes the CO2 bioconversion pathways and carbon chain elongation processes in MES, together with energy supply and utilization. The factors affecting MES performance, including physical, chemical, and biological aspects, are summarized, and the strategies to promote and regulate bioconversion in MES are explored. Finally, challenges and perspectives concerning microbial electrochemical carbon sequestration are proposed, and suggestions for future research are also provided. This review provides theoretical foundation and technical support for further development and industrial application of MES for CO2 reduction.

Bubble column photobioreactor (BCPR) for cultivating microalgae and microalgal consortium (Co-CC) with additional CO2 supply for enhancing biomass, lipid, and preferable fatty acids production

The present study has designed and developed a 5 L bubble column photobioreactor (BCPR) to investigate two microalgal strains Chlorella sp. S-01, Chlorella sp. S-02 and their consortium Co-CC (Chlorella sp. S-01 + Chlorella sp. S-02) at 0.03, 5, and 10% CO2 supply for biomass and lipid production. The dry cell weight of Chlorella sp. S-01, Chlorella sp. S-02 and Co-CC were, respectively about 1.41, 1.32, and 1.39 g/L on the 20th day without CO2 supply, while it was 1.76, 1.61, and 1.87 g/L, respectively at 10% CO2 supply and similarly, chlorophyll-a content was higher in 10% CO2 supplied condition over control. Interestingly, Co-CC grown at all the CO2 concentrations showed similar lipid content between 19.30 and 1F9.41%. As an integrated refinery approach, de-oiled biomass of Co-CC was subjected to carbohydrates and protein estimation and found that 46.2% and 30.80% in 10% CO2 supply condition in BCPR. Lipid extracted from the Co-CC grown under 0.03, 5, and 10% CO2 supply in 5L BCPR was converted to biodiesel, and the biodiesel yield was estimated to be 62.78%. Further, the fatty acid profile of Co-CC grown at 10% CO2 showed higher levels of C16:0, C16:1, C18:1, and monounsaturated fatty acids contents over other CO2 supplied conditions. Biodiesel of Co-CC showed favourable fuel properties such as density, higher heating value, oxidative stability, CFPP, viscosity, degree of unsaturation, saponification value, and cetane number, which were also in accordance with ASTM, and EN, biodiesel standards.

Perspectives for Using CO2 as a Feedstock for Biomanufacturing of Fuels and Chemicals

Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions-a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed.

A cellular platform for production of C4 monomers

Living organisms carry out a wide range of remarkable functions, including the synthesis of thousands of simple and complex chemical structures for cellular growth and maintenance. The manipulation of this reaction network has allowed for the genetic engineering of cells for targeted chemical synthesis, but it remains challenging to alter the program underlying their fundamental chemical behavior. By taking advantage of the unique ability of living systems to use evolution to find solutions to complex problems, we have achieved yields of up to ∼95% for three C4 commodity chemicals, n-butanol, 1,3-butanediol, and 4-hydroxy-2-butanone. Genomic sequencing of the evolved strains identified pcnB and rpoBC as two gene loci that are able to alter carbon flow by remodeling the transcriptional landscape of the cell, highlighting the potential of synthetic pathways as a tool to identify metabolic control points.

Design and Construction of Artificial Biological Systems for One-Carbon Utilization

The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.

Awakening the natural capability of psicose production in Escherichia coli

Due to the rampant rise in obesity and diabetes, consumers are desperately seeking for ways to reduce their sugar intake, but to date there are no options that are both accessible and without sacrifice of palatability. One of the most promising new ingredients in the food system as a non-nutritive sugar substitute with near perfect palatability is D-psicose. D-psicose is currently produced using an in vitro enzymatic isomerization of D-fructose, resulting in low yield and purity, and therefore requiring substantial downstream processing to obtain a high purity product. This has made adoption of D-psicose into products limited and results in significantly higher per unit costs, reducing accessibility to those most in need. Here, we found that Escherichia coli natively possesses a thermodynamically favorable pathway to produce D-psicose from D-glucose through a series of phosphorylation-epimerization-dephosphorylation steps. To increase carbon flux towards D-psicose production, we introduced a series of genetic modifications to pathway enzymes, central carbon metabolism, and competing metabolic pathways. In an attempt to maximize both cellular viability and D-psicose production, we implemented methods for the dynamic regulation of key genes including clustered regularly interspaced short palindromic repeats inhibition (CRISPRi) and stationary-phase promoters. The engineered strains achieved complete consumption of D-glucose and production of D-psicose, at a titer of 15.3 g L-1, productivity of 2 g L-1 h-1, and yield of 62% under test tube conditions. These results demonstrate the viability of whole-cell catalysis as a sustainable alternative to in vitro enzymatic synthesis for the accessible production of D-psicose.

Bacterial Membrane Vesicles for In Vitro Catalysis

The use of biological systems in manufacturing and medical applications has seen a dramatic rise in recent years as scientists and engineers have gained a greater understanding of both the strengths and limitations of biological systems. Biomanufacturing, or the use of biology for the production of biomolecules, chemical precursors, and others, is one particular area on the rise as enzymatic systems have been shown to be highly advantageous in limiting the need for harsh chemical processes and the formation of toxic products. Unfortunately, biological production of some products can be limited due to their toxic nature or reduced reaction efficiency due to competing metabolic pathways. In nature, microbes often secrete enzymes directly into the environment or encapsulate them within membrane vesicles to allow catalysis to occur outside the cell for the purpose of environmental conditioning, nutrient acquisition, or community interactions. Of particular interest to biotechnology applications, researchers have shown that membrane vesicle encapsulation often confers improved stability, solvent tolerance, and other benefits that are highly conducive to industrial manufacturing practices. While still an emerging field, this review will provide an introduction to biocatalysis and bacterial membrane vesicles, highlight the use of vesicles in catalytic processes in nature, describe successes of engineering vesicle/enzyme systems for biocatalysis, and end with a perspective on future directions, using selected examples to illustrate these systems' potential as an enabling tool for biotechnology and biomanufacturing.

Thermophilic Moorella thermoacetica as a platform microorganism for C1 gas utilization: physiology, engineering, and applications

In the context of the rapid development of low-carbon economy, there has been increasing interest in utilizing naturally abundant and cost-effective one-carbon (C1) substrates for sustainable production of chemicals and fuels. Moorella thermoacetica, a model acetogenic bacterium, has attracted significant attention due to its ability to utilize carbon dioxide (CO2) and carbon monoxide (CO) via the Wood-Ljungdahl (WL) pathway, thereby showing great potential for the utilization of C1 gases. However, natural strains of M. thermoacetica are not yet fully suitable for industrial applications due to their limitations in carbon assimilation and conversion efficiency as well as limited product range. Over the past decade, progresses have been made in the development of genetic tools for M. thermoacetica, accelerating the understanding and modification of this acetogen. Here, we summarize the physiological and metabolic characteristics of M. thermoacetica and review the recent advances in engineering this bacterium. Finally, we propose the future directions for exploring the real potential of M. thermoacetica in industrial applications.

Genomic Analysis of Leptolyngbya boryana CZ1 Reveals Efficient Carbon Fixation Modules

Cyanobacteria, one of the most widespread photoautotrophic microorganisms on Earth, have evolved an inorganic CO2-concentrating mechanism (CCM) to adapt to a variety of habitats, especially in CO2-limited environments. Leptolyngbya boryana, a filamentous cyanobacterium, is widespread in a variety of environments and is well adapted to low-inorganic-carbon environments. However, little is currently known about the CCM of L. boryana, in particular its efficient carbon fixation module. In this study, we isolated and purified the cyanobacterium CZ1 from the Xin'anjiang River basin and identified it as L. boryana by 16S rRNA sequencing. Genome analysis revealed that L. boryana CZ1 contains β-carboxysome shell proteins and form 1B of Rubisco, which is classify it as belonging to the β-cyanobacteria. Further analysis revealed that L. boryana CZ1 employs a fine CCM involving two CO2 uptake systems NDH-13 and NDH-14, three HCO3- transporters (SbtA, BicA, and BCT1), and two carboxysomal carbonic anhydrases. Notably, we found that NDH-13 and NDH-14 are located close to each other in the L. boryana CZ1 genome and are back-to-back with the ccm operon, which is a novel gene arrangement. In addition, L. boryana CZ1 encodes two high-affinity Na+/HCO3- symporters (SbtA1 and SbtA2), three low-affinity Na+-dependent HCO3- transporters (BicA1, BicA2, and BicA3), and a BCT1; it is rare for a single strain to encode all three bicarbonate transporters in such large numbers. Interestingly, L. boryana CZ1 also uniquely encodes two active carbonic anhydrases, CcaA1 and CcaA2, which are also rare. Taken together, all these results indicated that L. boryana CZ1 is more efficient at CO2 fixation. Moreover, compared with the reported CCM gene arrangement of cyanobacteria, the CCM-related gene distribution pattern of L. boryana CZ1 was completely different, indicating a novel gene organization structure. These results can enrich our understanding of the CCM-related gene arrangement of cyanobacteria, and provide data support for the subsequent improvement and increase in biomass through cyanobacterial photosynthesis.

Development of a Novel D-Lactic Acid Production Platform Based on Lactobacillus saerimneri TBRC 5746

D-Lactic acid is a chiral, three-carbon organic acid, that bolsters the thermostability of polylactic acid. In this study, we developed a microbial production platform for the high-titer production of D-lactic acid. We screened 600 isolates of lactic acid bacteria (LAB) and identified twelve strains that exclusively produced D-lactic acid in high titers. Of these strains, Lactobacillus saerimneri TBRC 5746 was selected for further development because of its homofermentative metabolism. We investigated the effects of high temperature and the use of cheap, renewable carbon sources on lactic acid production and observed a titer of 99.4 g/L and a yield of 0.90 g/g glucose (90% of the theoretical yield). However, we also observed L-lactic acid production, which reduced the product's optical purity. We then used CRISPR/dCas9-assisted transcriptional repression to repress the two Lldh genes in the genome of L. saerimneri TBRC 5746, resulting in a 38% increase in D-lactic acid production and an improvement in optical purity. This is the first demonstration of CRISPR/dCas9-assisted transcriptional repression in this microbial host and represents progress toward efficient microbial production of D-lactic acid.

Using a synthetic machinery to improve carbon yield with acetylphosphate as the core

In microbial cell factory, CO2 release during acetyl-CoA production from pyruvate significantly decreases the carbon atom economy. Here, we construct and optimize a synthetic carbon conserving pathway named as Sedoheptulose-1,7-bisphosphatase Cycle with Trifunctional PhosphoKetolase (SCTPK) in Escherichia coli. This cycle relies on a generalist phosphoketolase Xfspk and converts glucose into the stoichiometric amounts of acetylphosphate (AcP). Furthermore, genetic circuits responding to AcP positively or negatively are created. Together with SCTPK, they constitute a gene-metabolic oscillator that regulates Xfspk and enzymes converting AcP into valuable chemicals in response to intracellular AcP level autonomously, allocating metabolic flux rationally and improving the carbon atom economy of bioconversion process. Using this synthetic machinery, mevalonate is produced with a yield higher than its native theoretical yield, and the highest titer and yield of 3-hydroxypropionate via malonyl-CoA pathway are achieved. This study provides a strategy for improving the carbon yield of microbial cell factories.

Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor

Natural metabolism relies on chemical compartmentalization of two redox cofactors, NAD+ and NADP+, to orchestrate life-essential redox reaction directions. However, in whole cells the reliance on these canonical cofactors limits flexible control of redox reaction direction as these reactions are permanently tied to catabolism or anabolism. In cell-free systems, NADP+ is too expensive in large scale. We have previously reported the use of nicotinamide mononucleotide, (NMN+) as a low-cost, noncanonical redox cofactor capable of specific electron delivery to diverse chemistries. Here, we present Nox Ortho, an NMNH-specific water-forming oxidase, that completes the toolkit to modulate NMNH/NMN+ ratio. This work uncovers an enzyme design principle that succeeds in parallel engineering of six butanediol dehydrogenases as NMN(H)-orthogonal biocatalysts consistently with a 103 - 106 -fold cofactor specificity switch from NAD(P)+ to NMN+. We combine these to produce chiral-pure 2,3-butanediol (Bdo) isomers without interference from NAD(H) or NADP(H) in vitro and in E. coli cells. We establish that NMN(H) can be held at a distinct redox ratio on demand, decoupled from both NAD(H) and NADP(H) redox ratios in vitro and in vivo.

Biosynthesis pathways of expanding carbon chains for producing advanced biofuels

Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.

Consolidated bioprocessing for bioethanol production by metabolically engineered cellulolytic fungus Myceliophthora thermophila

Using cellulosic ethanol as fuel is one way to help achieve the world's decarbonization goals. However, the economics of the present technology are unfavorable, especially the cost of cellulose degradation. Here, we reprogram the thermophilic cellulosic fungus Myceliophthora thermophila to directly ferment cellulose into ethanol by mimicking the aerobic ethanol fermentation of yeast (the Crabtree effect), including optimizing the synthetic pathway, enhancing the glycolytic rate, inhibiting mitochondrial NADH shuttles, and knocking out ethanol consumption pathway. The final engineered strain produced 52.8 g/L ethanol directly from cellulose, and 39.8 g/L from corncob, without the need for any added cellulase, while the starting strain produced almost no ethanol. We also demonstrate that as the ethanol fermentation by engineered M. thermophila increases, the composition and expression of cellulases that facilitate the degradation of cellulose, especially cellobiohydrolases, changes. The simplified production process and significantly increased ethanol yield indicate that the fungal consolidated bioprocessing technology that we develop here (one-step, one-strain ethanol production) is promising for fueling sustainable carbon-neutral biomanufacturing in the future.

Different pre-treatments and kinetic models for bioethanol production from lignocellulosic biomass: A review

Lignocellulosic biomass is the generally explored substrate to produce bioethanol for environmental sustainability due to its availability in abundance. However, the complex network of cellulose-hemicellulose-lignin present in it makes its hydrolysis as a challenging task. To boost the effectiveness of conversion, biomass is pre-treated before enzymatic hydrolysis to alter or destroy its original composition. Enzymes like Cellulases are widely used for breaking down cellulose into fermentable sugars. Enzymatic hydrolysis is a complex process involving many influencing factors such as pH, temperature, substrate concentration. This review presents major four pre-treatment methods used for hydrolysing different substrates under varied reaction conditions along with their mechanism and limitations. A relative comparison of data analysis for most widely studied 10 kinetic models is briefly explained in terms of substrates used to get the brief insight about hydrolysis rates. The summary of pre-treatment methods and hydrolysis rates including cellulase enzyme kinetics will be the value addition for upcoming researchers for optimising the hydrolysis process.

Dimer-assisted mechanism of (un)saturated fatty acid decarboxylation for alkene production

The enzymatic decarboxylation of fatty acids (FAs) represents an advance toward the development of biological routes to produce drop-in hydrocarbons. The current mechanism for the P450-catalyzed decarboxylation has been largely established from the bacterial cytochrome P450 OleTJE. Herein, we describe OleTPRN, a poly-unsaturated alkene-producing decarboxylase that outrivals the functional properties of the model enzyme and exploits a distinct molecular mechanism for substrate binding and chemoselectivity. In addition to the high conversion rates into alkenes from a broad range of saturated FAs without dependence on high salt concentrations, OleTPRN can also efficiently produce alkenes from unsaturated (oleic and linoleic) acids, the most abundant FAs found in nature. OleTPRN performs carbon-carbon cleavage by a catalytic itinerary that involves hydrogen-atom transfer by the heme-ferryl intermediate Compound I and features a hydrophobic cradle at the distal region of the substrate-binding pocket, not found in OleTJE, which is proposed to play a role in the productive binding of long-chain FAs and favors the rapid release of products from the metabolism of short-chain FAs. Moreover, it is shown that the dimeric configuration of OleTPRN is involved in the stabilization of the A-A' helical motif, a second-coordination sphere of the substrate, which contributes to the proper accommodation of the aliphatic tail in the distal and medial active-site pocket. These findings provide an alternative molecular mechanism for alkene production by P450 peroxygenases, creating new opportunities for biological production of renewable hydrocarbons.

Recovery of methane and acetate during ex-situ biogas upgrading via novel dual-membrane aerated biofilm reactor

Biological biogas upgrading has been well-proven to be a promising approach for renewable bioenergy recovery, but hydrogen (H₂)-assisted ex-situ biogas upgrading is hindered by a large solubility discrepancy between H₂ and carbon dioxide (CO₂). This study established a new dual-membrane aerated biofilm reactor (dMBfR) to improve the upgrading efficiency. Results showed that dMBfR operated at 1.25 atm H₂ partial pressure, 1.5 atm biogas partial pressure, and 1.0 d hydraulic retention time could significantly improve the efficiency. The maximum methane purity of 97.6%, acetate production rate of 34.5 mmol L^-1d^-1, and H₂ and CO₂ utilization ratios of 96.5% and 96.3% were achieved. Further analysis showed that the improved performances of biogas upgrading and acetate recovery were positively correlated with the total abundances of functional microorganisms. Taken together, these results suggest that the dMBfR, which facilitates the precise CO₂ and H₂ supply, is an ideal approach for efficient biological biogas upgrading.

Target integration of an exogenous β-glucosidase enhances cellulose degradation and ethanol production in Clostridium cellulolyticum

The bacteria Clostridium cellulolyticum is a promising candidate for consolidated bioprocessing (CBP). However, genetic engineering is necessary to improve this organism's cellulose degradation and bioconversion efficiencies to meet standard industrial requirements. In this study, CRISPR-Cas9n was used to integrate an efficient β-glucosidase into the genome of C. cellulolyticum, disrupting lactate dehydrogenase (ldh) expression and reducing lactate production. The engineered strain showed a 7.4-fold increase in β-glucosidase activity, a 70% decrease in ldh expression, a 12% increase in cellulose degradation, and a 32% increase in ethanol production compared to wild type. Additionally, ldh was identified as a potential site for heterologous expression. These results demonstrate that simultaneous β-glucosidase integration and lactate dehydrogenase disruption is an effective strategy for increasing cellulose to ethanol bioconversion rates in C. cellulolyticum.

Biosynthesis of monoterpenoid and sesquiterpenoid as natural flavors and fragrances

Terpenoids are a large class of plant-derived compounds, that constitute the main components of essential oils and are widely used as natural flavors and fragrances. The biosynthesis approach presents a promising alternative route in terpenoid production compared to plant extraction or chemical synthesis. In the past decade, the production of terpenoids using biotechnology has attracted broad attention from both academia and the industry. With the growing market of flavor and fragrance, the production of terpenoids directed by synthetic biology shows great potential in promoting future market prospects. Here, we reviewed the latest advances in terpenoid biosynthesis. The engineering strategies for biosynthetic terpenoids were systematically summarized from the enzyme, metabolic, and cellular dimensions. Additionally, we analyzed the key challenges from laboratory production to scalable production, such as key enzyme improvement, terpenoid toxicity, and volatility loss. To provide comprehensive technical guidance, we collected milestone examples of biosynthetic mono- and sesquiterpenoids, compared the current application status of chemical synthesis and biosynthesis in terpenoid production, and discussed the cost drivers based on the data of techno-economic assessment. It is expected to provide critical insights into developing translational research of terpenoid biomanufacturing.

Fungal biotechnology: From yesterday to tomorrow

Fungi have been used to better the lives of everyday people and unravel the mysteries of higher eukaryotic organisms for decades. However, comparing progress and development stemming from fungal research to that of human, plant, and bacterial research, fungi remain largely understudied and underutilized. Recent commercial ventures have begun to gain popularity in society, providing a new surge of interest in fungi, mycelia, and potential new applications of these organisms to various aspects of research. Biotechnological advancements in fungal research cannot occur without intensive amounts of time, investments, and research tool development. In this review, we highlight past breakthroughs in fungal biotechnology, discuss requirements to advance fungal biotechnology even further, and touch on the horizon of new breakthroughs with the highest potential to positively impact both research and society.

Growth-coupled enzyme engineering through manipulation of redox cofactor regeneration

Enzymes need to be efficient, robust, and highly specific for their effective use in commercial bioproduction. These properties can be introduced using various enzyme engineering techniques, with random mutagenesis and directed evolution (DE) often being chosen when there is a lack of structural information -or mechanistic understanding- of the enzyme. The screening or selection step of DE is the limiting part of this process, since it must ideally be (ultra)-high throughput, specifically target the catalytic activity of the enzyme and have an accurately quantifiable metric for said activity. Growth-coupling selection strategies involve coupling a desired enzyme activity to cellular metabolism and therefore growth, where growth (rate) becomes the output metric. Redox cofactors (NAD⁺/NADH and NADP⁺/NADPH) have recently been identified as promising target molecules for growth coupling, owing to their essentiality for cellular metabolism and ubiquitous nature. Redox cofactor oxidation or reduction can be disrupted through metabolic engineering and the use of specific culturing conditions, rendering the cell inviable unless a 'rescue' reaction complements the imposed metabolic deficiency. Using this principle, enzyme variants displaying improved cofactor oxidation or reduction rates can be selected for through an increased growth rate of the cell. In recent years, several E. coli strains have been developed that are deficient in the oxidation or reduction of NAD⁺/NADH and NADP⁺/NADPH pairs, and of non-canonical redox cofactor pairs NMN⁺/NMNH and NCD⁺/NCDH, which provides researchers with a versatile toolbox of enzyme engineering platforms. A range of redox cofactor dependent enzymes have since been engineered using a variety of these strains, demonstrating the power of using this growth-coupling technique for enzyme engineering. This review aims to summarize the metabolic engineering involved in creating strains auxotrophic for the reduced or oxidized state of redox cofactors, and the resulting successes in using them for enzyme engineering. Perspectives on the unique features and potential future applications of this technique are also presented.

Enrichment of hydrogen-oxidizing bacteria using a hybrid biological-inorganic system

Hybrid biological-inorganic (HBI) systems comprising inorganic water-splitting catalysts and aerobic hydrogen-oxidizing bacteria (HOB) have previously been used for CO₂ conversion. In order to identify new biocatalysts for CO₂ conversion, the present study used an HBI system to enrich HOB directly from environmental samples. Three sediment samples (from a brackish water pond, a beach, and a tide pool) and two activated sludge samples (from two separate sewage plants) were inoculated into HBI systems using a cobalt phosphorus (Co-P) alloy and cobalt phosphate (CoPi) as inorganic catalysts with a fixed voltage of 2.0 V. The gas composition of the reactor headspaces and electric current were monitored. An aliquot of the reactor medium was transferred to a new reactor when significant consumption of H₂ and CO₂ was detected. This process was repeated twice (with three reactors in operation for each sample) to enrich HOB. Increased biomass concomitant with increased H₂ and CO₂ consumption was observed in the third reactor, indicating enrichment of HOB. 16S rRNA gene amplicon sequencing demonstrated enrichment of sequences related to HOB (including bacteria from Mycobacterium, Hydrogenophaga, and Xanthobacter genera) over successive sub-cultures. Finally, four different HOB belonging to the Mycobacterium, Hydrogenophaga, Xanthobacter, and Acidovorax genera were isolated from reactor media, representing potential candidates as HBI system biocatalysts.

Evaluation of 1,2-diacyl-3-acetyl triacylglycerol production in Yarrowia lipolytica

Plants produce many high-value oleochemical molecules. While oil-crop agriculture is performed at industrial scales, suitable land is not available to meet global oleochemical demand. Worse, establishing new oil-crop farms often comes with the environmental cost of tropical deforestation. The field of metabolic engineering offers tools to transplant oleochemical metabolism into tractable hosts while simultaneously providing access to molecules produced by non-agricultural plants. Here, we evaluate strategies for rewiring metabolism in the oleaginous yeast Yarrowia lipolytica to synthesize a foreign lipid, 3-acetyl-1,2-diacyl-sn-glycerol (acTAG). Oils made up of acTAG have a reduced viscosity and melting point relative to traditional triacylglycerol oils making them attractive as low-grade diesels, lubricants, and emulsifiers. This manuscript describes a metabolic engineering study that established acTAG production at g/L scale, exploration of the impact of lipid bodies on acTAG titer, and a techno-economic analysis that establishes the performance benchmarks required for microbial acTAG production to be economically feasible.

Environmental formaldehyde sensing at room temperature by smartphone-assisted and wearable plasmonic nanohybrids

Formaldehyde is a toxic and carcinogenic indoor air pollutant. Promising for its routine detection are gas sensors based on localized surface plasmon resonance (LSPR). Such sensors trace analytes by converting tiny changes in the local dielectric environment into easily readable, optical signals. Yet, this mechanism is inherently non-selective to volatile organic compounds (like formaldehyde) and yields rarely detection limits below parts-per-million concentrations. Here, we reveal that chemical reaction-mediated LSPR with nanohybrids of Ag/AgOx core-shell clusters on TiO2 enables highly selective formaldehyde sensing down to 5 parts-per-billion (ppb). Therein, AgOx is reduced by the formaldehyde to metallic Ag resulting in strong plasmonic signal changes, as measured by UV/Vis spectroscopy and confirmed by X-ray diffraction. This interaction is highly selective to formaldehyde over other aldehydes, alcohols, ketones, aromatic compounds (as confirmed by high-resolution mass spectrometry), inorganics, and quite robust to relative humidity changes. Since this sensor works at room temperature, such LSPR nanohybrids are directly deposited onto flexible wristbands to quantify formaldehyde between 40-500 ppb at 50% RH, even with a widely available smartphone camera (Pearson correlation coefficient r = 0.998). Such chemoresponsive coatings open new avenues for wearable devices in environmental, food, health and occupational safety applications, as demonstrated by an early field test in the pathology of a local hospital.