Turn air-captured CO2 with methanol into amino acid and pyruvate in an ATP/NAD(P)H-free chemoenzymatic system

Sequence and taxonomic feature evaluation facilitated the discovery of alcohol oxidases

Recent advancements in data technology offer immense opportunities for the discovery and development of new enzymes for the green synthesis of chemicals. Current protein databases predominantly prioritize overall sequence matches. The multi-scale features underpinning catalytic mechanisms and processes, which are scattered across various data sources, have not been sufficiently integrated to be effectively utilized in enzyme mining. In this study, we developed a sequence- and taxonomic-feature evaluation driven workflow to discover enzymes that can be expressed in E. coli and catalyze chemical reactions in vitro, using alcohol oxidase (AOX) for demonstration, which catalyzes the conversion of methanol to formaldehyde. A dataset of 21 reported AOXs was used to construct sequence scoring rules based on features, including sequence length, structural motifs, catalytic-related residues, binding residues, and overall structure. These scoring rules were applied to filter the results from HMM-based searches, yielding 357 candidate sequences of eukaryotic origin, which were categorized into six classes at 85 % sequence similarity. Experimental validation was conducted in two rounds on 31 selected sequences representing all classes. Among these selected sequences, 19 were expressed as soluble proteins in E. coli, and 18 of these soluble proteins exhibited AOX activity, as predicted. Notably, the most active recombinant AOX exhibited an activity of 8.65 ± 0.29 U/mg, approaching the highest activity of native eukaryotic enzymes. Compared to the established UniProt-annotation-based workflow, this feature-evaluation-based approach yielded a higher probability of highly active recombinant AOX (from 8.3 % to 19.4 %), demonstrating the efficiency and potential of this multi-dimensional feature evaluation method in accelerating the discovery of active enzymes.

Economic and sustainable revolution to facilitate one-carbon biomanufacturing

One-carbon (C1) biomanufacturing serves as a substitute for fossil-based feedstocks, aiming to de-fossilize chemical production and foster a circular carbon economy by recycling waste greenhouse gases. Here, we review the key economic and technical barriers associated with the commercialization of C1 biomanufacturing through case studies. Additionally, a viable roadmap to enhance cost competitiveness is unveiled, underscoring its potential to facilitate carbon neutrality as scalable and sustainable alternatives to traditional chemical production.

Cell-free synthesis of high-order carbohydrates from low-carbon molecules

Artificial conversion of CO2 into foods and chemicals offers a sustainable way to tackle population-related and environmental issues. Thermochemical and electrochemical methods for reducing CO2 to low-carbon molecules have made significant progress; however, it remains challenging to generate long-chain, structurally diverse carbohydrates, which are the most abundant substances in nature. Here, we report the successful design and realization of in vitro sucrose synthesis from C1 and C3 molecules through a thermodynamically favorable pathway with short reaction steps and low energy input. By engineering the phosphatase and sucrose synthase to improve their catalytic efficiency by 3- to 71-fold, and by optimizing the reaction system through an iterative scanning strategy, we achieved a high conversion yield of 86% and a specific synthetic rate of 5.7 g L-1 h-1. Additionally, we demonstrated the cell-free starch synthesis without the need for dextrin primers, achieving a superior C1-to-starch synthesis rate compared to previously developed multienzyme systems. Building upon this platform, we further extended methanol conversion to a variety of sugars, especially for cellooligosaccharides with a degree of polymerization of Cn≥18. Together, our system provides a promising, plant-independent route for de novo synthesis of structure-diversified oligosaccharides and polysaccharides.

Electrically Driven Biocatalysis for Sustainable CO2-to-Chemicals Transformation

The catalytic transformation of CO2 into value-added chemicals has become a critical strategy for mitigating environmental issues and generating economic benefits. Although substantial progress has been made in renewable electricity-driven CO2 conversion into C1/C2 products, the efficient synthesis of high-value, and long-chain compounds remains a significant challenge. Biosynthesis offers a feasible route for producing long-chain value-added products at mild conditions. Consequently, the integration of electrocatalysis with bioconversion has emerged as a promising approach for sustainable CO2 conversion. This short review outlines recent advances in the sustainable synthesis of long-chain compounds from CO2 via electrically driven biocatalysis, highlighting innovative coupling strategies that combine electrochemical and biochemical processes. Furthermore, the remaining challenges and prospects are tentatively discussed for further advancing CO2-based sustainable synthesis.

Cascade Catalytic Systems for Converting CO2 into C2+ Products

The excessive emission and continuous accumulation of CO2 have precipitated serious social and environmental issues. However, CO2 can also serve as an abundant, inexpensive, and non-toxic renewable C1 carbon source for synthetic reactions. To achieve carbon neutrality and recycling, it is crucial to convert CO2 into value-added products through chemical pathways. Multi-carbon (C2+) products, compared to C1 products, offer a broader range of applications and higher economic returns. Despite this, converting CO2 into C2+ products is difficult due to its stability and the high energy required for C-C coupling. Cascade catalytic reactions offer a solution by coordinating active components, promoting intermediate transfers, and facilitating further transformations. This method lowers energy consumption. Recent advancements in cascade catalytic systems have allowed for significant progress in synthesizing C2+ products from CO2. This review highlights the features and advantages of cascade catalysis strategies, explores the synergistic effects among active sites, and examines the mechanisms within these systems. It also outlines future prospects for CO2 cascade catalytic synthesis, offering a framework for efficient CO2 utilization and the development of next-generation catalytic systems.

Behavior, mechanisms, and applications of low-concentration CO2 in energy media

This review explores the behavior of low-concentration CO2 (LCC) in various energy media, such as solid adsorbents, liquid absorbents, and catalytic surfaces. It delves into the mechanisms of diffusion, adsorption, and catalytic reactions, while analyzing the potential applications and challenges of these properties in technologies like air separation, compressed gas energy storage, and CO2 catalytic conversion. Given the current lack of comprehensive analyses, especially those encompassing multiscale studies of LCC behavior, this review aims to provide a theoretical foundation and data support for optimizing CO2 capture, storage, and conversion technologies, as well as guidance for the development and application of new materials. By summarizing recent advancements in LCC separation techniques (e.g., cryogenic air separation and direct air carbon capture) and catalytic conversion technologies (including thermal catalysis, electrochemical catalysis, photocatalysis, plasma catalysis, and biocatalysis), this review highlights their importance in achieving carbon neutrality. It also discusses the challenges and future directions of these technologies. The findings emphasize that advancing the efficient utilization of LCC not only enhances CO2 reduction and resource utilization efficiency, promoting the development of clean energy technologies, but also provides an economically and environmentally viable solution for addressing global climate change.

Unlocking Efficient Electrosynthesis of α-Amino Acids: Adsorption Geometry Modulation and Electronic Structure Reconstruction in the Ag/Cu Bimetallic System

Electrosynthesis of α-amino acids from α-keto acids is a promising strategy but faces challenges such as high reduction potential and limited efficiency due to sluggish reaction kinetics and competitive side reactions. Here, this study presents a bimetallic Ag/Cu nanowires (NWs) catalyst that effectively addresses these issues, demonstrating an exceptionally low onset-potential of -0.18 V versus RHE for alanine electrosynthesis and achieving a remarkable alanine yield of 690 µmol h-1 cm-2. The reaction reaches 94.71% conversion within 2.5 h and yields gram-scale alanine powder over ten cycles. Theoretical calculations reveal that Ag incorporation exerts additional weak interactions with intermediates and modulates their adsorption geometries. Simultaneously, electron transfer between Ag and Cu reconstructs the catalyst's electronic structure. These modifications enhance the adsorption and activation of intermediates, significantly lowering the energy barrier for the potential-determining step. Additionally, the presence of Ag effectively suppresses the competitive hydrogen evolution reaction, thus improving the selectivity for alanine production. This Ag/Cu NWs catalyst also exhibits broad applicability for synthesizing various α-amino acids. This study presents a novel strategy for enhancing electrosynthesis efficiency by modulating the catalyst's electronic properties and intermediate adsorption behaviors, providing valuable theoretical insights and technical support for sustainable chemical production.

Carbon Negative Synthesis of Amino Acids Using a Cell-Free-Based Biocatalyst

Biological systems can directly upgrade carbon dioxide (CO2) into chemicals. The CO2 fixation rate of autotrophic organisms, however, is too slow for industrial utility, and the breadth of engineered metabolic pathways for the synthesis of value-added chemicals is too limited. Biotechnology workhorse organisms with extensively engineered metabolic pathways have recently been engineered for CO2 fixation. Yet, their low carbon fixation rate, compounded by the fact that living organisms split their carbon between cell growth and chemical synthesis, has led to only cell growth with no chemical synthesis achieved to date. Here, we engineer a lysate-based cell-free expression (CFE)-based multienzyme biocatalyst for the carbon negative synthesis of the industrially relevant amino acids glycine and serine from CO2 equivalents─formate and bicarbonate─and ammonia. The formate-to-serine biocatalyst leverages tetrahydrofolate (THF)-dependent formate fixation, reductive glycine synthesis, serine synthesis, and phosphite dehydrogenase-dependent NAD(P)H regeneration to convert 30% of formate into serine and glycine, surpassing the previous 22% conversion using a purified enzyme system. We find that (1) the CFE-based biocatalyst is active even after 200-fold dilution, enabling higher substrate loading and product synthesis without incurring additional cell lysate cost, (2) NAD(P)H regeneration is pivotal to driving forward reactions close to thermodynamic equilibrium, (3) balancing the ratio of the formate-to-serine pathway genes added to the CFE is key to improving amino acid synthesis, and (4) efficient THF recycling enables lowering the loading of this cofactor, reducing the cost of the CFE-based biocatalyst. To our knowledge, this is the first synthesis of amino acids that can capture CO2 equivalents for the carbon negative synthesis of amino acids using a CFE-based biocatalyst. Looking ahead, the CFE-based biocatalyst process could be extended beyond serine to pyruvate, a key intermediate, to access a variety of chemicals from aromatics and terpenes to alcohols and polymers.

Process simulation and evaluation of scaled-up biocatalytic systems: Advances, challenges, and future prospects

With the increased demand for bio-based products and the rapid development of biomanufacturing technologies, biocatalytic reactions including microorganisms and enzyme based, have become promising approaches. Prior to the scale-up of production process, environmental and economic feasibility analysis are essential for the development of a sustainable and intelligent bioeconomy in the context of industry 4.0. To achieve these goals, process simulation supports system optimization, improves energy and resource utilization efficiencies, and supports digital bioprocessing. However, due to the insufficient understanding of cellular metabolism and interaction mechanisms, there is still a lack of rational and transparent simulation tools to efficiently simulate, control, and optimize microbial/enzymatic reaction processes. Therefore, there is an urgent need to develop frameworks that integrate kinetic modeling, process simulation, and sustainability analysis for bioreaction simulations and their optimization. This review summarizes and compares the advantages and disadvantages of different process simulation software and models in simulating biocatalytic processes, identifies the limitations of traditional reaction kinetics models, and proposes the requirement of simulations close to real reactions. In addition, we explore the current state of kinetic modeling at the microscopic scale and how process simulation can be linked to kinetic models of cellular metabolism and computational fluid dynamics modeling. Finally, this review discusses the requirement of sensitivity analysis and how machine learning can assist with optimization of simulations to improve energy efficiency and product yields from techno-economic and life cycle assessment perspectives.

Formaldehyde: An Essential Intermediate for C1 Metabolism and Bioconversion

Formaldehyde is an intermediate metabolite of methylotrophic microorganisms that can be obtained from formate and methanol through oxidation-reduction reactions. Formaldehyde is also a one-carbon (C1) compound with high uniquely reactive activity and versatility, which is more amenable to further biocatalysis. Biosynthesis of high-value-added chemicals using formaldehyde as an intermediate is theoretically feasible and promising. This review focuses on the design of the biosynthesis of high-value-added chemicals using formaldehyde as an essential intermediate. The upstream biosynthesis and downstream bioconversion pathways of formaldehyde as an intermediate metabolite are described in detail, aiming to highlight the important role of formaldehyde in the transition from inorganic to organic carbon and carbon chain elongation. In addition, challenges and future directions of formaldehyde as an intermediate for the chemicals are discussed, with the expectation of providing ideas for the utilization of C1.

Genomic synergistic efficient carbon fixation and nitrogen removal induced by excessive inorganic carbon in the anammox-centered coupling system

Given the significance of HCO3- for autotrophic anammox bacteria (AnAOB), excessive HCO3- was always provided in anammox-related systems and engineering applications. However, its impact mechanism on anammox process at genome-level remains unknown. This study firstly established an anammox-centered coupling system that entails heterotrophic partial denitrification (PD) and hydrolytic acidification (A-PDHA) fed mainly with inorganic carbon (high HCO3- concentration and low C/N ratio). Metagenomic binning and metatranscriptomics analyses indicated that high HCO3- concentration enhanced expression of natural most efficient phosphoenolpyruvate (PEP) carboxylase within AnAOB, by up to 30.59 folds. This further induced AnAOB to achieve high-speed carbon-fixing reaction through cross-feeding of phosphate and PEP precursors with heterotrophs. Additionally, the enhanced activity of transporters and catalytic enzymes (up to 4949-fold) induced by low C/N ratio enabled heterotrophs to eliminate extracellular accumulated energy precursors mainly derived from carbon fixation products of AnAOB. This maintained high-speed carbon-fixing reaction within AnAOB and supplemented heterotrophs with organics. Moreover, assimilated energy precursors stimulated nitrogen metabolism enzymes, especially NO2- reductase (968.14 times), in heterotrophs. This established an energy-saving PD-A process mediated by interspecies NO shuttle. These variation resulted in efficient nitrogen removal (>95 %) and reduced external organic carbon demand (67 %) in A-PDHA system. This study unveils the great potential of an anammox-centered autotrophic-heterotrophic coupling system for achieving cost-effective nitrogen removal and enhancing carbon fixation under excessive HCO3- doses.

Moniezia benedeni drives the SNAP-25 expression of the enteric nerves in sheep's small intestine

BACKGROUND

The neuroimmune network plays a crucial role in regulating mucosal immune homeostasis within the digestive tract. Synaptosome-associated protein 25 (SNAP-25) is a presynaptic membrane-binding protein that activates ILC2s, initiating the host's anti-parasitic immune response.

METHODS

To investigate the effect of Moniezia benedeni (M. benedeni) infection on the distribution of SNAP-25 in the sheep's small intestine, the recombinant plasmid pET-28a-SNAP-25 was constructed and expressed in BL21, yielding the recombinant protein. Then, the rabbit anti-sheep SNAP-25 polyclonal antibody was prepared and immunofluorescence staining was performed with it. The expression levels of SNAP-25 in the intestines of normal and M. benedeni-infected sheep were detected by ELISA.

RESULTS

The results showed that the SNAP-25 recombinant protein was 29.3 KDa, the titer of the prepared immune serum reached 1:128,000. It was demonstrated that the rabbit anti-sheep SNAP-25 polyclonal antibody could bind to the natural protein of sheep SNAP-25 specifically. The expression levels of SNAP-25 in the sheep's small intestine revealed its primary presence in the muscular layer and lamina propria, particularly around nerve fibers surrounding the intestinal glands. Average expression levels in the duodenum, jejunum, and ileum were 130.32 pg/mg, 185.71 pg/mg, and 172.68 pg/mg, respectively. Under conditions of M. benedeni infection, the spatial distribution of SNAP-25-expressing nerve fibers remained consistent, but its expression level in each intestine segment was increased significantly (P < 0.05), up to 262.02 pg/mg, 276.84 pg/mg, and 326.65 pg/mg in the duodenum, jejunum, and ileum, and it was increased by 101.06%, 49.07%, and 89.16% respectively.

CONCLUSIONS

These findings suggest that M. benedeni could induce the SNAP-25 expression levels in sheep's intestinal nerves significantly. The results lay a foundation for further exploration of the molecular mechanism by which the gastrointestinal nerve-mucosal immune network perceives parasites in sheep.

Heterotrophic and autotrophic production of L-isoleucine and L-valine by engineered Cupriavidus necator H16

Advancement in commodity chemical production from carbon dioxide (CO2) offers a promising path towards sustainable development goal. Cupriavidus necator is an ideal host to convert CO2 into high-value chemicals, thereby achieving this target. Here, C. necator was engineered for heterotrophic and autotrophic production of L-isoleucine and L-valine. Citramalate synthase was introduced to simplify isoleucine synthesis pathway. Blocking poly-hydroxybutyrate biosynthesis resulted in significant accumulation of isoleucine and valine. Besides, strategies like key enzymes screening and overexpressing, reducing power balancing and feedback inhibition removing were applied in strain modification. Finally, the maximum isoleucine and valine titers of the best isoleucine-producing and valine-producing strains reached 857 and 972 mg/L, respectively, in fed-batch fermentation using glucose as substrate, and 105 and 319 mg/L, respectively, in autotrophic fermentation using CO2 as substrate. This study provides a feasible solution for developing C. necator as a microbial factory to produce amino acids from CO2.

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.

Artificial carbon assimilation: From unnatural reactions and pathways to synthetic autotrophic systems

Synthetic biology is being increasingly used to establish novel carbon assimilation pathways and artificial autotrophic strains that can be used in low-carbon biomanufacturing. Currently, artificial pathway design has made significant progress from advocacy to practice within a relatively short span of just over ten years. However, there is still huge scope for exploration of pathway diversity, operational efficiency, and host suitability. The accelerated research process will bring greater opportunities and challenges. In this paper, we provide a comprehensive summary and interpretation of representative one-carbon assimilation pathway designs and artificial autotrophic strain construction work. In addition, we propose some feasible design solutions based on existing research results and patterns to promote the development and application of artificial autotrophy.

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.

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.