Generation of an Escherichia coli strain growing on methanol via the ribulose monophosphate cycle

Rewiring the methanol assimilation pathway in the methylotrophic yeast Pichia pastoris for high-level production of erythritol

Methanol, which is non-food competing, abundant, inexpensive, and potentially renewable, serves as an ideal alternative feedstock for biomanufacturing. Although engineered methylotrophic yeasts have successfully achieved gram-scale production of C2 (acetyl-CoA), C3 (pyruvate), and C6 (fructose-6-phosphate) building blocks from methanol, the production of C4-based (i.e. erythrose-4-phosphate) chemicals remains unexplored. This study demonstrates high-level methanol-to-erythritol production by rewiring the methanol assimilation pathway of Pichia pastoris, achieved through trimming and strengthening the carbon rearrangement network (CRN). Notably, we introduced a bacterial ribulose monophosphate (RuMP) pathway in addition to the native xylulose monophosphate (XuMP) pathway of P. pastoris, creating a hybrid network that significantly improved erythritol production and reduced pentitol byproduct formation. Combining these strategies generated a high-producing recombinant strain, achieving titers up to 31.5 g/L in fermentor culture. This study validates the feasibility of engineering P. pastoris for the efficient conversion of methanol to valuable erythrose-4-phosphate (E4P)-based chemicals. The CRN rewiring strategies employed here offer a valuable reference for engineering methylotrophic cell factories for the production of a wide range of chemicals from methanol.

Hybrid Methylotrophic Pathway in Serratia marcescens for Sustainable Terpenoid Biosynthesis

Terpenoids are valuable chemicals used across industries. Methanol, a nonsugar-based feedstock, offers an eco-friendly approach to terpenoid production. In this study, a hybrid methylotrophic pathway was engineered in Serratia marcescens (S. marcescens) HBQA7, which is tolerant to both methanol and terpenoid compounds. The pathway utilizes bacterial methanol dehydrogenase (Mdh) and yeast dihydroxyacetone synthase (Das) to produce monoterpenes and sesquiterpenes from methanol and xylose. 13C labeling experiments identified the optimal enzyme pair: Mdh from Acinetobacter gerneri and Das from Pichia angusta, achieving 7.63% 13C enrichment of the central metabolic intermediate pyruvate. Deletion of pentose phosphate pathway genes (rpiAB) enhanced methanol utilization, achieving 22.99% 13C enrichment. Optimization of the mevalonate (MVA) biosynthetic pathway enabled the production of 5.12 g/L mevalonate in shake flask culture from methanol and xylose. Further construction of a haloarchaea-type MVA pathway enabled the production of geraniol (574.12 mg/L) and (-)-α-bisabolol (1256.41 mg/L) in shake flask cultures. This study demonstrates the first methanol conversion into valuable terpenoids in S. marcescens.

Awakening of the RuMP cycle for partial methylotrophy in the thermophile Parageobacillus thermoglucosidasius

Given sustainability and scalability concerns of using sugar feedstocks for microbial bioproduction of bulk chemicals, widening the feedstock range for microbial cell factories is of high interest. Methanol is a one-carbon alcohol that stands out as an alternative feedstock for the bioproduction of chemicals, as it is electron-rich, water-miscible and can be produced from several renewable resources. Bioconversion of methanol into products under thermophilic conditions (>50 °C) could be highly advantageous for industrial biotechnology. Although progress is being made with natural, thermophilic methylotrophic microorganisms, they are not yet optimal for bioproduction and establishing alternative thermophilic methylotrophic bioproduction platforms can widen possibilities. Hence, we set out to implement methanol assimilation in the emerging thermophilic model organism Parageobacillus thermoglucosidasius. We engineered P. thermoglucosidasius to be strictly dependent for its growth on methanol assimilation via the core of the highly efficient ribulose monophosphate (RuMP) cycle, while co-assimilating ribose. Surprisingly, this did not require heterologous expression of RuMP enzymes. Instead, by laboratory evolution we awakened latent, native enzyme activities to form the core of the RuMP cycle. We obtained fast methylotrophic growth in which ∼17 % of biomass was strictly obtained from methanol. This work lays the foundation for developing a versatile thermophilic bioproduction platform based on renewable methanol.

Design and implementation of aerobic and ambient CO2-reduction as an entry-point for enhanced carbon fixation

The direct reduction of CO2 into one-carbon molecules is key to highly efficient biological CO2-fixation. However, this strategy is currently restricted to anaerobic organisms and low redox potentials. In this study, we introduce the CORE cycle, a synthetic metabolic pathway that converts CO2 to formate at aerobic conditions and ambient CO2 levels, using only NADPH as a reductant. Combining theoretical pathway design and analysis, enzyme bioprospecting and high-throughput screening, modular assembly and adaptive laboratory evolution, we realize the CORE cycle in vivo and demonstrate that the cycle supports growth of E. coli by supplementing C1-metabolism and serine biosynthesis from CO2. We further analyze the theoretical potential of the CORE cycle as a new entry-point for carbon in photorespiration and autotrophy. Overall, our work expands the solution space for biological carbon reduction, offering a promising approach to enhance CO2 fixation processes such as photosynthesis, and opening avenues for synthetic autotrophy.

Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection

Auxotrophic metabolic sensors (AMS) are microbial strains modified so that biomass formation correlates with the availability of specific metabolites. These sensors are essential for bioengineering (e.g., in growth-coupled designs) but creating them is often a time-consuming and low-throughput process that can be streamlined by in silico analysis. Here, we present a systematic workflow for designing, implementing, and testing versatile AMS based on Escherichia coli. Glyoxylate, a key metabolite in (synthetic) CO2 fixation and carbon-conserving pathways, served as the test analyte. Through iterative screening of a compact metabolic model, we identify non-trivial growth-coupled designs that result in six AMS with a wide sensitivity range for glyoxylate, spanning three orders of magnitude in the detected analyte concentration. We further adapt these E. coli AMS for sensing glycolate and demonstrate their utility in both pathway engineering (testing a key metabolic module for carbon assimilation via glyoxylate) and environmental monitoring (quantifying glycolate produced by photosynthetic microalgae). Adapting this workflow to the sensing of different metabolites could facilitate the design and implementation of AMS for diverse biotechnological applications.

Evolution-assisted engineering of E. coli enables growth on formic acid at ambient CO2 via the Serine Threonine Cycle

Atmospheric CO2 poses a major threat to life on Earth by causing global warming and climate change. On the other hand, it can be considered as a resource that is scalable enough to establish a circular carbon economy. Accordingly, technologies to capture and convert CO2 into reduced one-carbon (C1) compounds (e.g. formic acid) are developing and improving fast. Driven by the idea of creating sustainable bioproduction platforms, natural and synthetic C1-utilization pathways are engineered into industrially relevant microbes. The realization of synthetic C1-assimilation cycles in living organisms is a promising but challenging endeavour. Here, we engineer the Serine Threonine Cycle, a synthetic C1-assimilation cycle in Escherichia coli to achieve growth on formic acid. Our stepwise engineering approach in tailored selection strains combined with adaptive laboratory evolution experiments enabled formatotrophic growth of the organism. Whole genome sequencing and reverse engineering allowed us to determine the key mutations linked to pathway activity. The Serine Threonine Cycle strains created in this work use formic acid as sole carbon and energy source and can grow at ambient CO2 cultivation conditions. This work sets an example for the engineering of complex C1-assimilation cycles in heterotrophic microbes.

Cell-Free Systems to Mimic and Expand Metabolism

Cell-free synthetic biology incorporates purified components and/or crude cell extracts to carry out metabolic and genetic programs. While protein synthesis has historically been the primary focus, more metabolism researchers are now turning toward cell-free systems either to prototype pathways for cellular implementation or to design new-to-nature reaction networks that incorporate environmentally relevant substrates or new energy sources. The ability to design, build, and test enzyme combinations in vitro has accelerated efforts to understand metabolic bottlenecks and engineer high-yielding pathways. However, only a small fraction of metabolic possibilities has been explored in cell-free systems, and extracts from model organisms remain the most common starting points. Expanding the scope of cell-free metabolism to include extracts from new organisms, alternative metabolic pathways, and non-natural chemistries will enhance our ability to understand and engineer bio-based chemical conversions.

C1 photochemotrophy - rethinking one-carbon metabolism in phototrophs

Excessive CO2 emissions, caused by an imbalance between carbon oxidation and reduction, drive climate change. To address this, we propose photochemotrophic metabolism as an alternative to both canonical photosynthesis and synthetic one-carbon (C1) metabolism in heterotrophs. In photochemotrophy, naturally phototrophic microorganisms such as cyanobacteria serve as the chassis to assimilate chemically reduced and soluble C1 compounds such as formate or methanol by using carbon fixation cycles that are more efficient than the native Calvin cycle. Key potential advantages of photochemotrophy include enhanced carbon fixation efficiency, utilization of storable carbon compounds, retention of energy from the original CO2 reduction, and decoupling of carbon delivery and electron source. This proposed strategy positions photochemotrophic cyanobacteria as a promising tool for advancing the bioeconomy.

Seven critical challenges in synthetic one-carbon assimilation and their potential solutions

Synthetic C1 assimilation holds the promise of facilitating carbon capture while mitigating greenhouse gas emissions, yet practical implementation in microbial hosts remains relatively limited. Despite substantial progress in pathway design and prototyping, most efforts stay at the proof-of-concept stage, with frequent failures observed even under in vitro conditions. This review identifies seven major barriers constraining the deployment of synthetic C1 metabolism in microorganisms and proposes targeted strategies for overcoming these issues. A primary limitation is the low catalytic activity of carbon-fixing enzymes, particularly carboxylases, which restricts the overall pathway performance. In parallel, challenges in expressing multiple heterologous genes-especially those encoding metal-dependent or oxygen-sensitive enzymes-further hinder pathway functionality. At the systems level, synthetic C1 pathways often exhibit poor flux distribution, limited integration with the host metabolism, accumulation of toxic intermediates, and disruptions in redox and energy balance. These factors collectively reduce biomass formation and compromise product yields in biotechnological setups. Overcoming these interconnected challenges is essential for moving synthetic C1 assimilation beyond conceptual stages and enabling its application in scalable, efficient bioprocesses towards a circular bioeconomy.

A synthetic methylotroph achieves accelerated cell growth by alleviating transcription-replication conflicts

Microbial utilization of methanol for valorization is an effective way to advance green bio-manufacturing technology. Although synthetic methylotrophs have been developed, strategies to enhance their cell growth rate and internal regulatory mechanism remain underexplored. In this study, we design a synthetic methanol assimilation (SMA) pathway containing only six enzymes linked to central carbon metabolism, which does not require energy and carbon emissions. Through rational design and laboratory evolution, E. coli harboring with the SMA pathway is converted into a synthetic methylotroph. By self-adjusting the expression of TOPAI (topoisomerase I inhibitor) to alleviate transcriptional-replication conflicts (TRCs), the doubling time of methylotrophic E. coli is reduced to 4.5 h, approaching that of natural methylotrophs. This work has the potential to overcome the growth limitation of C1-assimilating microbes and advance the development of a circular carbon economy.

Advancements in Biological Conversion of C1 Feedstocks: Sustainable Bioproduction and Environmental Solutions

The use of one-carbon (C1) feedstocks, including carbon dioxide (CO2), carbon monoxide (CO), formate (HCO2H), methanol (CH3OH), and methane (CH4), presents a significant opportunity for sustainable bioproduction and environmental conservation. This Perspective explores the development of biological methods for converting C1 feedstocks into valuable products, emphasizing major progress from engineering native C1 assimilation pathways to the creation of synthetic autotrophs and methylotrophs that utilize these carbon sources. Additionally, we discuss hybrid approaches that merge biological and electrochemical systems, particularly for the conversion of CO2. This Perspective underscores the importance of C1 bioconversion in promoting sustainable biotechnological strategies for a low-carbon future.

Harnessing noncanonical redox cofactors to advance synthetic assimilation of one-carbon feedstocks

One-carbon (C1) feedstocks, such as carbon monoxide (CO), formate (HCO2H), methanol (CH3OH), and methane (CH4), can be obtained either through stepwise electrochemical reduction of CO2 with renewable electricity or via processing of organic side streams. These C1 substrates are increasingly investigated in biotechnology as they can contribute to a circular carbon economy. In recent years, noncanonical redox cofactors (NCRCs) emerged as a tool to generate synthetic electron circuits in cell factories to maximize electron transfer within a pathway of interest. Here, we argue that expanding the use of NCRCs in the context of C1-driven bioprocesses will boost product yields and facilitate challenging redox transactions that are typically out of the scope of natural cofactors due to inherent thermodynamic constraints.

Evolutionary engineering of methylotrophic E. coli enables fast growth on methanol

As methanol can be derived from either CO2 or methane, methanol economy can play an important role in combating climate change. In this scenario, rapid utilization of methanol by an industrial microorganism is the first and crucial step for efficient utilization of the C1 feedstock chemical. Here, we report the development of a methylotrophic E. coli strain with a doubling time of 3.5 hours under optimal conditions, comparable or faster than native model methylotrophs Methylorubrum extorquens AM1 (Td~4hr) and Bacillus methanolicus at 37°C (Td~5hr). To accomplish this, we develop a bacterial artificial chromosome (BAC) with dynamic copy number variation (CNV) to facilitate overcoming the formaldehyde-induced DNA-protein cross-linking (DPC) problem in the evolution process. We track the genome variations of 75 cultures along the evolution process by next-generation sequencing, and identified the features of the fast-growing strain. After stabilization, the final strain (SM8) grows to 20 g/L of cell mass within 77 hrs in a bioreactor. This study illustrates the potential of dynamic CNV as an evolution tool and synthetic methylotrophs as a platform for sustainable biotechnological applications.

A machine learning framework for extracting information from biological pathway images in the literature

There have been significant advances in literature mining, allowing for the extraction of target information from the literature. However, biological literature often includes biological pathway images that are difficult to extract in an easily editable format. To address this challenge, this study aims to develop a machine learning framework called the "Extraction of Biological Pathway Information" (EBPI). The framework automates the search for relevant publications, extracts biological pathway information from images within the literature, including genes, enzymes, and metabolites, and generates the output in a tabular format. For this, this framework determines the direction of biochemical reactions, and detects and classifies texts within biological pathway images. Performance of EBPI was evaluated by comparing the extracted pathway information with manually curated pathway maps. EBPI will be useful for extracting biological pathway information from the literature in a high-throughput manner, and can be used for pathway studies, including metabolic engineering.

Phosphoribosylpyrophosphate synthetase as a metabolic valve advances Methylobacterium/Methylorubrum phyllosphere colonization and plant growth

The proficiency of phyllosphere microbiomes in efficiently utilizing plant-provided nutrients is pivotal for their successful colonization of plants. The methylotrophic capabilities of Methylobacterium/Methylorubrum play a crucial role in this process. However, the precise mechanisms facilitating efficient colonization remain elusive. In the present study, we investigate the significance of methanol assimilation in shaping the success of mutualistic relationships between methylotrophs and plants. A set of strains originating from Methylorubrum extorquens AM1 are subjected to evolutionary pressures to thrive under low methanol conditions. A mutation in the phosphoribosylpyrophosphate synthetase gene is identified, which converts it into a metabolic valve. This valve redirects limited C1-carbon resources towards the synthesis of biomass by up-regulating a non-essential phosphoketolase pathway. These newly acquired bacterial traits demonstrate superior colonization capabilities, even at low abundance, leading to increased growth of inoculated plants. This function is prevalent in Methylobacterium/Methylorubrum strains. In summary, our findings offer insights that could guide the selection of Methylobacterium/Methylorubrum strains for advantageous agricultural applications.

Design, construction and optimization of formaldehyde growth biosensors with broad application in biotechnology

Formaldehyde is a key metabolite in natural and synthetic one-carbon metabolism. To facilitate the engineering of formaldehyde-producing enzymes, the development of sensitive, user-friendly, and cost-effective detection methods is required. In this study, we engineered Escherichia coli to serve as a cellular biosensor capable of detecting a broad range of formaldehyde concentrations. Using both natural and promiscuous formaldehyde assimilation enzymes, we designed three distinct E. coli growth biosensor strains that depend on formaldehyde for cell growth. These strains were engineered to be auxotrophic for one or several essential metabolites that could be produced through formaldehyde assimilation. The respective assimilating enzyme was expressed from the genome to compensate the auxotrophy in the presence of formaldehyde. We first predicted the formaldehyde dependency of the biosensors by flux balance analysis and then analysed it experimentally. Subsequent to strain engineering, we enhanced the formaldehyde sensitivity of two biosensors either through adaptive laboratory evolution or modifications at metabolic branch points. The final set of biosensors demonstrated the ability to detect formaldehyde concentrations ranging approximately from 30 μM to 13 mM. We demonstrated the application of the biosensors by assaying the in vivo activity of different methanol dehydrogenases in the most sensitive strain. The fully genomic nature of the biosensors allows them to be deployed as "plug-and-play" devices for high-throughput screenings of extensive enzyme libraries. The formaldehyde growth biosensors developed in this study hold significant promise for advancing the field of enzyme engineering, thereby supporting the establishment of a sustainable one-carbon bioeconomy.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

A rationally designed miniature of soluble methane monooxygenase enables rapid and high-yield methanol production in Escherichia coli

Soluble methane monooxygenase (sMMO) oxidizes a wide range of carbon feedstocks (C1 to C8) directly using intracellular NADH and is a useful means in developing green routes for industrial manufacturing of chemicals. However, the high-throughput biosynthesis of active recombinant sMMO and the ensuing catalytic oxidation have so far been unsuccessful due to the structural and functional complexity of sMMO, comprised of three functionally complementary components, which remains a major challenge for its industrial applications. Here we develop a catalytically active miniature of sMMO (mini-sMMO), with a turnover frequency of 0.32 s-1, through an optimal reassembly of minimal and modified components of sMMO on catalytically inert and stable apoferritin scaffold. We characterise the molecular characteristics in detail through in silico and experimental analyses and verifications. Notably, in-situ methanol production in a high-cell-density culture of mini-sMMO-expressing recombinant Escherichia coli resulted in higher yield and productivity (~ 3.0 g/L and 0.11 g/L/h, respectively) compared to traditional methanotrophic production.

A synthetic methylotrophic Escherichia coli as a chassis for bioproduction from methanol

Methanol synthesized from captured greenhouse gases is an emerging renewable feedstock with great potential for bioproduction. Recent research has raised the prospect of methanol bioconversion to value-added products using synthetic methylotrophic Escherichia coli, as its metabolism can be rewired to enable growth solely on the reduced one-carbon compound. Here we describe the generation of an E. coli strain that grows on methanol at a doubling time of 4.3 h-comparable to many natural methylotrophs. To establish bioproduction from methanol using this synthetic chassis, we demonstrate biosynthesis from four metabolic nodes from which numerous bioproducts can be derived: lactic acid from pyruvate, polyhydroxybutyrate from acetyl coenzyme A, itaconic acid from the tricarboxylic acid cycle and p-aminobenzoic acid from the chorismate pathway. In a step towards carbon-negative chemicals and valorizing greenhouse gases, our work brings synthetic methylotrophy in E. coli within reach of industrial applications.

Artificial Methylotrophic Cells via Bottom-Up Integration of a Methanol-Utilizing Pathway

Methanol has gained substantial attention as a substrate for biomanufacturing due to plentiful stocks and nonreliance on agriculture, and it can be sourced renewably. However, due to inevitable complexities in cell metabolism, microbial methanol conversion requires further improvement before industrial applicability. Here, we present a novel, parallel strategy using artificial cells to provide a simplified and well-defined environment for methanol utilization as artificial methylotrophic cells. We compartmentalized a methanol-utilizing enzyme cascade, including NAD-dependent methanol dehydrogenase (Mdh) and pyruvate-dependent aldolase (KHB aldolase), in cell-sized lipid vesicles using the inverted emulsion method. The reduction of cofactor NAD+ to NADH was used to quantify the conversion of methanol within individual artificial methylotrophic cells via flow cytometry. Compartmentalization of the reaction cascade in liposomes led to a 4-fold higher NADH production compared with bulk enzyme experiments, and the incorporation of KHB aldolase facilitated another 2-fold increase above the Mdh-only reaction. This methanol-utilizing platform can serve as an alternative route to speed up methanol biological conversion, eventually shifting sugar-based bioproduction toward a sustainable methanol bioeconomy.

Creating new-to-nature carbon fixation: A guide

Synthetic biology aims at designing new biological functions from first principles. These new designs allow to expand the natural solution space and overcome the limitations of naturally evolved systems. One example is synthetic CO2-fixation pathways that promise to provide more efficient ways for the capture and conversion of CO2 than natural pathways, such as the Calvin Benson Bassham (CBB) cycle of photosynthesis. In this review, we provide a practical guideline for the design and realization of such new-to-nature CO2-fixation pathways. We introduce the concept of "synthetic CO2-fixation", and give a general overview over the enzymology and topology of synthetic pathways, before we derive general principles for their design from their eight naturally evolved analogs. We provide a comprehensive summary of synthetic carbon-assimilation pathways and derive a step-by-step, practical guide from the theoretical design to their practical implementation, before ending with an outlook on new developments in the field.

Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzyme's activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle's electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.

Engineering Escherichia coli for cost-effective production of medium-chain fatty acids from soy whey using an optimized galactose-based autoinduction system

Medium-chain fatty acids (MCFAs) are essential chemical feedstocks. Microbial production of MCFAs offers an attractive alternative to conventional methods, but the costly media and external inducers limit its practical application. To address this issue and make MCFA production more cost-effective, an E.coli platform was developed using soy whey as a medium and galactose as an autoinducer. We first designed an efficient, stringent, homogeneous, and robust galactose-based autoinduction system for the expression of pathway enzymes by rationally engineering the promoter of the galactose-proton symporter (GalP). Subsequently, the intracellular acetyl-CoA availability and NADH regeneration were enhanced to improve the reversal of the β-oxidation cycle. The resulting strain yielded 8.20 g/L and 16.42 g/L MCFA in pH-controlled batch fermentation and fed-batch fermentation with glucose added using soy whey as medium, respectively. This study provided a cost-effective and promising platform for MCFA production, as well as future strain development for other value-added chemicals production.

Leveraging the Proximity and Distribution of Cu-Cs Sites for Direct Conversion of Methanol to Esters/Aldehydes

Methanol serves as a versatile building-block for various commodity chemicals, and the development of industrially promising strategies for its conversion remains the ultimate goal in methanol chemistry. In this study, we design a dual Cu-Cs catalytic system that enables a one-step direct conversion of methanol and methyl acetate/ethanol into high value-added esters/aldehydes, with customized chain length and saturation by leveraging the proximity and distribution of Cu-Cs sites. Cu-Cs at a millimeter-scale intimacy triggers methanol dehydrogenation and condensation, involving proton transfer, aldol formation, and aldol condensation, to obtain unsaturated esters and aldehydes with selectivities of 76.3 % and 31.1 %, respectively. Cu-Cs at a micrometer-scale intimacy significantly promotes mass transfer of intermediates across catalyst interfaces and their subsequent hydrogenation to saturated esters and aldehydes with selectivities of 67.6 % and 93.1 %, respectively. Conversely, Cu-Cs at a nanometer-scale intimacy alters reaction pathway with a similar energy barrier for the rate-determining step, but blocks the acidic-basic sites and diverts the reaction to byproducts. More importantly, an unprecedented quadruple tandem catalytic production of methyl methacrylate (MMA) is achieved by further tailoring Cu and Cs distribution across the reaction bed in the configuration of Cu-Cs||Cs, outperforming the existing industrial processes and saving at least 15 % of production costs.

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.

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.

Next-generation feedstocks methanol and ethylene glycol and their potential in industrial biotechnology

Microbial fermentation processes are expected to play an important role in reducing dependence on fossil-based raw materials for the production of everyday chemicals. In order to meet the growing demand for biotechnological products in the future, alternative carbon sources that do not compete with human nutrition must be exploited. The chemical conversion of the industrially emitted greenhouse gas CO2 into microbially utilizable platform chemicals such as methanol represents a sustainable strategy for the utilization of an abundant carbon source and has attracted enormous scientific interest in recent years. A relatively new approach is the microbial synthesis of products from the C2-compound ethylene glycol, which can also be synthesized from CO2 and non-edible biomass and, in addition, can be recovered from plastic waste. Here we summarize the main chemical routes for the synthesis of methanol and ethylene glycol from sustainable resources and give an overview of recent metabolic engineering work for establishing natural and synthetic microbial assimilation pathways. The different metabolic routes for C1 and C2 alcohol-dependent bioconversions were compared in terms of their theoretical maximum yields and their oxygen requirements for a wide range of value-added products. Assessment of the process engineering challenges for methanol and ethylene glycol-based fermentations underscores the theoretical advantages of new synthetic metabolic routes and advocates greater consideration of ethylene glycol, a C2 substrate that has received comparatively little attention to date.

The oxygen-tolerant reductive glycine pathway assimilates methanol, formate and CO2 in the yeast Komagataella phaffii

The current climatic change is predominantly driven by excessive anthropogenic CO2 emissions. As industrial bioprocesses primarily depend on food-competing organic feedstocks or fossil raw materials, CO2 co-assimilation or the use of CO2-derived methanol or formate as carbon sources are considered pathbreaking contributions to solving this global problem. The number of industrially-relevant microorganisms that can use these two carbon sources is limited, and even fewer can concurrently co-assimilate CO2. Here, we search for alternative native methanol and formate assimilation pathways that co-assimilate CO2 in the industrially-relevant methylotrophic yeast Komagataella phaffii (Pichia pastoris). Using 13C-tracer-based metabolomic techniques and metabolic engineering approaches, we discover and confirm a growth supporting pathway based on native enzymes that can perform all three assimilations: namely, the oxygen-tolerant reductive glycine pathway. This finding paves the way towards metabolic engineering of formate and CO2 utilisation to produce proteins, biomass, or chemicals in yeast.

The potential of CO2-based production cycles in biotechnology to fight the climate crisis

Rising CO2 emissions have pushed scientists to develop new technologies for a more sustainable bio-based economy. Microbial conversion of CO2 and CO2-derived carbon substrates into valuable compounds can contribute to carbon neutrality and sustainability. Here, we discuss the potential of C1 carbon sources as raw materials to produce energy, materials, and food and feed using microbial cell factories. We provide an overview of potential microbes, natural and synthetic C1 utilization pathways, and compare their metabolic driving forces. Finally, we sketch a future in which C1 substrates replace traditional feedstocks and we evaluate the costs associated with such an endeavor.

Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy

A true circular carbon economy must upgrade waste greenhouse gases. C1-based biomanufacturing is an attractive solution, in which one carbon (C1) molecules (e.g. CO2, formate, methanol, etc.) are converted by microbial cell factories into value-added goods (i.e. food, feed, and chemicals). To render C1-based biomanufacturing cost-competitive, we must adapt microbial metabolism to perform chemical conversions at high rates and yields. To this end, the biotechnology community has undertaken two (seemingly opposing) paths: optimizing natural C1-trophic microorganisms versus engineering synthetic C1-assimilation de novo in model microorganisms. Here, we pose how these approaches can instead create synergies for strengthening the competitiveness of C1-based biomanufacturing as a whole.

The cofactor challenge in synthetic methylotrophy: bioengineering and industrial applications

Methanol is a promising feedstock for industrial bioproduction: it can be produced renewably and has high solubility and limited microbial toxicity. One of the key challenges for its bio-industrial application is the first enzymatic oxidation step to formaldehyde. This reaction is catalysed by methanol dehydrogenases (MDH) that can use NAD⁺, O₂ or pyrroloquinoline quinone (PQQ) as an electron acceptor. While NAD-dependent MDH are simple to express and have the highest energetic efficiency, they exhibit mediocre kinetics and poor thermodynamics at ambient temperatures. O₂-dependent methanol oxidases require high oxygen concentrations, do not conserve energy and thus produce excessive heat as well as toxic H₂O₂. PQQ-dependent MDH provide a good compromise between energy efficiency and good kinetics that support fast growth rates without any drawbacks for process engineering. Therefore, we argue that this enzyme class represents a promising solution for industry and outline engineering strategies for the implementation of these complex systems in heterologous hosts.

Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo

Formate can be envisioned at the core of a carbon-neutral bioeconomy, where it is produced from CO₂ by (electro-)chemical means and converted into value-added products by enzymatic cascades or engineered microbes. A key step in expanding synthetic formate assimilation is its thermodynamically challenging reduction to formaldehyde. Here, we develop a two-enzyme route in which formate is activated to formyl phosphate and subsequently reduced to formaldehyde. Exploiting the promiscuity of acetate kinase and N-acetyl-γ-glutamyl phosphate reductase, we demonstrate this phosphate (P_i)-based route in vitro and in vivo. We further engineer a formyl phosphate reductase variant with improved formyl phosphate conversion in vivo by suppressing cross-talk with native metabolism and interface the P_i route with a recently developed formaldehyde assimilation pathway to enable C2 compound formation from formate as the sole carbon source in Escherichia coli. The P_i route therefore offers a potent tool in expanding the landscape of synthetic formate assimilation.

Engineering Escherichia coli to Utilize Erythritol as Sole Carbon Source

Erythritol, one of the natural sugar alcohols, is widely used as a sugar substitute sweetener in food industries. Humans themselves are not able to catabolize erythritol and their gut microbes lack related catabolic pathways either to metabolize erythritol. Here, Escherichia coli (E. coli) is engineered to utilize erythritol as sole carbon source aiming for defined applications. First, the erythritol metabolic gene cluster is isolated and the erythritol-binding transcriptional repressor and its DNA-binding site are experimentally characterized. Transcriptome analysis suggests that carbohydrate metabolism-related genes in the engineered E. coli are overall upregulated. In particular, the enzymes of transaldolase (talA and talB) and transketolase (tktA and tktB) are notably overexpressed (e.g., the expression of tktB is improved by nearly sixfold). By overexpression of the four genes, cell growth can be increased as high as three times compared to the cell cultivation without overexpression. Finally, engineered E. coli strains can be used as a living detector to distinguish erythritol-containing soda soft drinks and can grow in the simulated intestinal fluid supplemented with erythritol. This work is expected to inspire the engineering of more hosts to respond and utilize erythritol for broad applications in metabolic engineering, synthetic biology, and biomedical engineering.

Paving the way for synthetic C1 - Metabolism in Pseudomonas putida through the reductive glycine pathway

One-carbon (C1) compounds such as methanol, formate, and CO₂ are alternative, sustainable microbial feedstocks for the biobased production of chemicals and fuels. In this study, we engineered the carbon metabolism of the industrially important bacterium Pseudomonas putida to modularly assimilate these three substrates through the reductive glycine pathway. First, we demonstrated the functionality of the C1-assimilation module by coupling the growth of auxotrophic strains to formate assimilation. Next, we extended the module in the auxotrophic strains from formate to methanol-dependent growth using both NAD and PQQ-dependent methanol dehydrogenases. Finally, we demonstrated, for the first time, engineered CO₂-dependent formation of part of the biomass through CO₂ reduction to formate by the native formate dehydrogenase, which required short-term evolution to rebalance the cellular NADH/NAD ⁺ ratio. This research paves the way to further engineer P. putida towards full growth on formate, methanol, and CO₂ as sole feedstocks, thereby substantially expanding its potential as a sustainable and versatile cell factory.

In vivo implementation of a synthetic metabolic pathway for the carbon-conserving conversion of glycolaldehyde to acetyl-CoA

Ethylene glycol (EG) derived from plastic waste or CO₂ can serve as a substrate for microbial production of value-added chemicals. Assimilation of EG proceeds though the characteristic intermediate glycolaldehyde (GA). However, natural metabolic pathways for GA assimilation have low carbon efficiency when producing the metabolic precursor acetyl-CoA. In alternative, the reaction sequence catalyzed by EG dehydrogenase, d-arabinose 5-phosphate aldolase, d-arabinose 5-phosphate isomerase, d-ribulose 5-phosphate 3-epimerase (Rpe), d-xylulose 5-phosphate phosphoketolase, and phosphate acetyltransferase may enable the conversion of EG into acetyl-CoA without carbon loss. We investigated the metabolic requirements for in vivo function of this pathway in Escherichia coli by (over)expressing constituting enzymes in different combinations. Using ¹³C-tracer experiments, we first examined the conversion of EG to acetate via the synthetic reaction sequence and showed that, in addition to heterologous phosphoketolase, overexpression of all native enzymes except Rpe was required for the pathway to function. Since acetyl-CoA could not be reliably quantified by our LC/MS-method, the distribution of isotopologues in mevalonate, a stable metabolite that is exclusively derived from this intermediate, was used to probe the contribution of the synthetic pathway to biosynthesis of acetyl-CoA. We detected strong incorporation of ¹³C carbon derived from labeled GA in all intermediates of the synthetic pathway. In presence of unlabeled co-substrate glycerol, 12.4% of the mevalonate (and therefore acetyl-CoA) was derived from GA. The contribution of the synthetic pathway to acetyl-CoA production was further increased to 16.1% by the additional expression of the native phosphate acyltransferase enzyme. Finally, we demonstrated that conversion of EG to mevalonate was feasible albeit at currently extremely small yields.

Leveraging substrate flexibility and product selectivity of acetogens in two-stage systems for chemical production

Carbon dioxide (CO2 ) stands out as sustainable feedstock for developing a circular carbon economy whose energy supply could be obtained by boosting the production of clean hydrogen from renewable electricity. H2 -dependent CO2 gas fermentation using acetogenic microorganisms offers a viable solution of increasingly demonstrated value. While gas fermentation advances to achieve commercial process scalability, which is currently limited to a few products such as acetate and ethanol, it is worth taking the best of the current state-of-the-art technology by its integration within innovative bioconversion schemes. This review presents multiple scenarios where gas fermentation by acetogens integrate into double-stage biotechnological production processes that use CO2 as sole carbon feedstock and H2 as energy carrier for products' synthesis. In the integration schemes here reviewed, the first stage can be biotic or abiotic while the second stage is biotic. When the first stage is biotic, acetogens act as a biological platform to generate chemical intermediates such as acetate, formate and ethanol that become substrates for a second fermentation stage. This approach holds the potential to enhance process titre/rate/yield metrics and products' spectrum. Alternatively, when the first stage is abiotic, the integrated two-stage scheme foresees, in the first stage, the catalytic transformation of CO2 into C1 products that, in the second stage, can be metabolized by acetogens. This latter scheme leverages the metabolic flexibility of acetogens in efficient utilization of the products of CO2 abiotic hydrogenation, namely formate and methanol, to synthesize multicarbon compounds but also to act as flexible catalysts for hydrogen storage or production.

Engineering and adaptive laboratory evolution of Escherichia coli for improving methanol utilization based on a hybrid methanol assimilation pathway

Engineering Escherichia coli for efficient methanol assimilation is important for developing methanol as an emerging next-generation feedstock for industrial biotechnology. While recent attempts to engineer E. coli as a synthetic methylotroph have achieved great success, most of these works are based on the engineering of the prokaryotic ribulose monophosphate (RuMP) pathway. In this study, we introduced a hybrid methanol assimilation pathway which consists of prokaryotic methanol dehydrogenase (Mdh) and eukaryotic xylulose monophosphate (XuMP) pathway enzyme dihydroxyacetone synthase (Das) into E. coli and reprogrammed E. coli metabolism to improve methanol assimilation by combining rational design and adaptive laboratory evolution. By deletion and down-regulation of key genes in the TCA cycle and glycolysis to increase the flux toward the cyclic XuMP pathway, methanol consumption and the assimilation of methanol to biomass were significantly improved. Further improvements in methanol utilization and cell growth were achieved via adaptive laboratory evolution and a final evolved strain can grow on methanol with only 0.1 g/L yeast extract as co-substrate. ¹³C-methanol labeling assay demonstrated significantly higher labeling in intracellular metabolites in glycolysis, TCA cycle, pentose phosphate pathway, and amino acids. Transcriptomics analysis showed that the expression of fba, dhak, and part of pentose phosphate pathway genes were highly up-regulated, suggesting that the rational engineering strategies and adaptive evolution are effective for activating the cyclic XuMP pathway. This study demonstrated the feasibility and provided new strategies to construct synthetic methylotrophy of E. coli based on the hybrid methanol assimilation pathway with Mdh and Das.

Recent progress in the engineering of C1-utilizing microbes

The global climate crisis has led to the transition toward the sustainable production of chemicals and fuels with a low carbon footprint. Microbial utilization of one-carbon (C1) substrates, such as carbon dioxide, carbon monoxide, methane, formate, and methanol, may be a promising replacement for the current fossil fuel-based industry. However, natural C1-utilizing microbes are currently unsuitable for industrial applications because of their slow growth and low carbon conversion efficiency, which results in low productivity and yield. Here, we review the recent achievements in engineering C1-utilizing microbes with improved carbon assimilation efficiency and describe the development of synthetic microorganisms by introducing natural C1 assimilation pathways in non-C1-utilizing microbes. Finally, we outline the future directions for realizing the industrial potential of C1-utilizing microbes.

Developing methylotrophic microbial platforms for a methanol-based bioindustry

Methanol, a relatively cheap and renewable single-carbon feedstock, has gained considerable attention as a substrate for the bio-production of commodity chemicals. Conventionally produced from syngas, along with emerging possibilities of generation from methane and CO2, this C1 substrate can serve as a pool for sequestering greenhouse gases while supporting a sustainable bio-economy. Methylotrophic organisms, with the inherent ability to use methanol as the sole carbon and energy source, are competent candidates as platform organisms. Accordingly, methanol bioconversion pathways have been an attractive target for biotechnological and bioengineering interventions in developing microbial cell factories. This review summarizes the recent advances in methanol-based production of various bulk and value-added chemicals exploiting the native and synthetic methylotrophic organisms. Finally, the current challenges and prospects of streamlining these methylotrophic platforms are discussed.

Efficient fatty acid synthesis from methanol in methylotrophic yeast

Methanol is an attractive C1 feedstock with high abundance and low cost in bio-manufacturing. However, the metabolic construction of cell factories to utilize methanol for chemicals production remains a challenge due to the toxic intermediates and complicated metabolic pathways. The group of Zhou rescued methylotrophic yeast from cell death and achieved high-level production of free fatty acids from methanol through a combination of adaptive laboratory evolution, rational metabolic engineering and multi-omics analysis.