Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering

Exploration of formate as a liquid organic hydrogen carrier in biohydrogen production through evolutionary and process engineering of hyperthermophilic archaeon

Hydrogen (H2) is considered a promising renewable energy source, but its storage and delivery present significant challenges. Liquid organic hydrogen carriers (LOHC) offer a potential solution to this problem, with formate as a top candidate for LOHC. This study focused on developing technology for biological H2 production from formate by utilizing the hyperthermophilic archaeon Thermococcus onnurineus NA1. An engineered strain, WTF-350 T, was developed through adaptive evolution using formate and exhibited 3.6-4.0 times enhanced cell growth, formate consumption, and H2 production compared to the wild-type strain. Optimizing fermentation processes through pH-stat, fed-batch mode, and pyruvate supplementation led to a 2.0-2.5 times increase in cell density and H2 production rate. Moreover, formic acid, produced by the electroreduction of carbon dioxide (CO2), was found to be an effective feedstock for biohydrogen production. This study successfully demonstrated the potential of integrating CO2 electroreduction and biohydrogen production for a sustainable hydrogen economy.

Pathways to sustainability: a quantitative comparison of aerobic and anaerobic C1 bioconversion routes

One-carbon (C1) substrates are attractive feedstocks for biological upgrading as part of a circular, carbon-negative bioeconomy. Nature has evolved a diverse set of C1-trophs that use a variety of pathways. Additionally, intensive effort has recently been invested in developing synthetic C1 assimilation pathways. This complicated landscape presents the question: "What pathways should be used to produce what products from what C1 substrates?" To guide the selection, we calculate and compare maximal theoretical yields for a range of bioproducts from different C1 feedstocks and pathways. The results highlight emerging opportunities to apply metabolic engineering to specific C1 pathways to improve pathway performance. Since the C1 landscape is dynamic, with new discoveries in the biochemistry of native pathways and new synthetic alternatives rapidly emerging, we present detailed procedures for these yield calculations to enable others to easily adapt them to additional scenarios as a foundation for establishing industrially relevant production strains.

Optimizing Cupriavidus necator H16 as a host for aerobic C1 conversion

Biological systems capable of converting CO2 or CO2-derived, single-carbon (C1) compounds can be used to reduce or reverse carbon emissions while establishing a circular bioeconomy to provide sustainable sources of the fuels, foods, and materials humanity relies on. A robust bioeconomy will rely upon a variety of microorganisms capable of assimilating C1 compounds and converting them to valuable products at industrial scale. While anaerobic microbes are ideal hosts for production of short-chain acids and alcohols, microbes capable of aerobic respiration are well suited for biosynthesis of higher molecular weight products. One such organism is the gram-negative soil bacterium Cupriavidus necator, which has been utilized in commercial production of biopolymers for decades. More recently, its capability of robust, aerobic growth on CO2 has inspired research efforts that have advanced it toward becoming one of the leading bacterial hosts for C1-based biomanufacturing. This review highlights those efforts in the context of the characteristics that have historically made C. necator an excellent host for industrial bioconversion processes: its metabolic versatility, ability to grow rapidly to high cell densities, and genetic amenability.

Efficient production of salicylic acid through CmeR-PcmeO biosensor-assisted multiplexing pathway optimization in Escherichia coli

To address the challenge of microbial tolerance in industrial biomanufacturing, we developed an adaptive evolution strategy for Escherichia coli W3110 to enhance its salicylic acid (SA) tolerance. Utilizing a CmeR-PcmeO biosensor-enabled high-throughput screening system, we isolated an SA-tolerant variant (W3110K-4) that exhibited a 2.3-fold increase in tolerance (from 0.9 to 2.1 g/L) and a 2.1-fold improvement in SA production (from 283 to 588.1 mg/L). Subsequently, the designed sensors were combined with multi-pathway sgRNA arrays to dynamically modulate the other three branched-chain acid derivatives, achieving a balance between biomass growth and rapid SA production in the adaptively evolved strain, resulting in a maximum SA yield of 1477.8 mg/L, which represents a 30% improvement over the non-evolved control strain W3110K-W2 (1138.2 mg/L) using the same metabolic strategy. Whole-genome sequencing revealed that adaptive mutations in genes such as ducA* and anti-drug resistance C2 mutation genes (ymdA*, ymdB*, clsC*, csgB*, csgA*, and csgC*) play a key role in enhancing SA tolerance and productivity. Notably, the evolved strain W3110K-4 exhibits significant resistance to bacteriophages, making it a promising candidate for large-scale SA fermentation. This work develops and expands the CmeR-PcmeO system, proposes new insights into improved strains through biosensor screening, guided multi-pathway metabolism, and adaptive evolution, and provides a paradigm for engineers to obtain engineered strains.

Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16

Cupriavidus necator H16 is a facultative chemolithotroph capable of using CO2 as a carbon source, making it a promising organism for carbon-negative biomanufacturing of petroleum-based product alternatives. In contrast to model microbes, genetic engineering technologies are limited in C. necator, constraining its utility in basic and applied research. Here, we developed a genome engineering technology to efficiently mobilize, integrate, and express synthetic genetic elements (SGEs) in C. necator. We tested the chromosomal expression of four inducible promoters to optimize an engineered genetic landing pad for tunable gene expression. To demonstrate utility, we employed the SGE system to design, mobilize, and express eight heterologous inorganic carbon uptake pathways in C. necator. We demonstrated all inorganic carbon uptake systems' upregulated intracellular bicarbonate concentrations under heterotrophic conditions. This work establishes the utility of the SGE strategy for expedited integration and tunable expression of heterologous pathways, and enhances intracellular bicarbonate concentrations in C. necator.

Recent advances in synthetic biology toolkits and metabolic engineering of Ralstonia eutropha H16 for production of value-added chemicals

Ralstonia eutropha H16, a facultative chemolithoautotrophic Gram-negative bacterium, demonstrates remarkable metabolic flexibility by utilizing either diverse organic substrates or CO2 as the sole carbon source, with H2 serving as the electron donor under aerobic conditions. The capacity of carbon and energy metabolism of R. eutropha H16 enabled development of synthetic biology technologies and strategies to engineer its metabolism for biosynthesis of value-added chemicals. This review firstly outlines the development of synthetic biology tools tailored for R. eutropha H16, including construction of expression vectors, regulatory elements, and transformation techniques. The availability of comprehensive omics data (i.e., transcriptomic, proteomic, and metabolomic) combined with the fully annotated genome sequence provides a robust genetic framework for advanced metabolic engineering. These advancements facilitate efficient reprogramming metabolic network of R. eutropha. The potential of R. eutropha as a versatile microbial platform for industrial biotechnology is further underscored by its ability to utilize a wide range of carbon sources for the production of value-added chemicals through both autotrophic and heterotrophic pathways. The integration of state-of-the-art genetic and genomic engineering tools and strategies with high cell-density fermentation processes enables engineered R. eutropha as promising microbial cell factories for optimizing carbon fluxes and expanding the portfolio of bio-based products.

Physiological role of the FDH1 gene in methylotrophic yeast Komagataella phaffii and carbon recovery as formate during methylotrophic growth of the fdh1-deletion strain

During methylotrophic growth of Komagataella phaffii, a large amount of carbon is lost as CO2. In this study, we aimed to construct a recovery system for carbon atoms, which emit as CO2 along the methanol dissimilation pathway in the form of formate when using strain fdh1Δ, the deletion mutant of formate dehydrogenase gene (FDH1). Strain fdh1Δ showed a severe growth defect when using methanol as the sole carbon source. However, using YPM medium (1 % yeast extract, 2 % peptone and 1 % methanol) with pH adjustment, the strain recovered methylotrophic growth and methanol utilization, accumulating high levels of extracellular formate in the medium. In strain fdh1Δ, the final carbon conversion rate of formate from methanol reached 12.9 % by batch cultivation. Moreover, by fed-batch cultivation in a jar fermentor, the formate productivity of strain fdh1Δ achieved approximately 540 mM. These results indicated that strain fdh1Δ possessed a high potential for recovering carbon atoms as formate, which can be a valuable precursor for various industrial applications.

One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle

One-carbon feedstocks such as formate could be promising renewable substrates for sustainable microbial production of food, fuels and chemicals. Here we replace the native energy-inefficient Calvin-Benson-Bassham cycle in Cupriavidus necator with the more energy-efficient reductive glycine pathway for growth on formate and CO2. In chemostats, our engineered strain reached a 17% higher biomass yield than the wild type and a yield higher than any natural formatotroph using the Calvin cycle. This shows the potential of synthetic metabolism to realize sustainable, bio-based production.

Metabolic engineering of microorganisms for carbon dioxide utilization

The escalating climate crisis underscores the urgent need for sustainable development, with CO2 utilization emerging as a pivotal approach to mitigating greenhouse gas emissions. Among various technological approaches, metabolic engineering of microorganisms for CO2 utilization offers significant potential. This review covers the engineering of endogenous CO2 fixation pathways, the construction of novel synthetic pathways, and strategies to optimize metabolic flux, enhance cofactor availability, and manipulate regulatory genes to improve CO2 assimilation efficiency. It also explores the roles of evolutionary engineering, enzyme engineering, and CO2 concentrating mechanisms in improving CO2 fixation. Additionally, the review underscores advancements in converting CO2 into valuable products such as biofuels, bioplastics, and chemicals using both native and synthetic autotrophic microorganisms.

Physiology-informed use of Cupriavidus necator in biomanufacturing: a review of advances and challenges

Biomanufacturing offers a potentially sustainable alternative to deriving chemicals from fossil fuels. However, traditional biomanufacturing, which uses sugars as feedstocks, competes with food production and yields unfavourable land use changes, so more sustainable options are necessary. Cupriavidus necator is a chemolithoautotrophic bacterium capable of consuming carbon dioxide and hydrogen as sole carbon and energy sources, or formate as the source of both. This autotrophic metabolism potentially makes chemical production using C. necator sustainable and attractive for biomanufacturing. Additionally, C. necator natively fixes carbon in the form of poly-3-hydroxybutyrate, which can be processed to make biodegradable plastic. Recent progress in development of modelling and synthetic biology tools have made C. necator much more usable as a biomanufacturing chassis. However, these tools and applications are often limited by a lack of consideration for the unique physiology and metabolic features of C. necator. As such, further work is required to better understand the intricate mechanisms that allow it to prioritise generalization over specialization. In this review, progress toward physiology-informed engineering of C. necator across several dimensions is critically discussed, and recommendations for moving toward a physiological approach are presented. Arguments for metabolic specialization, more focus on autotrophic fermentation, C. necator-specific synthetic biology tools, and modelling that goes beyond constraints are presented based on analysis of existing literature.

Production of α-amylase from gluconate and carbon dioxide by protein synthesis and secretion optimization in Cupriavidus necator H16

Chemoautotrophic Cupriavidus necator H16 has a strong protein synthesis ability and has been used to produce intracellular protein products. However, studies optimizing its secretion system and the producing extracellular enzyme products (EEPs) are lacking. Here, we focused on investigating the feasibility of synthesizing and secreting EEPs in C. necator H16, using α-amylase as a prototype. α-Amylase expression optimization, genome modification, and secretion system engineering were performed to construct and optimize the α-amylase-producing engineering C. necator H16. Finally, the optimized engineering strain could produce α-amylase, with the α-amylase activity per unit cells reaching up to 5.54 U/OD600 using gluconate as substrate, which was 29.2-fold compared with that of initial engineering strain. Additionally, when using carbon dioxide as substrate, the α-amylase activity per unit cells of engineered strain reached 4.26 U/OD600. Overall, this study demonstrates the feasibility of developing C. necator H16 as a host for autotrophic production of α-amylase.

Unlocking the potential of Cupriavidus necator H16 as a platform for bioproducts production from carbon dioxide

The rapid global increase in fossil fuel and energy consumption has resulted in the accumulation of greenhouse gases, especially carbon dioxide (CO2), thus contributing to climate change. Therefore, transforming CO2 into valuable products could yield beneficial outcomes. In this review, the capabilities of Cupriavidus necator H16, a light-independent chemoautotrophic bacterium, as a host platform for the transformation of CO2 into diverse products are explored. We begin by examining the progress in synthetic biology toolkits, gas fermentation technologies, and engineering approaches, considering the chemoautotrophic metabolic traits of C. necator to enhance the capacity of the strain for CO2 fixation. Additionally, recent research focused on the metabolic engineering of C. necator H16 for the conversion of CO2 into biodegradable plastics, biofuels, bioactive compounds, and single-cell proteins was reviewed. Finally, we address the limitations affecting the advancement and utilization of C. necator H16 strain, such as inefficiencies and the range of product types, and offer several recommendations for enhancement. This review acts as a resource for the development of C. necator H16 cell factories and the industrial manufacture of products derived from CO2.

Lignin valorization to bioplastics with an aromatic hub metabolite-based autoregulation system

Exploring microorganisms with downstream synthetic advantages in lignin valorization is an effective strategy to increase target product diversity and yield. This study ingeniously engineers the non-lignin-degrading bacterium Ralstonia eutropha H16 (also known as Cupriavidus necator H16) to convert lignin, a typically underutilized by-product of biorefinery, into valuable bioplastic polyhydroxybutyrate (PHB). The aromatic metabolism capacities of R. eutropha H16 for different lignin-derived aromatics (LDAs) are systematically characterized and complemented by integrating robust functional modules including O-demethylation, aromatic aldehyde metabolism and the mitigation of by-product inhibition. A pivotal discovery is the regulatory element PcaQ, which is highly responsive to the aromatic hub metabolite protocatechuic acid during lignin degradation. Based on the computer-aided design of PcaQ, we develop a hub metabolite-based autoregulation (HMA) system. This system can control the functional genes expression in response to heterologous LDAs and enhance metabolism efficiency. Multi-module genome integration and directed evolution further fortify the strain's stability and lignin conversion capacities, leading to PHB production titer of 2.38 g/L using heterologous LDAs as sole carbon source. This work not only marks a leap in bioplastic production from lignin components but also provides a strategy to redesign the non-LDAs-degrading microbes for efficient lignin valorization.

Adaptive laboratory evolution and metabolic engineering of Cupriavidus necator for improved catabolism of volatile fatty acids

Bioconversion of high-volume waste streams into value-added products will be an integral component of the growing bioeconomy. Volatile fatty acids (VFAs) (e.g., butyrate, valerate, and hexanoate) are an emerging and promising waste-derived feedstock for microbial carbon upcycling. Cupriavidus necator H16 is a favorable host for conversion of VFAs into various bioproducts due to its diverse carbon metabolism, ease of metabolic engineering, and use at industrial scales. Here, we report that a common strategy to improve product titers in C. necator, deletion of the polyhydroxybutyrate (PHB) biosynthetic operon, results in a significant growth defect on VFA substrates. Using adaptive laboratory evolution, we identify mutations to the regulator gene phaR, the two-component response regulator-histidine kinase pair encoded by H16_A1372/H16_A1373, and the tripartite transporter assembly encoded by H16_A2296-A2298 as causative for improved growth on VFA substrates. Deletion of phaR and H16_A1373 led to significantly reduced NADH abundance accompanied by large changes to expression of genes involved in carbon metabolism, balance of electron carriers, and oxidative stress tolerance that may be responsible for improved growth of these engineered strains. These results provide insight into the role of PHB biosynthesis in carbon and energy metabolism and highlight a key role for the regulator PhaR in global regulatory networks. By combining mutations, we generated platform strains with significant growth improvements on VFAs, which can enable improved conversion of waste-derived VFA substrates to target bioproducts.

The energy metabolism of Cupriavidus necator in different trophic conditions

The "knallgas" bacterium Cupriavidus necator is attracting interest due to its extremely versatile metabolism. C. necator can use hydrogen or formic acid as an energy source, fixes CO2 via the Calvin-Benson-Bassham (CBB) cycle, and grows on organic acids and sugars. Its tripartite genome is notable for its size and duplications of key genes (CBB cycle, hydrogenases, and nitrate reductases). Little is known about which of these isoenzymes and their cofactors are actually utilized for growth on different substrates. Here, we investigated the energy metabolism of C. necator H16 by growing a barcoded transposon knockout library on succinate, fructose, hydrogen (H2/CO2), and formic acid. The fitness contribution of each gene was determined from enrichment or depletion of the corresponding mutants. Fitness analysis revealed that (i) some, but not all, molybdenum cofactor biosynthesis genes were essential for growth on formate and nitrate respiration. (ii) Soluble formate dehydrogenase (FDH) was the dominant enzyme for formate oxidation, not membrane-bound FDH. (iii) For hydrogenases, both soluble and membrane-bound enzymes were utilized for lithoautotrophic growth. (iv) Of the six terminal respiratory complexes in C. necator H16, only some are utilized, and utilization depends on the energy source. (v) Deletion of hydrogenase-related genes boosted heterotrophic growth, and we show that the relief from associated protein cost is responsible for this phenomenon. This study evaluates the contribution of each of C. necator's genes to fitness in biotechnologically relevant growth regimes. Our results illustrate the genomic redundancy of this generalist bacterium and inspire future engineering strategies.IMPORTANCEThe soil bacterium Cupriavidus necator can grow on gas mixtures of CO2, H2, and O2. It also consumes formic acid as carbon and energy source and various other substrates. This metabolic flexibility comes at a price, for example, a comparatively large genome (6.6 Mb) and a significant background expression of lowly utilized genes. In this study, we mutated every non-essential gene in C. necator using barcoded transposons in order to determine their effect on fitness. We grew the mutant library in various trophic conditions including hydrogen and formate as the sole energy source. Fitness analysis revealed which of the various energy-generating iso-enzymes are actually utilized in which condition. For example, only a few of the six terminal respiratory complexes are used, and utilization depends on the substrate. We also show that the protein cost for the various lowly utilized enzymes represents a significant growth disadvantage in specific conditions, offering a route to rational engineering of the genome. All fitness data are available in an interactive app at https://m-jahn.shinyapps.io/ShinyLib/.

Functional plasticity of HCO3- uptake and CO2 fixation in Cupriavidus necator H16

Despite its prominence, the ability to engineer Cupriavidus necator H16 for inorganic carbon uptake and fixation is underexplored. We tested the roles of endogenous and heterologous genes on C. necator inorganic carbon metabolism. Deletion of β-carbonic anhydrase can had the most deleterious effect on C. necator autotrophic growth. Replacement of this native uptake system with several classes of dissolved inorganic carbon (DIC) transporters from Cyanobacteria and chemolithoautotrophic bacteria recovered autotrophic growth and supported higher cell densities compared to wild-type (WT) C. necator in batch culture. Strains expressing Halothiobacillus neopolitanus DAB2 (hnDAB2) and diverse rubisco homologs grew in CO2 similarly to the wild-type strain. Our experiments suggest that the primary role of carbonic anhydrase during autotrophic growth is to support anaplerotic metabolism, and an array of DIC transporters can complement this function. This work demonstrates flexibility in HCO3- uptake and CO2 fixation in C. necator, providing new pathways for CO2-based biomanufacturing.

Utilization of formic acid by extremely thermoacidophilic archaea species

The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO2, is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1-2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.

Synthetic biology toolkit of Ralstonia eutropha (Cupriavidus necator)

Synthetic biology encompasses many kinds of ideas and techniques with the common theme of creating something novel. The industrially relevant microorganism, Ralstonia eutropha (also known as Cupriavidus necator), has long been a subject of metabolic engineering efforts to either enhance a product it naturally makes (polyhydroxyalkanoate) or produce novel bioproducts (e.g., biofuels and other small molecule compounds). Given the metabolic versatility of R. eutropha and the existence of multiple molecular genetic tools and techniques for the organism, development of a synthetic biology toolkit is underway. This toolkit will allow for novel, user-friendly design that can impart new capabilities to R. eutropha strains to be used for novel application. This article reviews the different synthetic biology techniques currently available for modifying and enhancing bioproduction in R. eutropha. KEY POINTS: • R. eutropha (C. necator) is a versatile organism that has been examined for many applications. • Synthetic biology is being used to design more powerful strains for bioproduction. • A diverse synthetic biology toolkit is being developed to enhance R. eutropha's capabilities.

Fast-track adaptive laboratory evolution of Cupriavidus necator H16 with divalent metal cations

Microbial strain improvement through adaptive laboratory evolution (ALE) has been a key strategy in biotechnology for enhancing desired phenotypic traits. In this Biotech Method paper, we present an accelerated ALE (aALE) workflow and its successful implementation in evolving Cupriavidus necator H16 for enhanced tolerance toward elevated glycerol concentrations. The method involves the deliberate induction of genetic diversity through controlled exposure to divalent metal cations, enabling the rapid identification of improved variants. Through this approach, we observed the emergence of robust variants capable of growing in high glycerol concentration environments, demonstrating the efficacy of our aALE workflow. When cultivated in 10% v/v glycerol, the adapted variant Mn-C2-B11, selected through aALE, achieved a final OD600 value of 56.0 and a dry cell weight of 15.2 g L-1, compared to the wild type (WT) strain's final OD600 of 39.1 and dry cell weight of 8.4 g L-1. At an even higher glycerol concentration of 15% v/v, Mn-C2-B11 reached a final OD600 of 48.9 and a dry cell weight of 12.7 g L-1, in contrast to the WT strain's final OD600 of 9.0 and dry cell weight of 3.1 g L-1. Higher glycerol consumption by Mn-C2-B11 was also confirmed by high-performance liquid chromatography (HPLC) analysis. This adapted variant consumed 34.5 times more glycerol compared to the WT strain at 10% v/v glycerol. Our method offers several advantages over other reported ALE approaches, including its independence from genetically modified strains, specialized genetic tools, and potentially carcinogenic DNA-modifying agents. By utilizing divalent metal cations as mutagens, we offer a safer, more efficient, and cost-effective alternative for expansion of genetic diversity. With its ability to foster rapid microbial evolution, aALE serves as a valuable addition to the ALE toolbox, holding significant promise for the advancement of microbial strain engineering and bioprocess optimization.

From sustainable feedstocks to microbial foods

Climate change-induced alterations in weather patterns, such as frequent and severe heatwaves, cold waves, droughts, floods, heavy rain and storms, are reducing crop yields and agricultural productivity. At the same time, greenhouse gases arising from food production and supply account for almost 30% of anthropogenic emissions. This vicious circle is producing a global food crisis. Sustainable food resources and production systems are needed now, and microbial foods are one possible solution. In this Perspective, we highlight the most promising technologies, and carbon and energy sources, for microbial food production.

Establishing CRISPRi for Programmable Gene Repression and Genome Evolution in Cupriavidus necator

Cupriavidus necator H16 is a "Knallgas" bacterium with the ability to utilize various carbon sources and has been employed as a versatile microbial cell factory to produce a wide range of value-added compounds. However, limited genome engineering, especially gene regulation methods, has constrained its full potential as a microbial production platform. The advent of CRISPR/Cas9 technology has shown promise in addressing this limitation. Here, we developed an optimized CRISPR interference (CRISPRi) system for gene repression in C. necator by expressing a codon-optimized deactivated Cas9 (dCas9) and appropriate single guide RNAs (sgRNAs). CRISPRi was proven to be a programmable and controllable tool and could successfully repress both exogenous and endogenous genes. As a case study, we decreased the accumulation of polyhydroxyalkanoate (PHB) via CRISPRi and rewired the carbon fluxes to the synthesis of lycopene. Additionally, by disturbing the expression of DNA mismatch repair gene mutS with CRISPRi, we established CRISPRi-Mutator for genome evolution, rapidly generating mutant strains with enhanced hydrogen peroxide tolerance and robustness in microbial electrosynthesis (MES) system. Our work provides an efficient CRISPRi toolkit for advanced genetic manipulation and optimization of C. necator cell factories for diverse biotechnology applications.

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.

Comparison of wild-type KT2440 and genome-reduced EM42 Pseudomonas putida strains for muconate production from aromatic compounds and glucose

Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome reduction has been previously conducted, resulting in P. putida strain EM42, which exhibited characteristics that could be advantageous for production strains. Here, we compared P. putida KT2440- and EM42-derived strains for cis,cis-muconic acid production from an aromatic compound, p-coumarate, and in separate strains, from glucose. To our surprise, the EM42-derived strains did not outperform the KT2440-derived strains in muconate production from either substrate. In bioreactor cultivations, KT2440- and EM42-derived strains produced muconate from p-coumarate at titers of 45 g/L and 37 g/L, respectively, and from glucose at 20 g/L and 13 g/L, respectively. To provide additional insights about the differences in the parent strains, we analyzed growth profiles of KT2440 and EM42 on aromatic compounds as the sole carbon and energy sources. In general, the EM42 strain exhibited reduced growth rates but shorter growth lags than KT2440. We also observed that EM42-derived strains resulted in higher growth rates on glucose compared to KT2440-derived strains, but only at the lowest glucose concentrations tested. Transcriptomics revealed that genome reduction in EM42 had global effects on transcript levels and showed that the EM42-derived strains that produce muconate from glucose exhibit reduced modulation of gene expression in response to changes in glucose concentrations. Overall, our results highlight that additional studies are warranted to understand the effects of genome reduction on microbial metabolism and physiology, especially when intended for use in production strains.

A scalable membrane electrode assembly architecture for efficient electrochemical conversion of CO2 to formic acid

The electrochemical reduction of carbon dioxide to formic acid is a promising pathway to improve CO2 utilization and has potential applications as a hydrogen storage medium. In this work, a zero-gap membrane electrode assembly architecture is developed for the direct electrochemical synthesis of formic acid from carbon dioxide. The key technological advancement is a perforated cation exchange membrane, which, when utilized in a forward bias bipolar membrane configuration, allows formic acid generated at the membrane interface to exit through the anode flow field at concentrations up to 0.25 M. Having no additional interlayer components between the anode and cathode this concept is positioned to leverage currently available materials and stack designs ubiquitous in fuel cell and H2 electrolysis, enabling a more rapid transition to scale and commercialization. The perforated cation exchange membrane configuration can achieve >75% Faradaic efficiency to formic acid at <2 V and 300 mA/cm2 in a 25 cm2 cell. More critically, a 55-hour stability test at 200 mA/cm2 shows stable Faradaic efficiency and cell voltage. Technoeconomic analysis is utilized to illustrate a path towards achieving cost parity with current formic acid production methods.

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.

Problems and corresponding strategies for converting CO2 into value-added products in Cupriavidus necator H16 cell factories

Elevated CO2 emissions have substantially altered the worldwide climate, while the excessive reliance on fossil fuels has exacerbated the energy crisis. Therefore, the conversion of CO2 into fuel, petroleum-based derivatives, drug precursors, and other value-added products is expected. Cupriavidus necator H16 is the model organism of the "Knallgas" bacterium and is considered to be a microbial cell factory as it can convert CO2 into various value-added products. However, the development and application of C. necator H16 cell factories has several limitations, including low efficiency, high cost, and safety concerns arising from the autotrophic metabolic characteristics of the strains. In this review, we first considered the autotrophic metabolic characteristics of C. necator H16, and then categorized and summarized the resulting problems. We also provided a detailed discussion of some corresponding strategies concerning metabolic engineering, trophic models, and cultivation mode. Finally, we provided several suggestions for improving and combining them. This review might help in the research and application of the conversion of CO2 into value-added products in C. necator H16 cell factories.

Robotic workflows for automated long-term adaptive laboratory evolution: improving ethanol utilization by Corynebacterium glutamicum

BACKGROUND

Adaptive laboratory evolution (ALE) is known as a powerful tool for untargeted engineering of microbial strains and genomics research. It is particularly well suited for the adaptation of microorganisms to new environmental conditions, such as alternative substrate sources. Since the probability of generating beneficial mutations increases with the frequency of DNA replication, ALE experiments are ideally free of constraints on the required duration of cell proliferation.

RESULTS

Here, we present an extended robotic workflow for performing long-term evolution experiments based on fully automated repetitive batch cultures (rbALE) in a well-controlled microbioreactor environment. Using a microtiter plate recycling approach, the number of batches and thus cell generations is technically unlimited. By applying the validated workflow in three parallel rbALE runs, ethanol utilization by Corynebacterium glutamicum ATCC 13032 (WT) was significantly improved. The evolved mutant strain WT_EtOH-Evo showed a specific ethanol uptake rate of 8.45 ± 0.12 mmolEtOH gCDW-1 h-1 and a growth rate of 0.15 ± 0.01 h-1 in lab-scale bioreactors. Genome sequencing of this strain revealed a striking single nucleotide variation (SNV) upstream of the ald gene (NCgl2698, cg3096) encoding acetaldehyde dehydrogenase (ALDH). The mutated basepair was previously predicted to be part of the binding site for the global transcriptional regulator GlxR, and re-engineering demonstrated that the identified SNV is key for enhanced ethanol assimilation. Decreased binding of GlxR leads to increased synthesis of the rate-limiting enzyme ALDH, which was confirmed by proteomics measurements.

CONCLUSIONS

The established rbALE technology is generally applicable to any microbial strain and selection pressure that fits the small-scale cultivation format. In addition, our specific results will enable improved production processes with C. glutamicum from ethanol, which is of particular interest for acetyl-CoA-derived products.

Engineering the biological conversion of formate into crotonate in Cupriavidus necator

To advance the sustainability of the biobased economy, our society needs to develop novel bioprocesses based on truly renewable resources. The C1-molecule formate is increasingly proposed as carbon and energy source for microbial fermentations, as it can be efficiently generated electrochemically from CO2 and renewable energy. Yet, its biotechnological conversion into value-added compounds has been limited to a handful of examples. In this work, we engineered the natural formatotrophic bacterium C. necator as cell factory to enable biological conversion of formate into crotonate, a platform short-chain unsaturated carboxylic acid of biotechnological relevance. First, we developed a small-scale (150-mL working volume) cultivation setup for growing C. necator in minimal medium using formate as only carbon and energy source. By using a fed-batch strategy with automatic feeding of formic acid, we could increase final biomass concentrations 15-fold compared to batch cultivations in flasks. Then, we engineered a heterologous crotonate pathway in the bacterium via a modular approach, where each pathway section was assessed using multiple candidates. The best performing modules included a malonyl-CoA bypass for increasing the thermodynamic drive towards the intermediate acetoacetyl-CoA and subsequent conversion to crotonyl-CoA through partial reverse β-oxidation. This pathway architecture was then tested for formate-based biosynthesis in our fed-batch setup, resulting in a two-fold higher titer, three-fold higher productivity, and five-fold higher yield compared to the strain not harboring the bypass. Eventually, we reached a maximum product titer of 148.0 ± 6.8 mg/L. Altogether, this work consists in a proof-of-principle integrating bioprocess and metabolic engineering approaches for the biological upgrading of formate into a value-added platform chemical.

Heterologous expression of formate dehydrogenase enables photoformatotrophy in the emerging model microalga, Picochlorum renovo

Rising global greenhouse gas emissions and the impacts of resultant climate change necessitate development and deployment of carbon capture and conversion technologies. Amongst the myriad of bio-based conversion approaches under evaluation, a formate bio-economy has recently been proposed, wherein CO2-derived formate serves as a substrate for concurrent carbon and energy delivery to microbial systems. To date, this approach has been explored in chemolithotrophic and heterotrophic organisms via native or engineered formatotrophy. However, utilization of this concept in phototrophic organisms has yet to be reported. Herein, we have taken the first steps to establish formate utilization in Picochlorum renovo, a recently characterized eukaryotic microalga with facile genetic tools and promising applied biotechnology traits. Plastidial heterologous expression of a formate dehydrogenase (FDH) enabled P. renovo growth on formate as a carbon and energy source. Further, FDH expression enhanced cultivation capacity on ambient CO2, underscoring the potential for bypass of conventional CO2 capture and concentration limitations. This work establishes a photoformatotrophic cultivation regime that leverages light energy-driven formate utilization. The resultant photosynthetic formate platform has widespread implications for applied phototrophic cultivation systems and the bio-economy at large.