Production of acetoin from renewable resources under heterotrophic and mixotrophic conditions

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 Soil-Like Material Enhances CO2 Bio-Valorization into Chemicals in Gas Fermentation

Gas fermentation offers a carbon-neutral route for producing industrial feedstocks using autotrophic microbes to convert carbon dioxide (CO2) in waste gases, such as industrial emissions and biogas, into valuable chemicals or biofuels. However, slow microbial metabolism owing to low gaseous solubility causes significant challenges in gas fermentation. Although chemical or genetic manipulations have been explored to improve gas fermentation, they are either nonsustainable or complex. Herein, an artificial soil-like material (SLM) inspired by natural soil was fabricated to improve the growth and metabolism ofCupriavidus necatorfor enhanced poly-β-hydroxybutyrate (PHB) biosynthesis from CO2 and hydrogen (H2). Porous SLM comprises low-cost nanoclay, boehmite, and starch and serves as a biocarrier to facilitate the colonization of bacteria and delivery of CO2 to bacteria. With 3.0 g/L SLM addition, the solubility of CO2 in water increased by ∼4 times and biomass and PHB production boosted by 29 and 102%, respectively, in the 24 h culture. In addition, a positive modulation was observed in the metabolism of PHB biosynthesis. PHB biosynthesis-associated gene expression was found to be enhanced in response to the SLM addition. The concentrations of intermediates in the metabolic pathway of PHB biosynthesis, such as pyruvate and acetyl-CoA, as well as reducing energy (ATP and NADPH) significantly increased with SLM addition. SLM also demonstrated the merits of easy fabrication, high stability, recyclability, and plasticity, thereby indicating its considerable potential for large-scale application in gas fermentation.

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.

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.

Chemoautotroph Cupriavidus necator as a potential game-changer for global warming and plastic waste problem: A review

Cupriavidus necator, a versatile microorganism found in both soil and water, can have both heterotrophic and lithoautotrophic metabolisms depending on environmental conditions. C. necator has been extensively examined for producing Polyhydroxyalkanoates (PHAs), the promising polyester alternatives to petroleum-based synthetic polymers because it has a superior ability for accumulating a considerable amount of PHAs from renewable resources. The development of metabolically engineered C. necator strains has led to their application for synthesizing biopolymers, biofuels and biochemicals such as ethanol, isobutanol and higher alcohols. Bio-based processes of recombinant C. necator have made much progress in production of these high-value products from biomass wastes, plastic wastes and even waste gases. In this review, we discuss the potential of C. necator as promising platform host strains that provide a great opportunity for developing a waste-based circular bioeconomy.