Recent progress in the synthesis of advanced biofuel and bioproducts

Design of experiment approach to boost volatile production from kiwi byproducts

Design of Experiments (DoE), is a tool to explore relationships between factors and responses of a system. DoE and response surface methodology are increasingly used in different fields, but their application are limited in the valorization of residual biomass and agro-industrial by-products. Agro-industrial biomass residues can be eco-friendly converted into high-value compounds through bioprocesses. This approach identified key factors and predicted optimal conditions for enhancing microbial growth and the production of specific compounds or volatile classes. Lactiplantibacillus plantarum 4193 and Lacticaseibacillus paracasei 2243, were identified as the best starters while the production of methyl heptenone is influenced by fermentation time and pH. This out-turn in the generation of aromatically rich biomass, which can be utilised as a food ingredient or for the extraction of specific volatile compounds, and employed as flavouring agents. This study underlines the potential of fermentation in maximizing the value of unripe kiwi biomass.

Semi-continuous biomanufacturing for maximizing the production of complex chemicals and fuels: a case study of amorpha-4,11-diene

Biomanufacturing is emerging as a key technology for the sustainable production of chemicals, materials, and food ingredients using engineered microbes. However, despite billions of dollars of investment, few processes have been successfully commercialized due to a lack of attention on industrial-scale bioprocess design and innovation. In this study, we address this challenge through the development of a novel semi-continuous bioprocess for the production of the terpene amorpha-4,11-diene (AMD4,11) using engineered Escherichia coli. Using a hydrophilic membrane for product and biomass retention, we successfully decoupled production at low growth rates (~0.01 1/h) and improved reactor productivity up to 166 mg/lReactor h, threefold compared with traditional fed-batch fermentations. When cell recycling was implemented, we showed sustained production at the highest conversion yield and production rate for up to three cycles, demonstrating the robustness of both the strain and the process and highlighting the potential for new bioprocess strategies to improve the economic viability of industrial biomanufacturing.

BioCloneBot: A versatile, low-cost, and open-source automated liquid handler

Liquid handler systems can provide significant benefits to researchers by automating laboratory work, however, their unaffordable price provides a steep barrier to entry. Therefore, we provide the BioCloneBot, a versatile, low-cost, and open-source automated liquid handler. This system can be easily built with 3D-printed parts and readily available commercial components. The BioCloneBot is highly adaptive to user needs and facilitates various liquid handling tasks in research and diagnostics. Its user-friendly interface and programmable nature make it suitable for a wide range of applications, from small-scale experiments to larger laboratory setups. By utilizing BioCloneBot, researchers and scientists can streamline their liquid handling processes without the financial constraints posed by traditional systems. In this paper, we detail the design, construction, and validation of BioCloneBot, showcasing its precise control, accuracy, and repeatability in various liquid handling tasks. The open-source nature of the system encourages collaboration and customization, enabling researchers to contribute and adapt the technology to specific experimental requirements.

Transcription factor-based biosensor: A molecular-guided approach for advanced biofuel synthesis

As a sustainable and renewable alternative to petroleum fuels, advanced biofuels shoulder the responsibility of energy saving, emission reduction and environmental protection. Traditional engineering of cell factories for production of advanced biofuels lacks efficient high-throughput screening tools and regulating systems, impeding the improvement of cellular productivity and yield. Transcription factor-based biosensors have been widely applied to monitor and regulate microbial cell factory products due to the advantages of fast detection and in-situ screening. This review updates the design and application of transcription factor-based biosensors tailored for advanced biofuels and related intermediates. The construction and genetic parts selection principle of biosensors are discussed. Strategies to enhance the performance of biosensor, including regulating promoter strength and RBS strength, optimizing plasmid copy number, implementing genetic amplifier, and modulating the structure of transcription factor, have also been summarized. We further review the application of biosensors in high-throughput screening of new metabolic engineering targets, evolution engineering, confirmation of protein function, and dynamic regulation of metabolic flux for higher production of advanced biofuels. At last, we discuss the current limitations and future trends of transcription factor-based biosensors.

Microbial biotechnology and beyond: A roadmap for sustainable development and climate mitigation in the transition from fossil fuels to green chemistry

Our planet, which operates as a closed system, is facing increasing entropy due to human activities such as the overexploitation of natural resources and fossil fuel use. The COP28 in Dubai emphasized the urgency to abandon fossil fuels, recognizing them as the primary cause of human-induced environmental changes, while highlighting the need to transition to renewable energies. We promote the crucial role of microbes for sustaining biogenic cycles to combat climate change and the economic potential of synthetic biology tools for producing diverse non-fossil fuels and chemicals, thus contributing to emission reduction in transport and industry. The shift to 'green chemistry' encounters challenges, derived from the availability of non-food residues and waste (mainly lignocellulosic) as raw material, the construction of cost-effective bioprocessing plants, product recovery from fermentation broths and the utilization of leftover lignin residues for synthesizing new chemicals, aligning with circular economy and sustainable development goals. To meet the Paris Agreement goals, an urgent global shift to low-carbon, renewable sources is imperative, ultimately leading to the cessation of our reliance on fossil fuels.

Design of a dual-responding genetic circuit for high-throughput identification of L-threonine-overproducing Escherichia coli

L-threonine is a crucial amino acid that is extensively employed in the realms of food, animal feed and pharmaceuticals. Unfortunately, the lack of an appropriate biosensor has hindered the establishment of a robust high-throughput screening (HTS) system for the identification of the desired strains from random mutants. In this study, a dual-responding genetic circuit that capitalizes on the L-threonine inducer-like effect, the L-threonine riboswitch, and a signal amplification system was designed for the purpose of screening L-threonine overproducers. This platform effectively enhanced the performance of the enzyme and facilitated the identification of high L-threonine-producing strains from a random mutant library. Consequently, pathway optimization and directed evolution of the key enzyme enhanced L-threonine production by 4 and 7-fold, respectively. These results demonstrate the potential of biosensor design for dynamic metabolite detection and offer a promising tool for HTS and metabolic regulation for the development of L-threonine-hyperproducing strains.

'Dark' CO2 fixation in succinate fermentations enabled by direct CO2 delivery via hollow fiber membrane carbonation

Anaerobic succinate fermentations can achieve high-titer, high-yield performance while fixing CO2 through the reductive branch of the tricarboxylic acid cycle. To provide the needed CO2, conventional media is supplemented with significant (up to 60 g/L) bicarbonate (HCO3-), and/or carbonate (CO32-) salts. However, producing these salts from CO2 and natural ores is thermodynamically unfavorable and, thus, energetically costly, which reduces the overall sustainability of the process. Here, a series of composite hollow fiber membranes (HFMs) were first fabricated, after which comprehensive CO2 mass transfer measurements were performed under cell-free conditions using a novel, constant-pH method. Lumen pressure and total HFM surface area were found to be linearly correlated with the flux and volumetric rate of CO2 delivery, respectively. Novel HFM bioreactors were then constructed and used to comprehensively investigate the effects of modulating the CO2 delivery rate on succinate fermentations by engineered Escherichia coli. Through appropriate tuning of the design and operating conditions, it was ultimately possible to produce up to 64.5 g/L succinate at a glucose yield of 0.68 g/g; performance approaching that of control fermentations with directly added HCO3-/CO32- salts and on par with prior studies. HFMs were further found to demonstrate a high potential for repeated reuse. Overall, HFM-based CO2 delivery represents a viable alternative to the addition of HCO3-/CO32- salts to succinate fermentations, and likely other 'dark' CO2-fixing fermentations.

Mining natural products for advanced biofuels and sustainable bioproducts

Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.