Biosynthesis of monoethylene glycol in Saccharomyces cerevisiae utilizing native glycolytic enzymes

Prospects for carbon-negative biomanufacturing

Biomanufacturing has the potential to reduce demand for petrochemicals and mitigate climate change. Recent studies have also suggested that some of these products can be net carbon negative, effectively removing CO₂ from the atmosphere and locking it up in products. This review explores the magnitude of carbon removal achievable through biomanufacturing and discusses the likely fate of carbon in a range of target molecules. Solvents, cleaning agents, or food and pharmaceutical additives will likely re-release their carbon as CO₂ at the end of their functional lives, while carbon incorporated into non-compostable polymers can result in long-term sequestration. Future research can maximize its impact by focusing on reducing emissions, achieving performance advantages, and enabling a more circular carbon economy.

New pathways and metabolic engineering strategies for microbial synthesis of diols

Diols are important bulk chemicals that are widely used in polymer, cosmetics, fuel, food, and pharmaceutical industries. The development of bioprocess to produce diols from renewable feedstocks has gained much interest in recent years and is contributing to reducing the carbon footprint of the chemical industry. Although bioproduction of some natural diols such as 1,3-propanediol and 2,3-butanediol has been commercialized, microbial production of most other diols is still challenging due to the lack of natural biosynthetic pathways. This review describes the recent efforts in the development of novel synthetic pathways and metabolic engineering strategies for the biological production of C2∼C5 diols. We also discussed the main challenges and future perspectives for the microbial processes toward industrial application.

Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production in Clostridium autoethanogenum

The platform chemical ethylene glycol (EG) is used to manufacture various commodity chemicals of industrial importance, but largely remains synthesized from fossil fuels. Although several novel metabolic pathways have been reported for its bioproduction in model organisms, none has been reported for gas-fermenting, non-model acetogenic chassis organisms. Here, we describe a novel, synthetic biochemical pathway to convert acetate into EG in the industrially important gas-fermenting acetogen,Clostridium autoethanogenum. We not only developed a computational workflow to design and analyze hundreds of novel biochemical pathways for EG production but also demonstrated a successful pathway construction in the chosen host. The EG production was achieved using a two-plasmid system to bypass unfeasible expression levels and potential toxic enzymatic interactions. Although only a yield of 0.029 g EG/g fructose was achieved and therefore requiring further strain engineering efforts to optimize the designed strain, this work demonstrates an important proof-of-concept approach to computationally design and experimentally implement fully synthetic metabolic pathways in a metabolically highly specific, non-model host organism.

Production and waste treatment of polyesters: application of bioresources and biotechniques

Chemical resources and techniques have long been used in the history of bulk polyester production and still dominate today's chemical industry. The sustainable development of the polyester industry demands more renewable resources and environmentally benign polyester products. Accordingly, the rapid development of biotechnology has enabled the production of an extensive range of aliphatic and aromatic polyesters from renewable bio-feedstocks. This review addresses the production of representative commercial polyesters (polyhydroxyalkanoates, polylactic acid, poly ε-caprolactone, polybutylene succinate, polyethylene terephthalate, polybutylene terephthalate, polypropylene terephthalate, polyethylene furandicarboxylate, polypropylene furandicarboxylate, and polybutylene furandicarboxylate) or their monomers (lactic acid, succinic acid, 1,4-butanediol, ethylene glycol, terephthalic acid, 1,3-propanediol, and 2,5-furandicarboxylic acid) from renewable bioresources. In addition, this review summarizes advanced biotechniques in the treatment of polyester wastes, representing the near-term trends and future opportunities for waste-to-value recycling and the remediation of polyester wastes under sustainable models. For future prospects, it is essential to further expand: non-food bioresources, optimize bioprocesses and biotechniques in the preparation of bioderived or biodegradable polyesters with promising: material performance, biodegradability, and low production cost.

Systematic Metabolic Engineering for the Production of Azaphilones in Monascus purpureus HJ11

Fungal azaphilones have attracted considerable interest as they exhibit great potential in food and pharmacological industries. However, there is a severe bottleneck in the low production in wild strains and the ability to genetically engineer azaphilone-producing fungi. Using Monascus azaphilones (MAs) as an example, we demonstrate a systematic metabolic engineering strategy for improving the production of MAs. In this study, Monascus purpureus HJ11 was systematically engineered through a combination of promoter engineering, gene knockout, rate-limiting enzyme overexpression, repression of the competing pathway, enzyme engineering, and metabolic rebalance. The maximum yield and titer of MAs successfully increased to 906 mg/g dry cell weight (DCW) and 14.6 g/L, respectively, 2.6 and 3.7 times higher than those reported in the literature. Our successful model not only offers a practical and efficient way to improve the azaphilone production but also sheds light on the potential of systematic metabolic engineering in nonmodel fungi as a chassis for the production of high-value chemicals.

Contribution of Fermentation Technology to Building Blocks for Renewable Plastics

Large-scale worldwide production of plastics requires the use of large quantities of fossil fuels, leading to a negative impact on the environment. If the production of plastic continues to increase at the current rate, the industry will account for one fifth of global oil use by 2050. Bioplastics currently represent less than one percent of total plastic produced, but they are expected to increase in the coming years, due to rising demand. The usage of bioplastics would allow the dependence on fossil fuels to be reduced and could represent an opportunity to add some interesting functionalities to the materials. Moreover, the plastics derived from bio-based resources are more carbon-neutral and their manufacture generates a lower amount of greenhouse gasses. The substitution of conventional plastic with renewable plastic will therefore promote a more sustainable economy, society, and environment. Consequently, more and more studies have been focusing on the production of interesting bio-based building blocks for bioplastics. However, a coherent review of the contribution of fermentation technology to a more sustainable plastic production is yet to be carried out. Here, we present the recent advancement in bioplastic production and describe the possible integration of bio-based monomers as renewable precursors. Representative examples of both published and commercial fermentation processes are discussed.

Development of aldolase-based catalysts for the synthesis of organic chemicals

Aldol chemicals are synthesized by condensation reactions between the carbon units of ketones and aldehydes using aldolases. The efficient synthesis of diverse organic chemicals requires intrinsic modification of aldolases via engineering and design, as well as extrinsic modification through immobilization or combination with other catalysts. This review describes the development of aldolases, including their engineering and design, and the selection of desired aldolases using high-throughput screening, to enhance their catalytic properties and perform novel reactions. Aldolase-containing catalysts, which catalyze the aldol reaction combined with other enzymatic and/or chemical reactions, can efficiently synthesize diverse complex organic chemicals using inexpensive and simple materials as substrates. We also discuss the current challenges and emerging solutions for aldolase-based catalysts.

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Enzyme substrate promiscuity has significant implications for metabolic engineering. The ability to predict the space of possible enzymatic side reactions is crucial for elucidating underground metabolic networks in microorganisms, as well as harnessing novel biosynthetic capabilities of enzymes to produce desired chemicals. Reaction rule-based cheminformatics platforms have been implemented to computationally enumerate possible promiscuous reactions, relying on existing knowledge of enzymatic transformations to inform novel reactions. However, past versions of curated reaction rules have been limited by a lack of comprehensiveness in representing all possible transformations, as well as the need to prune rules to enhance computational efficiency in pathway expansion. To this end, we curated a set of 1224 most generalized reaction rules, automatically abstracted from atom-mapped MetaCyc reactions and verified to uniquely cover all common enzymatic transformations. We developed a framework to systematically identify and correct redundancies and errors in the curation process, resulting in a minimal, yet comprehensive, rule set. These reaction rules were capable of reproducing more than 85% of all reactions in the KEGG and BRENDA databases, for which a large fraction of reactions is not present in MetaCyc. Our rules exceed all previously published rule sets for which reproduction was possible in this coverage analysis, which allows for the exploration of a larger space of known enzymatic transformations. By leveraging the entire knowledge of possible metabolic reactions through generalized enzymatic reaction rules, we are able to better utilize underground metabolic pathways and accelerate novel biosynthetic pathway design to enable bioproduction towards a wider range of new molecules.

Omics-Driven Biotechnology for Industrial Applications

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.

Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae

Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.

Bio-Polyethylene (Bio-PE), Bio-Polypropylene (Bio-PP) and Bio-Poly(ethylene terephthalate) (Bio-PET): Recent Developments in Bio-Based Polymers Analogous to Petroleum-Derived Ones for Packaging and Engineering Applications

In recent year, there has been increasing concern about the growing amount of plastic waste coming from daily life. Different kinds of synthetic plastics are currently used for an extensive range of needs, but in order to reduce the impact of petroleum-based plastics and material waste, considerable attention has been focused on "green" plastics. In this paper, we present a broad review on the advances in the research and development of bio-based polymers analogous to petroleum-derived ones. The main interest for the development of bio-based materials is the strong public concern about waste, pollution and carbon footprint. The sustainability of those polymers, for general and specific applications, is driven by the great progress in the processing technologies that refine biomass feedstocks in order to obtain bio-based monomers that are used as building blocks. At the same time, thanks to the industrial progress, it is possible to obtain more versatile and specific chemical structures in order to synthetize polymers with ad-hoc tailored properties and functionalities, with engineering applications that include packaging but also durable and electronic goods. In particular, three types of polymers were described in this review: Bio-polyethylene (Bio-PE), bio-polypropylene (Bio-PP) and Bio-poly(ethylene terephthalate) (Bio-PET). The recent advances in their development in terms of processing technologies, product development and applications, as well as their advantages and disadvantages, are reported.

Bio-Polyethylene (Bio-PE), Bio-Polypropylene (Bio-PP) and Bio-Poly(ethylene terephthalate) (Bio-PET): Recent Developments in Bio-Based Polymers Analogous to Petroleum-Derived Ones for Packaging and Engineering Applications

In recent year, there has been increasing concern about the growing amount of plastic waste coming from daily life. Different kinds of synthetic plastics are currently used for an extensive range of needs, but in order to reduce the impact of petroleum-based plastics and material waste, considerable attention has been focused on "green" plastics. In this paper, we present a broad review on the advances in the research and development of bio-based polymers analogous to petroleum-derived ones. The main interest for the development of bio-based materials is the strong public concern about waste, pollution and carbon footprint. The sustainability of those polymers, for general and specific applications, is driven by the great progress in the processing technologies that refine biomass feedstocks in order to obtain bio-based monomers that are used as building blocks. At the same time, thanks to the industrial progress, it is possible to obtain more versatile and specific chemical structures in order to synthetize polymers with ad-hoc tailored properties and functionalities, with engineering applications that include packaging but also durable and electronic goods. In particular, three types of polymers were described in this review: Bio-polyethylene (Bio-PE), bio-polypropylene (Bio-PP) and Bio-poly(ethylene terephthalate) (Bio-PET). The recent advances in their development in terms of processing technologies, product development and applications, as well as their advantages and disadvantages, are reported.

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 10¹¹ tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.

Mixed carbon substrates: a necessary nuisance or a missed opportunity?

Although fermentation with single carbon sources is the preferred mode of operation in current industrial biotechnology, the use of multiple substrates has been continuously investigated throughout the years. Generally, microbial metabolism varies significantly when cells are presented with mixed carbon substrates compared to a single carbon-energy source, as different nutrients interact in complex ways within the metabolic network. By exploiting these distinct modes of interaction, researchers have identified unique opportunities to optimize metabolism using mixed carbon sources. Here we review situations where process yield and productivity are markedly improved through the judicious introduction of substrate mixtures. Our goal is to illustrate that with proper design of the choice of substrates and the way they are introduced to cultures, metabolic optimization with mixed substrates can be a unique strategy that complements genetic engineering techniques to enhance cell performance beyond what is accomplished in single substrate fermentations.

Microbial Genes for a Circular and Sustainable Bio-PET Economy

Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for the synthesis of novel PET as well as become a potential carbon source for microorganisms. In addition, microorganisms and biomass can be used for the synthesis of the constituent monomers of PET from renewable sources. The combination of both biodegradation and biosynthesis would enable a completely circular bio-PET economy beyond the conventional recycling processes. Circular strategies like this could contribute to significantly decreasing the environmental impact of our dependence on this polymer. Here we review the efforts made towards turning PET into a viable feedstock for microbial transformations. We highlight current bottlenecks in degradation of the polymer and metabolism of the monomers, and we showcase fully biological or semisynthetic processes leading to the synthesis of PET from sustainable substrates.

Biotechnological production of glycolic acid and ethylene glycol: current state and perspectives

Glycolic acid (GA) and ethylene glycol (EG) are versatile two-carbon organic chemicals used in multiple daily applications. GA and EG are currently produced by chemical synthesis, but their biotechnological production from renewable resources has received a substantial interest. Several different metabolic pathways by using genetically modified microorganisms, such as Escherichia coli, Corynebacterium glutamicum and yeast have been established for their production. As a result, the yield of GA and EG produced from sugars has been significantly improved. Here, we describe the recent advancement in metabolic engineering efforts focusing on metabolic pathways and engineering strategies used for GA and EG production.