Table of Contents
Overview
Definition and Scope
Metabolic engineering is defined as the science of rewiring the metabolism of cells to enhance the production of native metabolites or to enable cells to produce new products. This field encompasses a wide range of applications, including the generation of fuels, chemicals, foods, feeds, and pharmaceuticals, thereby significantly impacting various industries such as chemical, agriculture, food, pharmaceutical, and energy sectors.[5.1] Since its inception over 30 years ago, metabolic engineering has rapidly evolved through its integration with molecular biology, systems biology, and synthetic biology, which has greatly advanced the biotechnology industry.[3.1] The discipline aims to improve the production of economically valuable molecules through genetic manipulation of microbial metabolism, facilitating industrial-level molecule production.[5.1] Recent advancements in metabolic engineering (ME) have significantly contributed to the sustainable production of chemicals, health, and environmental improvements, as summarized by a research team from KAIST, which reviewed the field's 30-year history.[2.1] This review highlights various examples of ME's progress and its contributions to addressing global challenges, including climate change, environmental pollution, and food and energy shortages.[2.1] The findings indicate that metabolic engineering plays a crucial role in the development of bio-based sustainable chemicals, clean energy, and bioremediation, positioning it as a key solution to pressing issues faced by aging societies.[2.1] Furthermore, the research discusses future challenges and perspectives, emphasizing that metabolic engineering will continue to be vital in promoting sustainability and addressing health challenges in the coming years.[13.1] Moreover, systems metabolic engineering (SysME) has emerged as an enabling technology that optimizes cellular performance to produce bioproducts with higher titres, productivities, and yields.[16.1] This approach aligns with the United Nations' Sustainable Development Goals (SDGs), which advocate for international cooperation towards sustainable development and improving the quality of life while protecting the environment.[14.1]Key Principles and Techniques
Metabolic engineering is a multidisciplinary field that combines principles from systems biology, synthetic biology, and traditional metabolic engineering to enhance the production of biofuels, chemicals, and natural products. This integration has led to significant advancements in the development of microbial cell factories, which are engineered organisms capable of efficiently converting renewable resources into valuable products.[8.1] Recent advancements in systems metabolic engineering have significantly enhanced the development of industrially competitive strains by integrating systems biology, synthetic biology, and evolutionary engineering with traditional metabolic engineering. This integration has expedited the creation of highly productive microbial cell factories, exemplified by early efforts to develop Escherichia coli strains capable of overproducing l-valine and l-threonine within a decade.[28.1] Furthermore, recent tools and strategies have been employed for enzyme, genetic module, pathway, flux, genome, and cell-level engineering, which are supported by illustrative examples.[7.1] Notably, systems biology tools such as genome-scale metabolic models (GEMs), along with machine learning-assisted pathway design and deep learning-based enzyme design, have been developed to provide a comprehensive understanding of cellular systems and facilitate accurate predictions, thereby enhancing the potential of systems metabolic engineering.[7.1] Metabolic engineering is increasingly recognized for its potential to address global challenges such as climate change and environmental pollution. The exacerbation of climate change and air pollution has underscored the urgent need to replace fossil fuels with clean and sustainable energy sources. Metabolic engineering provides innovative strategies to engineer diverse organisms for the production of biofuels from renewable carbon sources, thereby facilitating a transition away from fossil fuel dependency.[17.1] Additionally, concerns regarding future oil supplies and climate change are driving interest in sustainable alternative sources of energy and chemicals, with biomass emerging as a renewable feedstock capable of replacing a significant fraction of petroleum used today.[18.1] Furthermore, metabolic engineering plays a critical role in bioremediation by harnessing the metabolic activities of microorganisms to degrade pollutants, thus contributing to environmental restoration.[20.1] This approach is increasingly recognized as a cost-effective and environmentally friendly solution for cleaning up contaminated sites, including those affected by pesticides and antibiotics.[22.1] Emerging technologies in metabolic engineering also offer precise methods for restoring soil to a fertile and contaminant-free state, highlighting its importance in environmental sustainability.[21.1] The field of metabolic engineering is increasingly influential in the development of personalized medicine, particularly through the application of pharmacometabolomics. This evolving research area aims to achieve tailored therapeutic regimes by predicting and evaluating responses to drug treatments based on individual metabolic fingerprints.[1.1] The ability to correlate metabolic phenotypes into subgroups that exhibit different responses is becoming a reality through metabolomics, which plays a crucial role in the advancement of personalized healthcare systems.[2.1] Furthermore, the design of synthetic gene networks and prototype therapeutic circuits is expected to significantly impact future gene- and cell-based therapies, ushering in a new era of drug discovery. These innovations may enable the development of personalized therapies that utilize synthetic genomes for specific drug synthesis and delivery, ultimately enhancing treatment for complex diseases.[1.1] As these principles and techniques continue to evolve, they demonstrate substantial potential to address both industrial and societal healthcare needs effectively.In this section:
History
Early Developments
The early developments in metabolic engineering marked significant milestones that laid the foundation for the field as it is known today. One of the pivotal achievements was the reconstruction of the Escherichia coli pathway for the conversion of the amino acid tryptophan into the plant-derived dye indigo, which represented a key milestone in metabolic engineering.[44.1] This success was followed by several instances of engineering E. coli metabolism to overproduce various aromatic compounds, showcasing the potential of metabolic engineering to enhance microbial production capabilities.[44.1] Over the past three decades, metabolic engineering has rapidly evolved, benefiting from its integration with molecular biology, systems biology, and synthetic biology.[46.1] This interdisciplinary approach has significantly advanced the biotechnology industry, enabling the production of high-value chemicals derived from both primary and secondary metabolism.[45.1] Notably, the development of methodologies such as flux balance analysis has allowed researchers to elucidate intracellular metabolic controls, further enhancing the understanding of metabolic pathways.[45.1] A comprehensive review of the 30-year history of metabolic engineering highlights the contributions of this discipline to sustainability and health, emphasizing its role in producing bio-based sustainable chemicals and clean energy.[2.1] Researchers have noted that metabolic engineering will increasingly address critical global challenges, including climate change, environmental pollution, and health issues associated with aging populations.[49.1] The early developments in metabolic engineering have prominently featured Escherichia coli, which is recognized as a veteran in industrial biotechnology. This organism has been utilized for groundbreaking applications, including the overproduction of the amino acid l-threonine and the first recombinant synthesis of human insulin, establishing E. coli as one of the best-studied microbes in the field.[68.1] Multiple researchers have reported the use of pathway engineering to generate E. coli strains capable of accumulating various metabolic precursors, such as pyruvate, acetyl-CoA, malonyl-CoA, mevalonate, and shikimate, which provides a promising guideline for designing strains that can produce a variety of useful chemicals.[66.1] Furthermore, both metabolic engineering and synthetic biology have made significant advances in biotechnology, contributing to the resolution of challenges in the production of pharmaceuticals, vaccines, and chemical compounds.[70.1]Evolution of Techniques
The evolution of techniques in metabolic engineering has been significantly influenced by advancements in synthetic biology and systems biology. Synthetic biology has emerged as a powerful discipline for creating novel biological systems, particularly in the subfield of metabolic pathway and product engineering, which has facilitated the development of engineered organisms with optimized metabolic pathways.[53.1] This integration of synthetic biology has led to smarter construct designs and higher yields of valuable chemicals, exemplified by the engineering of Saccharomyces cerevisiae to produce casbene, a diterpene precursor of many medically relevant terpenoids.[54.1] Recent advancements in systems metabolic engineering have further enhanced the capabilities of metabolic engineering by targeting various biological components of host cells. This approach has enabled the creation of highly productive microbial cell factories through the application of tools and strategies such as enzyme engineering, genetic module design, and genome-scale metabolic models (GEMs).[63.1] These innovations have allowed for a more comprehensive understanding of cellular systems, leading to accurate predictions and improved designs for metabolic pathways.[55.1] The evolution of metabolic engineering has significantly advanced the production of biofuels, chemicals, and natural products, facilitating a transition from fossil-resource-dependent processes to sustainable bio-based methods. Over the past decade, advancements in metabolic engineering and synthetic biology have provided a range of tools and strategies for constructing efficient microbial cell factories, which are essential for this transition.[63.1] Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized the sustainable production of fuels and materials through the creation of these efficient microbial cell factories.[77.1] Recent developments in systems metabolic engineering have focused on targeting different biological components of host cells, enabling the creation of highly productive microbial cell factories.[55.1] Furthermore, innovative tools such as genome-scale metabolic models and machine learning-assisted pathway design have been developed to enhance the potential of systems metabolic engineering by providing a comprehensive understanding of cellular systems and accurate predictions.[55.1] These advancements underscore the critical role of metabolic engineering in addressing global challenges, including climate change and resource scarcity, by promoting sustainable production practices.[65.1] The evolution of plant metabolic engineering is increasingly recognized as a vital component in addressing global challenges such as climate change and food security. This field focuses on customizing plant metabolism to enhance nutrient bioavailability, exemplified by efforts to increase iron content in crops, which can help combat malnutrition.[61.1] As technological capabilities advance, metabolic engineering is expected to expand the utility of plants beyond traditional sugar feedstocks, enabling the direct production of valuable compounds such as pharmaceuticals, renewable fuels, and commodity chemicals.[64.1] Furthermore, the integration of engineered enzymes is being explored to improve carbon capture, bioremediation, and the generation of renewable feedstocks, highlighting the potential for innovative strategies to enhance environmental sustainability.[76.1] Overall, the development of novel metabolic pathways and the enhancement of production yields are crucial for creating sustainable solutions within the realm of metabolic pathway engineering.[78.1]In this section:
Recent Advancements
Breakthroughs in Genetic Engineering
Recent advancements in metabolic engineering have led to significant breakthroughs in genetic engineering, particularly in the development of microbial cell factories. Systems metabolic engineering, which merges metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has transformed the sustainable production of fuels and materials by creating efficient microbial cell factories.[89.1] This integration has facilitated the use of advanced tools and strategies, including genome-scale metabolic models (GEMs), machine learning (ML)-assisted pathway design, and deep learning (DL)-based enzyme design, which enhance the understanding of cellular systems and improve predictive capabilities.[86.1] The application of biosensors has emerged as a pivotal strategy in high-throughput metabolic engineering, enabling the identification of novel genotype-phenotype relationships and the evolution of microbial cell factories for increased production of various chemicals, biofuels, and secondary metabolites.[88.1] Recent developments in biosensor engineering have yielded innovative tools for small molecule screening, driven by efforts in data mining, directed evolution, and rational re-engineering of transcription factors (TFs) and riboswitches.[92.1] These biosensors play crucial roles in optimizing microbial production strains through high-throughput screening, adaptive laboratory evolution, and dynamic pathway control.[93.1] Moreover, the integration of metabolic circuits with TF-based biosensors has proven to be a robust solution for enhancing the production of target chemicals in engineered microbial strains.[95.1] As many biosensors are still in the proof-of-concept stage, ongoing research is focused on their potential applications in metabolic engineering to accelerate the development of cell factories.[94.1] New strategies have also been developed to balance metabolic flux within target pathways by tuning gene expression through the engineering of promoters, ribosome binding sites, and intergenic regions, allowing for simultaneous optimization of metabolic pathways while maintaining cellular fitness.[116.1]Integration of Artificial Intelligence
The integration of artificial intelligence (AI) and machine learning (ML) into metabolic engineering has significantly transformed the field, particularly in optimizing metabolic pathways and enhancing the efficiency of microbial cell factories. The increasing availability of bio big data, such as omics data, has facilitated the application of machine learning techniques across various stages of systems metabolic engineering, including host strain selection, metabolic pathway reconstruction, metabolic flux optimization, and fermentation processes.[108.1] Machine learning models are particularly valuable in identifying patterns within large datasets, which can lead to the development of more efficient microbial cell factories. These models enable the optimization of metabolic pathways by allowing for adjustments that enhance outputs while minimizing inputs.[110.1] Traditional mathematical kinetic models, which have been used to predict pathway dynamics, are often time-consuming to develop and require significant biological expertise. In contrast, machine learning approaches can learn pathway dynamics directly from data examples, streamlining the modeling process.[111.1] Moreover, the application of machine learning extends to critical stages of metabolic engineering, such as process scale-up and downstream processing. Here, ML-based methods can select optimal growth conditions and process parameters from extensive experimental datasets, ultimately maximizing titer, rate, and yield.[112.1] The combination of mechanistic and machine learning models has also been proposed for predictive engineering, particularly in the optimization of specific metabolic processes, such as tryptophan metabolism.[113.1] As artificial intelligence (AI) technologies advance, they are projected to facilitate more accurate diagnoses and cost-effective treatments in various fields, including metabolic engineering.[109.1] Machine learning (ML) and deep learning, both subsets of AI, play a crucial role in this evolution by enabling adjustments to metabolic pathways in living organisms, thereby optimizing outputs while minimizing inputs.[109.1] Furthermore, AI and ML are revolutionizing metabolic engineering by enhancing the design of robust microbial strains and accelerating the development of sustainable bioproduction systems.[128.1] This integration of AI technologies is expected to significantly improve the efficiency of microbial cell factories, ultimately leading to more effective metabolic engineering practices.[128.1]Applications
Biofuels and Chemicals Production
Metabolic engineering has significantly advanced the production of biofuels and chemicals, facilitating a transition from fossil fuel dependency to sustainable bio-based processes. This field focuses on the genetic manipulation of microbial metabolism to enhance the production of economically valuable molecules, which has been beneficial across various industries, including chemical, agriculture, food, pharmaceutical, and energy sectors.[136.1] Microbial cell factories, such as Saccharomyces cerevisiae and Aspergillus niger, have a long-standing history in natural fermentation processes for producing essential chemicals like ethanol and citric acid.[137.1] Recent advancements in metabolic engineering have enabled the development of these microbial cell factories to efficiently produce biofuels and other chemicals, thereby supporting the creation of green and sustainable production methods.[138.1] To enhance chemical production through metabolic engineering, a variety of computational tools have been developed to identify genetic strategies for optimizing strain designs. These tools, including metabolic flux analysis and genome-scale metabolic models, are essential for predicting genetic modifications that can lead to increased yields of desired products.[139.1] Recent advancements in systems metabolic engineering have focused on different biological components of the host cell, enabling the creation of highly productive microbial cell factories.[148.1] Additionally, the integration of machine learning-assisted pathway design and deep learning-based enzyme design has significantly improved the capabilities of these systems biology tools, providing a comprehensive understanding of cellular systems and facilitating accurate predictions.[148.1] Furthermore, the development of synthetic biology tools, such as CRISPR/Cas9, along with novel concepts like dynamic control, has further advanced metabolic engineering efforts by allowing for more precise strain designs.[139.1] The ongoing research in metabolic engineering also emphasizes the utilization of carbon dioxide as a feedstock, which is crucial for developing sustainable bioproduction methods. This involves engineering endogenous CO2 fixation pathways and constructing novel synthetic pathways to improve CO2 assimilation efficiency.[153.1] Overall, the application of metabolic engineering in biofuels and chemicals production not only enhances productivity but also contributes to addressing environmental challenges associated with traditional fossil fuel processes.Health and Pharmaceuticals
Metabolic engineering has gained recognition over the past decade as a valuable tool in the discovery and development of new natural-product drugs. This integration with traditional drug discovery processes offers significant advantages, particularly in the efficient and cost-effective production of various secondary metabolites with pharmacological value, derived from both plants and microorganisms.[164.1] Furthermore, the goals of metabolic engineering, such as identifying genes that confer specific phenotypes, align conceptually and methodologically with central issues in drug discovery and functional genomics.[165.1] This synergy not only enhances the drug discovery process but also addresses critical challenges in the field. Recent advancements in CRISPR-derived genome editing technologies have established these methods as the preferred choice for genome engineering in various organisms, particularly those relevant to industrial applications.[140.1] The development of CRISPR technology has resolved several challenges associated with previous pathway engineering and genome editing techniques, allowing for the optimal construction of metabolic pathways that minimize negative effects while maximizing catalytic efficiency.[141.1] As a result, the ambitious engineering aims of synthetic biology are rapidly becoming a reality, driven by improvements in genome editing and the identification and optimization of biosynthetic building blocks.[140.1] These advancements are expected to significantly enhance the efficiency and scalability of pharmaceutical compound production in the future.[140.1] Moreover, engineered microorganisms are increasingly being utilized as microbial cell factories to enhance the synthesis of chemical compounds, including natural products and antibiotics. This shift is driven by the limitations of wild-type strains, which often lack the metabolic capacity needed for efficient production.[166.1] The application of synthetic biology tools in this context has shown promise in revitalizing antibiotic discovery, particularly in the fight against multidrug-resistant (MDR) pathogens.[168.1]Challenges And Future Directions
Sustainability and Economic Viability
The integration of unconventional feedstocks and non-model organisms is increasingly recognized as a pivotal strategy for advancing sustainability in metabolic engineering. These unconventional feedstocks, such as hemicellulosic sugars and carbon dioxide, are gaining traction due to their potential to support advanced bioproduct synthesis while minimizing environmental impact.[198.1] The careful selection of substrate-organism-product combinations is essential for achieving environmentally and economically sustainable outcomes in metabolic engineering.[199.1] This approach not only illuminates new avenues for sustainable practices but also enhances the diversity of products that can be synthesized. Self-assembly approaches in metabolic engineering address critical challenges such as ineffective sequential catalysis, side reactions, and the untimely supply of cofactors, which can hinder production efficiency.[200.1] These strategies have been explored for aggregating multiple enzymes within the same pathway, thereby improving sequential catalytic efficiency and enabling high-level production of desired products.[201.1] To effectively tackle existing challenges in metabolic engineering, future strategies must account for all aspects of product synthesis, including the transcriptome, translatome, proteome, and reactome.[202.1] This comprehensive approach is essential for enhancing the performance and stability of assembly systems in metabolic engineering endeavors. Synthetic biology has significantly advanced the development of metabolic control strategies and has accelerated the creation of efficient microbial cell factories.[203.1] Recent research highlights the integration of the glyoxylate shunt pathway into mammalian liver cells and mice, which has been explored for its effects on fatty acid metabolism and overall whole-body metabolism.[204.1] This work exemplifies the potential of synthetic biology to address metabolic imbalances and enhance metabolic regulation in engineered systems. In the field of metabolic engineering, traditional model organisms such as Escherichia coli and Saccharomyces cerevisiae have been extensively utilized due to their advantageous characteristics, including low safety risks, rapid growth rates, and high tractability.[210.1] However, these organisms exhibit limitations in their ability to biosynthesize certain carboxylic acid platform chemicals.[210.1] Consequently, non-conventional yeasts like Yarrowia lipolytica and Kluyveromyces marxianus are emerging as promising alternatives for the production of value-added chemicals.[211.1] Yarrowia lipolytica, in particular, is recognized for its potential as a valuable host for producing a diverse array of both lipid and non-lipid chemical products, despite the challenges posed by its unique genetics.[212.1] Recent advances in metabolic engineering tools have facilitated improved genetic manipulation in this organism, enhancing its utility in various applications.[212.1] The exploration of these non-conventional hosts is expanding the scope of metabolic engineering applications, with a focus on producing a variety of valuable chemicals, including fuels, cosmetics, and pharmaceuticals.[213.1]Regulatory and Ethical Considerations
Regulatory and ethical considerations in metabolic engineering are increasingly important as the field continues to evolve. Despite significant advancements, metabolic pathway engineering encounters several challenges, including pathway toxicity, metabolic imbalances, and limited knowledge of complex cellular networks.[183.1] Addressing these challenges is essential for ensuring the safety and efficacy of applications in this area. Future efforts will focus on implementing advanced computational tools, exploring non-conventional organisms, and enhancing the understanding of these complex systems.[183.1] Metabolic pathway engineering has made significant strides; however, it continues to face challenges such as pathway toxicity, metabolic imbalances, and a limited understanding of complex cellular networks.[183.1] To address these issues, advanced computational tools, including metabolic flux analysis and genome-scale metabolic models, have been developed to predict genetic modifications that enhance chemical production.[185.1] Additionally, self-assembly approaches have been employed to tackle problems like ineffective sequential catalysis, side reactions, and the untimely supply of cofactors.[184.1] The integration of synthetic biology tools, such as CRISPR/Cas9, along with novel concepts like dynamic control and cell-free metabolic engineering, has further advanced metabolic engineering efforts.[185.1] Future directions will likely focus on exploring non-conventional organisms and improving our understanding of metabolic pathways to overcome existing challenges.[183.1] As the field continues to evolve, addressing these regulatory and ethical challenges will be essential to foster public trust and ensure responsible innovation in metabolic engineering practices.Tools And Methodologies
Synthetic Biology Tools
Synthetic biology tools have significantly advanced the field of metabolic engineering, enabling the precise manipulation of microbial metabolism for various applications. One of the most notable advancements is the development of the CRISPR-Cas9 system, which has revolutionized genetic editing by allowing for targeted modifications in microbial genomes. This tool is particularly valued for its precision and efficiency, facilitating significant improvements in microbial functions and applications across multiple domains, including agriculture and pharmaceuticals.[236.1] In recent years, significant advancements in synthetic biology have been achieved through the development of various computational tools aimed at enhancing strain design and predicting genetic modifications for improved chemical production. Among these tools are metabolic flux analysis, genome-scale metabolic models (GEMs), and algorithms such as OptKnock, which collectively facilitate the identification of optimal genetic designs for metabolic engineering.[225.1] GEMs, in particular, are powerful tools that enable the mathematical simulation of metabolism across archaea, bacteria, and eukaryotic organisms. They quantitatively define the relationship between genotype and phenotype by integrating diverse types of Big Data, including genomics, metabolomics, and transcriptomics.[231.1] Furthermore, there have been numerous metabolic engineering efforts focused on developing engineered strains of Yarrowia lipolytica with enhanced lipid yields, showcasing the practical applications of these computational tools in real-world scenarios.[229.1] Moreover, advanced mass metabolomics methods, including isotope flux analysis and untargeted metabolomics, are employed to characterize metabolic pathways and guide the engineering of synthetic bioproduction pathways. These methods have shown great potential in developing metabolomics-directed synthetic bioproduction, further enhancing the capabilities of metabolic engineering.[224.1]Case Studies
Successful Microbial Cell Factories
Successful microbial cell factories are a cornerstone of metabolic engineering, enabling the industrial-scale production of valuable chemicals from renewable resources. A prominent example is the collaboration between DuPont and Tate & Lyle, which has advanced from a pilot fermentation process to constructing a plant with a 100,000-ton annual capacity for feedstock chemicals production.[259.1] This illustrates the practical application of metabolic engineering in developing efficient microbial strains for high-yield production. Over recent decades, numerous case studies have documented the successful production of microbially derived chemicals at various scales, categorized as industrial (greater than 50 g/L), medium (5-50 g/L), and lab scale (0-5 g/L). These studies underscore the versatility of engineered microorganisms in chemical synthesis.[260.1] Systems metabolic engineering has been pivotal in developing high-performance strains for producing a diverse range of bioproducts, including bulk and fine chemicals, polymers, biofuels, and natural products.[261.1] The engineering of microorganisms focuses on enhancing the synthesis of chemical compounds, as wild-type strains often lack the necessary metabolic capacity. This has led to the development of tools and strategies to optimize metabolic pathways, crucial for bio-based production of natural products like drugs, nutraceuticals, and pigments.[262.1] Key techniques include pathway manipulation methods such as gene overexpression, silencing, and knockouts to improve target metabolite yields.[271.1] To further improve microbial cell factory efficiency, computational tools like metabolic flux analysis and genome-scale metabolic models have been developed to predict genetic modifications that enhance chemical production.[272.1] Additionally, advancements in synthetic biology, including CRISPR/Cas9 technology and dynamic control systems, have significantly contributed to precise microbial strain engineering.[272.1]Innovations in Organic Acid Production
DuPont Tate & Lyle Bio Products has made significant strides in the field of metabolic engineering, particularly in the production of organic acids such as 1,3-propanediol (1,3-PDO). This joint venture was the first to achieve production at a scale of thousands of metric tons per year using a metabolically engineered host, with commercial production of 1,3-PDO from corn starch commencing in 2006. Nearly a decade later, the company reported ongoing progress in expanding production capabilities, demonstrating the potential for large-scale industrial applications of metabolic engineering.[267.1] Recent advancements in cell-free metabolic engineering have shown significant progress, including the development of pathways that extend beyond eight enzyme steps, achieving near theoretical mass yields, and demonstrating volumetric productivities of several grams per liter per hour, with successful scale-up into hundreds of liters.[263.1] The enzymatic hydrolysis process has been effectively scaled up and utilized in industrial-scale plants operated by Beta Renewables, while DuPont Tate & Lyle Bio Products has produced microbial 1,3-propanediol (1,3-PDO) from corn-derived sugars since 2006, achieving an annual production of approximately 63,500 kilotonnes.[266.1] This illustrates the practical applications of metabolic engineering in the industrial production of organic acids, as well as the ongoing challenges in scaling these innovative processes, which include the need for new technologies to enable metabolic engineering to be scaled up to the industrial level.[265.1] Recent advancements in metabolic engineering and synthetic biology have provided a range of tools and strategies for constructing efficient microbial cell factories, significantly enhancing the sustainable production of organic acids and other bioproducts.[276.1] Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized this field by enabling the creation of highly productive microbial cell factories tailored for industrial applications.[276.1] However, many engineered strains encounter challenges such as redox imbalance and excess metabolic burden, which can lead to poor product yields.[279.1] To address these issues, significant developments have been made in the co-cultivation of multiple engineered strains, allowing for the distribution of metabolic burdens and ultimately improving product yields.[279.1] Furthermore, addressing these imbalances to enhance target pathway flux represents a major challenge for metabolic engineers, who traditionally identify and remove bottlenecks in pathway design through sequential optimization campaigns.[281.1]In this section:
References
[1] PDF — Credit: The Korea Advanced Institute of Science and Technology (KAIST) 1/3 A research team comprised of Gi Bae Kim, Dr. So Young Choi, Dr. In Jin Cho, Da-Hee Ahn, and Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering at KAIST have summarized the 30-year history of metabolic engineering, highlighting examples of recent progress in the field and contributions to sustainability and health. DOI: 10.1016/j.tibtech.2022.12.014 Provided by The Korea Advanced Institute of Science and Technology (KAIST) Citation: An overview of the 30-year history of metabolic engineering (2023, January 25) retrieved 24 September 2024 from https://phys.org/news/2023-01-overview-year-history-metabolic.html This document is subject to copyright.
[2] An overview of the 30-year history of metabolic engineering - Phys.org — A research team comprised of Gi Bae Kim, Dr. So Young Choi, Dr. In Jin Cho, Da-Hee Ahn, and Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering at KAIST have summarized the 30-year history of metabolic engineering, highlighting examples of recent progress in the field and contributions to sustainability and health. Metabolic engineering's contributions to bio-based sustainable chemicals and clean energy, health, and bioremediation were also reviewed. By looking back on the 30+ years of metabolic engineering, we aimed to highlight the contributions of metabolic engineering to achieve sustainability and good health." He added, "Metabolic engineering will play an increasingly important role as a key solution to the climate crisis, environmental pollution, food and energy shortages, and health problems in aging societies."
[3] [Thirty years development of metabolic engineering: a review] — Since its establishment 30 years ago, the discipline of metabolic engineering has developed rapidly based on its deep integration with molecular biology, systems biology and synthetic biology successively, which has greatly contributed to advancing and upgrading biotechnology industry. This review f …
[5] Metabolic Engineering: Methodologies and Applications — Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy
[7] Recent advances in systems metabolic engineering — Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides a review of the recent tools and strategies used for enzyme-, genetic module-, pathway-, flux-, genome-, and cell-level engineering, supported by illustrative examples. Additionally, various systems biology tools, such as genome-scale metabolic models (GEMs), machine learning (ML)-assisted pathway design, and deep learning (DL)-based enzyme design, have been developed to enhance the potential of systems metabolic engineering by providing a comprehensive understanding of cellular systems and accurate predictions 5, 6. Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production
[8] Metabolic engineering: Tools and applications - PMC — Metabolic engineering plays a pivotal role in the development of microbial cell factories for efficient production of biofuels, chemicals, and natural products, which facilitate the transition from fossil-resource dependent processes to green and sustainable bio-based processes. This special issue was aimed to showcase some recent advances in developing novel synthetic biology tools and screening techniques for metabolic engineering, strategies on engineering of microbial cell factories for sustainable feedstock utilization, and the production of representative chemicals. Metabolic engineering strategies for microbial utilization of methanol [J] Eng. Microbiol. 9.Lu H., Villada J.C., Lee P.K.H. Modular metabolic engineering for biobased chemical production [J] Trends Biotechnol. Combinatorial metabolic engineering of Saccharomyces cerevisiae for improved production of 7-dehydrocholesterol [J] Eng. Microbiol.
[13] PDF — to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed. Metabolic engineering to address global challenges ME (see Glossary) has been studied in earnest since the early 1990s and has made remarkable progress over the past 30 years.
[14] Systems metabolic engineering as an enabling technology in ... — With pressing issues arising in recent years, the United Nations proposed 17 Sustainable Development Goals (SDG s) as an agenda urging international cooperations for sustainable development.In this perspective, we examine the roles of systems metabolic engineering (SysME) and its contribution to improving the quality of life and protecting our environment, presenting how this field of study
[16] Systems metabolic engineering as an enabling technology in ... — Systems metabolic engineering (SysME) is an enabling technology for optimizing cellular performance to produce better bioproducts to higher titres with higher productivities and yields. ... Assembly is a set of measurable goals ranging from ending world poverty and hunger to combating climate change by 2030 (see Jang et al. in the same issue
[17] Metabolic engineering strategies toward production of biofuels — Exacerbation of climate change and air pollution around the world have emphasized the necessity of replacing fossil fuels with clean and sustainable energy. Metabolic engineering has provided strategies to engineer diverse organisms for the production of biofuels from renewable carbon sources.
[18] Metabolic engineering: enabling technology of a bio-based economy — Concerns about future oil supplies and climate change are fueling interest in sustainable alternative sources of energy and chemicals. Biomass is a renewable feedstock that has the potential to replace a significant fraction of petroleum used today. Advances in metabolic engineering and biotechnology have made it possible to engineer microorganisms capable of converting simple sugars derived
[20] The Role of Bioremediation in Achieving Environmental Sustainability — Microorganisms and enzymes play a crucial role in bioremediation processes, facilitating the breakdown of pollutants and contributing to environmental restoration. ... P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, et al. Enzymes, in vivo biocatalysis, and metabolic engineering for enabling a circular economy and
[21] Engineering of Plants, Microbes and Their Metabolites for Soil ... — The emerging technologies of metabolic engineering and next generation sequencing offer precise and effective methods to restore the fertile and contaminant-free state of the soil. ... 19.7 Metabolite Engineering and Its Role in Soil ... is an important agent of soil bioremediation. The engineering of enzymes through recombinant DNA technology
[22] Engineering microbiomes for enhanced bioremediation — Microbial bioremediation, which harnesses the metabolic activities of microbes to degrade OPs, is increasingly recognized as a cost-effective and environment-friendly solution for cleaning up contaminated sites, including pesticides (such as glyphosate and atrazine), antibiotics (such as amoxicillin and ciprofloxacin), polycyclic aromatic
[28] Systems Metabolic Engineering Strategies: Integrating Systems and ... — The emergence of systems metabolic engineering - which integrates systems biology, synthetic biology, and evolutionary engineering with traditional metabolic engineering - has expedited the development of industrially competitive strains, as exemplified by initial works on developing Escherichia coli strains to overproduce l-valine and l-threonine in 10 person-years.
[44] Engineering Cellular Metabolism - Cell Press — Reconstruction of the E. coli pathway for conversion of the amino acid tryptophan into the plant-derived dye indigo represented a key milestone in metabolic engineering (Murdock et al., 1993). Following this, there were several successful cases of engineering E. coli metabolism to overproduce aromatics.
[45] Metabolic Engineering - SpringerLink — In this chapter, important milestones of implementing experimental and computational metabolic engineering concepts are reviewed. Key examples include the production of high-value chemicals derived from primary and secondary metabolism and elucidation of intracellular metabolic controls through flux balance analysis.
[46] [Thirty years development of metabolic engineering: a review] — Since its establishment 30 years ago, the discipline of metabolic engineering has developed rapidly based on its deep integration with molecular biology, systems biology and synthetic biology successively, which has greatly contributed to advancing and upgrading biotechnology industry. This review f …
[49] An overview of the 30-year history of metabolic engineering - Phys.org — A research team comprised of Gi Bae Kim, Dr. So Young Choi, Dr. In Jin Cho, Da-Hee Ahn, and Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering at KAIST have summarized the 30-year history of metabolic engineering, highlighting examples of recent progress in the field and contributions to sustainability and health. Metabolic engineering's contributions to bio-based sustainable chemicals and clean energy, health, and bioremediation were also reviewed. By looking back on the 30+ years of metabolic engineering, we aimed to highlight the contributions of metabolic engineering to achieve sustainability and good health." He added, "Metabolic engineering will play an increasingly important role as a key solution to the climate crisis, environmental pollution, food and energy shortages, and health problems in aging societies."
[53] Synthetic Metabolism: Engineering Biology at the Protein and Pathway ... — Synthetic biology has emerged as a powerful discipline for the creation of novel biological systems (Endy, 2005; Pleiss, 2006), particularly within the subfield of metabolic pathway and product engineering (Keasling, 2008; Savage et al., 2008).Continuing efforts to characterize and understand natural enzymes and pathways have opened the door for the building of synthetic pathways toward
[54] Editorial: Synthetic Biology-Guided Metabolic Engineering — Among the successes of Synthetic Biology and Metabolic Engineering, the ability to achieve smarter construct design and higher yields of valuable chemicals needs to be considered. As one example, Callari et al. engineered Saccharomyces cerevisiae to produce the diterpene casbene, precursor of many terpenoids of medical interest. The authors
[55] Recent advances in systems metabolic engineering — Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides a review of the recent tools and strategies used for enzyme-, genetic module-, pathway-, flux-, genome-, and cell-level engineering, supported by illustrative examples. Additionally, various systems biology tools, such as genome-scale metabolic models (GEMs), machine learning (ML)-assisted pathway design, and deep learning (DL)-based enzyme design, have been developed to enhance the potential of systems metabolic engineering by providing a comprehensive understanding of cellular systems and accurate predictions 5, 6. Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production
[61] Plant Metabolic Engineering for Enhanced Nutrition and Food Security ... — In the face of climate change and the increasing problem of food security, plant metabolic engineering stands out as the most ... metabolic engineering can be customized to improve nutrient bioavailability. For example, increasing iron content in crops ... solutions to addressing malnutrition. Climate change poses a significant threat to global
[63] Metabolic engineering for sustainability and health — Over the past decade, advances in metabolic engineering and synthetic biology have provided a range of tools and strategies for the construction of efficient microbial cell factories (Choi et al., 2019; Kim et al., 2023; Ko et al., 2020). Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized the sustainable production of fuels and materials through the creation of efficient microbial cell factories. Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides an overview of the current advancements in the bio-based production of polyamide monomers using metabolically engineered microorganisms and the bio-based polyamides synthesized using those monomers are reviewed.
[64] Towards a sustainable bio-based economy: Redirecting primary metabolism ... — Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology - PMC As our technological capabilities improve, metabolic engineering efforts may expand the utility of plants beyond sugar feedstocks through the direct production of target compounds, including pharmaceuticals, renewable fuels, and commodity chemicals. Plant metabolic engineering and synthetic biology may provide a means to begin altering plant metabolism to produce various co-products to help offset costs and expand the application of feedstock crops. Recent studies have also demonstrated how stacking strategies can boost production levels overall; thus, in many ways, plant metabolic engineering is catching up and simultaneously learning from microbial studies, which will be key to the overall success of plant synthetic biology efforts in the future.
[65] Metabolic engineering: Tools and applications - PMC — Metabolic engineering plays a pivotal role in the development of microbial cell factories for efficient production of biofuels, chemicals, and natural products, which facilitate the transition from fossil-resource dependent processes to green and sustainable bio-based processes. This special issue was aimed to showcase some recent advances in developing novel synthetic biology tools and screening techniques for metabolic engineering, strategies on engineering of microbial cell factories for sustainable feedstock utilization, and the production of representative chemicals. Metabolic engineering strategies for microbial utilization of methanol [J] Eng. Microbiol. 9.Lu H., Villada J.C., Lee P.K.H. Modular metabolic engineering for biobased chemical production [J] Trends Biotechnol. Combinatorial metabolic engineering of Saccharomyces cerevisiae for improved production of 7-dehydrocholesterol [J] Eng. Microbiol.
[66] Engineering metabolic pathways in Escherichia coli for constructing a ... — Multiple researchers have reported the use of pathway engineering to generate strains capable of accumulating various metabolic precursors, including pyruvate, acetyl-CoA, malonyl-CoA, mevalonate and shikimate. The aim of this review provides a promising guideline for designing E. coli strains capable of producing a variety of useful chemicals.
[68] Systems metabolic engineering of Escherichia coli for the heterologous ... — Escherichia coli is a veteran in industrial biotechnology. Several decades ago, groundbreaking applications described the use of E. coli for the overproduction of the amino acid l-threonine and the first recombinant synthesis of human insulin .Owing to its outstanding importance as an industrial producer and model strain, E. coli is probably the best-studied organism among all microbes.
[70] Metabolic Engineering and Synthetic Biology: Synergies, Future, and ... — Both metabolic engineering and synthetic biology are two promising areas that have made great advances in biotechnology and have contributed significantly toward the resolution of problems in production of drugs, vaccines, chemical compounds, etc. (Khalil and Collins, 2010). In addition, these fields have advanced our knowledge regarding life
[76] Engineering Enzymes for Environmental Sustainability — Topics include the use of engineered enzymes for improving carbon capture and utilisation, bioremediation, plastic deconstruction, and renewable feedstock generation. Successes, challenges, and opportunities for future enzyme engineering campaigns to improve environmental sustainability are discussed.
[77] Metabolic engineering for sustainability and health — Over the past decade, advances in metabolic engineering and synthetic biology have provided a range of tools and strategies for the construction of efficient microbial cell factories (Choi et al., 2019; Kim et al., 2023; Ko et al., 2020). Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized the sustainable production of fuels and materials through the creation of efficient microbial cell factories. Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides an overview of the current advancements in the bio-based production of polyamide monomers using metabolically engineered microorganisms and the bio-based polyamides synthesized using those monomers are reviewed.
[78] PDF — novel metabolic pathways, enhance production yields, and develop sustainable solutions. In this article, it will delve into the field of metabolic pathway engineering, exploring its principles, methodologies, and promising applications. Principles of metabolic pathway engineering Metabolic pathway engineering involves the rational redesign
[86] Recent advances in systems metabolic engineering — Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides a review of the recent tools and strategies used for enzyme-, genetic module-, pathway-, flux-, genome-, and cell-level engineering, supported by illustrative examples. Additionally, various systems biology tools, such as genome-scale metabolic models (GEMs), machine learning (ML)-assisted pathway design, and deep learning (DL)-based enzyme design, have been developed to enhance the potential of systems metabolic engineering by providing a comprehensive understanding of cellular systems and accurate predictions 5, 6. Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production
[88] Recent advances in high-throughput metabolic engineering: Generation of ... — The engineering strategy brought by biosensors is also termed high-throughput metabolic engineering (Dietrich et al., 2010), which has been applied to reveal novel genotype-phenotype relationships and evolve microbial cell factories to increase the production of commodity chemicals, secondary metabolites, biofuels, etc. (Zeng et al., 2020).
[89] Recent advances in systems metabolic engineering - PubMed — Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized the sustainable production of fuels and materials through the creation of efficient microbial cell factories. Recent advancements in systems …
[92] Searching for the optimal microbial factory: high-throughput biosensors ... — This review has explored recent advancements in the field of biosensor engineering for small molecule screening of microbial cell factories. Efforts in data mining, directed evolution and rational re-engineering of TFs and riboswitches have yielded novel biosensors for high-value compounds.
[93] Tailor-made transcriptional biosensors for optimizing microbial cell ... — Biosensor applications for optimizing microbial cell factories. Transcriptional biosensors are used mainly to perform one of three key functions in the development and optimization of microbial production strains with industrial significance, namely, high-throughput screening, adaptive laboratory evolution and dynamic pathway control [44, 83
[94] Development of biosensors and their application in metabolic engineering — As many biosensors are still in the 'proof-of-concept' stage, this review will also address aspects regarding their potential application in a metabolic engineering context to accelerate cell factory development. Finally, recent examples on integration of biosensors into genetic circuit regulation will be discussed.
[95] Extended Metabolic Biosensor Design for Dynamic Pathway Regulation of ... — As shown in this study, the integration of metabolic circuits and TF-based biosensors in pathway regulation is a robust solution for the high-performance production of target chemicals in the engineered microbial strains that are currently designed in modern biofoundries (Carbonell et al., 2018). Our analysis of the dynamic response of a cell
[108] Machine learning applications in systems metabolic engineering — Machine learning applications in systems metabolic engineering - ScienceDirect In recent years, increasing availability of bio big data, for example, omics data, has led to active application of machine learning techniques across various stages of systems metabolic engineering, including host strain selection, metabolic pathway reconstruction, metabolic flux optimization, and fermentation. As the use of machine learning in systems metabolic engineering will become more widespread in accordance with the ever-increasing volume of bio big data, future prospects are also provided for the successful applications of machine learning. In this context, here we review recent contributions of machine learning in gene annotation and host strain selection, metabolic pathway reconstruction, metabolic flux optimization, and fermentation, which constitute the key factors of systems metabolic engineering (Figure 1).
[109] Machine Learning Approaches in Metabolic Pathway Predictions and Drug ... — In the near future, AI technologies are expected to facilitate more accurate diagnoses and cost-effective treatments. Machine learning (ML) and deep learning, both subsets of AI, enable adjustments to metabolic pathways in living organisms, optimizing outputs while minimizing inputs.
[110] Machine learning for metabolic pathway optimization: A review — Optimizing the metabolic pathways of microbial cell factories is essential for establishing viable biotechnological production processes. However, due to the limited understanding of the complex setup of cellular machinery, building efficient microbial cell factories remains tedious and time-consuming. Machine learning (ML), a powerful tool capable of identifying patterns within large datasets
[111] A machine learning approach to predict metabolic pathway dynamics from ... — Mathematical kinetic models have been traditionally used to predict pathway dynamics, but they take a long time to develop and require significant biological expertize. Here, we substitute traditional kinetic models with a machine learning approach that is able to learn pathway dynamics straight from data examples.
[112] Recent advances in machine learning applications in metabolic engineering — have developed rapidly, the motivation of applying machine learning (ML) techniques in synthetic biology and ML-based designer cell factory development has started to become an obvious approach (Perakakis et al., 2018). Thus, data-driven ML models are highly efficient in metabolic engineering applications from predicting a novel pathway to creating a designer strain with optimal RBS sequences or promoter strength for improved yield. Additionally, ML-based methods are being applied in crucial metabolic engineering stages like process scale-up and other downstream processing where optimal growth conditions and process parameters can be selected from large experimental datasets to obtain maximum titer, rate, and yield (Baladehi et al., 2021; Czajka et al., 2021; Lv et al., 2022; Oyetunde et al., 2019).
[113] Recent advances in machine learning applications in metabolic engineering — Recent advances in machine learning applications in metabolic engineering - PubMed Recent advances in machine learning applications in metabolic engineering Recent advances in machine learning applications in metabolic engineering Machine learning (ML) coupled with the available metabolic engineering test instances and omics data brings a comprehensive and multidisciplinary approach that enables scientists to evaluate various parameters for effective strain design. The combinative interplay between the ML algorithms and biological datasets through knowledge engineering have guided the recent advancements in applications such as CRISPR/Cas systems, gene circuits, protein engineering, metabolic pathway reconstruction, and bioprocess engineering. Systems Metabolic Engineering Meets Machine Learning: A New Era for Data-Driven Metabolic Engineering. Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism. Zhang J, et al.
[116] Customized optimization of metabolic pathways by combinatorial ... — In addition, new strategies have been developed to balance the metabolic flux within a target pathway by tuning pathway gene expression through engineering of the promoters , ribosome binding sites and intergenic regions . These new approaches have enabled simultaneous optimization of a metabolic pathway to a certain degree.
[128] The Transformative Role of Artificial Intelligence in Metabolic Engineering — Artificial intelligence (AI) and machine learning (ML) are revolutionizing metabolic engineering by enabling the design of robust microbial strains, optimizing metabolic pathways, and accelerating the development of sustainable bioproduction systems.
[136] Metabolic Engineering: Methodologies and Applications — Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy
[137] Systematic Applications of Metabolomics in Metabolic Engineering — 1. Introduction. Organisms such as Saccharomyces cerevisiae and Aspergillus niger have a long history of commercial use in natural fermentation processes to produce chemicals such as ethanol and citric acid. Traditional bioprocess engineering entails the design and optimization of the equipment and procedures necessary to efficiently manufacture these and other biologically derived products.
[138] Metabolic engineering: Tools and applications - PMC — Metabolic engineering plays a pivotal role in the development of microbial cell factories for efficient production of biofuels, chemicals, and natural products, which facilitate the transition from fossil-resource dependent processes to green and sustainable bio-based processes. This special issue was aimed to showcase some recent advances in developing novel synthetic biology tools and screening techniques for metabolic engineering, strategies on engineering of microbial cell factories for sustainable feedstock utilization, and the production of representative chemicals. Metabolic engineering strategies for microbial utilization of methanol [J] Eng. Microbiol. 9.Lu H., Villada J.C., Lee P.K.H. Modular metabolic engineering for biobased chemical production [J] Trends Biotechnol. Combinatorial metabolic engineering of Saccharomyces cerevisiae for improved production of 7-dehydrocholesterol [J] Eng. Microbiol.
[139] PDF — To accelerate strain design, several important computational tools, such as metabolic flux analysis, genome-scale metabolic models, and related algorithms like OptKnock, have been established to predict genetic modifications that can lead to higher chemical production.22−26 Development of synthetic biology tools, such as protein engineering and clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9), and novel concepts, such as dynamic control and cell-free metabolic engineering, has further facilitated metabolic engineering endeavors.27−33 More recently, important milestones included metabolic engineering efforts in nonmodel organisms, utilization of C1 compounds, and incorporation of machine learning (ML) techniques.34−37 In this review, we first describe the strategies and tools used in metabolic engineering with a focus on the DBTL cycle in the model organisms E.
[140] CRISPR-derived genome editing technologies for metabolic engineering — CRISPR-derived genome editing technologies for metabolic engineering - ScienceDirect CRISPR-derived genome editing technologies for metabolic engineering Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas) systems now have become the first choice for genome engineering in many organisms including industrially relevant ones for construction of cell factories as well as discovery and evaluation of relevant genes and pathways. Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy Using CRISPR-Cas 9 genome editing technology Multiplex gene disruption by targeted base editing of yarrowia lipolytica genome using cytidine deaminase combined with the CRISPR/Cas9 system We particularly put emphasis on reviewing some successful implementations in metabolic pathway engineering via CRISPR-based genome editing tools.
[141] CRISPR-based metabolic pathway engineering - PubMed — CRISPR-based metabolic pathway engineering Metab Eng. 2021 Jan:63:148-159. doi: 10.1016/j ... pathways must be constructed optimally to minimize these negative effects and maximize catalytic efficiency. With the development of CRISPR technology, some of the problems of previous pathway engineering and genome editing techniques were resolved
[148] Recent advances in systems metabolic engineering — Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides a review of the recent tools and strategies used for enzyme-, genetic module-, pathway-, flux-, genome-, and cell-level engineering, supported by illustrative examples. Additionally, various systems biology tools, such as genome-scale metabolic models (GEMs), machine learning (ML)-assisted pathway design, and deep learning (DL)-based enzyme design, have been developed to enhance the potential of systems metabolic engineering by providing a comprehensive understanding of cellular systems and accurate predictions 5, 6. Tools and strategies of systems metabolic engineering for the development of microbial cell factories for chemical production
[153] Metabolic engineering of microorganisms for carbon dioxide utilization ... — Metabolic engineering of microorganisms for carbon dioxide utilization - ScienceDirect Metabolic engineering of microorganisms for carbon dioxide utilization 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. This review delves into the latest advancements in CO2 utilization through metabolic engineering, emphasizing the integration of natural and synthetic pathways and recent trends in sustainable bioproduction using CO2. This work is supported by the Development of platform technologies of microbial cell factories for the next-generation biorefineries project (2022M3J5A1056117), and Development of advanced synthetic biology source technologies for leading the biomanufacturing industry project (RS-2024-00399424) from National Research Foundation supported by the Korean Ministry of Science and ICT.
[164] Metabolic pathway engineering: Perspectives and applications — Metabolic engineering of both plant and microorganism helps to get different secondary metabolites with pharmacological values. It leads to efficient and cost effective drug discovery process , .In the first part of this review, we have discussed metabolic engineering perspectives from application point of view.
[165] Lessons from metabolic engineering for functional genomics and drug ... — The metabolic engineering goal of identifying genes that confer a particular phenotype is conceptually and methodologically congruent with central issues in drug discovery and functional genomics.
[166] Recent trends in metabolic engineering for microbial production of ... — Engineered microorganisms are being developed that can be utilized for enhanced synthesis of various chemical compounds as microbial cell factories because wild-type microbial strain has not had enough metabolic capacity to produce natural products , , . Here in this article, we have discussed various tools that could be explored to engineer metabolic pathways in the interest of a bioeconomy, such as bio-based production of natural drugs, nutraceuticals, pigments, aromatic compounds and biofuels. Growing concerns over the traditional fermentation process, restricted petroleum resources linked with conservational complications and advancements in tools and strategies of metabolic engineering are encouraging the use of metabolically engineered microorganisms for the industrial production of natural products such as drugs, nutraceuticals, pigments, aromatic compounds, biofuels etc.
[168] Metabolic engineering approaches for the biosynthesis of antibiotics — In this paper, we review recent tools and strategies in metabolic engineering and synthetic biology for antibiotic discovery and the efficient production of antibiotics, their derivatives, and analogs, along with representative examples. These metabolic engineering and synthetic biology strategies offer promising potential to revitalize the discovery and development of new antibiotics, providing renewed hope in humanity’s fight against MDR pathogenic bacteria. Recent discovery of natural antibiotics as well as metabolic engineering and synthetic biology strategies for the development of novel antibiotic derivatives are discussed. Although engineering large BGCs in actinomycetes remains challenging, new synthetic biology tools and strategies are continuously being developed to facilitate the engineering of these highly potent hosts for industrial-scale antibiotic production. J Antibiot. J Antibiot.
[183] PDF — Challenges and future directions Despite significant progress, metabolic pathway engineering faces challenges, including pathway toxicity, metabolic imbalances, and limited knowledge of complex cellular networks. Future efforts will focus on addressing these challenges by implementing advanced computational tools, exploring non-conventional organisms, and enhancing the understanding of
[184] Self-assembly systems to troubleshoot metabolic engineering challenges — Self-assembly approaches address metabolic engineering issues such as ineffective sequential catalysis, side reactions, and untimely supply of cofactors.
[185] PDF — To accelerate strain design, several important computational tools, such as metabolic flux analysis, genome-scale metabolic models, and related algorithms like OptKnock, have been established to predict genetic modifications that can lead to higher chemical production.22−26 Development of synthetic biology tools, such as protein engineering and clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9), and novel concepts, such as dynamic control and cell-free metabolic engineering, has further facilitated metabolic engineering endeavors.27−33 More recently, important milestones included metabolic engineering efforts in nonmodel organisms, utilization of C1 compounds, and incorporation of machine learning (ML) techniques.34−37 In this review, we first describe the strategies and tools used in metabolic engineering with a focus on the DBTL cycle in the model organisms E.
[198] Sustainable metabolic engineering requires a perfect trifecta — Unconventional feedstocks (e.g. hemicellulosic sugars and CO 2) and non-model organisms are increasingly gaining traction for advanced bioproduct synthesis due to their specialized metabolic modes. Judicious selection of the substrate-organism-product combination will illuminate the untapped territory of sustainable metabolic engineering.
[199] Sustainable metabolic engineering requires a perfect trifecta — A perfect trifecta of substrate, product, and organism is prerequisite for an environmentally and economically sustainable metabolic engineering endeavor. With broad spectra of substrates, products, and organisms in nature, careful consideration, including technoeconomic analysis of the combinations of these three components of metabolic engineering, can lead to a quantum leap in biotechnology by eliciting synergies. Fuel ethanol production from lignocellulose: a challenge for metabolic engineering and process integration The integration of artificial intelligence with metabolic engineering to facilitate precise and data-driven design of biosynthetic pathways is also discussed, along with the identification of current limitations and proposition of strategies for optimizing biosystems, thereby propelling the field of chemical biology towards sustainable chemical production.
[200] Self-assembly systems to troubleshoot metabolic engineering challenges — Self-assembly approaches address metabolic engineering issues such as ineffective sequential catalysis, side reactions, and untimely supply of cofactors. ... The directions of scaffold modification are presented. ... These weaknesses limit the application of scaffolds in metabolic engineering. Future work may concentrate on the modification of
[201] Self-assembly systems to troubleshoot metabolic engineering ... - PubMed — In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively
[202] The Need for Integrated Approaches in Metabolic Engineering — FUTURE DIRECTIONS TOWARD INTEGRATED APPROACHES IN METABOLIC ENGINEERING. To tackle the existing challenges in metabolic engineering, strategies need to account for all aspects of product synthesis in which control can be exerted: the transcriptome, the translatome, the proteome, and the reactome . First, engineering the transcriptome involves
[203] New synthetic biology tools for metabolic control - ScienceDirect — Advances in synthetic biology have contributed to metabolic control strategies and accelerated the development of efficient microbial cell factories. In this review, recent findings for the metabolic regulation of engineered cell are reviewed, focusing on three aspects: metabolic model, CRISPR technology, and genetic circuits.
[204] Synthetic biology: applications come of age - PMC - PubMed Central (PMC) — Operating at the interface of synthetic biology and metabolic engineering, Liao and colleagues 97 recently introduced the glyoxylate shunt pathway into mammalian liver cells and mice to explore its effects on fatty acid metabolism and, more broadly, on whole-body metabolism. Remarkably, the researchers found that when transplanted into mammals
[210] Next-generation metabolic engineering of non-conventional microbial ... — E. coli and S. cerevisiae have been the most widely used workhorses for metabolic engineering in production of value-added biochemicals owing to their advantageous characteristics, such as low safety risks, fast growth rates and high tractability (Yu et al., 2014).However, they lack several traits that limit their abilities to biosynthesize carboxylic acid platform chemicals.
[211] Considering Strain Variation and Non-Type Strains for Yeast Metabolic ... — Abstract. A variety of yeast species have been considered ideal hosts for metabolic engineering to produce value-added chemicals, including the model organism Saccharomyces cerevisiae, as well as non-conventional yeasts including Yarrowia lipolytica, Kluyveromyces marxianus, and Pichia pastoris.However, the metabolic capacity of these microbes is not simply dictated or implied by genus or
[212] Metabolic engineering in the host Yarrowia lipolytica - PubMed — The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host.
[213] Non-conventional hosts for the production of fuels and chemicals — In this review, we explore recent advances in the use of nonconventional hosts for the production of a variety of fuel, cosmetics, perfumes, food, and pharmaceuticals. Specifically, we highlight twenty-seven popular molecules with a special focus on recent progress and metabolic engineering strategies to enable improved production of fuels and
[224] Dynamic Metabolomics for Engineering Biology: Accelerating Learning ... — Metabolomics is a powerful tool to rationally guide the metabolic engineering of synthetic bioproduction pathways. Current reports indicate great potential to further develop metabolomics-directed synthetic bioproduction. Advanced mass metabolomics methods including isotope flux analysis, untargeted metabolomics, and system-wide approaches are assisting the characterization of metabolic
[225] PDF — To accelerate strain design, several important computational tools, such as metabolic flux analysis, genome-scale metabolic models, and related algorithms like OptKnock, have been established to predict genetic modifications that can lead to higher chemical production.22−26 Development of synthetic biology tools, such as protein engineering and clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9), and novel concepts, such as dynamic control and cell-free metabolic engineering, has further facilitated metabolic engineering endeavors.27−33 More recently, important milestones included metabolic engineering efforts in nonmodel organisms, utilization of C1 compounds, and incorporation of machine learning (ML) techniques.34−37 In this review, we first describe the strategies and tools used in metabolic engineering with a focus on the DBTL cycle in the model organisms E.
[229] In silico identification of metabolic engineering strategies for ... — Accordingly, many metabolic engineering efforts have been made to develop engineered strains of Y. lipolytica with higher lipid yields. Genome-scale model of metabolism (GEM) is a powerful tool for identifying novel genetic designs for metabolic engineering.
[231] Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big ... — Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics).
[236] Genetic Engineering in Bacteria, Fungi, and Oomycetes, Taking ... - MDPI — The advent of advanced genetic tools, such as CRISPR-Cas9, has revolutionized the ability to precisely edit microbial genomes, allowing for targeted modifications that can lead to significant improvements in microbial functions and applications . CRISPR-Cas9 has emerged as a groundbreaking tool in genetic engineering, particularly for bacteria, due to its precision and efficiency in editing genomes (Table 1). Additionally, ongoing research into improving the specificity and efficiency of CRISPR-Cas systems, as well as developing novel gene-editing tools, is expected to enhance the precision of bacterial genetic modifications. The CRISPR-Cas9 system has emerged as a transformative tool in the genetic engineering of fungi, enabling precise genome editing that has significantly advanced both basic research and industrial applications (Table 1). Nødvig, C.S.; Nielsen, J.B.; Kogle, M.E.; Mortensen, U.H. A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi.
[259] Metabolic Engineering - Applications, Methods, and Challenges — This is a successful example of using metabolic engineering to establish an industrial strain for commercial production of feedstock chemicals from renewable resources. DuPont and Tate & Lyle (formerly A.E. Staley) have completed their pilot fermentation process study and begun building their first plant, with a capacity of 100,000 tons/yr.
[260] Metabolic engineering of strains: from industrial-scale to lab-scale ... — A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5-50 g/L), and lab-scale (0-5 g/L).
[261] Tools and strategies of systems metabolic engineering for the ... — When developing microbial strains by systems metabolic engineering (e.g., the second upstream process), it is extremely important to consider the first upstream, midstream, and downstream processes together for the overall optimization of the entire process (Fig. 1).3 The advent of systems metabolic engineering promoted the development of high-performance strains producing various bioproducts, including bulk chemicals, fine chemicals, polymers and materials, biofuels, and natural products (Fig. 1).
[262] Recent trends in metabolic engineering for microbial production of ... — Engineered microorganisms are being developed that can be utilized for enhanced synthesis of various chemical compounds as microbial cell factories because wild-type microbial strain has not had enough metabolic capacity to produce natural products , , . Here in this article, we have discussed various tools that could be explored to engineer metabolic pathways in the interest of a bioeconomy, such as bio-based production of natural drugs, nutraceuticals, pigments, aromatic compounds and biofuels. Growing concerns over the traditional fermentation process, restricted petroleum resources linked with conservational complications and advancements in tools and strategies of metabolic engineering are encouraging the use of metabolically engineered microorganisms for the industrial production of natural products such as drugs, nutraceuticals, pigments, aromatic compounds, biofuels etc.
[263] Scaling up of renewable chemicals - ScienceDirect — DuPont Tate & Lyle Bio Products, LLC: ... Progress in developing cell-free metabolic engineering includes demonstrations of pathways extending beyond 8 enzyme steps, near theoretical mass yields, volumetric productivities of several g/L/hour and scale-up into the hundreds of liters. ... Scale-up challenges are usually dependent on whether the
[265] Engineering Cellular Metabolism - Cell Press — Here, we will review the current status and challenges of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome
[266] A review on commercial-scale high-value products that can be produced ... — The enzymatic hydrolysis process has been scaled up and used in the industrial-scale plants operated by Beta Renewables ... DuPont Tate & Lyle Bio Products have produced microbial 1,3-PDO from corn derivate sugars since 2006 at a 63,500-kilotonne per ... An example of a successful metabolic engineering project is the production of 1,3
[267] Extremely thermophilic microorganisms as metabolic engineering ... — A joint venture between Dupont and Tate & Lyle was the first to achieve a scale in the thousands of metric tons per year of a commodity chemical using a metabolically engineered host. Production of 1,3-propanediol from corn starch commenced in 2006 and, nearly a decade later, the company reports progress on expanding production.
[271] Metabolic Engineering for Plant Secondary Metabolites Production - Springer — Key focuses on metabolic engineering include pathway manipulation techniques such as gene overexpression, gene silencing, and gene knockouts or knock-ins. These techniques adjust the levels of specific enzymes and other proteins involved in the metabolic pathways, thereby enhancing the production of target metabolites.
[272] PDF — To accelerate strain design, several important computational tools, such as metabolic flux analysis, genome-scale metabolic models, and related algorithms like OptKnock, have been established to predict genetic modifications that can lead to higher chemical production.22−26 Development of synthetic biology tools, such as protein engineering and clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9), and novel concepts, such as dynamic control and cell-free metabolic engineering, has further facilitated metabolic engineering endeavors.27−33 More recently, important milestones included metabolic engineering efforts in nonmodel organisms, utilization of C1 compounds, and incorporation of machine learning (ML) techniques.34−37 In this review, we first describe the strategies and tools used in metabolic engineering with a focus on the DBTL cycle in the model organisms E.
[276] Metabolic engineering for sustainability and health — Over the past decade, advances in metabolic engineering and synthetic biology have provided a range of tools and strategies for the construction of efficient microbial cell factories (Choi et al., 2019; Kim et al., 2023; Ko et al., 2020). Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized the sustainable production of fuels and materials through the creation of efficient microbial cell factories. Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides an overview of the current advancements in the bio-based production of polyamide monomers using metabolically engineered microorganisms and the bio-based polyamides synthesized using those monomers are reviewed.
[279] Optimizing Metabolic Pathways for the Improved Production of Natural ... — Optimizing Metabolic Pathways for the Improved Production of Natural Products - ScienceDirect Chapter Eight - Optimizing Metabolic Pathways for the Improved Production of Natural Products Improvement of catechin production in Escherichia coli through combinatorial metabolic engineering Recent advances in metabolic engineering enable the production of high-value chemicals via expressing complex biosynthetic pathways in a single microbial host. However, many engineered strains suffer from poor product yields due to redox imbalance and excess metabolic burden, and require compartmentalization of the pathway for optimal function. To address this problem, significant developments have been made towards co-cultivation of more than one engineered microbial strains to distribute metabolic burden between the co-cultivation partners and improve the product yield.
[281] Combinatorial pathway optimization for streamlined metabolic engineering — Addressing the aforementioned imbalances to enable and improve target pathway flux and eventually create microbial cell factories for industrial application represents a major challenge for metabolic engineers .Classically this has been done by identifying major bottlenecks in the initial pathway design and subsequently removing these individually by sequential optimization campaigns