Abstract:Metabolic engineering is the use of recombinant DNA technology, synthetic biology and genome editing to modify the cellular networks including metabolic, gene regulatory, and signaling networks of an organism. It can achieve the desirable goals such as enhanced production of metabolites, and improve the capability of biomanufacturing pharmaceuticals, biofuels and biochemicals as well as other biotechnology products. In order to comprehend the status of metabolic engineering in past 30 years, we published this special issue to review the progress and trends of metabolic engineering from the four aspects of overall development, key technologies, host engineering and product engineering, respectively, for laying the foundation for the further development of metabolic engineering.

Abstract: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 firstly analyzes the current status of academic research and China’s competence in the area of metabolic engineering according to the data of papers published in SCI-indexed journals in the past 30 years. Subsequently, the article summarizes the development of systems biology methods and enabling technologies of synthetic biology and their applications in metabolic engineering in the past 10 years. Finally, the major challenges and future perspectives for the development of metabolic engineering are briefly discussed.

Abstract:In 1990s, Bailey and Stephanopoulos put forward the concept of classic metabolic engineering, aiming to use DNA recombination technology to rewire metabolic network to achieve improved cell performance and increased target products. In the last 30 years since the birth of metabolic engineering, life science have flourished, and new disciplines such as genomics, systems biology and synthetic biology have emerged, injecting new connotations and vitality into the development of metabolic engineering. Classic metabolic engineering research has entered into an unprecedented stage of systems metabolic engineering. The application of synthetic biology tools and strategies, such as omics technology, genomic-scale metabolic model, parts assembly, circuits design, dynamic control, genome editing and many others, have greatly improved the design, build, and rewiring capabilities of complex metabolism. The intervention of machine learning and the combination of evolutionary engineering and metabolic engineering will further promote the development of systems metabolic engineering. This paper analyzes the development of metabolic engineering in the past 30 years and summarizes the novel theories, techniques, strategies, and applications of metabolic engineering that have emerged over the past 30 years.

Abstract:13C metabolic flux analysis (13C-MFA) enables the precise quantification of intracellular metabolic reaction rates by analyzing the distribution of mass isotopomers of proteinogenic amino acids or intracellular metabolites through 13C labeling experiments. 13C-MFA has received much attention as it can help systematically understand cellular metabolic characteristics, guide metabolic engineering design and gain mechanistic insights into pathophysiology. This article reviews the advances of 13C-MFA in the past 30 years and discusses its potential and future perspective, with a focus on its application in industrial biotechnology and biomedicine.

Abstract:Genome-scale metabolic network model (GSMM) is becoming an important tool for studying cellular metabolic characteristics, and remarkable advances in relevant theories and methods have been made. Recently, various constraint-based GSMMs that integrated genomic, transcriptomic, proteomic, and thermodynamic data have been developed. These developments, together with the theoretical breakthroughs, have greatly contributed to identification of target genes, systems metabolic engineering, drug discovery, understanding disease mechanism, and many others. This review summarizes how to incorporate transcriptomic, proteomic, and thermodynamic-constraints into GSMM, and illustrates the shortcomings and challenges of applying each of these methods. Finally, we illustrate how to develop and refine a fully integrated GSMM by incorporating transcriptomic, proteomic, and thermodynamic constraints, and discuss future perspectives of constraint-based GSMM.

Abstract:The regulation of the expression of genes involved in metabolic pathways, termed as metabolic regulation, is vital to construct efficient microbial cell factories. With the continuous breakthroughs in synthetic biology, the mining and artificial design of high-quality regulatory elements have substantially improved our ability to modify and regulate cellular metabolic networks and its activities. The research on metabolic regulation has also evolved from the static regulation of single genes to the intelligent and precise dynamic regulation at the systems level. This review briefly summarizes the advances of metabolic regulation technologies in the past 30 years.

Abstract:As an important model industrial microorganism, Escherichia coli has been widely used in pharmaceutical, chemical industry and agriculture. In the past 30 years, a variety of new strategies and techniques, including artificial intelligence, gene editing, metabolic pathway assembly, and dynamic regulation have been used to design, construct, and optimize E. coli cell factories, which remarkably improved the efficiency for biotechnological production of chemicals. In this review, three key aspects for constructing E. coli cell factories, including pathway design, pathway assembly and regulation, and optimization of global cellular performance, are summarized. The technologies that have played important roles in metabolic engineering of E. coli, as well as their future applications, are discussed.

Abstract:Since its birth in the early 1990s, metabolic engineering technology has gone 30 years rapid development. As one of the preferred chassis for metabolic engineering, S. cerevisiae cells have been engineered into microbial cell factories for the production of a variety of bulk chemicals and novel high value-added bioactive compounds. In recent years, synthetic biology, bioinformatics, machine learning and other technologies have also greatly contributed to the technological development and applications of metabolic engineering. This review summarizes the important technological development for metabolic engineering of S. cerevisiae in the past 30 years. Firstly, classical metabolic engineering tools and strategies were reviewed, followed by reviewing systems metabolic engineering and synthetic biology driven metabolic engineering approaches. The review is concluded with discussing future perspectives for metabolic engineering of S. cerevisiae in the light of state-of-the-art technological development.

Abstract:Corynebacterium glutamicum is an important workhorse of industrial biotechnology, especially for amino acid bioindustry. This bacterium is being used to produce various amino acids at a level of over 6 million tons per year. In recent years, enabling technologies for C. glutamicum metabolic engineering have been developed and improved, which accelerated construction and optimization of microbial cell factoriers, expanding spectra of substrates and products, and facilitated basic researches on C. glutamicum. With these technologies, C. glutamicum has become one of the ideal microbial chasses. This review summarizes recent key technological developments of enabling technologies for C. glutamicum metabolic engineering and focuses on establishment and applications of CRISPR-based genome editing, gene expression regulation, adaptive laboratory evolution, and biosensor technologies.

Abstract:As a typical food safety industrial model strain, Bacillus subtilis has been widely used in the field of metabolic engineering due to its non-pathogenicity, strong ability of extracellular protein secretion and no obvious codon preference. In recent years, with the rapid development of molecular biology and genetic engineering technology, a variety of research strategies and tools have been used to construct B. subtilis chassis cells for efficient synthesis of biological products. This review introduces the research progress of B. subtilis from the aspects of promoter engineering, gene editing, genetic circuit, cofactor engineering and pathway enzyme assembly. Then, we also summarized the application of B. subtilis in the production of biological products. Finally, the future research directions of B. subtilis are prospected.

Abstract:Filamentous fungi are important industrial microorganisms that play important roles in the production of bio-based products such as organic acids, proteins and secondary metabolites. The development of metabolic engineering and its enabling techniques have greatly promoted the design, construction and application of filamentous fungal cell factories. This article systematically reviews the development of filamentous fungal cell factories constructed through metabolic engineering, and discusses the challenges and future perspectives for systems metabolic engineering of filamentous fungi.

Abstract:Over the past 30 years, Yarrowia lipolytica, Kluyveromyces, Pichia, Candida, Hansenula and other non-conventional yeasts have attracted wide attention because of their desirable phenotypes, such as rapid growth, capability of utilizing multiple substrates, and stress tolerance. A variety of synthetic biology tools are being developed for exploitation of their unique phenotypes, making them potential cell factories for the production of recombinant proteins and renewable bio-based chemicals. This review summarizes the gene editing tools and the metabolic engineering strategies recently developed for non-conventional yeasts. Moreover, the challenges and future perspectives for developing non-conventional yeasts into efficient cell factories for the production of useful products through metabolic engineering are discussed.

Abstract:Fermentative production of amino acids is one of the pillars of the fermentation industry in China. Recently, with the fast development of metabolic engineering and synthetic biology technologies, the metabolic engineering for production of amino acids has been flourishing. Conventional forward metabolic engineering, reversed metabolic engineering based on omics data and in silico simulation, and evolutionary metabolic engineering mimicking the natural evolution, have shown increasingly promising applications. A series of highly efficient and robust amino acids-producing strains have been developed and applied in the industrial production of amino acids. The increasingly fierce market competition has put forward new requirements for strain breeding and selection, such as developing high value-added amino acids, dynamic regulation of cellular metabolism, and adapting to the requirements of new process. This review summarizes the advances and prospects in metabolic engineering for the production of amino acids.

Abstract:Tetracarbon organic acids are important platform chemicals that are widely used in the food, chemical, medicine, material industries and agriculture. Compared with the traditional petrochemical process, the production of tetracarbon organic acids by microbial fermentation is more promising due to milder reaction conditions, greener process and better environmental compatibility. This review summarizes the biosynthetic pathways and metabolic mechanisms for the production of tetracarbon organic acids, and illustrates recent advances, challenges, and future perspectives in the production of tetracarbon organic acids by naturally selected or purposefully engineered strains.

Abstract:Higher alcohols that contain more than two carbon atoms have better fuel properties than ethanol, making them important supplements and alternatives to fossil fuels. Using microbes to produce higher alcohols from renewable biomass can alleviate the current energy and environmental crises, and has become a major future direction for green biomanufacturing. Since natural microbes can only produce a few higher alcohols in small amounts, it is necessary to reconstruct the synthetic pathways for higher alcohols in model industrial strains through metabolic engineering and synthetic biology to overcome the metabolic bottlenecks. A series of milestones have been accomplished in past decades. The authors of this review have witnessed the entire journey of this field from its first success to the leaping development. On the 30th anniversary of the founding of the discipline of metabolic engineering, this review dates back to the great milestones in achieving heterologous production of higher alcohols in non-native strains. The design and optimization of high alcohol biosynthetic pathways, the expansion of feedstock, the engineering of host strains and the industrialization process are summarized. This review aims to draw further attention to microbial synthesis of higher alcohols, inspire the development of novel techniques and strategies of metabolic engineering, and promote the innovation and upgrade of China’s biofuel industry.

Abstract:14- to 16-membered macrolide antibiotics (MA) are clinically important anti-infective drugs. With the rapid emergence of bacterial resistance, there is an urgent need to develop novel MA to counter drug-resistant bacteria. The targeted optimization of MA can be guided by analyzing the interaction between the MA and its ribosomal targets, and the desired MA derivatives can be obtained efficiently when combining with the rapidly developed metabolic engineering approaches. In the past 30 years, metabolic engineering approaches have shown great advantages in engineering the biosynthesis of MA to create new derivatives and to improve their production. These metabolic engineering approaches include modification of the structural domains of the polyketide synthase (PKS) and post-PKS modification enzymes as well as combinatorial biosynthesis. In addition, the R&D (including the evaluation of its antimicrobial activities and the optimization through metabolic engineering) of carrimycin, a new 16-membered macrolide drug, are described in details in this review.

Abstract:Vitamins are organic substances that are essential for the maintenance of life activities. Generally, vitamins need to be obtained from the diet or from some synthetic source as the body cannot synthesize vitamins, or the amounts of the synthesized vitamins are insufficient. At present, vitamins are widely used in medicine, food additives, feed additives, cosmetics and other fields, and the global demand for vitamins is constantly growing. Vitamins can be produced from chemical or microbial synthesis. Chemical synthesis usually requires harsh reaction conditions, produces serious wastes, and creates great potential safety hazard. In contrast, microbial synthesis of vitamins is greener, safer, and requires much less energy input. This review summarizes the advances in metabolic engineering for vitamins production in the past 30 years, with a focus on production of water-soluble vitamins (vitamins B1, B2, B3, B5, B6, B7, B9, B12 and vitamin C precursors) and lipid-soluble vitamins (vitamin A, precursors of vitamin D, vitamin E and vitamin K). Moreover, the bottlenecks for fermentative production of vitamins are discussed, and future perspectives for developing next generation vitamins producing strains using synthetic biotechnology are prospected.

Abstract:Metabolic engineering has been developed for nearly 30 years since the early 1990s, and it has given a great impetus to microbial strain breeding and improvement. Aromatic chemicals are a variety of important chemicals that can be produced by microbial fermentation and are widely used in the pharmaceutical, food, feed, and material industry. Microbial cells can be engineered to accumulate a variety of useful aromatic chemicals in a targeted manner through rational engineering of the biosynthetic pathways of shikimate and the derived aromatic amino acids. This review summarizes the metabolic engineering strategies and biosynthetic pathways for the production of aromatic chemicals developed in the past 30 years, with the aim to provide a valuable reference and promote the research in this field.

Abstract:Polyhydroxyalkanoate (PHA) is a family of biodegradable polyesters synthesized by microorganisms. It has various monomer structures and physical properties with broad application prospects. However, its large-scale production is still hindered by the high cost. In the past 30 years, metabolic engineering approach has been used to tune the metabolic flux, engineer and introduce pathways. The efficiency of PHA synthesis by microorganisms has been significantly improved, and the diversity of PHA monomer, structure and substrate have also been enriched. Meanwhile, by changing cell morphology and PHA particle size, more efficient downstream production process has achieved and PHA production costs have been reduced. In recent years, “Next generation industrial biotechnology” (NGIB) based on extremophiles, especially halophilic Halomonas spp., has been rapidly developed. NGIB has achieved the opening and continuous production of PHA, which simplifies the production process and saves energy and fresh water. Combined with metabolic engineering, Halomonas spp. can be transformed into low-cost production platform of numerous PHA. It is expected to improve the market competitiveness and promote the commercialization of PHA.