Potential impact of synthetic biology on the development of microbial systems for the production of renewable fuels and chemicals

Exploiting synthetic biology platforms for enhanced biosynthesis of natural products in Yarrowia lipolytica

With the rapid development of synthetic biology, researchers can design, modify, or even synthesize microorganisms de novo, and microorganisms endowed with unnatural functions can be considered "artificial life" and facilitate the development of functional products. Based on this concept, researchers can solve critical problems related to the insufficient supply of natural products, such as low yields, long production cycles, and cumbersome procedures. Due to its superior performance and unique physiological and biochemical characteristics, Yarrowia lipolytica is a favorable chassis cell used for green biomanufacturing by numerous researchers. This paper mainly reviews the development of synthetic biology techniques for Y. lipolytica and summarizes the recent research progress on the synthesis of natural products in Y. lipolytica. This review will promote the continued innovative development of Y. lipolytica by providing theoretical guidance for research on the biosynthesis of natural products.

A review of synthetic biology tools in Yarrowia lipolytica

Yarrowia lipolytica is a non-conventional oleaginous yeast with great potential for industrial production. Y. lipolytica has a high propensity for flux through tricarboxylic acid cycle intermediates. Therefore, this host is currently being developed as a workhorse, and is rapidly emerging in biotechnology fields, especially for industrial chemical production, whole-cell bioconversion, and the treatment and recycling of industrial waste. In recent studies, Y. lipolytica has been rewritten and introduced with non-native metabolites of certain compounds of interest owing to the advancement in synthetic biology tools. In this review, we collate recent progress to present a detailed and insightful summary of the major developments in synthetic biology tools and techniques for Y. lipolytica, including promoters, terminators, selection markers, autonomously replicating sequences, DNA assembly techniques, genome editing techniques, and subcellular organelle engineering. This comprehensive overview would be a useful resource for future genetic engineering studies to improve the yield of desired metabolic products in Y. lipolytica.

Integrated proteomic and metabolomic analysis of a reconstructed three-species microbial consortium for one-step fermentation of 2-keto-l-gulonic acid, the precursor of vitamin C

Microbial consortia, with the merits of strong stability, robustness, and multi-function, played critical roles in human health, bioenergy, and food manufacture, etc. On the basis of ‘build a consortium to understand it’, a novel microbial consortium consisted of Gluconobacter oxydans, Ketogulonicigenium vulgare and Bacillus endophyticus was reconstructed to produce 2-keto-l-gulonic acid (2-KGA), the precursor of vitamin C. With this synthetic consortium, 73.7 g/L 2-KGA was obtained within 30 h, which is comparable to the conventional industrial method. A combined time-series proteomic and metabolomic analysis of the fermentation process was conducted to further investigate the cell–cell interaction. The results suggested that the existence of B. endophyticus and G. oxydans together promoted the growth of K. vulgare by supplying additional nutrients, and promoted the 2-KGA production by supplying more substrate. Meanwhile, the growth of B. endophyticus and G. oxydans was compromised from the competition of the nutrients by K. vulgare, enabling the efficient production of 2-KGA. This study provides valuable guidance for further study of synthetic microbial consortia.

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.

Bridging the gap between systems biology and synthetic biology

Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology.

Potential for green microalgae to produce hydrogen, pharmaceuticals and other high value products in a combined process

Green microalgae for several decades have been produced for commercial exploitation, with applications ranging from health food for human consumption, aquaculture and animal feed, to coloring agents, cosmetics and others. Several products from green algae which are used today consist of secondary metabolites that can be extracted from the algal biomass. The best known examples are the carotenoids astaxanthin and β-carotene, which are used as coloring agents and for health-promoting purposes. Many species of green algae are able to produce valuable metabolites for different uses; examples are antioxidants, several different carotenoids, polyunsaturated fatty acids, vitamins, anticancer and antiviral drugs. In many cases, these substances are secondary metabolites that are produced when the algae are exposed to stress conditions linked to nutrient deprivation, light intensity, temperature, salinity and pH. In other cases, the metabolites have been detected in algae grown under optimal conditions, and little is known about optimization of the production of each product, or the effects of stress conditions on their production. Some green algae have shown the ability to produce significant amounts of hydrogen gas during sulfur deprivation, a process which is currently studied extensively worldwide. At the moment, the majority of research in this field has focused on the model organism, Chlamydomonas reinhardtii, but other species of green algae also have this ability. Currently there is little information available regarding the possibility for producing hydrogen and other valuable metabolites in the same process. This study aims to explore which stress conditions are known to induce the production of different valuable products in comparison to stress reactions leading to hydrogen production. Wild type species of green microalgae with known ability to produce high amounts of certain valuable metabolites are listed and linked to species with ability to produce hydrogen during general anaerobic conditions, and during sulfur deprivation. Species used today for commercial purposes are also described. This information is analyzed in order to form a basis for selection of wild type species for a future multi-step process, where hydrogen production from solar energy is combined with the production of valuable metabolites and other commercial uses of the algal biomass.

Protein design in systems metabolic engineering for industrial strain development

Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering.

Synthetic biology triggers new era of antibiotics development

As a discipline to design and construct organisms with desired properties, synthetic biology has generated rapid progresses in the last decade. Combined synthetic biology with the traditional process, a new universal workflow for drug development has been becoming more and more attractive. The new methodology exhibits more efficient and inexpensive comparing to traditional methods in every aspect, such as new compounds discovery & screening, process design & drug manufacturing. This article reviews the application of synthetic biology in antibiotics development, including new drug discovery and screening, combinatorial biosynthesis to generate more analogues and heterologous expression of biosynthetic gene clusters with systematic engineering the recombinant microbial systems for large scale production.

Bioethanol from lignocellulosic biomass

China is suffering from a sustained shortage of crude oil supply, making fuel ethanol and other biofuels alternative solutions for this issue. However, taking into account the country's large population and dwindling arable land due to rapid urbanization, it is apparent that current fuel ethanol production from grain-based feedstocks is not sustainable, and lignocellulosic biomass, particularly agricultural residues that are abundantly available in China, is the only choice for China to further expand its fuel ethanol production, provided economically viable processes can be developed. In this chapter, cutting edge progress in bioethanol is reviewed, with a focus on the understanding of the molecular structure of the feedstock, leading pretreatment technologies, enzymatic hydrolysis of the cellulose component and strategies for the co-fermentation of the C5 and C6 sugars with engineered microorganisms. Finally, process integration and optimization is addressed with a case study on the COFCO Corporation's pilot plant, and challenges and perspectives for commercial production of bioethanol are highlighted.

Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development

The future of industrial biotechnology requires efficient development of highly productive and robust strains of microorganisms. Present praxis of strain development cannot adequately fulfill this requirement, primarily owing to the inability to control reactions precisely at a molecular level, or to predict reliably the behavior of cells upon perturbation. Recent developments in two areas of biology are changing the situation rapidly: structural biology has revealed details about enzymes and associated bioreactions at an atomic level; and synthetic biology has provided tools to design and assemble precisely controllable modules for re-programming cellular metabolic circuitry. However, because of different emphases, to date, these two areas have developed separately. A linkage between them is desirable to harness their concerted potential. We therefore propose structural synthetic biotechnology as a new field in biotechnology, specifically for application to the development of industrial microbial strains.

MISSA is a highly efficient in vivo DNA assembly method for plant multiple-gene transformation

We describe a highly efficient in vivo DNA assembly method, multiple-round in vivo site-specific assembly (MISSA), which facilitates plant multiple-gene transformation. MISSA is based on conjugational transfer, which is driven by donor strains, and two in vivo site-specific recombination events, which are mediated by inducible Cre recombinase and phage lambda site-specific recombination proteins in recipient strains, to enable in vivo transfer and in vivo assembly of multiple transgenic DNA. The assembly reactions can be performed circularly and iteratively through alternate use of the two specially designed donor vectors. As proof-of-principle experiments, we constructed a few plant multigene binary vectors. One of these vectors was generated by 15 rounds of MISSA reactions and was confirmed in transgenic Arabidopsis (Arabidopsis thaliana). As MISSA simplifies the tedious and time-consuming in vitro manipulations to a simple mixing of bacterial strains, it will greatly save time, effort, and expense associated with the assembly of multiple transgenic or synthetic DNA. The principle that underlies MISSA is applicable to engineering polygenic traits, biosynthetic pathways, or protein complexes in all organisms, such as Escherichia coli, yeast, plants, and animals. MISSA also has potential applications in synthetic biology, whether for basic theory or for applied biotechnology, aiming at the assembly of genetic pathways for the production of biofuels, pharmaceuticals, and industrial compounds from natural or synthetic DNA.

Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology

Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.

Construction and optimization of synthetic pathways in metabolic engineering

Metabolic engineering has enabled us to develop strains suitable for their use as microbial factories of chemicals and materials from renewable sources. It has recently become more powerful with the advanced in synthetic biology, which is allowing us to create novel and fine-controlled metabolic and regulatory circuits maximizing metabolic fluxes to the desired products in the strain being developed. This enables us to engineer host microorganisms to enhance their innate metabolic capabilities or to gain new capabilities in the production of target compounds. Here we review recently constructed synthetic pathways that have been successfully applied for producing non-innate chemicals and also discuss recent approaches developed to increase the efficiency of synthetic pathways for achieving higher productivities of desired bioproducts.

The path to next generation biofuels: successes and challenges in the era of synthetic biology

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.