Protein design in metabolic engineering and synthetic biology

Starting from experimental data on sequence, structure or biochemical properties of enzymes, protein design seeks to construct enzymes with desired activity, stability, specificity and selectivity. Two strategies are widely used to investigate sequence-structure-function relationships: statistical methods to analyse protein families or mutant libraries, and molecular modelling methods to study proteins and their interaction with ligands or substrates. On the basis of these methods, protein design has been successfully applied to fine-tune bottleneck enzymes in metabolic engineering and to design enzymes with new substrate spectra and new functions. However, constructing efficient metabolic pathways by integrating individual enzymes into a complex system is challenging. The field of synthetic biology is still in its infancy, but promising results have demonstrated the feasibility and usefulness of the concept.     

Opportunities for yeast metabolic engineering: Lessons from synthetic biology

Constant progress in genetic engineering has given rise to a number of promising areas of research that facilitated the expansion of industrial biotechnology. The field of metabolic engineering, which utilizes genetic tools to manipulate microbial metabolism to enhance the production of compounds of interest, has had a particularly strong impact by providing new platforms for chemical production. Recent developments in synthetic biology promise to expand the metabolic engineering toolbox further by creating novel biological components for pathway design. The present review addresses some of the recent advances in synthetic biology and how these have the potential to affect metabolic engineering in the yeast Saccharomyces cerevisiae. While S. cerevisiae for years has been a robust industrial organism and the target of multiple metabolic engineering trials, its potential for synthetic biology has remained relatively unexplored and further research in this field could strongly contribute to industrial biotechnology. This review also addresses are general considerations for pathway design, ranging from individual components to regulatory systems, overall pathway considerations and whole-organism engineering, with an emphasis on potential contributions of synthetic biology to these areas. Some examples of applications for yeast synthetic biology and metabolic engineering are also discussed.     

Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications

Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior. This extracellular space offers an addition route for synthetic biologists to apply their engineering principles to program cell-responsive modules within the extracellular space using biomaterials. In this review, we discuss how taking a bottom-up approach to build genetic circuits using DNA modules can be applied to biomaterials for controlling cell behavior from the extracellular milieu. We suggest that, by collectively controlling intrinsic and extrinsic signals in synthetic biology and biomaterials, tissue engineering outcomes can be improved.     

The future of metabolic engineering and synthetic biology: towards a systematic practice

Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as 'multivariate modular metabolic engineering' (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering.     

Synthetic tissue biology: tissue engineering meets synthetic biology

We propose the term "synthetic tissue biology" to describe the use of engineered tissues to form biological systems with metazoan-like complexity. The increasing maturity of tissue engineering is beginning to render this goal attainable. As in other synthetic biology approaches, the perspective is bottom-up; here, the premise is that complex functional phenotypes (on par with those in whole metazoan organisms) can be effected by engineering biology at the tissue level. To be successful, current efforts to understand and engineer multicellular systems must continue, and new efforts to integrate different tissues into a coherent structure will need to emerge. The fruits of this research may include improved understanding of how tissue systems can be integrated, as well as useful biomedical technologies not traditionally considered in tissue engineering, such as autonomous devices, sensors, and manufacturing.     

Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology

The microbial production of biofuels is a promising avenue for the development of viable processes for the generation of fuels from sustainable resources. In order to become cost and energy effective, these processes must utilize organisms that can be optimized to efficiently produce candidate fuels from a variety of feedstocks. Escherichia coli has become a promising host organism for the microbial production of biofuels in part due to the ease at which this organism can be manipulated. Advancements in metabolic engineering and synthetic biology have led to the ability to efficiently engineer E. coli as a biocatalyst for the production of a wide variety of potential biofuels from several biomass constituents. This review focuses on recent efforts devoted to engineering E. coli for the production of biofuels, with emphasis on the key aspects of both the utilization of a variety of substrates as well as the synthesis of several promising biofuels. Strategies for the efficient utilization of carbohydrates, carbohydrate mixtures, and noncarbohydrate carbon sources will be discussed along with engineering efforts for the exploitation of both fermentative and nonfermentative pathways for the production of candidate biofuels such as alcohols and higher carbon biofuels derived from fatty acid and isoprenoid pathways. Continued advancements in metabolic engineering and synthetic biology will help improve not only the titers, yields, and productivities of biofuels discussed herein, but also increase the potential range of compounds that can be produced.     

Systems and synthetic biology approaches to cell division

Cells proliferate by division into similar daughter cells, a process that lies at the heart of cell biology. Extensive research on cell division has led to the identification of the many components and control elements of the molecular machinery underlying cellular division. Here we provide a brief review of prokaryotic and eukaryotic cell division and emphasize how new approaches such as systems and synthetic biology can provide valuable new insight.     

Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Proteomics approaches to the systems biology of cardiovascular diseases

Proteins play a central role in a systems view of biologic processes. This review provides an overview of proteomics from a systems perspective. We survey the key tools and methodologies used, present examples of how these are currently being used in the systems biology context, and discuss future directions.     

细胞焦亡法破碎微生物细胞在合成生物学与代谢工程的应用

【背景】细胞焦亡是一种细胞程序性死亡。在古菌和细菌中,gasdermin同源蛋白（GSDM）能够被特定的活化caspase （protease）酶切,从而激活类似于细胞焦亡的效应,产生细胞破碎效果。【目的】合成生物学、代谢工程和生物制造等应用过程中,细胞破碎是不可或缺的一步。利用细胞焦亡法破碎细胞取代传统的破碎方法,可以简化操作、提高生产效益。【方法】在大肠杆菌（Escherichia coli） BW25113中共表达protease和不同来源的GSDM,选择有明显细胞焦亡效应即来源Runella sp.的GSDM进行蛋白截短改造,使其在诱导表达蛋白截短体GSDMJD后能直接激活细胞焦亡效应。对GSDMJD进行过表达优化,获得可控大肠杆菌细胞焦亡菌株。进一步以重组表达蔗糖磷酸化酶为研究模型,验证本系统应用于细胞破碎释放蛋白的效果。【结果】实现了大肠杆菌中细胞焦亡的人为可控。焦亡菌株在诱导表达焦亡相关蛋白2 h后大肠杆菌细胞破碎死亡,内容物释放。将上述系统和超声法应用于制备蔗糖磷酸化酶粗酶液,细胞焦亡法制备的粗酶液的相对酶活显著高于超声法制备的粗酶液。在制备粗酶液的菌液OD₆₀₀值为2.0时,细胞焦亡法制备的粗酶液相对酶活最高并且相较于超声法制备粗酶液,提高了60%的相对酶活。【结论】细胞焦亡提供了一种更加简单快捷、绿色环保的微生物细胞破碎方式,为合成生物学与代谢工程的发展奠定了基础。