Synthetic Biology Toolkits for Metabolic Engineering of Cyanobacteria

Cyanobacteria are of great importance to Earth's ecology. Due to their capability in photosynthesis and C1 metabolism, they are ideal microbial chassis that can be engineered for direct conversion of carbon dioxide and solar energy into biofuels and biochemicals. Facilitated by the elucidation of the basic biology of the photoautotrophic microbes and rapid advances in synthetic biology, genetic toolkits have been developed to enable implementation of nonnatural functionalities in engineered cyanobacteria. Hence, cyanobacteria are fast becoming an emerging platform in synthetic biology and metabolic engineering. Herein, the progress made in the synthetic biology toolkits for cyanobacteria and their utilization for transforming cyanobacteria into microbial cell factories for sustainable production of biofuels and biochemicals is outlined. Current techniques in heterologous gene expression, strategies in genome editing, and development of programmable regulatory parts and modules for engineering cyanobacteria towards biochemical production are discussed and prospected. As cyanobacteria synthetic biology is still in its infancy, apart from the achievements made, the difficulties and challenges in applying and developing genetic toolkits in cyanobacteria for biochemical production are also evaluated.     

Current methods for the maturation of induced pluripotent stem cellderived cardiomyocytes

Induced pluripotent stem cells(iPSCs) were first generated by Yamanaka and colleagues over a decade ago. Since then, iPSCs have been successfully differentiated into many distinct cell types, enabling tissue-, disease-, and patientspecific in vitro modelling. Cardiovascular disease is the greatest cause of mortality worldwide but encompasses rarer disorders of conduction and myocardial function for which a cellular model of study is ideal. Although methods to differentiate iPSCs into beating cardiomyocytes(iPSC-CMs) have recently been adequately optimized and commercialized, the resulting cells remain largely immature with regards to their structure and function,demonstrating fetal gene expression, disorganized morphology, reliance on predominantly glycolytic metabolism and contractile characteristics that differ from those of adult cardiomyocytes. As such, disease modelling using iPSC-CMs may be inaccurate and of limited utility. However, this limitation is widely recognized, and numerous groups have made substantial progress in addressing this problem. This review highlights successful methods that have been developed for the maturation of human iPSC-CMs using small molecules,environmental manipulation and 3-dimensional(3 D) growth approaches.     

Biosynthesis of the anti‐diabetic metabolite montbretin A: glucosylation of the central intermediate mini‐MbA

Type 2 diabetes (T2D) affects over 320 million people worldwide. Healthy lifestyles, improved drugs and effective nutraceuticals are different components of a response against the growing T2D epidemic. The specialized metabolite montbretin A (MbA) is being developed for treatment of T2D and obesity due to its unique pharmacological activity as a highly effective and selective inhibitor of the human pancreatic α‐amylase. MbA is an acylated flavonol glycoside found in small amounts in montbretia (Crocosmia × crocosmiiflora) corms. MbA cannot be obtained in sufficient quantities for drug development from its natural source or by chemical synthesis. To overcome these limitations through metabolic engineering, we are investigating the genes and enzymes of MbA biosynthesis. We previously reported the first three steps of MbA biosynthesis from myricetin to myricetin 3‐O‐(6′‐O‐caffeoyl)‐glucosyl rhamnoside (mini‐MbA). Here, we describe the sequence of reactions from mini‐MbA to MbA, and the discovery and characterization of the gene and enzyme responsible for the glucosylation of mini‐MbA. The UDP‐dependent glucosyltransferase CcUGT3 (UGT703E1) catalyzes the 1,2‐glucosylation of mini‐MbA to produce myricetin 3‐O‐(glucosyl‐6′‐O‐caffeoyl)‐glucosyl rhamnoside. Co‐expression of CcUGT3 with genes for myricetin and mini‐MbA biosynthesis in Nicotiana benthamiana validated its biological function and expanded the set of genes available for metabolic engineering of MbA.     

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Bacteria that engage in long‐standing associations with particular hosts are expected to evolve host‐specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep‐branching host‐specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate‐related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate‐related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization.     

体外多酶分子机器的现状和最新进展

体外多酶分子机器遵循所设计的多酶催化路径,将若干种纯化或部分纯化的酶元件进行合理的优化与适配,高效地在体外将特定的底物转化为目标化合物。体外多酶分子机器反应系统呈现元件化和模块化的特点,在设计、组装和调控方面具有较高的自由度。近年来,体外多酶分子机器在实现反应过程的精准调控和提高产品得率方面的优势逐渐体现,展示了其在生物制造领域重要的应用潜力。对体外多酶分子机器的相关研究已成为合成生物学的一个重要分支领域,日益受到广泛的关注。文中系统地综述了基于酶元件/模块的体外多酶分子机器的构建策略,以及改善该分子机器中酶元件/模块之间适配性的研究进展,并分析了该生物制造平台的发展前景与挑战。     

面向工业生物技术的系统生物学

工业生物技术是以微生物细胞工厂利用可再生的生物原料来生产能源、材料与化学品等的生物技术,在解决资源、能源与环境等问题方面起着越来越重要的作用。系统生物学是全面解析微生物细胞工厂及其发酵过程从"黑箱"到"白箱"的重要研究方法。系统生物学借助基因组、转录组、蛋白质组、代谢组以及代谢流组等多组学数据,可解析微生物细胞工厂在RNA、蛋白与代谢物等不同水平上的变化规律与调控机制。目前,系统生物学在微生物细胞工厂的设计创建与发酵工艺优化中起着越来越重要的指导作用,许多成功应用实例不断涌现,推动着工业生物技术的快速发展。文中重点综述基因组、转录组、蛋白质组、代谢组与代谢流组以及基因组规模的网络模型等各组学技术的最新发展及其在工业生物技术尤其是菌株改造与发酵优化中的应用,并就工业生物技术中系统生物学的未来发展方向进行展望。     

粘合材料及其在生物医学中的应用：进展与展望

粘合材料作为一种重要的辅助材料,在工业包装、海洋工程以及生物医药等多个领域都有广泛的应用需求。天然存在的粘合剂如贻贝足丝粘合蛋白等具有良好的生物相容性和生物可降解性,但因其来源受限及在生理环境下较弱的粘合性能,因此在生物医药领域的应用受到了限制。从自然生物的粘合现象中汲取灵感,各种利用化学或生物合成方法制备的仿生粘合材料应运而生,针对生物医药领域的特定需求,一些新兴粘合材料在生物相容性、生物可降解性以及组织粘附等方面都表现出在医药领域应用的潜力。展望未来,受自然粘合材料兼具环境响应、自我再生和自修复等特征的启迪,各种生物灵感和生物仿生粘合材料的开发势必是未来的发展热点,而合成生物学技术为创建具有上述特征的活体粘合材料提供了新的可能。     

合成支架在代谢工程中的研究进展

代谢工程作为通过引入外源合成途径或改造优化代谢网络,进行高附加值的天然代谢产物生物合成的技术,已经得到广泛应用。但随着目标合成产物的结构日渐复杂,构建多基因的从头合成途径造成宿主生物代谢失衡与中间产物对宿主细胞产生毒害作用等一系列问题发生的可能性也随之增加。为解决这些问题合成支架策略应运而生,合成支架将途径酶共定位以提高局部酶和代谢物的浓度,来增强代谢通量并限制中间产物与宿主细胞环境间的相互作用,成为生物催化和合成生物学研究的热点之一。尽管由核酸、蛋白质构成的合成支架策略已经应用于多种代谢物的异源合成,并取得了不同程度的成功,但合成支架的精确组装仍然是一项艰巨的任务。文中详细介绍了合成支架技术的研究现状,详细阐述了合成支架技术的原理和实例,并初步探讨了其应用前景。     

CRISPR/Cas9在放线菌合成生物学研究中的应用和发展

放线菌是活性天然产物和抗生素药物的重要来源。利用合成生物学高效地开发其中丰富的天然产物资源,将为加速新药开发奠定坚实的基础。CRISPR/Cas9作为一种多功能基因编辑系统,因其便捷高效而被广泛应用于真核生物的遗传操作。但在原核生物尤其是放线菌中的应用仍处于起步阶段,机遇和挑战并存。本综述总结了目前CRISPR/Cas9系统在放线菌基因编辑和调控,以及活性天然产物的产量提升、生物合成机制解析和资源开发等方面的研究进展。同时,也对该系统在应用中面临的包括重组修复效率低,以及靶向切割效率不足等关键挑战进行了分析,并提出了相应的优化解决方法。随着CRISPR/Cas9在放线菌应用中的不断完善和发展,将极大地推动放线菌的合成生物学研究,促进其中天然产物资源的有效挖掘和应用开发。     

Randomness in microtubule dynamics: an error that requires correction or an inherent plasticity required for normal cellular function?

Microtubules (MTs) play roles in regulating the mechanical structure and dynamics of cells. While MTs appear to be highly ordered structures, recent data suggest some randomness in their structure and dynamics. Part of this inherent randomness is attributed to errors and correction mechanisms are being investigated to overcome these ‘mistakes.’ However, this randomness may also be part of the normal intracellular function of MTs. It is possible that random events in MT structure and dynamics may contribute to their normal function and may even be part of an improved efficacy mechanism. An alternative view, wherein MT and kinetochore errors are part of required cell plasticity, is also discussed. These data may further support the concept of randomness in biological pathways as part of self‐organization or accurate and enhanced function.