Plasticity of a key metabolic pathway in fungi

Beta oxidation is the principal metabolic pathway for fatty acid degradation. The pathway is virtually universally present throughout eukaryotes yet displays different forms in enzyme architecture, substrate specificity, and subcellular location. In this review, we examine beta oxidation across the fungal kingdom by conducting a large-scale in silico screen and localization prediction for all relevant enzymes in >50 species. The survey reveals that fungi exhibit an astounding diversity of beta oxidation pathways and shows that the combined presence of distinct mitochondrial and peroxisomal pathways is the prevailing and likely ancestral type of beta oxidation in fungi. In addition, the available information indicates that the mitochondrial pathway was lost in the common ancestor of Saccharomycetes. Finally, we infer the existence of a hybrid peroxisomal pathway in several Sordariomycetes, including Neurospora crassa. In these cases, a typically mitochondrion-located enzyme compensates for the lack of a peroxisomal one. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production

Interest in thermophilic bacteria as live-cell catalysts in biofuel and biochemical industry has surged in recent years, due to their tolerance of high temperature and wide spectrum of carbon-sources that include cellulose. However their direct employment as microbial cellular factories in the highly demanding industrial conditions has been hindered by uncompetitive biofuel productivity, relatively low tolerance to solvent and osmic stresses, and limitation in genome engineering tools. In this work we review recent advances in dissecting and engineering the metabolic and regulatory networks of thermophilic bacteria for improving the traits of key interest in biofuel industry: cellulose degradation, pentose–hexose co-utilization, and tolerance of thermal, osmotic, and solvent stresses. Moreover, new technologies enabling more efficient genetic engineering of thermophiles were discussed, such as improved electroporation, ultrasound-mediated DNA delivery, as well as thermo-stable plasmids and functional selection systems. Expanded applications of such technological advancements in thermophilic microbes promise to substantiate a synthetic biology perspective, where functional parts, module, chassis, cells and consortia were modularly designed and rationally assembled for the many missions at industry and nature that demand the extraordinary talents of these extremophiles.     

Advances in engineering algae for biofuel production

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Modular co-culture engineering,a new approach for metabolic engineering

With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed.     

Metabolic engineering of E. coli for pyocyanin production

Pyocyanin is a secondary metabolite from Pseudomonas aeruginosa that belongs to the class of phenazines, which are aromatic nitrogenous compounds with numerous biological functions. Besides its antifungal and antimicrobial activities, pyocyanin is a remarkable redox-active molecule with potential applications ranging from the pharma industry to the development of microbial fuel cells. Nevertheless, pyocyanin production has been restricted to P. aeruginosa strains, limiting its practical applicability. In this study, the pyocyanin biosynthetic pathway was engineered for the first time for high level production of this compound in a heterologous host. Escherichia coli cells harboring the nine-gene pathway divided into two plasmids were able to produce and secrete pyocyanin at higher levels than some Pseudomonas aeruginosa strains. The influence of culture and induction parameters were evaluated, and the optimized conditions led to an increase of 3.5-fold on pyocyanin accumulation. Pathway balancing was achieved by testing a set of plasmids with different copy numbers to optimize the expression levels of pyocyanin biosynthetic genes, resulting in a fourfold difference in product titer among the engineered strains. Further improvements were achieved by co-expression of Vitreoscilla hemoglobin Vhb, which relieved oxygen limitations and led to a final titer of 18.8 mg/L pyocyanin. These results show promise to use E. coli for phenazines production, and the engineered strain developed here has the potential to be used in electro-fermentation systems where pyocyanin plays a role as electron-shuttle.     

Emerging strategies of lignin engineering and degradation for cellulosic biofuel production

Ethanol and other biofuels produced from lignocellulosic biomass represent a renewable, more carbon-balanced alternative to both fossil fuels and corn-derived or sugarcane-derived ethanol. Unfortunately, the presence of lignin in plant cell walls impedes the breakdown of cell wall polysaccharides to simple sugars and the subsequent conversion of these sugars to usable fuel. Recent advances in the understanding of lignin composition, polymerization, and regulation have revealed new opportunities for the rational manipulation of lignin in future bioenergy crops, augmenting the previous successful approach of manipulating lignin monomer biosynthesis. Furthermore, recent studies on lignin degradation in nature may provide novel resources for the delignification of dedicated bioenergy crops and other sources of lignocellulosic biomass.     

Importance of systems biology in engineering microbes for biofuel production

Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.     

Selection, breeding and engineering of microalgae for bioenergy and biofuel production

Microalgal production technologies are seen as increasingly attractive for bioenergy production to improve fuel security and reduce CO(2) emissions. Photosynthetically derived fuels are a renewable, potentially carbon-neutral and scalable alternative reserve. Microalgae have particular promise because they can be produced on non-arable land and utilize saline and wastewater streams. Furthermore, emerging microalgal technologies can be used to produce a range of products such as biofuels, protein-rich animal feeds, chemical feedstocks (e.g. bioplastic precursors) and higher-value products. This review focuses on the selection, breeding and engineering of microalgae for improved biomass and biofuel conversion efficiencies.     

Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol

Biofuels provide a potential route to avoiding the global political instability and environmental issues that arise from reliance on petroleum. Currently, most biofuel is in the form of ethanol generated from starch or sugar, but this can meet only a limited fraction of global fuel requirements. Conversion of cellulosic biomass, which is both abundant and renewable, is a promising alternative. However, the cellulases and pretreatment processes involved are very expensive. Genetically engineering plants to produce cellulases and hemicellulases, and to reduce the need for pretreatment processes through lignin modification, are promising paths to solving this problem, together with other strategies, such as increasing plant polysaccharide content and overall biomass.     

Expanding the metabolic engineering toolbox with directed evolution

Cellular systems can be engineered into factories that produce high-value chemicals from renewable feedstock. Such an approach requires an expanded toolbox for metabolic engineering. Recently, protein engineering and directed evolution strategies have started to play a growing and critical role within metabolic engineering. This review focuses on the various ways in which directed evolution can be applied in conjunction with metabolic engineering to improve product yields. Specifically, we discuss the application of directed evolution on both catalytic and non-catalytic traits of enzymes, on regulatory elements, and on whole genomes in a metabolic engineering context. We demonstrate how the goals of metabolic pathway engineering can be achieved in part through evolving cellular parts as opposed to traditional approaches that rely on gene overexpression and deletion. Finally, we discuss the current limitations in screening technology that hinder the full implementation of a metabolic pathway-directed evolution approach.     

代谢工程在维生素生产中的应用及研究进展

维生素是维持人体生命活动必需的一类有机物质,机体本身一般不能合成或合成量不足,因此需经食物或其他强化产品获取。目前,维生素产品已广泛应用于医药、食品添加剂、饲料添加剂、化妆品等领域,而且全球对维生素的需求也是呈逐年增长态势。维生素的生产方法主要包括化学合成法和生物合成法。化学合成法通常安全隐患大、反应条件严苛、废物污染严重,相比之下,代谢工程生产维生素绿色环保安全、能耗低,因此建立微生物细胞工厂具有重大的科学意义和应用需求。文中回顾了近30年来代谢工程在维生素生产领域的研究进展,详细阐述了水溶性维生素(维生素B1、B2、B3、B5、B6、B7、B9、B12和维生素C的前体)和脂溶性维生素(维生素A、维生素D的前体、维生素E和维生素K)的生物合成研究现状,并对其发酵生产的瓶颈进行了探讨,最后对合成生物技术创建维生素生产菌种进行了展望。