Metabolic engineering--a genetic toolbox for small molecule organic synthesis

Metabolic engineering is an emerging field that exploits biosynthetic machinery as a means to genetically design small molecule production within heterologous host organisms. Molecular design and synthesis with biological tools has lagged behind total synthesis technology for about seventy-five years and owes its existence to relatively new molecular biology techniques. Here the field of metabolic engineering is explained as a comparison to total organic synthesis, including the sequence of scientific events leading up to successful implementation and future goals in the field. It is expected that metabolic engineering will take a place alongside traditional organic synthesis as a powerful means to design and create small organic molecules.     

Metabolic engineering is key to a sustainable chemical industry

The depletion of fossil fuel stocks will prohibit their use as the main feedstock of future industrial processes. Biocatalysis is being increasingly used to reduce fossil fuel reliance and to improve the sustainability, efficiency and cost of chemical production. Even with their current small market share, biocatalyzed processes already generate approximately US$50 billion and it has been estimated that they could be used to produce up to 20% of fine chemicals by 2020. Until the advent of molecular biological technologies, the compounds that were readily accessible from renewable biomass were restricted to naturally-occurring metabolites. However, metabolic engineering has considerably broadened the range of compounds now accessible, providing access to compounds that cannot be otherwise reliably sourced, as well as replacing established chemical processes. This review presents the case for continued efforts to promote the adoption of biocatalyzed processes, highlighting successful examples of industrial chemical production from biomass and/or via biocatalyzed processes. A selection of emerging technologies that may further extend the potential and sustainability of biocatalysis are also presented. As the field matures, metabolic engineering will be increasingly crucial in maintaining our quality of life into a future where our current resources and feedstocks cannot be relied upon.     

Interrogating Plant-Microbe Interactions with Chemical Tools: Click Chemistry Reagents for Metabolic Labeling and Activity-Based Probes

Continued expansion of the chemical biology toolbox presents many new and diverse opportunities to interrogate the fundamental molecular mechanisms driving complex plant–microbe interactions. This review will examine metabolic labeling with click chemistry reagents and activity-based probes for investigating the impacts of plant-associated microbes on plant growth, metabolism, and immune responses. While the majority of the studies reviewed here used chemical biology approaches to examine the effects of pathogens on plants, chemical biology will also be invaluable in future efforts to investigate mutualistic associations between beneficial microbes and their plant hosts.     

Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: A Review

Flavonoids belong to a class of plant secondary metabolites that have a polyphenol structure. Flavonoids show extensive biological activity, such as antioxidative, anti-inflammatory, anti-mutagenic, anti-cancer, and antibacterial properties, so they are widely used in the food, pharmaceutical, and nutraceutical industries. However, traditional sources of flavonoids are no longer sufficient to meet current demands. In recent years, with the clarification of the biosynthetic pathway of flavonoids and the development of synthetic biology, it has become possible to use synthetic metabolic engineering methods with microorganisms as hosts to produce flavonoids. This article mainly reviews the biosynthetic pathways of flavonoids and the development of microbial expression systems for the production of flavonoids in order to provide a useful reference for further research on synthetic metabolic engineering of flavonoids. Meanwhile, the application of co-culture systems in the biosynthesis of flavonoids is emphasized in this review.     

以亮氨酸合成为例刍议代谢中的生物化学相似性规律

生物体内纷杂多样的代谢过程存在诸多规律可循。本文以亮氨酸代谢为例提供一种教学的新模式。结合其他学科知识从基础代谢角度归纳总结生物代谢中化学原理的内在规律;同时,通过对比不同代谢路径中类似酶在进化上的相似性,发现自然界选择这种代谢方式的规律和原因。这种对比不同代谢路径异同的教学模式,可以帮助学生总结生物代谢不同路径之间的内在规律,加深对相关代谢过程的理解,同时也避免生物化学代谢过程杂乱无章、无迹可寻的错误印象,并增加学习过程的趣味性和思辨性。作为对基础生物化学和生物工程等相关课程中代谢过程教学的改革探索,希望对培养21世纪高素质人才有助。     

Synthetische Biologie

Synthetic Biology continues the work done in genetic engineering and molecular biology. It pursues an engineering approach in intervening in biological processes on various levels (genes, metabolic pathways, cells) or constructing them de novo. In biotechnology, synthetic biology aims at cost‐saving methods and very pure products. However, this new field raises questions about ethical, legal and social implications.     

Advancements in biocatalysis: From computational to metabolic engineering

Through several waves of technological research and un-matched innovation strategies, bio-catalysis has been widely used at the industrial level. Because of the value of enzymes, methods for producing value-added compounds and industrially-relevant fine chemicals through biological methods have been developed. A broad spectrum of numerous biochemical pathways is catalyzed by enzymes, including enzymes that have not been identified. However, low catalytic efficacy, low stability, inhibition by non-cognate substrates, and intolerance to the harsh reaction conditions required for some chemical processes are considered as major limitations in applied bio-catalysis. Thus, the development of green catalysts with multi-catalytic features along with higher efficacy and induced stability are important for bio-catalysis. Implementation of computational science with metabolic engineering, synthetic biology, and machine learning routes offers novel alternatives for engineering novel catalysts. Here, we describe the role of synthetic biology and metabolic engineering in catalysis. Machine learning algorithms for catalysis and the choice of an algorithm for predicting protein-ligand interactions are discussed. The importance of molecular docking in predicting binding and catalytic functions is reviewed. Finally, we describe future challenges and perspectives.     

Transition Metal‐Free Reduction of Activated Alkenes Using a Living Microorganism

Microorganisms can be programmed to perform chemical synthesis via metabolic engineering. However, despite an increasing interest in the use of de novo metabolic pathways and designer whole‐cells for small molecule synthesis, the inherent synthetic capabilities of native microorganisms remain underexplored. Herein, we report the use of unmodified E. coli BL21(DE3) cells for the reduction of keto‐acrylic compounds and apply this whole‐cell biotransformation to the synthesis of aminolevulinic acid from a lignin‐derived feedstock. The reduction reaction is rapid, chemo‐, and enantioselective, occurs under mild conditions (37 °C, aqueous media), and requires no toxic transition metals or external reductants. This study demonstrates the remarkable promiscuity of central metabolism in bacterial cells and how these processes can be leveraged for synthetic chemistry without the need for genetic manipulation.     

Designer Micelles Accelerate Flux Through Engineered Metabolism in E. coli and Support Biocompatible Chemistry

Synthetic biology has enabled the production of many value‐added chemicals via microbial fermentation. However, the problem of low product titers from recombinant pathways has limited the utility of this approach. Methods to increase metabolic flux are therefore critical to the success of metabolic engineering. Here we demonstrate that vitamin E‐derived designer micelles, originally developed for use in synthetic chemistry, are biocompatible and accelerate flux through a styrene production pathway in Escherichia coli. We show that these micelles associate non‐covalently with the bacterial outer‐membrane and that this interaction increases membrane permeability. In addition, these micelles also accommodate both heterogeneous and organic‐soluble transition metal catalysts and accelerate biocompatible cyclopropanation in vivo. Overall, this work demonstrates that these surfactants hold great promise for further application in the field of synthetic biotechnology, and for expanding the types of molecules that can be readily accessed from renewable resources via the combination of microbial fermentation and biocompatible chemistry.     

Radiometallated peptides for molecular imaging and targeted therapy

In developed countries, cancer is the second leading cause of death, being only surpassed by cardiovascular diseases. To develop tumor-targeted tools to localize and treat cancer at an early stage is a multidisciplinary area fuelled by the convergence of biology, medicine, chemistry, physics and engineering. Chemists, in particular, play a critical role in this effort, as they are continuously challenged to use innovative chemical strategies to develop 'smart drugs'. The in vitro observation that peptide receptors are overexpressed in certain tumors, as compared to endogenous expression levels, has prompted the use of such receptors as targets and the design of radiolabelled peptide-based tools for targeted nuclear molecular imaging and therapy. Such approach has gained increased interest over the last two decades, driven in particular by the success of OctreoScan(?) and by the increasing knowledge concerning overexpression of regulatory peptide receptors in tumor tissues. Selected peptides that target a variety of disease related receptors are in place and have been labeled with different radiometals, using mainly the bifunctional approach. This review begins by summarizing some relevant aspects of the coordination chemistry of the metals studied for labeling peptides. Then, we provide an overview of the chemical strategies explored to improve the biological performance of different families of radiometallated peptides for nuclear molecular imaging and/or targeted radionuclide tumor therapy.     

Total synthesis approaches to natural product derivatives based on the combination of chemical synthesis and metabolic engineering

Secondary metabolites are an extremely diverse and important group of natural products with industrial and biomedical implications. Advances in metabolic engineering of both native and heterologous secondary metabolite producing organisms have allowed the directed synthesis of desired novel products by exploiting their biosynthetic potentials. Metabolic engineering utilises knowledge of cellular metabolism to alter biosynthetic pathways. An important technique that combines chemical synthesis with metabolic engineering is mutasynthesis (mutational biosynthesis; MBS), which advanced from precursor-directed biosynthesis (PDB). Both techniques are based on the cellular uptake of modified biosynthetic intermediates and their incorporation into complex secondary metabolites. Mutasynthesis utilises genetically engineered organisms in conjunction with feeding of chemically modified intermediates. From a synthetic chemist's point of view the concept of mutasynthesis is highly attractive, as the method combines chemical expertise with Nature's synthetic machinery and thus can be exploited to rapidly create small libraries of secondary metabolites. However, in each case, the method has to be critically compared with semi- and total synthesis in terms of practicability and efficiency. Recent developments in metabolic engineering promise to further broaden the scope of outsourcing chemically demanding steps to biological systems.     

On the study of nonlinear dynamics of complex chemical reaction systems

When driven far from equilibrium,nonlinear chemical reactions often show a variety of self-organization behavior,including chemical oscillations,waves,chaos and patterns[1].Recently,the study of such nonlinear phenomena in‘complex’systems,such as the li…     

Noncovalent interactions in inorganic supramolecular chemistry based in heavy metals. Quantum chemistry point of view

Complexity is a concept that is being considered in chemistry as it has shown potential to reveal interesting phenomena. Thus, it is possible to study chemical phenomena in a new approach called systems chemistry. The systems chemistry has an organization and function, which are regulated by the interactions among its components. At the simplest level, noncovalent interactions between molecules can lead to the emergence of large structures. Consequently, it is possible to go from the molecular to the supramolecular systems chemistry, which aims to develop chemical systems highly complex through intra- and intermolecular forces. Proper use of the interactions previously mentioned allow a glimpse of supramolecular system chemistry in many tasks such as structural properties reflecting certain behaviors in the chemistry of materials, for example, electrical and optical, processes of molecular recognition and among others. In the last time, within this area, inorganic supramolecular systems chemistry has been developed. Those systems have a structural orientation which is defined by certain forces that predominate in the associations among molecules. It is possible to recognize these forces as hydrogen bonding, π-π stacking, halogen bonding, electrostatic, hydrophobic, charge transfer, metal coordination, and metallophilic interactions. The presence of these forces in supramolecular system yields certain properties such as light absorption and luminescence. The quantum theoretical modeling plays an important role in the designing of the supramolecular system. The goal is to apply supramolecular principles in order to understand the associated forces in many inorganic molecules that include heavy metals for instance gold, platinum, and mercury. Relevant systems will be studied in detail, considering functional aspects such as enhanced coordination of functionalized molecular self-assembly, electronic and optoelectronic properties.     

Selective Host Molecules Obtained by Dynamic Adaptive Chemistry

Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis–optimization process. The second was the use of a “brutal force” approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, “rational design” often resulted in time‐consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. “Combinatorial chemistry” suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry.     

Interfacing Microbial Styrene Production with a Biocompatible Cyclopropanation Reaction

The introduction of new reactivity into living organisms is a major challenge in synthetic biology. Despite an increasing interest in both the development of small‐molecule catalysts that are compatible with aqueous media and the engineering of enzymes to perform new chemistry in vitro, the integration of non‐native reactivity into metabolic pathways for small‐molecule production has been underexplored. Herein we report a biocompatible iron(III) phthalocyanine catalyst capable of efficient olefin cyclopropanation in the presence of a living microorganism. By interfacing this catalyst with E. coli engineered to produce styrene, we synthesized non‐natural phenyl cyclopropanes directly from D ‐glucose in single‐vessel fermentations. This process is the first example of the combination of nonbiological carbene‐transfer reactivity with cellular metabolism for small‐molecule production.     

分子动力学模拟在聚合物热解中的应用

分子动力学模拟作为分子模拟的重要分支已经在化学、化工、材料、生物等领域受到了广泛的关注。介绍了分子动力学模拟的基本原理,阐述了分子动力学模拟在高分子聚合物热解反应机理研究中的应用。实例表明:在研究物质化学反应机理方面,分子动力学模拟是一种有效的研究手段。     

Perspectives for Biotechnological Production and Utilization of Biopolymers: Metabolic Engineering of Polyhydroxyalkanoate Biosynthesis Pathways as a Successful Example

This article provides an overview of biopolymers, classed according to their chemical structures, function and occurrence, the principles of biosynthesis and metabolism in organisms. It will then focus on polyhydroxyalkanoates (PHA) for which technical applications in several areas are currently considered. PHAs represent a complex class of bacterial polyesters consisting of various hydroxyalkanoic acids that are synthesized by bacteria as storage compounds for energy and carbon if a carbon source is present in excess. Poly(3‐hydroxybutyrate), poly(3HB), is just one example. Most other PHAs are only synthesized if pathways exist which mediate between central intermediates of the metabolism or special precursor substrates on one side and coenzyme A thioesters of hydroxyalkanoic acids, which are the substrates of the PHA synthase catalyzing the polymerization, on the other side. During the last decade, basic and applied research have revealed much knowledge about the biochemical and molecular basis of the enzymatic processes for the synthesis of PHAs in microorganisms. The combination of detailed physiological studies, utilization of the overwhelming information provided by the numerous genome sequencing projects, application of recombinant DNA technology, engineering of metabolic pathways or enzymes and molecular breeding techniques applied to plants have provided new perspectives to produce these technically interesting biopolymers by novel or significantly improved biotechnological processes or by agriculture. Some examples for successful in vivo and in vitro engineering of pathways suitable for the synthesis and biotechnological production of PHAs consisting of medium‐chain‐length 3‐hydroxyalkanoic acids and short‐chain‐length hydroxyalkanoic acids will be provided.     

Computer-Assisted Molecular Design (CAMD)—An Overview

A new instrument, long established as CAD in engineering, is beginning to make its presence felt in chemical research laboratories: Computer-Assisted Molecular Design (CAMD). The combined use of computer graphics and theoretical chemistry is opening up new perspectives in molecular research. Structures and properties of molecules such as spacefilling, charge distribution, or dynamic behavior can be determined and used for comparison. For research on complex systems like biomolecules (protein engineering), this new approach turns out to be indispensable.     

化学生物学在生物芯片技术中的角色

化学生物学是一个新兴的化学与生物学的交叉学科.它的基本任务是揭示生命运动的化学本质,发展生命调控的化学方法,提供生命研究的化学技术.本文以化学生物学在生物芯片技术发展中扮演的角色为例讨论当前化学生物学发展的特点.     

From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry

Supramolecular chemistry has developed over the last forty years as chemistry beyond the molecule. Starting with the investigation of the basis of molecular recognition, it has explored the implementation of molecular information in the programming of chemical systems towards self-organisation processes, that may occur either on the basis of design or with selection of their components. Supramolecular entities are by nature constitutionally dynamic by virtue of the lability of non-covalent interactions. Importing such features into molecular chemistry, through the introduction of reversible bonds into molecules, leads to the emergence of a constitutional dynamic chemistry, covering both the molecular and supramolecular levels. It considers chemical objects and systems capable of responding to external solicitations by modification of their constitution through component exchange or reorganisation. It thus opens the way towards an adaptive and evolutive chemistry, a further step towards the chemistry of complex matter.