Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation

Glycogen and starch are the major readily accessible energy storage compounds in nearly all living organisms. Glycogen is a very large branched glucose homopolymer containing about 90% alpha-1,4-glucosidic linkages and 10% alpha-1,6 linkages. Its synthesis and degradation constitute central pathways in the metabolism of living cells regulating a global carbon/energy buffer compartment. Glycogen biosynthesis involves the action of several enzymes among which glycogen synthase catalyzes the synthesis of the alpha-1,4-glucose backbone. We now report the first crystal structure of glycogen synthase in the presence and absence of adenosine diphosphate. The overall fold and the active site architecture of the protein are remarkably similar to those of glycogen phosphorylase, indicating a common catalytic mechanism and comparable substrate-binding properties. In contrast to glycogen phosphorylase, glycogen synthase has a much wider catalytic cleft, which is predicted to undergo an important interdomain 'closure' movement during the catalytic cycle. The structures also provide useful hints to shed light on the allosteric regulation mechanisms of yeast/mammalian glycogen synthases.     

Constraints-based genome-scale metabolic simulation for systems metabolic engineering

Random mutagenesis and selection approaches used traditionally for the development of industrial strains have largely been complemented by metabolic engineering, which allows purposeful modification of metabolic and cellular characteristics by using recombinant DNA and other molecular biological techniques. As systems biology advances as a new paradigm of research thanks to the development of genome-scale computational tools and high-throughput experimental technologies including omics, systems metabolic engineering allowing modification of metabolic, regulatory and signaling networks of the cell at the systems-level is becoming possible. In silico genome-scale metabolic model and its simulation play increasingly important role in providing systematic strategies for metabolic engineering. The in silico genome-scale metabolic model is developed using genomic annotation, metabolic reactions, literature information, and experimental data. The advent of in silico genome-scale metabolic model brought about the development of various algorithms to simulate the metabolic status of the cell as a whole. In this paper, we review the algorithms developed for the system-wide simulation and perturbation of cellular metabolism, discuss the characteristics of these algorithms, and suggest future research direction.     

Complex systems in metabolic engineering

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微生物合成鸟氨酸的代谢工程研究进展

鸟氨酸是一种非蛋白氨基酸,对氨态氮的排出及解除氨中毒有重要的作用,可用于功能性饮料、减肥保健产品及护肝抗癌药品等,在医疗、保健、食品等领域具有广泛的应用前景。本文系统地总结目前微生物合成鸟氨酸的研究现状,介绍鸟氨酸的分解代谢和合成代谢途径,及其所涉及的关键酶,详细阐述利用代谢工程改造鸟氨酸生产菌的思路,及其所涉及的代谢工程技术和最新研究进展,展望微生物合成鸟氨酸的代谢工程未来发展方向。     

Regulated multicistronic expression technology for mammalian metabolic engineering

Contemporary basic research is rapidly revealing increasingly complex molecular regulatory networks which are often interconnected via key signal integrators. These connections among regulatory and catalytic networks often frustrate bioengineers as promising metabolic engineering strategies are bypassed by compensatory metabolic responses or cause unexpected, undesired outcomes such as apoptosis, product protein degradation or inappropriate post- translational modification. Therefore, for metabolic engineering to achieve greater success in mammalian cell culture processes and to become important for future applications such as gene therapy and tissue engineering, this technology must be enhanced to allow simultaneous, in cases conditional, reshaping of metabolic pathways to access difficult-to-attain cell states. Recent advances in this new territory of multigene metabolic engineering are intimately linked to the development of multicistronic expression technology which allows the simultaneous, and in some cases, regulated expression of several genes in mammalian cells. Here we review recent achievements in multicistronic expression technology in view of multigene metabolic engineering. This revised version was published online in August 2006 with corrections to the Cover Date.     

Bioremediation through microbes: systems biology and metabolic engineering approach

Today, environmental pollution is a serious problem, and bioremediation can play an important role in cleaning contaminated sites. Remediation strategies, such as chemical and physical approaches, are not enough to mitigate pollution problems because of the continuous generation of novel recalcitrant pollutants due to anthropogenic activities. Bioremediation using microbes is an eco-friendly and socially acceptable alternative to conventional remediation approaches. Many microbes with a bioremediation potential have been isolated and characterized but, in many cases, cannot completely degrade the targeted pollutant or are ineffective in situations with mixed wastes. This review envisages advances in systems biology (SB), which enables the analysis of microbial behavior at a community level under different environmental stresses. By applying a SB approach, crucial preliminary information can be obtained for metabolic engineering (ME) of microbes for their enhanced bioremediation capabilities. This review also highlights the integrated SB and ME tools and techniques for bioremediation purposes.     

New pathways and metabolic engineering strategies for microbial synthesis of diols

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A method for continuous monitoring of phosphorylase b activity during glycogen degradation and synthesis

Phosphorylase b (1,4-α-glucaniorthophosphate glucosyltransferase, EC. 2.4.1.1) catalyzes the glycogen synthesis and degradation reaction. It is the latter which is the physiological function of the enzyme. Its action may be described by a random order bi-bi kinetic mechanism. The rate-limiting step is an interconversion between ternary complexes (1).Activity determination can be carried out in the direction of glycogen synthesis by measuring the amount of inorganic phosphate (P_j) released during the reaction (2). This method requires termination of the enzyme action after an appropriate time interval and only yields information about the total amount of the product without giving details of the time course of the process. In the reverse direction, the glycogen degradation can be followed in a more complicated and indirect way by coupled reactions of additional enzymes (3).The present communication describes a convenient method for continuous monitoring of the reaction in both directions with a fluorescence spectrometer.     

Heterologous expression and metabolic engineering tools for improving terpenoids production

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Towards systems metabolic engineering of microorganisms for amino acid production

Microorganisms capable of efficient production of amino acids have traditionally been developed by random mutation and selection method, which might cause unwanted physiological changes in cellular metabolism. Rational genome-wide metabolic engineering based on systems and synthetic biology tools, which is termed 'systems metabolic engineering', is rising as an alternative to overcome these problems. Recently, several amino acid producers have been successfully developed by systems metabolic engineering, where the metabolic engineering procedures were performed within a systems biology framework, and entire metabolic networks, including complex regulatory circuits, were engineered in an integrated manner. Here we review the current status of systems metabolic engineering successfully applied for developing amino acid producing strains and discuss future prospects.     

Machine learning applications in systems metabolic engineering

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Towards systems metabolic engineering in Pichia pastoris

The methylotrophic yeast Pichia pastoris is firmly established as a host for the production of recombinant proteins, frequently outperforming other heterologous hosts. Already, a sizeable amount of systems biology knowledge has been acquired for this non-conventional yeast. By applying various omics-technologies, productivity features have been thoroughly analyzed and optimized via genetic engineering. However, challenging clonal variability, limited vector repertoire and insufficient genome annotation have hampered further developments. Yet, in the last few years a reinvigorated effort to establish P. pastoris as a host for both protein and metabolite production is visible. A variety of compounds from terpenoids to polyketides have been synthesized, often exceeding the productivity of other microbial systems. The clonal variability was systematically investigated and strategies formulated to circumvent untargeted events, thereby streamlining the screening procedure. Promoters with novel regulatory properties were discovered or engineered from existing ones. The genetic tractability was increased via the transfer of popular manipulation and assembly techniques, as well as the creation of new ones. A second generation of sequencing projects culminated in the creation of the second best functionally annotated yeast genome. In combination with landmark physiological insights and increased output of omics-data, a good basis for the creation of refined genome-scale metabolic models was created. The first application of model-based metabolic engineering in P. pastoris showcased the potential of this approach. Recent efforts to establish yeast peroxisomes for compartmentalized metabolite synthesis appear to fit ideally with the well-studied high capacity peroxisomal machinery of P. pastoris. Here, these recent developments are collected and reviewed with the aim of supporting the establishment of systems metabolic engineering in P. pastoris.     

Partly ordered synthesis and degradation of glycogen in cultured rat myotubes.

The following questions concerning glycogen synthesis and degradation were examined in cultured rat myotubes. 1) Is synthesis and degradation of the individual glycogen molecule a strictly ordered process, with the last glucosyl unit incorporated into the molecule being the first to be released (the last-in-first-out principle), or is it a random process? 2) Are all glycogen molecules in skeletal muscle synthesized and degraded in phase (simultaneous order) or out of phase (sequential order)? Basal glycogen stores were minimized by fasting and were subsequently replenished in two intervals, the first (0-0.5 h) with tritium-labeled and the second (0.5-3 h) with carbon-labeled glucose as precursor. Glycogen degradation was initiated by addition of forskolin. The kinetics of glycogen accumulation as well as degradation could be approximated by monoexponential equations with rate constants of 0.81 and 1.39 h(-1), respectively. The degradation of glycogen largely followed the last-in-first-out principle, particularly in the initial period. Analysis of the size of the glycogen molecules and the beta-dextrin limit during glycogen accumulation and degradation showed that both synthesis and degradation of glycogen molecules are largely sequential and the small deviation from this order is most pronounced at the beginning of the accumulation and at the end of the degradation period. This pattern may reflect the number of synthase and phosphorylase molecules and fits well with the role of glycogen in skeletal muscle as a readily available energy store and with the known structure of the glycogen molecule. It is emphasized that the observed nonlinear relation between the change in glycogen concentration and release of label during glycogen degradation may have important practical consequences for interpretation of experimental data.     

Protein engineering for metabolic engineering: Current and next-generation tools

Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. We review advances in selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use; produce non-natural amino acids, alcohols, and carboxylic acids; and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes.     

Potential of metabolic engineering in bacterial nanosilver synthesis

The widespread applications of silver nanoparticles in present days demand an industrial-scale production process. The ability of bacteria to synthesise silver nanoparticles can be exploited to overcome many shortcomings associated with conventional production processes, such as high cost and nanoparticle toxicity. However, lack of a standardised protocol and suboptimal yield remain a major obstacle for bacterial synthesis route. A potential, yet unexplored, solution to this problem could be envisioned through rewiring of the metabolic network to direct cellular resources towards the product of interest. Mathematical modelling of metabolic pathway is the key to understand and manipulate the cellular metabolism for enhanced production of desired metabolite(s). The present study provides a perspective on the scope of metabolic engineering approaches to enhance bacterial synthesis of silver nanoparticles.     

Manipulating gene expression for the metabolic engineering of plants.

Introducing and expressing foreign genes in plants present many technical challenges that are not encountered with microbial systems. This review addresses the variety of issues that must be considered and the variety of options that are available, in terms of choosing transformation systems and designing recombinant transgenes to ensure appropriate expression in plant cells. Tissue specificity and proper developmental regulation, as well as proper subcellular localization of products, must be dealt with for successful metabolic engineering in plants..