Advancing metabolic engineering through systems biology of industrial microorganisms

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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.     

Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

Industrial biotechnology is a rapidly growing field. With the increasing shift towards a bio-based economy, there is rising demand for developing efficient cell factories that can produce fuels, chemicals, pharmaceuticals, materials, nutraceuticals, and even food ingredients. The yeast Saccharomyces cerevisiae is extremely well suited for this objective. As one of the most intensely studied eukaryotic model organisms, a rich density of knowledge detailing its genetics, biochemistry, physiology, and large-scale fermentation performance can be capitalized upon to enable a substantial increase in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given.     

Expanding chemical biology of 2-oxoglutarate oxygenases

Beyond established roles in collagen biosynthesis, hypoxic signaling and fatty acid metabolism, recent reports have now revealed roles for human 2-oxoglutarate-dependent oxygenases in histone and nucleic acid demethylation and in signaling protein hydroxylation. The emerging role of these oxygenases in enabling a multiplicity of histone modifications has some analogy with their role in enabling structural diversity in secondary metabolism.     

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.     

Predicting drug side-effects by chemical systems biology

The publication of the highest-quality and best-annotated personal genome yet tells us much about sequencing technology, something about genetic ancestry, but still little of medical relevance.     

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。     

Synthetic biology and the development of tools for metabolic engineering

Synthetic biology can significantly advance metabolic engineering by contributing tools (minimal hosts, vectors, genetic controllers, characterized enzymes). The development of these tools significantly reduced the costs and time to develop the antimalarial drug artemisinin, but the availability of more tools could have reduced these costs substantially.     

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.     

Expanding the concepts and tools of metabolic engineering to elucidate cancer metabolism

The metabolic engineer's toolbox, comprising stable isotope tracers, flux estimation and analysis, pathway identification, and pathway kinetics and regulation, among other techniques, has long been used to elucidate and quantify pathways primarily in the context of engineering microbes for producing small molecules of interest. Recently, these tools are increasingly finding use in cancer biology due to their unparalleled capacity for quantifying intracellular metabolism of mammalian cells. Here, we review basic concepts that are used to derive useful insights about the metabolism of tumor cells, along with a number of illustrative examples highlighting the fundamental contributions of these methods to elucidating cancer cell metabolism. This area presents unique opportunities for metabolic engineering to expand its portfolio of applications into the realm of cancer biology and help develop new cancer therapies based on a new class of metabolically derived targets. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression

Despite substantial progress in synthetic biology, we still lack the ability to engineer anything as complex as Nature has. One of the many reasons is that we lack the requisite tools for independently controlling the expression of multiple genes in parallel. While our toolbox is still spare, the situation is rapidly changing. This opinion discusses some recent approaches and open challenges in designing orthogonal regulators of gene expression in bacteria.     

Complex systems in metabolic engineering

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