Engineering metabolism through dynamic control

Venayak, Naveen; Anesiadis, Nikolaos; Cluett, William R.; Mahadevan, Radhakrishnan

doi:10.1016/j.copbio.2014.12.022

Cited by 182 publications

(161 citation statements)

References 78 publications

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“…However, the drain of metabolites from essential pathways and/or product toxicity could inhibit cell growth, exerting a negative effect on the production of the target chemical by decreasing volumetric productivity. Therefore, a proper balance between growth rate and production flux is important to achieve both high yield and productivity (28).…”

mentioning

confidence: 99%

Improvement of Glucose Uptake Rate and Production of Target Chemicals by Overexpressing Hexose Transporters and Transcriptional Activator Gcr1 in Saccharomyces cerevisiae

Kim

Song

Hahn

2015

Appl Environ Microbiol

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Metabolic engineering to increase the glucose uptake rate might be beneficial to improve microbial production of various fuels and chemicals. In this study, we enhanced the glucose uptake rate in Saccharomyces cerevisiae by overexpressing hexose transporters (HXTs). Among the 5 tested HXTs (Hxt1, Hxt2, Hxt3, Hxt4, and Hxt7), overexpression of high-affinity transporter Hxt7 was the most effective in increasing the glucose uptake rate, followed by moderate-affinity transporters Hxt2 and Hxt4. Deletion of STD1 and MTH1, encoding corepressors of HXT genes, exerted differential effects on the glucose uptake rate, depending on the culture conditions. In addition, improved cell growth and glucose uptake rates could be achieved by overexpression of GCR1, which led to increased transcription levels of HXT1 and ribosomal protein genes. All genetic modifications enhancing the glucose uptake rate also increased the ethanol production rate in wild-type S. cerevisiae. Furthermore, the growth-promoting effect of GCR1 overexpression was successfully applied to lactic acid production in an engineered lactic acid-producing strain, resulting in a significant improvement of productivity and titers of lactic acid production under acidic fermentation conditions. Saccharomyces cerevisiae has been used as an important cell factory for production of fuels and chemicals (1, 2). Although yeast can utilize a wide range of carbon sources, glucose is the most widely preferred carbon source for yeast fermentation (3). Glucose uptake in S. cerevisiae is elaborately regulated to adapt cellular metabolism in response to ever-changing environmental conditions (3, 4). However, to achieve high titers and productivity of target chemicals using metabolically engineered yeast cells, it may be beneficial to inactivate, circumvent, or modify some of such natural regulatory mechanisms.The first regulatory step of glucose uptake is the facilitated diffusion of glucose through hexose transporters (HXTs) in the plasma membrane (4, 5). S. cerevisiae contains 18 HXT family members of hexose transporters, Hxt1 to Hxt17 and Gal2, among which Hxt1 to Hxt7 function as major glucose transporters (6). Expression of the HXTs, all of which exhibit different levels of glucose affinity, is differentially regulated depending on extracellular glucose concentrations (7-9). Hxt1 (K m ϭ ϳ100 mM) and Hxt3 (K m ϭ ϳ30 to 60 mM) are classified as low-affinity glucose transporters. HXT1 is highly induced in the presence of high (Ͼ1%) concentrations of glucose, whereas HXT3 is induced by both low and high levels of glucose. When the glucose concentrations are lowered to around 0.1%, HXT2 and HXT4, encoding moderate-affinity glucose transporters (K m ϭ ϳ5 to 10 mM), are expressed (10). HXT6 and HXT7, encoding highly homologous glucose transporters with very high glucose affinity (K m ϭ ϳ1 mM), are expressed just before the depletion of glucose in the medium (11). Expression of HXT5, encoding a moderate-affinity transporter (K m ϭ ϳ10 mM), is not regulated by extracellular glucose ...

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confidence: 99%

Improvement of Glucose Uptake Rate and Production of Target Chemicals by Overexpressing Hexose Transporters and Transcriptional Activator Gcr1 in Saccharomyces cerevisiae

Kim

Song

Hahn

2015

Appl Environ Microbiol

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“…Hence, the most advanced ideal system for metabolic engineering is via dynamic control of metabolic pathways to eliminate metabolic imbalances. 125,126 To achieve this, the commonly used systems are quorum sensing that modulates gene expression based on cell population, and genetic switches like AND gate or toggle switch that induce gene expres sion when certain inducers are present. 127 The quorum sensing system has been successfully incorporated into 1,4butanediol (BD) biosynthesis pathway in E. coli and achieved autonomous BD production.…”

Section: Strategies In Metabolic Engineering Of Glycolysismentioning

confidence: 99%

Glycolysis and Its Metabolic Engineering Applications

Wang¹,

Yan²

2017

Engineering Microbial Metabolism for Chemical Synthesis

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IntroductionMicroorganisms play a pivotal role in the degradation of complex carbon sources in nature and could survive in different conditions due to the genetically coined cellular metabolism. Cellular metabolism of microorg anisms is defined as the sum of biochemical processes that involves the conversion of environmental nutrients into simple biosynthetic building blocks and energy in the cells. Within these metabolic processes, catabo lism is responsible for breakdown of complex molecules into simple molecules, producing energy, reducing power, and precursor intermedi ates for other metabolic processes like anabolism. The central catabolic pathways include Embden-Meyerhof-Parnas (EMP) pathway, pentose phosphate (PP) pathway, Entner-Doudoroff (ED) pathway, and the tricar boxylic acid (TCA) cycle. The EMP pathway, also known as glycolysis

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“…through a protein burden effect [117]. 'Dynamic metabolic engineering' or 'dynamic control' strategies [118,119] have been proposed to control gene expression and enzyme activity dynamically such as to allow trade-offs between growth and production. Models that predict the impact of genetic modifications on growth rate were developed recently [120,121].…”

Section: Dynamic Control and Control-theoretic Analysismentioning

confidence: 99%

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

Murabito

Westerhoff

2016

J. R. Soc. Interface.

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Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

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Engineering metabolism through dynamic control

Cited by 182 publications

References 78 publications

Improvement of Glucose Uptake Rate and Production of Target Chemicals by Overexpressing Hexose Transporters and Transcriptional Activator Gcr1 in Saccharomyces cerevisiae

Improvement of Glucose Uptake Rate and Production of Target Chemicals by Overexpressing Hexose Transporters and Transcriptional Activator Gcr1 in Saccharomyces cerevisiae

Glycolysis and Its Metabolic Engineering Applications

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

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