Combining Gal4p-mediated expression enhancement and directed evolution of isoprene synthase to improve isoprene production in Saccharomyces cerevisiae.

Abstract:

:Current studies on microbial isoprene biosynthesis have mostly focused on regulation of the upstream mevalonic acid (MVA) or methyl-erythritol-4-phosphate (MEP) pathway. However, the downstream bottleneck restricting isoprene biosynthesis capacity caused by the weak expression and low activity of plant isoprene synthase (ISPS) under microbial fermentation conditions remains to be alleviated. Here, based on a previously constructed Saccharomyces cerevisiae strain with enhanced precursor supply, we strengthened the downstream pathway through increasing both the expression and activity of ISPS to further improve isoprene production. Firstly, a two-level expression enhancement system was developed for the PGAL1-controlled ISPS by overexpression of GAL 4. Meanwhile, the native GAL1/7/10 promoters were deleted to avoid competition for the transcriptional activator Gal4p, and GAL80 was disrupted to eliminate the dependency of gene expression on galactose induction. The IspS expression was obviously elevated upon enhanced Gal4p supply, and the isoprene production was improved from 6.0mg/L to 23.6mg/L in sealed-vial cultures with sucrose as carbon source. Subsequently, a novel high-throughput screening method was developed based on precursor toxicity and used for ISPS directed evolution towards enhanced catalytic activity. Combinatorial mutagenesis of the resulting ISPS mutants generated the best mutant ISPSM4, introduction of which into the GAL4-overexpressing strain YXM29 achieved 50.2mg/L of isoprene in sealed vials, and the isoprene production reached 640mg/L and 3.7g/L in aerobic batch and fed-batch fermentations, respectively. These results demonstrated the effectiveness of the proposed combinatorial engineering strategy in isoprene biosynthesis, which might also be feasible and instructive for biotechnological production of other valuable chemicals.

journal_name

Metab Eng

journal_title

Metabolic engineering

authors

Wang F,Lv X,Xie W,Zhou P,Zhu Y,Yao Z,Yang C,Yang X,Ye L,Yu H

doi

10.1016/j.ymben.2016.12.011

subject

Has Abstract

pub_date

2017-01-01 00:00:00

pages

257-266

eissn

1096-7176

issn

1096-7184

pii

S1096-7176(16)30201-4

journal_volume

39

pub_type

杂志文章
  • Engineering microbes for isoprene production.

    abstract::Isoprene is facing a growing global market due to its wide industrial applications. Current industrial production of isoprene is almost entirely petroleum-based, which is influenced by the shrinking C5 supply, while the natural emission of isoprene is predominantly contributed by plants. To bridge the need gap, a high...

    journal_title:Metabolic engineering

    pub_type: 杂志文章,评审

    doi:10.1016/j.ymben.2016.07.005

    authors: Ye L,Lv X,Yu H

    更新日期:2016-11-01 00:00:00

  • Reconstitution of EPA and DHA biosynthesis in arabidopsis: iterative metabolic engineering for the synthesis of n-3 LC-PUFAs in transgenic plants.

    abstract::An iterative approach to optimising the accumulation of non-native long chain polyunsaturated fatty acids in transgenic plants was undertaken in Arabidopsis thaliana. The contribution of a number of different transgene enzyme activities was systematically determined, as was the contribution of endogenous fatty acid me...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2013.03.001

    authors: Ruiz-Lopez N,Haslam RP,Usher SL,Napier JA,Sayanova O

    更新日期:2013-05-01 00:00:00

  • Engineering Escherichia coli to produce branched-chain fatty acids in high percentages.

    abstract::Branched-chain fatty acids (BCFAs) are key precursors of branched-chain fuels, which have cold-flow properties superior to straight chain fuels. BCFA production in Gram-negative bacterial hosts is inherently challenging because it competes directly with essential and efficient straight-chain fatty acid (SCFA) biosynth...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2016.07.003

    authors: Bentley GJ,Jiang W,Guamán LP,Xiao Y,Zhang F

    更新日期:2016-11-01 00:00:00

  • 13C metabolic flux analysis of microbial and mammalian systems is enhanced with GC-MS measurements of glycogen and RNA labeling.

    abstract::13C metabolic flux analysis (13C-MFA) is a widely used tool for quantitative analysis of microbial and mammalian metabolism. Until now, 13C-MFA was based mainly on measurements of isotopic labeling of amino acids derived from hydrolyzed biomass proteins and isotopic labeling of extracted intracellular metabolites. Her...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2016.06.007

    authors: Long CP,Au J,Gonzalez JE,Antoniewicz MR

    更新日期:2016-11-01 00:00:00

  • Chromosome engineering of the TCA cycle in Halomonas bluephagenesis for production of copolymers of 3-hydroxybutyrate and 3-hydroxyvalerate (PHBV).

    abstract::Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a promising biopolyester with good mechanical properties and biodegradability. Large-scale production of PHBV is still hindered by the high production cost. CRISPR/Cas9 method was used to engineer the TCA cycle in Halomonas bluephagenesis on its chromosome for pro...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2019.03.006

    authors: Chen Y,Chen XY,Du HT,Zhang X,Ma YM,Chen JC,Ye JW,Jiang XR,Chen GQ

    更新日期:2019-07-01 00:00:00

  • A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism.

    abstract::We present a model-based method, designated Inverse Metabolic Control Analysis (IMCA), which can be used in conjunction with classical Metabolic Control Analysis for the analysis and design of cellular metabolism. We demonstrate the capabilities of the method by first developing a comprehensively curated kinetic model...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2016.04.002

    authors: Savoglidis G,da Silveira Dos Santos AX,Riezman I,Angelino P,Riezman H,Hatzimanikatis V

    更新日期:2016-09-01 00:00:00

  • A dynamic metabolite valve for the control of central carbon metabolism.

    abstract::Successful redirection of endogenous resources into heterologous pathways is a central tenet in the creation of efficient microbial cell factories. This redirection, however, may come at a price of poor biomass accumulation, reduced cofactor regeneration and low recombinant enzyme expression. In this study, we propose...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2012.08.006

    authors: Solomon KV,Sanders TM,Prather KL

    更新日期:2012-11-01 00:00:00

  • Metabolome, transcriptome and metabolic flux analysis of arabinose fermentation by engineered Saccharomyces cerevisiae.

    abstract::One of the challenges in strain improvement by evolutionary engineering is to subsequently determine the molecular basis of the improved properties that were enriched from the natural genetic variation during the selective conditions. This study focuses on Saccharomyces cerevisiae IMS0002 which, after metabolic and ev...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2010.08.003

    authors: Wisselink HW,Cipollina C,Oud B,Crimi B,Heijnen JJ,Pronk JT,van Maris AJ

    更新日期:2010-11-01 00:00:00

  • Metabolic engineering to enhance the value of plants as green factories.

    abstract::The promise of plants to serve as the green factories of the future is ever increasing. Plants have been used traditionally for construction, energy, food and feed. Bioactive compounds primarily derived from specialized plant metabolism continue to serve as important scaffold molecules for pharmaceutical drug producti...

    journal_title:Metabolic engineering

    pub_type: 杂志文章,评审

    doi:10.1016/j.ymben.2014.11.005

    authors: Yuan L,Grotewold E

    更新日期:2015-01-01 00:00:00

  • Overexpression of a novel endogenous NADH kinase in Aspergillus nidulans enhances growth.

    abstract::The complete genome sequence of the filamentous fungi Aspergillus nidulans has paved the way for fundamental research on this industrially important species. To the best of our knowledge, this is the first time a gene encoding for ATP-dependent NADH kinase (ATP:NADH 2'-phosphotransferase, EC 2.7.1.86) has been identif...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2008.08.008

    authors: Panagiotou G,Grotkjaer T,Hofmann G,Bapat PM,Olsson L

    更新日期:2009-01-01 00:00:00

  • Metabolomics-driven approach to solving a CoA imbalance for improved 1-butanol production in Escherichia coli.

    abstract::High titer 1-butanol production in Escherichia coli has previously been achieved by overexpression of a modified clostridial 1-butanol production pathway and subsequent deletion of native fermentation pathways. This strategy couples growth with production as 1-butanol pathway offers the only available terminal electro...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2017.04.003

    authors: Ohtake T,Pontrelli S,Laviña WA,Liao JC,Putri SP,Fukusaki E

    更新日期:2017-05-01 00:00:00

  • Design and application of genetically-encoded malonyl-CoA biosensors for metabolic engineering of microbial cell factories.

    abstract::Malonyl-CoA is the basic building block for synthesizing a range of important compounds including fatty acids, phenylpropanoids, flavonoids and non-ribosomal polyketides. Centering around malonyl-CoA, we summarized here the various metabolic engineering strategies employed recently to regulate and control malonyl-CoA ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章,评审

    doi:10.1016/j.ymben.2017.10.011

    authors: Johnson AO,Gonzalez-Villanueva M,Wong L,Steinbüchel A,Tee KL,Xu P,Wong TS

    更新日期:2017-11-01 00:00:00

  • Metabolic flux rearrangement in the amino acid metabolism reduces ammonia stress in the α1-antitrypsin producing human AGE1.HN cell line.

    abstract::This study focused on metabolic changes in the neuronal human cell line AGE1.HN upon increased ammonia stress. Batch cultivations of α(1)-antitrypsin (A1AT) producing AGE1.HN cells were carried out in media with initial ammonia concentrations ranging from 0mM to 5mM. Growth, A1AT production, metabolite dynamics and fi...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2012.01.001

    authors: Priesnitz C,Niklas J,Rose T,Sandig V,Heinzle E

    更新日期:2012-03-01 00:00:00

  • Engineering Saccharomyces cerevisiae for production of simvastatin.

    abstract::Simvastatin is a semisynthetic cholesterol-lowering medication and one of the top-selling statins in the world. Currently, industrial production of simvastatin acid (SVA) is a multistep process starting from the natural product lovastatin. For this reason, there is significant interest in direct production of simvasta...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.09.005

    authors: Bond CM,Tang Y

    更新日期:2019-01-01 00:00:00

  • 13C metabolic flux analysis at a genome-scale.

    abstract::Metabolic models used in 13C metabolic flux analysis generally include a limited number of reactions primarily from central metabolism. They typically omit degradation pathways, complete cofactor balances, and atom transition contributions for reactions outside central metabolism. This study addresses the impact on pr...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.08.006

    authors: Gopalakrishnan S,Maranas CD

    更新日期:2015-11-01 00:00:00

  • Improvement of a CrtO-type of beta-carotene ketolase for canthaxanthin production in Methylomonas sp.

    abstract::Two types of non-homologous beta-carotene ketolases (CrtW and CrtO) were previously described. We report improvement of a CrtO-type of beta-carotene ketolase for canthaxanthin production in a methylotrophic bacterium, Methylomonas sp. 16a, which could use the C1 substrate (methane or methanol) as sole carbon and energ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2007.05.004

    authors: Tang XS,Shyr J,Tao L,Sedkova N,Cheng Q

    更新日期:2007-07-01 00:00:00

  • Overproduction of free fatty acids in E. coli: implications for biodiesel production.

    abstract::Whereas microbial fermentation processes for producing ethanol and related alcohol biofuels are well established, biodiesel (methyl esters of fatty acids) is exclusively derived from plant oils. Slow cycle times for engineering oilseed metabolism and the excessive accumulation of glycerol as a byproduct are two major ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2008.08.006

    authors: Lu X,Vora H,Khosla C

    更新日期:2008-11-01 00:00:00

  • Spatial organization of enzymes for metabolic engineering.

    abstract::As synthetic pathways built from exogenous enzymes become more complicated, the probability of encountering undesired interactions with host organisms increases, thereby lowering product titer. An emerging strategy to combat this problem is to spatially organize pathway enzymes into multi-protein complexes, where high...

    journal_title:Metabolic engineering

    pub_type: 杂志文章,评审

    doi:10.1016/j.ymben.2011.09.003

    authors: Lee H,DeLoache WC,Dueber JE

    更新日期:2012-05-01 00:00:00

  • An evolutionary metabolic engineering approach for enhancing lipogenesis in Yarrowia lipolytica.

    abstract::Lipogenic organisms provide an ideal platform for biodiesel and oleochemical production. Through our previous rational metabolic engineering efforts, lipogenesis titers in Yarrowia lipolytica were significantly enhanced. However, the resulting strain still suffered from decreased biomass generation rates. Here, we emp...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.02.003

    authors: Liu L,Pan A,Spofford C,Zhou N,Alper HS

    更新日期:2015-05-01 00:00:00

  • Complete genome sequence, metabolic model construction and phenotypic characterization of Geobacillus LC300, an extremely thermophilic, fast growing, xylose-utilizing bacterium.

    abstract::We have isolated a new extremely thermophilic fast-growing Geobacillus strain that can efficiently utilize xylose, glucose, mannose and galactose for cell growth. When grown aerobically at 72 °C, Geobacillus LC300 has a growth rate of 2.15 h(-1) on glucose and 1.52 h(-1) on xylose (doubling time less than 30 min). The...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.09.009

    authors: Cordova LT,Long CP,Venkataramanan KP,Antoniewicz MR

    更新日期:2015-11-01 00:00:00

  • Escherichia coli responds with a rapid and large change in growth rate upon a shift from glucose-limited to glucose-excess conditions.

    abstract::Glucose pulse experiments at seconds time scale resolution were performed in aerobic glucose-limited Escherichia coli chemostat cultures. The dynamic responses of oxygen-uptake and growth rate at seconds time scale were determined using a new method based on the dynamic liquid-phase mass balance for oxygen and the pse...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2011.03.003

    authors: Taymaz-Nikerel H,van Gulik WM,Heijnen JJ

    更新日期:2011-05-01 00:00:00

  • A phycocyanin·phellandrene synthase fusion enhances recombinant protein expression and β-phellandrene (monoterpene) hydrocarbons production in Synechocystis (cyanobacteria).

    abstract::Cyanobacteria can be exploited as photosynthetic platforms for heterologous generation of terpene hydrocarbons with industrial applications. Transformation of Synechocystis and heterologous expression of the β-phellandrene synthase (PHLS) gene alone is necessary and sufficient to confer to Synechocystis the ability to...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.09.010

    authors: Formighieri C,Melis A

    更新日期:2015-11-01 00:00:00

  • Metabolomics for high-resolution monitoring of the cellular physiological state in cell culture engineering.

    abstract::Cell culture engineering has to-date used transcriptomic, proteomic, and metabolic flux analyses, attempting to resolve significant questions regarding cell culture performance. Despite the foreseen positive impact, the metabolomic analytical platform has not yet been vastly deployed. Presently, there is no published ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2009.11.001

    authors: Chrysanthopoulos PK,Goudar CT,Klapa MI

    更新日期:2010-05-01 00:00:00

  • Human 293 cell metabolism in low glutamine-supplied culture: interpretation of metabolic changes through metabolic flux analysis.

    abstract::Metabolic flux analysis is a useful tool to analyze cell metabolism. In this study, we report the use of a metabolic model with 34 fluxes to study the 293 cell, in order to improve its growth capacity in a DMEM/F12 medium. A batch, fed-batch with glutamine feeding, fed-batch with essential amino acids, and finally a f...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1006/mben.2000.0152

    authors: Nadeau I,Sabatié J,Koehl M,Perrier M,Kamen A

    更新日期:2000-10-01 00:00:00

  • Using biopolymer bodies for encapsulation of hydrophobic products in bacterium.

    abstract::Producing some small hydrophobic molecules in microbes is challenging. Often these molecules cannot cross membranes, and thus their production may be limited by lack of storage space in the producing organism. This study reports a new technology for in vivo storage of valuable hydrophobic products in/on biopolymer bod...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2020.04.006

    authors: Liu Y,Low ZJ,Ma X,Liang H,Sinskey AJ,Stephanopoulos G,Zhou K

    更新日期:2020-09-01 00:00:00

  • Application of 2D-TOCSY NMR to the measurement of specific(13C-enrichments in complex mixtures of 13C-labeled metabolites.

    abstract::A 2D-NMR method based on zero-quantum filtered (ZQF-) TOtal Correlation SpectroscopY (TOCSY) was applied to measure 13C-enrichments in complex mixtures of 13C-labeled metabolites generated in carbon-labeling experiments. Using ZQF-TOCSY, more than 30 13C-enrichments could be potentially measured from the analysis of a...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2007.03.001

    authors: Massou S,Nicolas C,Letisse F,Portais JC

    更新日期:2007-05-01 00:00:00

  • Metabolic engineering of fatty acid biosynthesis in plants.

    abstract::Fatty acids are the most abundant form of reduced carbon chains available from nature and have diverse uses ranging from food to industrial feedstocks. Plants represent a significant renewable source of fatty acids because many species accumulate them in the form of triacylglycerol as major storage components in seeds...

    journal_title:Metabolic engineering

    pub_type: 杂志文章,评审

    doi:10.1006/mben.2001.0204

    authors: Thelen JJ,Ohlrogge JB

    更新日期:2002-01-01 00:00:00

  • Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways.

    abstract::Metabolic pathways in cells must be sufficiently robust to tolerate fluctuations in expression levels and changes in environmental conditions. Perturbations in expression levels may lead to system failure due to the disappearance of a stable steady state. Increasing evidence has suggested that biological networks have...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2014.06.006

    authors: Lee Y,Lafontaine Rivera JG,Liao JC

    更新日期:2014-09-01 00:00:00

  • Metabolic engineering of ammonium release for nitrogen-fixing multispecies microbial cell-factories.

    abstract::The biological nitrogen fixation carried out by some Bacteria and Archaea is one of the most attractive alternatives to synthetic nitrogen fertilizers. In this study we compared the effect of controlling the maximum activation state of the Azotobacter vinelandii glutamine synthase by a point mutation at the active sit...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2014.03.002

    authors: Ortiz-Marquez JC,Do Nascimento M,Curatti L

    更新日期:2014-05-01 00:00:00

  • Manipulating respiratory levels in Escherichia coli for aerobic formation of reduced chemical products.

    abstract::Optimizing the productivity of bioengineered strains requires balancing ATP generation and carbon atom conservation through fine-tuning cell respiration and metabolism. Traditional approaches manipulate cell respiration by altering air feeding, which are technically difficult especially in large bioreactors. An approa...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2011.09.006

    authors: Zhu J,Sánchez A,Bennett GN,San KY

    更新日期:2011-11-01 00:00:00