Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene.

Abstract:

:Saccharomyces cerevisiae is an efficient host for natural-compound production and preferentially employed in academic studies and bioindustries. However, S. cerevisiae exhibits limited production capacity for lipophilic natural products, especially compounds that accumulate intracellularly, such as polyketides and carotenoids, with some engineered compounds displaying cytotoxicity. In this study, we used a nature-inspired strategy to establish an effective platform to improve lipid oil-triacylglycerol (TAG) metabolism and enable increased lycopene accumulation. Through systematic traditional engineering methods, we achieved relatively high-level production at 56.2 mg lycopene/g cell dry weight (cdw). To focus on TAG metabolism in order to increase lycopene accumulation, we overexpressed key genes associated with fatty acid synthesis and TAG production, followed by modulation of TAG fatty acyl composition by overexpressing a fatty acid desaturase (OLE1) and deletion of Seipin (FLD1), which regulates lipid-droplet size. Results showed that the engineered strain produced 70.5 mg lycopene/g cdw, a 25% increase relative to the original high-yield strain, with lycopene production reaching 2.37 g/L and 73.3 mg/g cdw in fed-batch fermentation and representing the highest lycopene yield in S. cerevisiae reported to date. These findings offer an effective strategy for extended systematic metabolic engineering through lipid engineering.

journal_name

Metab Eng

journal_title

Metabolic engineering

authors

Ma T,Shi B,Ye Z,Li X,Liu M,Chen Y,Xia J,Nielsen J,Deng Z,Liu T

doi

10.1016/j.ymben.2018.11.009

subject

Has Abstract

pub_date

2019-03-01 00:00:00

pages

134-142

eissn

1096-7176

issn

1096-7184

pii

S1096-7176(18)30288-X

journal_volume

52

pub_type

杂志文章
  • Parallel capillary electrophoresis for the quantitative screening of fermentation broths containing natural products.

    abstract::Directed molecular evolution is a recursive process of controlled genetic diversification and functional screening. The success of this approach is dependent on both the quality of the genetic diversity and the ability to accurately screen a large population of individual genetic variants for those having improved fun...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2004.09.001

    authors: Kittell J,Borup B,Voladari R,Zahn K

    更新日期:2005-01-01 00:00:00

  • In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C≥4) products.

    abstract::The modularity and versatility of an engineered functional reversal of the β-oxidation cycle make it a promising platform for the synthesis of longer-chain (C≥4) products. While the pathway has recently been exploited for the production of n-alcohols and carboxylic acids, fully capitalizing on its potential for the sy...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2014.02.011

    authors: Cintolesi A,Clomburg JM,Gonzalez R

    更新日期:2014-05-01 00:00:00

  • Dynamical analysis of gene networks requires both mRNA and protein expression information.

    abstract::One of the important goals of biology is to understand the relationship between DNA sequence information and nonlinear cellular responses. This relationship is central to the ability to effectively engineer cellular phenotypes, pathways, and characteristics. Expression arrays for monitoring total gene expression based...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1006/mben.1999.0115

    authors: Hatzimanikatis V,Lee KH

    更新日期:1999-10-01 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

  • Dynamic consolidated bioprocessing for direct production of xylonate and shikimate from xylan by Escherichia coli.

    abstract::Numerous value-added chemicals can be produced using xylan as a feedstock. However, the product yields are limited by low xylan utilization efficiency, as well as by carbon flux competition between biomass production and biosynthesis. Herein, a dynamic consolidated bioprocessing strategy was developed, which coupled x...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2020.04.001

    authors: Gao C,Guo L,Ding Q,Hu G,Ye C,Liu J,Chen X,Liu L

    更新日期:2020-07-01 00:00:00

  • Construction of lycopene-overproducing Saccharomyces cerevisiae by combining directed evolution and metabolic engineering.

    abstract::Improved supply of farnesyl diphosphate (FPP) is often considered as a typical strategy for engineering Saccharomyces cerevisiae towards efficient terpenoid production. However, in the engineered strains with enhanced precursor supply, the production of the target metabolite is often impeded by insufficient capacity o...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.04.009

    authors: Xie W,Lv X,Ye L,Zhou P,Yu H

    更新日期:2015-07-01 00:00:00

  • Identification and engineering of the cytochalasin gene cluster from Aspergillus clavatus NRRL 1.

    abstract::Cytochalasins are a group of fungal secondary metabolites with diverse structures and bioactivities, including cytochalasin E produced by Aspergillus clavatus, which is a potent anti-angiogenic agent. Here, we report the identification and characterization of the cytochalasin gene cluster from A. clavatus NRRL 1. As a...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2011.09.008

    authors: Qiao K,Chooi YH,Tang Y

    更新日期:2011-11-01 00:00:00

  • CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production.

    abstract::Cyanobacteria hold promise as a cell factory for producing biofuels and bio-derived chemicals, but genome engineering of cyanobacteria such as Synechococcus elongatus PCC 7942 poses challenges because of their oligoploidy nature and long-term instability of the introduced gene. CRISPR-Cas9 is a newly developed RNA-gui...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2016.09.006

    authors: Li H,Shen CR,Huang CH,Sung LY,Wu MY,Hu YC

    更新日期:2016-11-01 00:00:00

  • Effect of puuC overexpression and nitrate addition on glycerol metabolism and anaerobic 3-hydroxypropionic acid production in recombinant Klebsiella pneumoniae ΔglpKΔdhaT.

    abstract::3-Hydroxypropionic acid (3-HP), an industrially important platform chemical, is used as a precursor during the production of many commercially important chemicals. Recently, recombinant strains of K. pneumoniae overexpressing an NAD(+)-dependent γ-glutamyl-γ-aminobutyraldehyde dehydrogenase (PuuC) enzyme of K. pneumon...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2012.09.004

    authors: Ashok S,Mohan Raj S,Ko Y,Sankaranarayanan M,Zhou S,Kumar V,Park S

    更新日期:2013-01-01 00:00:00

  • Introduction of a bacterial acetyl-CoA synthesis pathway improves lactic acid production in Saccharomyces cerevisiae.

    abstract::Acid-tolerant Saccharomyces cerevisiae was engineered to produce lactic acid by expressing heterologous lactate dehydrogenase (LDH) genes, while attenuating several key pathway genes, including glycerol-3-phosphate dehydrogenase1 (GPD1) and cytochrome-c oxidoreductase2 (CYB2). In order to increase the yield of lactic ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.09.006

    authors: Song JY,Park JS,Kang CD,Cho HY,Yang D,Lee S,Cho KM

    更新日期:2016-05-01 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

  • Efficient reduction of the formation of by-products and improvement of production yield of 2,3-butanediol by a combined deletion of alcohol dehydrogenase, acetate kinase-phosphotransacetylase, and lactate dehydrogenase genes in metabolically engineered Kl

    abstract::Klebsiella oxytoca KMS005 (∆adhE∆ackA-pta∆ldhA) was metabolically engineered to improve 2,3-butanediol (BDO) yield. Elimination of alcohol dehydrogenase E (adhE), acetate kinase A-phosphotransacetylase (ackA-pta), and lactate dehydrogenase A (ldhA) enzymes allowed BDO production as a primary pathway for NADH re-oxidat...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.04.004

    authors: Jantama K,Polyiam P,Khunnonkwao P,Chan S,Sangproo M,Khor K,Jantama SS,Kanchanatawee S

    更新日期:2015-07-01 00:00:00

  • A flexible state-space approach for the modeling of metabolic networks II: advanced interrogation of hybridoma metabolism.

    abstract::Having previously introduced the mathematical framework of topological metabolic analysis (TMA) - a novel optimization-based technique for modeling metabolic networks of arbitrary size and complexity - we demonstrate how TMA facilitates unique methods of metabolic interrogation. With the aid of several hybridoma metab...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2010.12.003

    authors: Baughman AC,Sharfstein ST,Martin LL

    更新日期:2011-03-01 00:00:00

  • Efficient mining of natural NADH-utilizing dehydrogenases enables systematic cofactor engineering of lysine synthesis pathway of Corynebacterium glutamicum.

    abstract::Increasing the availability of NADPH is commonly used to improve lysine production by Corynebacterium glutamicum since 4 mol of NADPH are required for the synthesis of 1 mol of lysine. Alternatively, engineering of enzymes in lysine synthesis pathway to utilize NADH directly can also be explored for cofactor balance d...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.11.006

    authors: Wu W,Zhang Y,Liu D,Chen Z

    更新日期:2019-03-01 00:00:00

  • Metabolic engineering of Rhizopus oryzae: effects of overexpressing pyc and pepc genes on fumaric acid biosynthesis from glucose.

    abstract::Fumaric acid, a dicarboxylic acid used as a food acidulant and in manufacturing synthetic resins, can be produced from glucose in fermentation by Rhizopus oryzae. However, the fumaric acid yield is limited by the co-production of ethanol and other byproducts. To increase fumaric acid production, overexpressing endogen...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2012.07.001

    authors: Zhang B,Skory CD,Yang ST

    更新日期:2012-09-01 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

  • Engineering of new-to-nature halogenated indigo precursors in plants.

    abstract::Plants are versatile chemists producing a tremendous variety of specialized compounds. Here, we describe the engineering of entirely novel metabolic pathways in planta enabling generation of halogenated indigo precursors as non-natural plant products. Indican (indolyl-β-D-glucopyranoside) is a secondary metabolite cha...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.02.003

    authors: Fräbel S,Wagner B,Krischke M,Schmidts V,Thiele CM,Staniek A,Warzecha H

    更新日期:2018-03-01 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

  • Engineering of α-1,3-fucosyltransferases for production of 3-fucosyllactose in Escherichia coli.

    abstract::Fucosyllactoses (FLs), present in human breast milk, have been reported to benefit human health immensely. Especially, 3-fucosyllactose (3-FL) has numerous benefits associated with a healthy gut ecosystem. Metabolic engineering of microorganisms is thought to be currently the only option to provide an economically fea...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.05.021

    authors: Yu J,Shin J,Park M,Seydametova E,Jung SM,Seo JH,Kweon DH

    更新日期:2018-07-01 00:00:00

  • A synthetic cGMP-sensitive gene switch providing Viagra(®)-controlled gene expression in mammalian cells and mice.

    abstract::Cyclic guanosine monophosphate (cGMP) is a universal second messenger that is synthesized from guanosine triphosphate (GTP) by guanylyl cyclases (GCs) and hydrolyzed into guanosine monophosphate (GMP) by phosphodiesterases (PDEs). Small-molecule drugs that induce high cGMP levels in specialized tissues by boosting GC ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.03.016

    authors: Kim T,Folcher M,Charpin-El Hamri G,Fussenegger M

    更新日期:2015-05-01 00:00:00

  • Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2,3-butanediol production from methane.

    abstract::Methane is considered a next-generation feedstock, and methanotrophic cell-based biorefinery is attractive for production of a variety of high-value compounds from methane. In this work, we have metabolically engineered Methylomicrobium alcaliphilum 20Z for 2,3-butanediol (2,3-BDO) production from methane. The enginee...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.04.010

    authors: Nguyen AD,Hwang IY,Lee OK,Kim D,Kalyuzhnaya MG,Mariyana R,Hadiyati S,Kim MS,Lee EY

    更新日期:2018-05-01 00:00:00

  • Isobutanol and 2-ketoisovalerate production by Klebsiella pneumoniae via a native pathway.

    abstract::Isobutanol is a valuable chemical and is considered a new generation biofuel. Construction of isobutanol synthesis pathways in bacteria is a hot topic in isobutanol production. Here, we show that an isobutanol synthesis pathway exists naturally in Klebsiella pneumoniae; however, this pathway is dormant in the wild-typ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2017.07.003

    authors: Gu J,Zhou J,Zhang Z,Kim CH,Jiang B,Shi J,Hao J

    更新日期:2017-09-01 00:00:00

  • Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis.

    abstract::Understanding in vivo regulation of photoautotrophic metabolism is important for identifying strategies to improve photosynthetic efficiency or re-route carbon fluxes to desirable end products. We have developed an approach to reconstruct comprehensive flux maps of photoautotrophic metabolism by computational analysis...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2011.08.002

    authors: Young JD,Shastri AA,Stephanopoulos G,Morgan JA

    更新日期:2011-11-01 00:00:00

  • Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli.

    abstract::We report improved NADPH flux and xylitol biosynthesis in engineered E. coli. Xylitol is produced from xylose via an NADPH dependent reductase. We utilize 2-stage dynamic metabolic control to compare two approaches to optimize xylitol biosynthesis, a stoichiometric approach, wherein competitive fluxes are decreased, a...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2021.01.005

    authors: Li S,Ye Z,Moreb EA,Hennigan JN,Castellanos DB,Yang T,Lynch MD

    更新日期:2021-01-16 00:00:00

  • Effect of glucose analog supplementation on metabolic flux distribution in anaerobic chemostat cultures of Escherichia coli.

    abstract::Previous work in our laboratories investigated the use of methyl alpha-glucoside (alpha-MG), a glucose analog that shares a phosphotransferase system with glucose, to modulate glucose uptake and therefore reduce acetate accumulation. The results of that study showed a significant improvement in batch culture performan...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1006/mben.1999.0141

    authors: Berríos-Rivera SJ,Yang YT,Bennett GN,San KY

    更新日期:2000-04-01 00:00:00

  • An engineered E.coli strain for the production of glycoglycerolipids.

    abstract::The glycolipid synthase MG517 from Mycoplasma genitalium catalyzes the glucosyl transfer from UDPGlc to diacylglycerol producing glycoglycerolipids (GGL) (Andrés et al., 2011). The enzyme was functional in E. coli accumulating GGL in the plasma membrane. A metabolic engineering strategy for GGL production was evaluate...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2012.06.001

    authors: Mora-Buyé N,Faijes M,Planas A

    更新日期:2012-09-01 00:00:00

  • Down-regulation of cold-inducible RNA-binding protein does not improve hypothermic growth of Chinese hamster ovary cells producing erythropoietin.

    abstract::Discovery of the cold-inducible RNA-binding protein (CIRP) in mouse fibroblasts suggests that growth suppression at hypothermic conditions is due to an active response by the cell rather than due to passive thermal effects. To determine the effect of down-regulated CIRP expression on cell growth and erythropoietin (EP...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2006.11.003

    authors: Hong JK,Kim YG,Yoon SK,Lee GM

    更新日期:2007-03-01 00:00:00

  • The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units.

    abstract::Based on the analysis of molecular interactions of proteins with DNA binding sites, a new approach to developing mathematical models describing gene expression is introduced. Detection of hierarchical structures in metabolic networks can be used to decompose complex reaction schemes. This will be achieved by assigning...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1006/mben.2000.0175

    authors: Kremling A,Gilles ED

    更新日期:2001-04-01 00:00:00

  • Estradiol stimulates the biosynthetic pathways of breast cancer cells: detection by metabolic flux analysis.

    abstract::Selective estrogen receptor (ER) modulators are highly successful breast cancer therapies, but they are not effective in patients with ER negative and selective estrogen receptor modulator (SERM)-resistant tumors. Understanding the mechanisms of estrogen-stimulated proliferation may provide a route to design estrogen-...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2006.06.005

    authors: Forbes NS,Meadows AL,Clark DS,Blanch HW

    更新日期:2006-11-01 00:00:00

  • Biotin-independent strains of Escherichia coli for enhanced streptavidin production.

    abstract::Biotin is an archetypal vitamin used as cofactor for carboxylation reactions found in all forms of life. However, biotin biosynthesis is an elaborate multi-enzymatic process and metabolically costly. Moreover, many industrially relevant organisms are incapable of biotin synthesis resulting in the requirement to supple...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2016.12.013

    authors: Jeschek M,Bahls MO,Schneider V,Marlière P,Ward TR,Panke S

    更新日期:2017-03-01 00:00:00