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 approach based on genetic regulation may better serve this purpose. With excess oxygen supply to the culture, we efficiently manipulated Escherichia coli cell respiration by adding different amount of coenzyme Q1 to strains lacking the ubiCA genes, which encode two critical enzymes for ubiquinone synthesis. As a proof-of-concept, the metabolic effect of the ubiCA gene knockout and coenzyme Q1 supplementation were characterized, and the metabolic profiles of the experimental strains showed clear correlations with coenzyme Q1 concentrations. Further proof-of-principle experiments were performed to illustrate that the approach can be used to optimize cell respiration for the production of chemicals of interest such as ethanol. This study showed that controlled respiration through genetic manipulation can be exploited to allow much larger operating windows for reduced product formation even under fully aerobic conditions.

journal_name

Metab Eng

journal_title

Metabolic engineering

authors

Zhu J,Sánchez A,Bennett GN,San KY

doi

10.1016/j.ymben.2011.09.006

subject

Has Abstract

pub_date

2011-11-01 00:00:00

pages

704-12

issue

6

eissn

1096-7176

issn

1096-7184

pii

S1096-7176(11)00096-6

journal_volume

13

pub_type

杂志文章
  • High-level production of valine by expression of the feedback inhibition-insensitive acetohydroxyacid synthase in Saccharomyces cerevisiae.

    abstract::Valine, which is one of the branched-chain amino acids (BCAAs) essential for humans, is widely used in animal feed, dietary supplements and pharmaceuticals. At the commercial level, valine is usually produced by bacterial fermentation from glucose. However, valine biosynthesis can also proceed in the yeast Saccharomyc...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.02.011

    authors: Takpho N,Watanabe D,Takagi H

    更新日期:2018-03-01 00:00:00

  • Metabolic engineering of Escherichia coli for production of L-aspartate and its derivative β-alanine with high stoichiometric yield.

    abstract::L-aspartate is an important 4-carbon platform compound that can be used as the precursor of numerous chemical products. The bioproduction of L-aspartate directly from biomass resources is expected to provide a more cost-competitive technique route. Yet little metabolic engineering work on this matter has been carried ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2019.04.012

    authors: Piao X,Wang L,Lin B,Chen H,Liu W,Tao Y

    更新日期:2019-07-01 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

  • 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

  • Elucidation and in planta reconstitution of the parthenolide biosynthetic pathway.

    abstract::Parthenolide, the main bioactive compound of the medicinal plant feverfew (Tanacetum parthenium), is a promising anti-cancer drug. However, the biosynthetic pathway of parthenolide has not been elucidated yet. Here we report on the isolation and characterization of all the genes from feverfew that are required for the...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2014.03.005

    authors: Liu Q,Manzano D,Tanić N,Pesic M,Bankovic J,Pateraki I,Ricard L,Ferrer A,de Vos R,van de Krol S,Bouwmeester H

    更新日期:2014-05-01 00:00:00

  • Metabolic fluxes and metabolic engineering.

    abstract::Metabolic engineering is the directed improvement of cellular properties through the modification of specific biochemical reactions or the introduction of new ones, with the use of recombinant DNA technology. As such, metabolic engineering emphasizes metabolic pathway integration and relies on metabolic fluxes as dete...

    journal_title:Metabolic engineering

    pub_type: 杂志文章,评审

    doi:10.1006/mben.1998.0101

    authors: Stephanopoulos G

    更新日期:1999-01-01 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

  • Step changes in leaf oil accumulation via iterative metabolic engineering.

    abstract::Synthesis and accumulation of plant oils in the entire vegetative biomass offers the potential to deliver yields surpassing those of oilseed crops. However, current levels still fall well short of those typically found in oilseeds. Here we show how transcriptome and biochemical analyses pointed to a futile cycle in a ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2016.12.007

    authors: Vanhercke T,Divi UK,El Tahchy A,Liu Q,Mitchell M,Taylor MC,Eastmond PJ,Bryant F,Mechanicos A,Blundell C,Zhi Y,Belide S,Shrestha P,Zhou XR,Ral JP,White RG,Green A,Singh SP,Petrie JR

    更新日期:2017-01-01 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

  • Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal.

    abstract::An engineered reversal of the β-oxidation cycle (r-BOX) and the fatty acid biosynthesis (FAB) pathway are promising biological platforms for advanced fuel and chemical production in part due to their iterative nature supporting the synthesis of various chain length products. While diverging in their carbon-carbon elon...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2017.11.003

    authors: Clomburg JM,Contreras SC,Chou A,Siegel JB,Gonzalez R

    更新日期:2018-01-01 00:00:00

  • Precise control of lycopene production to enable a fast-responding, minimal-equipment biosensor.

    abstract::Pigmented metabolites have great potential for use in biosensors that target low-resource areas, since sensor output can be interpreted without any equipment. However, full repression of pigment production when undesired is challenging, as even small amounts of enzyme can catalyze the production of large, visible amou...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2017.07.004

    authors: McNerney MP,Styczynski MP

    更新日期:2017-09-01 00:00:00

  • Identification and elimination of metabolic bottlenecks in the quinone modification pathway for enhanced coenzyme Q10 production in Rhodobacter sphaeroides.

    abstract::In this report, UbiE and UbiH in the quinone modification pathway (QMP) were identified in addition to UbiG as bottleneck enzymes in the CoQ10 biosynthesis by Rhodobacter sphaeroides. The CoQ10 content was enhanced after co-overexpression of UbiE and UbiG, however, accompanied by the accumulation of the intermediate 1...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.03.012

    authors: Lu W,Ye L,Lv X,Xie W,Gu J,Chen Z,Zhu Y,Li A,Yu H

    更新日期:2015-05-01 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

  • Generation of serum-stabilized retroviruses: reduction of alpha1,3gal-epitope synthesis in a murine NIH3T3-derived packaging cell line by expression of chimeric glycosyltransferases.

    abstract::Retroviral vectors released from mouse-derived packaging cell lines are inactivated in human sera by naturally occurring antibodies due to the recognition of Galalpha1,3Galbeta1,4GlcNAc (alphagal-epitope) decorated surface proteins. In this study, an extensive analysis of the glycosylation potential of NIH3T3-derived ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2005.02.004

    authors: Hansen W,Grabenhorst E,Nimtz M,Müller K,Conradt HS,Wirth M

    更新日期:2005-05-01 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

  • Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models.

    abstract::Rational metabolic engineering methods are increasingly employed in designing the commercially viable processes for the production of chemicals relevant to pharmaceutical, biotechnology, and food and beverage industries. With the growing availability of omics data and of methodologies capable to integrate the availabl...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2016.01.009

    authors: Andreozzi S,Chakrabarti A,Soh KC,Burgard A,Yang TH,Van Dien S,Miskovic L,Hatzimanikatis V

    更新日期:2016-05-01 00:00:00

  • A modular autoinduction device for control of gene expression in Bacillus subtilis.

    abstract::Intense synthesis of proteins and chemicals in engineered microbes impose metabolic burden, frequently leading to reduced growth and heterogeneous cell population. Thus, the correct balance between growth and production is important. Such balance can be engineered through dynamic control of pathways, but few broadly a...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2020.03.012

    authors: Corrêa GG,Lins MRDCR,Silva BF,de Paiva GB,Zocca VFB,Ribeiro NV,Picheli FP,Mack M,Pedrolli DB

    更新日期:2020-09-01 00:00:00

  • Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity.

    abstract::Cyanobacterial carboxysomes encapsulate carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Genetic deletion of the major structural proteins encoded within the ccm operon in Synechococcus sp. PCC 7002 (ΔccmKLMN) disrupts carboxysome formation and significantly affects cellular physiology...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2019.04.010

    authors: Abernathy MH,Czajka JJ,Allen DK,Hill NC,Cameron JC,Tang YJ

    更新日期:2019-07-01 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

  • 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

  • Genetic improvement of the microalga Phaeodactylum tricornutum for boosting neutral lipid accumulation.

    abstract::To obtain fast growing oil-rich microalgal strains has been urgently demanded for microalgal biofuel. Malic enzyme (ME), which is involved in pyruvate metabolism and carbon fixation, was first characterized in microalgae here. Overexpression of Phaeodactylum tricornutum ME (PtME) significantly enhanced the expression ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2014.10.002

    authors: Xue J,Niu YF,Huang T,Yang WD,Liu JS,Li HY

    更新日期:2015-01-01 00:00:00

  • Efficient production of saffron crocins and picrocrocin in Nicotiana benthamiana using a virus-driven system.

    abstract::Crocins and picrocrocin are glycosylated apocarotenoids responsible, respectively, for the color and the unique taste of the saffron spice, known as red gold due to its high price. Several studies have also shown the health-promoting properties of these compounds. However, their high costs hamper the wide use of these...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2020.06.009

    authors: Martí M,Diretto G,Aragonés V,Frusciante S,Ahrazem O,Gómez-Gómez L,Daròs JA

    更新日期:2020-09-01 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

  • Characteristics of methionine production by an engineered Corynebacterium glutamicum strain.

    abstract::A methionine-producing strain was derived from a lysine-producing Corynebacterium glutamicum through a process of genetic manipulation in order to assess its potential to synthesize and accumulate methionine during growth. The strain carries a deregulated hom gene (hom(FBR)) to abolish feedback inhibition of homoserin...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2007.05.001

    authors: Park SD,Lee JY,Sim SY,Kim Y,Lee HS

    更新日期:2007-07-01 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

  • 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 design for selective production of nicotinamide mononucleotide from glucose and nicotinamide.

    abstract::β-Nicotinamide mononucleotide (NMN) is, one of the nucleotide compounds, a precursor of NAD+ and has recently attracted attention as a nutraceutical. Here, we develop a whole-cell biocatalyst using Escherichia coli, which enabled selective and effective high production of NMN from the inexpensive feedstock substrates ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2020.11.008

    authors: Shoji S,Yamaji T,Makino H,Ishii J,Kondo A

    更新日期:2020-11-18 00:00:00

  • Cell-free styrene biosynthesis at high titers.

    abstract::Styrene is an important petroleum-derived molecule that is polymerized to make versatile plastics, including disposable silverware and foamed packaging materials. Finding more sustainable methods, such as biosynthesis, for producing styrene is essential due to the increasing severity of climate change as well as the l...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2020.05.009

    authors: Grubbe WS,Rasor BJ,Krüger A,Jewett MC,Karim AS

    更新日期:2020-09-01 00:00:00

  • Metabolic engineering of Corynebacterium glutamicum for the production of glutaric acid, a C5 dicarboxylic acid platform chemical.

    abstract::Corynebacterium glutamicum was metabolically engineered for the production of glutaric acid, a C5 dicarboxylic acid that can be used as platform building block chemical for nylons and plasticizers. C. glutamicum gabT and gabD genes and Pseudomonas putida davT and davD genes encoding 5-aminovalerate transaminase and gl...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.08.007

    authors: Kim HT,Khang TU,Baritugo KA,Hyun SM,Kang KH,Jung SH,Song BK,Park K,Oh MK,Kim GB,Kim HU,Lee SY,Park SJ,Joo JC

    更新日期:2019-01-01 00:00:00

  • A metabolic network analysis & NMR experiment design tool with user interface-driven model construction for depth-first search analysis.

    abstract::A Windows program for metabolic engineering analysis and experimental design has been developed. A graphical user interface enables the pictorial, "on-screen" construction of a metabolic network. Once a model is composed, balance equations are automatically generated. Model construction, modification and information e...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/s1096-7176(03)00023-5

    authors: Zhu T,Phalakornkule C,Ghosh S,Grossmann IE,Koepsel RR,Ataai MM,Domach MM

    更新日期:2003-04-01 00:00:00