Kinetic modelling reveals current limitations in the production of ethanol from xylose by recombinant Saccharomyces cerevisiae.

Abstract:

:Saccharomyces cerevisiae lacks the ability to ferment the pentose sugar xylose that is the second most abundant sugar in nature. Therefore two different xylose catabolic pathways have been heterologously expressed in S. cerevisiae. Whereas the xylose reductase (XR)-xylitol dehydrogenase (XDH) pathway leads to the production of the by-product xylitol, the xylose isomerase (XI) pathway results in significantly lower xylose consumption. In this study, kinetic models including the reactions ranging from xylose transport into the cell to the phosphorylation of xylulose to xylulose 5-P were constructed. They were used as prediction tools for the identification of putative targets for the improvement of xylose utilization in S. cerevisiae strains engineered for higher level of the non-oxidative pentose phosphate pathway (PPP) enzymes, higher xylulokinase and inactivated GRE3 gene encoding an endogenous NADPH-dependent aldose reductase. For both pathways, the in silico analyses identified a need for even higher xylulokinase (XK) activity. In a XR-XDH strain expressing an integrated copy of the Escherichia coli XK encoding gene xylB about a six-fold reduction of xylitol formation was confirmed under anaerobic conditions. Similarly overexpression of the xylB gene in a XI strain increased the aerobic growth rate on xylose by 21%. In contrast to the in silico predictions, the aerobic growth also increased 24% when the xylose transporter gene GXF1 from Candida intermedia was overexpressed together with xylB in the XI strain. Under anaerobic conditions, the XI strains overexpressing xylB gene and the combination of xylB and GFX1 genes consumed 27% and 37% more xylose than the control strain.

journal_name

Metab Eng

journal_title

Metabolic engineering

authors

Parachin NS,Bergdahl B,van Niel EW,Gorwa-Grauslund MF

doi

10.1016/j.ymben.2011.05.005

subject

Has Abstract

pub_date

2011-09-01 00:00:00

pages

508-17

issue

5

eissn

1096-7176

issn

1096-7184

pii

S1096-7176(11)00054-1

journal_volume

13

pub_type

杂志文章
  • Quantitative prediction of genome-wide resource allocation in bacteria.

    abstract::Predicting resource allocation between cell processes is the primary step towards decoding the evolutionary constraints governing bacterial growth under various conditions. Quantitative prediction at genome-scale remains a computational challenge as current methods are limited by the tractability of the problem or by ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.10.003

    authors: Goelzer A,Muntel J,Chubukov V,Jules M,Prestel E,Nölker R,Mariadassou M,Aymerich S,Hecker M,Noirot P,Becher D,Fromion V

    更新日期:2015-11-01 00:00:00

  • Engineering of carboligase activity reaction in Candida glabrata for acetoin production.

    abstract::Utilization of Candida glabrata overproducing pyruvate is a promising strategy for high-level acetoin production. Based on the known regulatory and metabolic information, acetaldehyde and thiamine were fed to identify the key nodes of carboligase activity reaction (CAR) pathway and provide a direction for engineering ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2013.12.005

    authors: Li S,Xu N,Liu L,Chen J

    更新日期:2014-03-01 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Engineering precursor flow for increased erythromycin production in Aeromicrobium erythreum.

    abstract::Metabolic engineering technology for industrial microorganisms is under development to create rational, more reliable, and more cost-effective approaches to strain improvement. Strain improvement is a critical component of the drug development process, yet the genetic basis for high production by industrial microorgan...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2004.03.003

    authors: Reeves AR,Cernota WH,Brikun IA,Wesley RK,Weber JM

    更新日期:2004-10-01 00:00:00

  • Metabolic transistor strategy for controlling electron transfer chain activity in Escherichia coli.

    abstract::A novel strategy to finely control a large metabolic flux by using a "metabolic transistor" approach was established. In this approach a small change in the level or availability of an essential component for the process is controlled by adding a competitive reaction that affects a precursor or an intermediate in its ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.01.002

    authors: Wu H,Tuli L,Bennett GN,San KY

    更新日期:2015-03-01 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

  • Multiplexed site-specific genome engineering for overproducing bioactive secondary metabolites in actinomycetes.

    abstract::Actinomycetes produce a large variety of pharmaceutically active compounds, yet production titers often require to be improved for discovery, development and large-scale manufacturing. Here, we describe a new technique, multiplexed site-specific genome engineering (MSGE) via the 'one integrase-multiple attB sites' con...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2017.01.004

    authors: Li L,Zheng G,Chen J,Ge M,Jiang W,Lu Y

    更新日期:2017-03-01 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

  • 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

  • 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

  • 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

  • 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

  • Functional expression of prokaryotic and eukaryotic genes in Escherichia coli for conversion of glucose to p-hydroxystyrene.

    abstract::The chemical monomer p-hydroxystyrene (pHS) is used for producing a number of important industrial polymers from petroleum-based feedstocks. In an alternative approach, the microbial production of pHS can be envisioned by linking together a number of different metabolic pathways, of which those based on using glucose ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2007.01.002

    authors: Qi WW,Vannelli T,Breinig S,Ben-Bassat A,Gatenby AA,Haynie SL,Sariaslani FS

    更新日期:2007-05-01 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

  • Improving recombinant bone morphogenetic protein-4 (BMP-4) production by autoregulatory feedback loop removal using BMP receptor-knockout CHO cell lines.

    abstract::A Chinese hamster ovary (CHO) cell line producing recombinant human bone morphogenetic protein-4 (rhBMP-4) (CHO-BMP-4), which expresses essential components of BMP signal transduction, underwent autocrine BMP-4 signaling. RNA seq analysis on CHO host cells (DG44) treated with rhBMP-4 (20 µg/mL) suggested that rhBMP-4 ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2018.11.003

    authors: Kim CL,Lee GM

    更新日期:2019-03-01 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

  • A real-time control system of gene expression using ligand-bound nucleic acid aptamer for metabolic engineering.

    abstract::Artificial control of bio-functions through regulating gene expression is one of the most important and attractive technologies to build novel living systems that are useful in the areas of chemical synthesis, nanotechnology, pharmacology, cell biology. Here, we present a novel real-time control system of gene regulat...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2017.06.002

    authors: Wang J,Cui X,Yang L,Zhang Z,Lv L,Wang H,Zhao Z,Guan N,Dong L,Chen R

    更新日期:2017-07-01 00:00:00

  • Determining contributions of exogenous glucose and fructose to de novo fatty acid and glycerol synthesis in liver and adipose tissue.

    abstract::The de novo synthesis of triglyceride (TG) fatty acids (FA) and glycerol can be measured with stable isotope tracers. However, these methods typically do not inform the contribution of a given substrate to specific pathways on these synthetic processes. We integrated deuterated water (2H2O) measurement of de novo lipo...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2019.08.018

    authors: Silva JCP,Marques C,Martins FO,Viegas I,Tavares L,Macedo MP,Jones JG

    更新日期:2019-12-01 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

  • Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis.

    abstract::Aromatic amino acids are precursors of numerous plant secondary metabolites with diverse biological functions. Many of these secondary metabolites are already being used as active pharmaceutical or nutraceutical ingredients, and there are numerous exploratory studies of other compounds with promising applications. p-C...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2015.08.003

    authors: Rodriguez A,Kildegaard KR,Li M,Borodina I,Nielsen J

    更新日期:2015-09-01 00:00:00

  • Metabolic engineering of β-oxidation in Penicillium chrysogenum for improved semi-synthetic cephalosporin biosynthesis.

    abstract::Industrial production of semi-synthetic cephalosporins by Penicillium chrysogenum requires supplementation of the growth media with the side-chain precursor adipic acid. In glucose-limited chemostat cultures of P. chrysogenum, up to 88% of the consumed adipic acid was not recovered in cephalosporin-related products, b...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2012.02.004

    authors: Veiga T,Gombert AK,Landes N,Verhoeven MD,Kiel JA,Krikken AM,Nijland JG,Touw H,Luttik MA,van der Toorn JC,Driessen AJ,Bovenberg RA,van den Berg MA,van der Klei IJ,Pronk JT,Daran JM

    更新日期:2012-07-01 00:00:00

  • Metabolic engineering of strains of Ralstonia eutropha and Pseudomonas putida for biotechnological production of 2-methylcitric acid.

    abstract::In this study strains of Ralstonia eutropha H16 and Pseudomonas putida KT2440 were engineered which are suitable for biotechnological production of 2-methylcitric acid (2MC). Analysis of a previous mutant of R. eutropha able to accumulate 2MC recommended this strain as a candidate for fermentative production of 2MC. T...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2006.05.007

    authors: Ewering C,Heuser F,Benölken JK,Brämer CO,Steinbüchel A

    更新日期:2006-11-01 00:00:00

  • Induction of a hypermetabolic state in cultured hepatocytes by glucagon and H2O2.

    abstract::Stress hormones and pro-inflammatory cytokines are putative signals triggering increased energy expenditure or "hypermetabolism" commonly observed in inflammatory states. Cytokines also cause the release of reactive oxidants by immune cells resident in tissues in vivo. Therefore, we hypothesized that oxidative stress ...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/s1096-7176(03)00042-9

    authors: Lee K,Berthiaume F,Stephanopoulos GN,Yarmush ML

    更新日期:2003-10-01 00:00:00

  • Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield.

    abstract::The potential to produce succinate aerobically in Escherichia coli would offer great advantages over anaerobic fermentation in terms of faster biomass generation, carbon throughput, and product formation. Genetic manipulations were performed on two aerobic succinate production systems to increase their succinate yield...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1016/j.ymben.2004.10.003

    authors: Lin H,Bennett GN,San KY

    更新日期:2005-03-01 00:00:00

  • The organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose.

    abstract::A mathematical model to describe carbon catabolite repression in Escherichia coli is developed and in part validated. The model is aggregated from two functional units describing glucose and lactose transport and degradation. Both units are members of the crp modulon and are under control of a global signal transducti...

    journal_title:Metabolic engineering

    pub_type: 杂志文章

    doi:10.1006/mben.2001.0199

    authors: Kremling A,Bettenbrock K,Laube B,Jahreis K,Lengeler JW,Gilles ED

    更新日期:2001-10-01 00:00:00