Abstract:
:Engineering cellular metabolism for improved production of valuable chemicals requires extensive modulation of bacterial genome to explore complex genetic spaces. Here, we report the development of a CRISPR-Cas9 based method for iterative genome editing and metabolic engineering of Escherichia coli. This system enables us to introduce various types of genomic modifications with near 100% editing efficiency and to introduce three mutations simultaneously. We also found that cells with intact mismatch repair system had reduced chance to escape CRISPR mediated cleavage and yielded increased editing efficiency. To demonstrate its potential, we used our method to integrate the β-carotene synthetic pathway into the genome and to optimize the methylerythritol-phosphate (MEP) pathway and central metabolic pathways for β-carotene overproduction. We collectively tested 33 genomic modifications and constructed more than 100 genetic variants for combinatorially exploring the metabolic landscape. Our best producer contained15 targeted mutations and produced 2.0 g/L β-carotene in fed-batch fermentation.
journal_name
Metab Engjournal_title
Metabolic engineeringauthors
Li Y,Lin Z,Huang C,Zhang Y,Wang Z,Tang YJ,Chen T,Zhao Xdoi
10.1016/j.ymben.2015.06.006subject
Has Abstractpub_date
2015-09-01 00:00:00pages
13-21eissn
1096-7176issn
1096-7184pii
S1096-7176(15)00075-0journal_volume
31pub_type
杂志文章abstract::Biosynthesis of Nylon 12 monomer using dodecanoic acid (DDA) or its esters as the renewable feedstock typically involves ω-hydroxylation, oxidation and ω-amination. The dependence of hydroxylation and oxidation-catalyzing enzymes on redox cofactors, and the requirement of L-alanine as the co-substrate and pyridoxal 5'...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2020.09.006
更新日期:2020-11-01 00:00:00
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
更新日期:2012-09-01 00:00:00
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 syntha...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2016.12.011
更新日期:2017-01-01 00:00:00
abstract::The metabolic engineering of natural products has begun to prosper in the past few years due to genomic research and the discovery of biosynthetic genes. While the biosynthetic pathways and genes for some isoprenoids have been known for many years, new pathways have been found and known pathways have been further inve...
journal_title:Metabolic engineering
pub_type: 杂志文章,评审
doi:10.1006/mben.2000.0168
更新日期:2001-01-01 00:00:00
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
更新日期:2015-05-01 00:00:00
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
更新日期:2003-04-01 00:00:00
abstract::A large number of CHO glycosylation mutants were isolated by Ricinus communis agglutinin-I (RCA-I). Complementation tests revealed that all these mutant lines possessed a dysfunctional N-acetylglucosaminyltransferase I (GnT I) gene. Sequencing analyses on the GnT I cDNAs isolated from 16 mutant lines led to the identi...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2010.03.002
更新日期:2010-07-01 00:00:00
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
更新日期:2006-11-01 00:00:00
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
更新日期:2013-01-01 00:00:00
abstract::Presented herein is a methodology for quantitatively analyzing the complex signaling network by resorting to colored Petri nets (CPN). The mathematical as well as Petri net models for two basic reaction types were established, followed by the extension to a large signal transduction system stimulated by epidermal grow...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2005.10.001
更新日期:2006-03-01 00:00:00
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
更新日期:2019-01-01 00:00:00
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
更新日期:2020-09-01 00:00:00
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
更新日期:2015-07-01 00:00:00
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
更新日期:2014-09-01 00:00:00
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
更新日期:2019-07-01 00:00:00
abstract::An innovative "biodrug" concept based on oral administration of living recombinant microorganisms as a vehicle to deliver active compounds directly into the digestive tract has recently been developed. To validate this concept, we studied a recombinant Saccharomyces cerevisiae strain in order to investigate its viabil...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2009.01.001
更新日期:2009-05-01 00:00:00
abstract::Anthocyanins are widely distributed, glycosylated, water-soluble plant pigments, which give many fruits and flowers their red, purple or blue colouration. Their beneficial effects in a dietary context have encouraged increasing use of anthocyanins as natural colourants in the food and cosmetic industries. However, the...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2018.06.004
更新日期:2018-07-01 00:00:00
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
更新日期:2006-11-01 00:00:00
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
更新日期:2016-09-01 00:00:00
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
更新日期:2020-11-18 00:00:00
abstract::Using the carbon isotope labeling technique, the response of cyanobacterial central carbon metabolism to the change in environmental conditions was investigated. Synechocystis was grown in the heterotrophic and mixotrophic cultures fed with 13C-labeled glucose. The labeling patterns of the amino acids in biomass hydro...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1006/mben.2002.0226
更新日期:2002-07-01 00:00:00
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
更新日期:2001-04-01 00:00:00
abstract::Mutations in succinate dehydrogenase (SDH) are associated with tumor development and neurodegenerative diseases. Only in tumors, loss of SDH activity is accompanied with the loss of complex I activity. Yet, it remains unknown whether the metabolic phenotype of SDH mutant tumors is driven by loss of complex I function,...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2016.11.005
更新日期:2017-09-01 00:00:00
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
更新日期:2019-01-01 00:00:00
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 prod...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2011.05.005
更新日期:2011-09-01 00:00:00
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
更新日期:2018-03-01 00:00:00
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
更新日期:2012-11-01 00:00:00
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
更新日期:2012-07-01 00:00:00
abstract::Isotopically nonstationary metabolic flux analysis (INST-MFA) provides a versatile platform to quantitatively assess in vivo metabolic activities of autotrophic systems. By applying INST-MFA to recombinant aldehyde-producing cyanobacteria, we identified metabolic alterations that correlated with increased strain perfo...
journal_title:Metabolic engineering
pub_type: 杂志文章
doi:10.1016/j.ymben.2020.03.007
更新日期:2020-07-01 00:00:00
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
更新日期:2019-03-01 00:00:00