Industrial systems biology and its impact on synthetic biology of yeast cell factories

被引:32
作者
Fletcher, Eugene [1 ,2 ]
Krivoruchko, Anastasia [1 ,2 ]
Nielsen, Jens [1 ,2 ,3 ]
机构
[1] Chalmers Univ Technol, Dept Biol & Biol Engn, Kemivagen 10, SE-41296 Gothenburg, Sweden
[2] Chalmers Univ Technol, Novo Nordisk Fdn, Ctr Biosustainabil, Kemivagen 10, SE-41296 Gothenburg, Sweden
[3] Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, DK-2970 Horsholm, Denmark
关键词
systems biology; yeast; synthetic biology; modeling; fine chemicals; metabolic engineering; IMPROVED VANILLIN PRODUCTION; SACCHAROMYCES-CEREVISIAE; BAKERS-YEAST; REGULATORY NETWORKS; MULTIPLE GENES; EXPRESSION; PATHWAY; MODEL; BIOSYNTHESIS; INTEGRATION;
D O I
10.1002/bit.25870
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. (C) 2015 Wiley Periodicals, Inc.
引用
收藏
页码:1164 / 1170
页数:7
相关论文
共 70 条
[51]   Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development [J].
Paddon, Chris J. ;
Keasling, Jay D. .
NATURE REVIEWS MICROBIOLOGY, 2014, 12 (05) :355-367
[52]   A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis [J].
Picotti, Paola ;
Clement-Ziza, Mathieu ;
Lam, Henry ;
Campbell, David S. ;
Schmidt, Alexander ;
Deutsch, Eric W. ;
Roest, Hannes ;
Sun, Zhi ;
Rinner, Oliver ;
Reiter, Lukas ;
Shen, Qin ;
Michaelson, Jacob J. ;
Frei, Andreas ;
Alberti, Simon ;
Kusebauch, Ulrike ;
Wollscheid, Bernd ;
Moritz, Robert L. ;
Beyer, Andreas ;
Aebersold, Ruedi .
NATURE, 2013, 494 (7436) :266-270
[53]   Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolyticale [J].
Qiao, Kangjian ;
Abidi, Syed Hussain Imam ;
Liu, Hongjuan ;
Zhang, Haoran ;
Chakraborty, Sagar ;
Watson, Nicki ;
Ajikumar, Parayil Kumaran ;
Stephanopoulos, Gregory .
METABOLIC ENGINEERING, 2015, 29 :56-65
[54]   The development and characterization of synthetic minimal yeast promoters [J].
Redden, Heidi ;
Alper, Hal S. .
NATURE COMMUNICATIONS, 2015, 6
[55]   Selection of chromosomal DNA libraries using a multiplex CRISPR system [J].
Ryan, Owen W. ;
Skerker, Jeffrey M. ;
Maurer, Matthew J. ;
Li, Xin ;
Tsai, Jordan C. ;
Poddar, Snigdha ;
Lee, Michael E. ;
DeLoache, Will ;
Dueber, John E. ;
Arkin, Adam P. ;
Cate, Jamie H. D. .
ELIFE, 2014, 3 :1-15
[56]   Genome scale models of yeast: towards standardized evaluation and consistent omic integration [J].
Sanchez, Benjamin J. ;
Nielsen, Jens .
INTEGRATIVE BIOLOGY, 2015, 7 (08) :846-858
[57]   Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering [J].
Sanchez, Rosa Garcia ;
Karhumaa, Kaisa ;
Fonseca, Cesar ;
Nogue, Violeta Sanchez ;
Almeida, Joao R. M. ;
Larsson, Christer U. ;
Bengtsson, Oskar ;
Bettiga, Maurizio ;
Hahn-Hagerdal, Barbel ;
Gorwa-Grauslund, Marie F. .
BIOTECHNOLOGY FOR BIOFUELS, 2010, 3
[58]   Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways [J].
Schulz, Juliane Caroline ;
Zampieri, Mattia ;
Wanka, Stefanie ;
von Mering, Christian ;
Sauer, Uwe .
SCIENCE SIGNALING, 2014, 7 (353)
[59]   Snf1 Is a Regulator of Lipid Accumulation in Yarrowia lipolytica [J].
Seip, John ;
Jackson, Raymond ;
He, Hongxian ;
Zhu, Quinn ;
Hong, Seung-Pyo .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2013, 79 (23) :7360-7370
[60]   Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions [J].
Sheng, Jiayuan ;
Feng, Xueyang .
FRONTIERS IN MICROBIOLOGY, 2015, 6