Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Ren, Shaogang ^a   Zeng, Bo ^a   Qian, Xiaoning ^a  

^a University of South Florida   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; ESCHERICHIA COLI; GENES; GENETIC PROGRAMMING; LINEARIZATION; METABOLIC ENGINEERING; METABOLISM; OPTIMIZATION; QUADRATIC PROGRAMMING;

BI-LEVEL OPTIMIZATION; BILEVEL PROGRAMMING PROBLEM; COMPUTATIONAL FRAMEWORK; FLUX BALANCE ANALYSIS; OPTIMIZATION PROBLEMS; OPTIMIZATION PROCEDURES; PIECEWISE LINEARIZATION; QUADRATIC PROGRAMMING PROBLEMS;

INTEGER PROGRAMMING;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; ESCHERICHIA COLI; GENE INACTIVATION; GENETICS; METABOLIC ENGINEERING; METABOLISM; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENE KNOCKOUT TECHNIQUES; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL;

EID: 84881493893     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S2-S17     Document Type: Article

References (19)

1. Haro M, de LV: Metabolic engineering of bacteria for environmental applications: Construction of Pseudomonas strains for biodegradation of 2-chlorotoluene. J Biotechnol 2001, 85:103-113.
2. Lu J, Sheahan C, Fu P: Metabolic engineering of algae for fourth generation biofuels production. Energy Environ Sci 2011, 4:2451-2466.
3. Broa C, Regenberga B, Förster J, Nielsen J: In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metabolic Engineering 2006, 8:102-111.
4. Ohta K, Beall DS, Mejia JP, Shanmugam KT, Ingram LO: Metabolic engineering of Klebsiella oxytoca M5A1 for ethanol production from xylose and glucose. Applied and Environmental Microbiology 1991, 57:2810-2815.
5. Steen EJ, Chan R, Prasad N, Myers S, Petzold CJ, Redding A, Ouellet M, Keasling JD: Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb Cell Fact 2008, 7:36.
6. Luengo JM, Garcia B, Sandoval A, Naharro G, Olivera ER: Bioplastics from microorganisms. Current Opinion in Microbiology 2003, 6:251-260.
7. Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY: Metabolic Engineering of Escherichia coli for En-hanced Production of Succinic Acid, Based on Genome Comparison and in silico Gene Knockout Simulation. Applied and Environmental Microbiology 2005, 71:7880-7887.
8. Stephanopoulos G, Aristidou A, Nielson J: Metabolic engineering principles and methodologies New York: Academic Press; 1998.
9. Barrett C, Kim T, Kim H, Palsson B, Lee S: Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotechnol 2006, 17:488-492.
10. Förster J, Famili I, Fu P, Palsson B, Nielsen J: Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13:244-253.
11. Segre D, Vitkup D, Church G: Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 2002, 99:15112-15117.
12. Shlomi T, Berkman O, Ruppin E: Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 2005, 102:7695-7700.
13. Burgard A, Pharkya P, Maranas C: OptKnock: A bi-level programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84:647-657.
14. Varma A, Palsson B: Metabolic flux balancing: Basic concepts, scientific and practical use. Bio/Technology 1994, 12:994-998.
15. Edwards JS, Palsson BO: The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 2000, 97:5528-5533.
16. Bazaraa MS, Jarvis JJ, Sherali HD: Linear programming and network flows USA: John Wiley & Sons; 2005.
17. IBM ILOG CPLEX Optimizer. [http://www-01.ibm.com/software/integration/ optimization/cplex-optimizer/].
18. Antoniewicz MR, Kraynie DF, Laffend LA, Joanna G, Joanne KK, Stephanopoulos Gregory: Metabolic flux analysis in a non-stationary system: Fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Genome Res 2007, 9(3):277-292.
19. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson B: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 2007, 3:121-138.