Computational Approaches in Metabolic Engineering

Overview

Journal J Biomed Biotechnol

Specialty Biology

Date 2011 May 18

PMID 21584279

Citations 9

Authors

Jennifer L Reed

Ryan S Senger

Maciek R Antoniewicz

Jamey D Young

Affiliations

Soon will be listed here.

Citing Articles

FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization.

Hassani L, Moosavi M, Setoodeh P, Zare H Microb Cell Fact. 2024; 23(1):37.

PMID: 38287320 PMC: 10823710. DOI: 10.1186/s12934-023-02277-x.

Improved 13C metabolic flux analysis in Escherichia coli metabolism: application of a high-resolution MS (GC-EI-QTOF) for comprehensive assessment of MS/MS fragments.

Richter C, Grafahrend-Belau E, Ziegler J, Raorane M, Junker B J Ind Microbiol Biotechnol. 2023; 50(1).

PMID: 37960978 PMC: 10716738. DOI: 10.1093/jimb/kuad039.

The metabolic origins of non-photorespiratory CO2 release during photosynthesis: a metabolic flux analysis.

Xu Y, Fu X, Sharkey T, Shachar-Hill Y, Walker A Plant Physiol. 2021; 186(1):297-314.

PMID: 33591309 PMC: 8154043. DOI: 10.1093/plphys/kiab076.

Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches.

Aghakhani S, Zerrouk N, Niarakis A Cancers (Basel). 2020; 13(1).

PMID: 33374292 PMC: 7795338. DOI: 10.3390/cancers13010035.

A Method to Constrain Genome-Scale Models with 13C Labeling Data.

Garcia Martin H, Kumar V, Weaver D, Ghosh A, Chubukov V, Mukhopadhyay A PLoS Comput Biol. 2015; 11(9):e1004363.

PMID: 26379153 PMC: 4574858. DOI: 10.1371/journal.pcbi.1004363.

References

Unrean P, Trinh C, Srienc F . Rational design and construction of an efficient E. coli for production of diapolycopendioic acid. Metab Eng. 2009; 12(2):112-22. PMC: 2875070. DOI: 10.1016/j.ymben.2009.11.002. View

Almaas E, Kovacs B, Vicsek T, Oltvai Z, Barabasi A . Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature. 2004; 427(6977):839-43. DOI: 10.1038/nature02289. View

Shastri A, Morgan J . A transient isotopic labeling methodology for 13C metabolic flux analysis of photoautotrophic microorganisms. Phytochemistry. 2007; 68(16-18):2302-12. DOI: 10.1016/j.phytochem.2007.03.042. View

Antoniewicz M, Kraynie D, Laffend L, Gonzalez-Lergier J, Kelleher J, Stephanopoulos G . Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Metab Eng. 2007; 9(3):277-92. PMC: 2048574. DOI: 10.1016/j.ymben.2007.01.003. View

Antoniewicz M, Kelleher J, Stephanopoulos G . Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng. 2006; 9(1):68-86. PMC: 1994654. DOI: 10.1016/j.ymben.2006.09.001. View

Pharkya P, Burgard A, Maranas C . OptStrain: a computational framework for redesign of microbial production systems. Genome Res. 2004; 14(11):2367-76. PMC: 525696. DOI: 10.1101/gr.2872004. View

Price N, Reed J, Palsson B . Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol. 2004; 2(11):886-97. DOI: 10.1038/nrmicro1023. View

Covert M, Palsson B . Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem. 2002; 277(31):28058-64. DOI: 10.1074/jbc.M201691200. View

Lun D, Rockwell G, Guido N, Baym M, Kelner J, Berger B . Large-scale identification of genetic design strategies using local search. Mol Syst Biol. 2009; 5:296. PMC: 2736654. DOI: 10.1038/msb.2009.57. View

10.

Moxley J, Jewett M, Antoniewicz M, Villas-Boas S, Alper H, Wheeler R . Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A. 2009; 106(16):6477-82. PMC: 2672541. DOI: 10.1073/pnas.0811091106. View

11.

Thiele I, Price N, Vo T, Palsson B . Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem. 2004; 280(12):11683-95. DOI: 10.1074/jbc.M409072200. View

12.

Becker S, Palsson B . Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol. 2008; 4(5):e1000082. PMC: 2366062. DOI: 10.1371/journal.pcbi.1000082. View

13.

Heinrich R, Rapoport T . A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem. 1974; 42(1):89-95. DOI: 10.1111/j.1432-1033.1974.tb03318.x. View

14.

Fong S, Palsson B . Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet. 2004; 36(10):1056-8. DOI: 10.1038/ng1432. View

15.

Schmidt , Marx , de Graaf AA , Wiechert , Sahm , Nielsen . 13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches . Biotechnol Bioeng. 1999; 58(2-3):254-7. DOI: 10.1002/(sici)1097-0290(19980420)58:2/3<254::aid-bit19>3.0.co;2-c. View

16.

Park J, Lee K, Kim T, Lee S . Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci U S A. 2007; 104(19):7797-802. PMC: 1857225. DOI: 10.1073/pnas.0702609104. View

17.

Alper H, Jin Y, Moxley J, Stephanopoulos G . Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng. 2005; 7(3):155-64. DOI: 10.1016/j.ymben.2004.12.003. View

18.

Bennett B, Kimball E, Gao M, Osterhout R, Van Dien S, Rabinowitz J . Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol. 2009; 5(8):593-9. PMC: 2754216. DOI: 10.1038/nchembio.186. View

19.

Kummel A, Panke S, Heinemann M . Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol. 2006; 2:2006.0034. PMC: 1681506. DOI: 10.1038/msb4100074. View

20.

Wahl S, Noh K, Wiechert W . 13C labeling experiments at metabolic nonstationary conditions: an exploratory study. BMC Bioinformatics. 2008; 9:152. PMC: 2373788. DOI: 10.1186/1471-2105-9-152. View