microbial metabolism metabolic engineering in post-genomic...
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Microbial MetabolismMetabolic Engineering in Post-Genomic EraChing-Tsan Huang (黃慶璨)Office: Agronomy Hall, Room 111Tel: (02) 33664454E-mail: [email protected]
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DefinitionA directed improvement of cellular properties through the modification of specific biochemical reaction with the use of recombinant DNA technology. Alteration of metabolic pathways to better understand and use cellular pathways for chemical transformation, energy transduction, and supramolecular assembly.
AimTo optimize a biotechnologically important process carried out by organisms.
DisciplineGenetics
Biochemistry Molecular BiologyPhysiology
Metabolic Engineering
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http://ocw.osaka-u.ac.jp/contents/19/Prof.%20Shimizu%201.pdf
Systems and Elements in a Cell
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ME before the Genomics Revolution
The Cell as a Production Line.
OptimizationThe flux through a metabolic pathway was thought to be controlled by rate-limiting step.
Alternation
A B C D E
E1 E2 E3 E4
mRNA1
DNA1
mRNA2
DNA2
mRNA3
DNA3
mRNA4
DNA4
D’ E’
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Metabolic flux analysis (MFA) and observability metabolic pathwayCell capability analysisOn-line metabolic flux analysisMetabolic control analysis (MCA) in complicated bionetworksExperimental determination of flux distribution by isotope labeling and trace experimentKinetic analysisIntegration of Bioinformatic data
Methodologies in Metabolic Engineering
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From Maps to Equations
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Metabolic Flux AnalysisThe calculation and analysis of the flux distribution of the entire biochemical reaction network in the system of study
http://karma.med.harvard.edu/wiki/User:JeremyZucker
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Metabolic Flux AnalysisMethodology for determining important cellular physiological characteristics from the network stoichiometryThe control of the flux tends to be distributed among multiple enzymes.
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Example of Metabolic Flux Analysis
Bioreaction Network of Central Carbon Metabolism
J. Bacteriol. 184: 152-164, 2002..
Basis of 13C Metabolic Flux Analysis
Tang et al., 2007. Nano Lett. 7(3):754-760.
Carbon Source13C1-C2-C3-C4-C5-C6
(labeled)
Intracellular fluxes
PP Pathway
Glycolysis
Measurable carbon labeling pattern of isotopomers
Amino Acids
TCA Cycle
Cell
Measurable extracellular fluxes
v1v3
v2
Metabolic Flux Distribution in Chemostat Cultures
J. Bacteriol. 184: 152-164, 2002..
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Example of ME by Alternation
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http://ocw.osaka-u.ac.jp/contents/19/Prof.%20Shimizu%201.pdf
Systems and Elements in Bioprocess
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http://ocw.osaka-u.ac.jp/contents/19/Prof.%20Shimizu%201.pdf
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http://karamatsu.shinshu-u.ac.jp/lab/ferment/index_e.htm
ME in the Post-Genomic EraThe Cell as a Production Organism.
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Genomics
Proteomics
Transcriptomics
Metabolomics
Phynotypes
The Era of OmicsWhat is possible
What appears to be happing
What makes it happen
What is happening
What is shown
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Metabolic Reconstruction from the GenomePhysiology without biochemistry
http://microgen.ouhsc.edu/s_mutans/s_mutans_pathways_large.png
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Metabolic Reconstructionht
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The Wheel of Biological Understanding
http://www.bioteach.ubc.ca/Bioinformatics/whatisbioinform/