Advances in metabolic modeling of oleaginous microalgae
Abstract
Production of biofuels and bioenergy precursors by phototrophic microorganisms, such as microalgae and cyanobacteria, is a promising alternative to conventional fuels obtained from non-renewable resources. Several species of microalgae have been investigated as potential candidates for the production of biofuels, for the most part due to their exceptional metabolic capability to accumulate large quantities of lipids. Constraint-based modeling, a systems biology approach that accurately predicts the metabolic phenotype of phototrophs, has been deployed to identify suitable culture conditions as well as to explore genetic enhancement strategies for bioproduction. Core metabolic models were employed to gain insight into the central carbon metabolism in photosynthetic microorganisms. More recently, comprehensive genome-scale models, including organelle-specifc information at high resolution, have been developed to gain new insight into the metabolism of phototrophic cell factories. As a result, we review the current state of the art of constraint-based modeling and computational method development and discuss how advanced models led to increased prediction accuracy and thus improved lipid production in microalgae.
- Authors:
-
- Univ. Nacional de Colombia (Colombia)
- Univ. of California, San Diego, La Jolla, CA (United States)
- Publication Date:
- Research Org.:
- Johns Hopkins Univ., Baltimore, MD (United States)
- Sponsoring Org.:
- USDOE Office of Energy Efficiency and Renewable Energy (EERE)
- OSTI Identifier:
- 1485595
- Grant/Contract Number:
- SC0012658
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biotechnology for Biofuels
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1754-6834
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Oleaginous phototrophs; Lipid production; Constraint‑based metabolic modeling; Central carbon metabolism
Citation Formats
Tibocha-Bonilla, Juan D., Zuñiga, Cristal, Godoy-Silva, Rubén D., and Zengler, Karsten. Advances in metabolic modeling of oleaginous microalgae. United States: N. p., 2018.
Web. doi:10.1186/s13068-018-1244-3.
Tibocha-Bonilla, Juan D., Zuñiga, Cristal, Godoy-Silva, Rubén D., & Zengler, Karsten. Advances in metabolic modeling of oleaginous microalgae. United States. https://doi.org/10.1186/s13068-018-1244-3
Tibocha-Bonilla, Juan D., Zuñiga, Cristal, Godoy-Silva, Rubén D., and Zengler, Karsten. Wed .
"Advances in metabolic modeling of oleaginous microalgae". United States. https://doi.org/10.1186/s13068-018-1244-3. https://www.osti.gov/servlets/purl/1485595.
@article{osti_1485595,
title = {Advances in metabolic modeling of oleaginous microalgae},
author = {Tibocha-Bonilla, Juan D. and Zuñiga, Cristal and Godoy-Silva, Rubén D. and Zengler, Karsten},
abstractNote = {Production of biofuels and bioenergy precursors by phototrophic microorganisms, such as microalgae and cyanobacteria, is a promising alternative to conventional fuels obtained from non-renewable resources. Several species of microalgae have been investigated as potential candidates for the production of biofuels, for the most part due to their exceptional metabolic capability to accumulate large quantities of lipids. Constraint-based modeling, a systems biology approach that accurately predicts the metabolic phenotype of phototrophs, has been deployed to identify suitable culture conditions as well as to explore genetic enhancement strategies for bioproduction. Core metabolic models were employed to gain insight into the central carbon metabolism in photosynthetic microorganisms. More recently, comprehensive genome-scale models, including organelle-specifc information at high resolution, have been developed to gain new insight into the metabolism of phototrophic cell factories. As a result, we review the current state of the art of constraint-based modeling and computational method development and discuss how advanced models led to increased prediction accuracy and thus improved lipid production in microalgae.},
doi = {10.1186/s13068-018-1244-3},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 11,
place = {United States},
year = {Wed Sep 05 00:00:00 EDT 2018},
month = {Wed Sep 05 00:00:00 EDT 2018}
}
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Table 1: Characteristics of current metabolic models of oleaginous microalgae
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journal, November 2008
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journal, April 2011
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journal, September 2017
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journal, April 2017
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Genome scale metabolic reconstruction of Chlorella variabilis for exploring its metabolic potential for biofuels
journal, August 2016
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Metabolic model of Synechococcus sp. PCC 7002: Prediction of flux distribution and network modification for enhanced biofuel production
journal, August 2016
- Hendry, John I.; Prasannan, Charulata B.; Joshi, Aditi
- Bioresource Technology, Vol. 213
RNA-Seq and metabolic flux analysis of Tetraselmis sp. M8 during nitrogen starvation reveals a two-stage lipid accumulation mechanism
journal, November 2017
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journal, November 2005
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Characterization of Scenedesmus obtusiusculus AT-UAM for high-energy molecules accumulation: deeper insight into biotechnological potential of strains of the same species
journal, March 2018
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Dynamic photosynthetic response of the microalga Scenedesmus obtusiusculus to light intensity perturbations
journal, September 2014
- Cabello, Juan; Morales, Marcia; Revah, Sergio
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Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production
journal, June 2015
- Baroukh, Caroline; Muñoz-Tamayo, Rafael; Bernard, Olivier
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Metabolic flux analysis of the hydrogen production potential in Synechocystis sp. PCC6803
journal, November 2009
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The biomass objective function
journal, June 2010
- Feist, Adam M.; Palsson, Bernhard O.
- Current Opinion in Microbiology, Vol. 13, Issue 3
Biofuels from microalgae—A review of technologies for production, processing, and extractions of biofuels and co-products
journal, February 2010
- Brennan, Liam; Owende, Philip
- Renewable and Sustainable Energy Reviews, Vol. 14, Issue 2, p. 557-577
Biodiesel from microalgae beats bioethanol
journal, March 2008
- Chisti, Yusuf
- Trends in Biotechnology, Vol. 26, Issue 3
Network reduction in metabolic pathway analysis: Elucidation of the key pathways involved in the photoautotrophic growth of the green alga Chlamydomonas reinhardtii
journal, July 2012
- Rügen, Marco; Bockmayr, Alexander; Legrand, Jack
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Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli
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Flux Balance Analysis of Photoautotrophic Metabolism
journal, December 2005
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- Biotechnology Progress, Vol. 21, Issue 6
Metabolic network reconstruction of Chlamydomonas offers insight into light‐driven algal metabolism
journal, January 2011
- Chang, Roger L.; Ghamsari, Lila; Manichaikul, Ani
- Molecular Systems Biology, Vol. 7, Issue 1
A protocol for generating a high-quality genome-scale metabolic reconstruction
journal, January 2010
- Thiele, Ines; Palsson, Bernhard Ø
- Nature Protocols, Vol. 5, Issue 1
The water-land-food nexus of first-generation biofuels
journal, March 2016
- Rulli, Maria Cristina; Bellomi, Davide; Cazzoli, Andrea
- Scientific Reports, Vol. 6, Issue 1
An integrative approach towards completing genome-scale metabolic networks
journal, January 2009
- Christian, Nils; May, Patrick; Kempa, Stefan
- Molecular BioSystems, Vol. 5, Issue 12
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis
journal, December 2016
- Broddrick, Jared T.; Rubin, Benjamin E.; Welkie, David G.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 51
Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
journal, October 2017
- Chen, Ke; Gao, Ye; Mih, Nathan
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 43
Genome-wide metabolic network reconstruction of the picoalga Ostreococcus
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