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Title: Optimization of Energy Flow Through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe

Abstract

Diatoms are important oceanic photosynthetic microorganisms, responsible for approximately 20% of all carbon fixation on Earth. Additionally, diatoms are attractive metabolic engineering candidates. This investigation leveraged Systems Biology techniques to advance our understanding of and potential to engineer diatoms for bioproducts of societal interest, such as biofuels. Systems Biology combines computational and experimental techniques to understand an organism at the whole-cell level as well as characterize the interface between the organism and its environment. Our research resulted in major contributions to the understanding of systems-level light-driven metabolism. Diatoms have a unique evolutionary history. As a result, existing understanding of photosynthetic metabolism may not be applicable to diatom physiology. We generated, validated, and published a high-quality metabolic model of diatom metabolism facilitating novel insights into these unique organisms. Additionally, we overcame a consistent challenge in the modeling of photosynthetic organisms by integrating light into metabolic models. This result allows realistic assessments of how the light environment affects cell physiology and metabolism, a necessary advancement for bioengineering. Next, we generated several methodologies for integrating large-scale datasets with models of metabolism. These “big data” approaches begin to address a constant challenge in biology, which is translating data into information and understanding. Finally, wemore » built web-based databases for housing, distributing, and visualizing systems-level biology data. These projects created an online ecosystem for sharing, analyzing, and characterizing metabolic information and is currently being used by public and private institutions. Photosynthetic bioengineering has the promise to create high-energy products with minimal inputs. Systems Biology has a long history of facilitating bioengineering of cellular metabolism. However, photosynthetic organisms are only sparsely present in this history. This project and its outputs have accelerated the application of proven Systems Biology techniques to light-driven metabolism. The resulting methodologies will accelerate public and private endeavors leveraging photosynthetic systems in the bioengineering of bioproducts such as biofuels or carbon sequestration.« less

Authors:
; ;
Publication Date:
Research Org.:
Dr. Bernhard O. Palsson
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Contributing Org.:
JCVI, La Joll, CA; Colorado State University, Fort Collins CO; Department of Pediatrics, University of California San Diego, La Jolla, CA; Division of Biological Sciences, University of California San Diego, La Jolla, CA.
OSTI Identifier:
1484079
Report Number(s):
DOE-SBRG-8701-1
DOE Contract Number:  
SC0008701
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS

Citation Formats

Palsson, Bernhard O., Broddrick, Jared T., and King, Zachary A. Optimization of Energy Flow Through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe. United States: N. p., 2018. Web. doi:10.2172/1484079.
Palsson, Bernhard O., Broddrick, Jared T., & King, Zachary A. Optimization of Energy Flow Through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe. United States. doi:10.2172/1484079.
Palsson, Bernhard O., Broddrick, Jared T., and King, Zachary A. Fri . "Optimization of Energy Flow Through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe". United States. doi:10.2172/1484079. https://www.osti.gov/servlets/purl/1484079.
@article{osti_1484079,
title = {Optimization of Energy Flow Through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe},
author = {Palsson, Bernhard O. and Broddrick, Jared T. and King, Zachary A.},
abstractNote = {Diatoms are important oceanic photosynthetic microorganisms, responsible for approximately 20% of all carbon fixation on Earth. Additionally, diatoms are attractive metabolic engineering candidates. This investigation leveraged Systems Biology techniques to advance our understanding of and potential to engineer diatoms for bioproducts of societal interest, such as biofuels. Systems Biology combines computational and experimental techniques to understand an organism at the whole-cell level as well as characterize the interface between the organism and its environment. Our research resulted in major contributions to the understanding of systems-level light-driven metabolism. Diatoms have a unique evolutionary history. As a result, existing understanding of photosynthetic metabolism may not be applicable to diatom physiology. We generated, validated, and published a high-quality metabolic model of diatom metabolism facilitating novel insights into these unique organisms. Additionally, we overcame a consistent challenge in the modeling of photosynthetic organisms by integrating light into metabolic models. This result allows realistic assessments of how the light environment affects cell physiology and metabolism, a necessary advancement for bioengineering. Next, we generated several methodologies for integrating large-scale datasets with models of metabolism. These “big data” approaches begin to address a constant challenge in biology, which is translating data into information and understanding. Finally, we built web-based databases for housing, distributing, and visualizing systems-level biology data. These projects created an online ecosystem for sharing, analyzing, and characterizing metabolic information and is currently being used by public and private institutions. Photosynthetic bioengineering has the promise to create high-energy products with minimal inputs. Systems Biology has a long history of facilitating bioengineering of cellular metabolism. However, photosynthetic organisms are only sparsely present in this history. This project and its outputs have accelerated the application of proven Systems Biology techniques to light-driven metabolism. The resulting methodologies will accelerate public and private endeavors leveraging photosynthetic systems in the bioengineering of bioproducts such as biofuels or carbon sequestration.},
doi = {10.2172/1484079},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2018},
month = {11}
}

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