Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels

ABSTRACT Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean’s primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory net...

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Autores principales:	Jennifer Levering, Christopher L. Dupont, Andrew E. Allen, Bernhard O. Palsson, Karsten Zengler
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba
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spelling	oai:doaj.org-article:a0a28495f0d94002ab7ff2edef6fcdba2021-12-02T18:15:43ZIntegrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels10.1128/mSystems.00142-162379-5077https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba2017-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00142-16https://doaj.org/toc/2379-5077ABSTRACT Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean’s primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom’s metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels. This transcriptional regulatory network was integrated with a recently published genome-scale metabolic model of Phaeodactylum tricornutum to explore the connectivity of the regulatory network and shared metabolites. The integrated regulatory and metabolic model revealed highly connected modules within carbon and nitrogen metabolism. P. tricornutum’s response to rising carbon levels was analyzed by using the recent genome-scale metabolic model with cross comparison to experimental manipulations of carbon dioxide. IMPORTANCE Using a systems biology approach, we studied the response of the marine diatom Phaeodactylum tricornutum to changing atmospheric carbon concentrations on an ocean-wide scale. By integrating an available genome-scale metabolic model and a newly developed transcriptional regulatory network inferred from transcriptome sequencing expression data, we demonstrate that carbon metabolism and nitrogen metabolism are strongly connected and the genes involved are coregulated in this model diatom. These tight regulatory constraints could play a major role during the adaptation of P. tricornutum to increasing carbon levels. The transcriptional regulatory network developed can be further used to study the effects of different environmental perturbations on P. tricornutum’s metabolism.Jennifer LeveringChristopher L. DupontAndrew E. AllenBernhard O. PalssonKarsten ZenglerAmerican Society for MicrobiologyarticlePhaeodactylum tricornutumcoregulated genesgenome-scale metabolic network reconstructionintegrated network modelingregulatory network inferenceMicrobiologyQR1-502ENmSystems, Vol 2, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology QR1-502
spellingShingle	Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology QR1-502 Jennifer Levering Christopher L. Dupont Andrew E. Allen Bernhard O. Palsson Karsten Zengler Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels
description	ABSTRACT Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean’s primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom’s metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels. This transcriptional regulatory network was integrated with a recently published genome-scale metabolic model of Phaeodactylum tricornutum to explore the connectivity of the regulatory network and shared metabolites. The integrated regulatory and metabolic model revealed highly connected modules within carbon and nitrogen metabolism. P. tricornutum’s response to rising carbon levels was analyzed by using the recent genome-scale metabolic model with cross comparison to experimental manipulations of carbon dioxide. IMPORTANCE Using a systems biology approach, we studied the response of the marine diatom Phaeodactylum tricornutum to changing atmospheric carbon concentrations on an ocean-wide scale. By integrating an available genome-scale metabolic model and a newly developed transcriptional regulatory network inferred from transcriptome sequencing expression data, we demonstrate that carbon metabolism and nitrogen metabolism are strongly connected and the genes involved are coregulated in this model diatom. These tight regulatory constraints could play a major role during the adaptation of P. tricornutum to increasing carbon levels. The transcriptional regulatory network developed can be further used to study the effects of different environmental perturbations on P. tricornutum’s metabolism.
format	article
author	Jennifer Levering Christopher L. Dupont Andrew E. Allen Bernhard O. Palsson Karsten Zengler
author_facet	Jennifer Levering Christopher L. Dupont Andrew E. Allen Bernhard O. Palsson Karsten Zengler
author_sort	Jennifer Levering
title	Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels
title_short	Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels
title_full	Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels
title_fullStr	Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels
title_full_unstemmed	Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels
title_sort	integrated regulatory and metabolic networks of the marine diatom <italic toggle="yes">phaeodactylum tricornutum</italic> predict the response to rising co<sub>2</sub> levels
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba
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Integrated Regulatory and Metabolic Networks of the Marine Diatom <italic toggle="yes">Phaeodactylum tricornutum</italic> Predict the Response to Rising CO<sub>2</sub> Levels

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