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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Gespeichert in:

Autor*in:	Jennifer Levering [verfasserIn] Christopher L. Dupont [verfasserIn] Andrew E. Allen [verfasserIn] Bernhard O. Palsson [verfasserIn] Karsten Zengler [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2017

Schlagwörter:	Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference

Übergeordnetes Werk:	In: mSystems - American Society for Microbiology, 2017, 2(2017), 1
Übergeordnetes Werk:	volume:2 ; year:2017 ; number:1

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1128/mSystems.00142-16

Katalog-ID:	DOAJ052402800

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allfields	10.1128/mSystems.00142-16 doi (DE-627)DOAJ052402800 (DE-599)DOAJa0a28495f0d94002ab7ff2edef6fcdba DE-627 ger DE-627 rakwb eng QR1-502 Jennifer Levering verfasserin aut 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 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology Christopher L. Dupont verfasserin aut Andrew E. Allen verfasserin aut Bernhard O. Palsson verfasserin aut Karsten Zengler verfasserin aut In mSystems American Society for Microbiology, 2017 2(2017), 1 (DE-627)84597212X (DE-600)2844333-0 23795077 nnns volume:2 year:2017 number:1 https://doi.org/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba kostenfrei https://journals.asm.org/doi/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/toc/2379-5077 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2017 1
spelling	10.1128/mSystems.00142-16 doi (DE-627)DOAJ052402800 (DE-599)DOAJa0a28495f0d94002ab7ff2edef6fcdba DE-627 ger DE-627 rakwb eng QR1-502 Jennifer Levering verfasserin aut 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 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology Christopher L. Dupont verfasserin aut Andrew E. Allen verfasserin aut Bernhard O. Palsson verfasserin aut Karsten Zengler verfasserin aut In mSystems American Society for Microbiology, 2017 2(2017), 1 (DE-627)84597212X (DE-600)2844333-0 23795077 nnns volume:2 year:2017 number:1 https://doi.org/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba kostenfrei https://journals.asm.org/doi/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/toc/2379-5077 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2017 1
allfields_unstemmed	10.1128/mSystems.00142-16 doi (DE-627)DOAJ052402800 (DE-599)DOAJa0a28495f0d94002ab7ff2edef6fcdba DE-627 ger DE-627 rakwb eng QR1-502 Jennifer Levering verfasserin aut 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 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology Christopher L. Dupont verfasserin aut Andrew E. Allen verfasserin aut Bernhard O. Palsson verfasserin aut Karsten Zengler verfasserin aut In mSystems American Society for Microbiology, 2017 2(2017), 1 (DE-627)84597212X (DE-600)2844333-0 23795077 nnns volume:2 year:2017 number:1 https://doi.org/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba kostenfrei https://journals.asm.org/doi/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/toc/2379-5077 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2017 1
allfieldsGer	10.1128/mSystems.00142-16 doi (DE-627)DOAJ052402800 (DE-599)DOAJa0a28495f0d94002ab7ff2edef6fcdba DE-627 ger DE-627 rakwb eng QR1-502 Jennifer Levering verfasserin aut 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 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology Christopher L. Dupont verfasserin aut Andrew E. Allen verfasserin aut Bernhard O. Palsson verfasserin aut Karsten Zengler verfasserin aut In mSystems American Society for Microbiology, 2017 2(2017), 1 (DE-627)84597212X (DE-600)2844333-0 23795077 nnns volume:2 year:2017 number:1 https://doi.org/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba kostenfrei https://journals.asm.org/doi/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/toc/2379-5077 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2017 1
allfieldsSound	10.1128/mSystems.00142-16 doi (DE-627)DOAJ052402800 (DE-599)DOAJa0a28495f0d94002ab7ff2edef6fcdba DE-627 ger DE-627 rakwb eng QR1-502 Jennifer Levering verfasserin aut 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 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference Microbiology Christopher L. Dupont verfasserin aut Andrew E. Allen verfasserin aut Bernhard O. Palsson verfasserin aut Karsten Zengler verfasserin aut In mSystems American Society for Microbiology, 2017 2(2017), 1 (DE-627)84597212X (DE-600)2844333-0 23795077 nnns volume:2 year:2017 number:1 https://doi.org/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/article/a0a28495f0d94002ab7ff2edef6fcdba kostenfrei https://journals.asm.org/doi/10.1128/mSystems.00142-16 kostenfrei https://doaj.org/toc/2379-5077 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2017 1
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authorswithroles_txt_mv	Jennifer Levering @@aut@@ Christopher L. Dupont @@aut@@ Andrew E. Allen @@aut@@ Bernhard O. Palsson @@aut@@ Karsten Zengler @@aut@@
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callnumber-first	Q - Science
author	Jennifer Levering
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topic_title	QR1-502 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 Phaeodactylum tricornutum coregulated genes genome-scale metabolic network reconstruction integrated network modeling regulatory network inference
topic	misc QR1-502 misc Phaeodactylum tricornutum misc coregulated genes misc genome-scale metabolic network reconstruction misc integrated network modeling misc regulatory network inference misc Microbiology
topic_unstemmed	misc QR1-502 misc Phaeodactylum tricornutum misc coregulated genes misc genome-scale metabolic network reconstruction misc integrated network modeling misc regulatory network inference misc Microbiology
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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
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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
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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
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title_auth	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	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.
abstractGer	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.
abstract_unstemmed	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.
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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
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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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