Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana
Abstract
Diatoms are one of the most productive and successful photosynthetic taxa on Earth and possess attributes such as rapid growth rates and production of lipids, making them candidate sources of renewable fuels. Despite their significance, few details of the mechanisms used to regulate growth and carbon metabolism are currently known, hindering metabolic engineering approaches to enhance productivity. To characterize the transcript level component of metabolic regulation, genome-wide changes in transcript abundance were documented in the model diatom Thalassiosira pseudonana on a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of coregulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes. Coordinated transcript level responses to silicon starvation are probably driven by signals linked to cell cycle progression and shifts in photophysiology. A mechanistic understanding of how this is accomplished will aid efforts to engineer metabolism for development of algal-derived biofuels.
- Authors:
-
- Univ. of California, San Diego, CA (United States). Scripps Institution of Oceanography; J. Craig Venter Inst. (JCVI), La Jolla, CA (United States)
- Univ. of California, San Diego, CA (United States). Scripps Institution of Oceanography
- Publication Date:
- Research Org.:
- Univ. of California, San Diego, CA (United States); J. Craig Venter Inst. (JCVI), La Jolla, CA (United States)
- Sponsoring Org.:
- USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office (BETO); USDOE Office of Science (SC), Biological and Environmental Research (BER); US Air Force Office of Scientific Research (AFOSR); National Science Foundation (NSF); California Energy Commission (United States); Gordon and Betty Moore Foundation (United States)
- OSTI Identifier:
- 1437597
- Grant/Contract Number:
- EE0001222; EE0003373; SC0006719; SC0008593; FA9550-08-1-0178; CBET-0903712; MCB-1024913; OCE-0727997; OCE-1140042; 500-10-039; GBMF3828
- Resource Type:
- Accepted Manuscript
- Journal Name:
- New Phytologist
- Additional Journal Information:
- Journal Volume: 210; Journal Issue: 3; Journal ID: ISSN 0028-646X
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; carbon metabolism; cell cycle; diatom; lipid metabolism; Thalassiosira pseudonana; transcriptomics
Citation Formats
Smith, Sarah R., Gle, Corine, Abbriano, Raffaela M., Traller, Jesse C., Davis, Aubrey, Trentacoste, Emily, Vernet, Maria, Allen, Andrew E., and Hildebrand, Mark. Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana. United States: N. p., 2016.
Web. doi:10.1111/nph.13843.
Smith, Sarah R., Gle, Corine, Abbriano, Raffaela M., Traller, Jesse C., Davis, Aubrey, Trentacoste, Emily, Vernet, Maria, Allen, Andrew E., & Hildebrand, Mark. Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana. United States. https://doi.org/10.1111/nph.13843
Smith, Sarah R., Gle, Corine, Abbriano, Raffaela M., Traller, Jesse C., Davis, Aubrey, Trentacoste, Emily, Vernet, Maria, Allen, Andrew E., and Hildebrand, Mark. Thu .
"Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana". United States. https://doi.org/10.1111/nph.13843. https://www.osti.gov/servlets/purl/1437597.
@article{osti_1437597,
title = {Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana},
author = {Smith, Sarah R. and Gle, Corine and Abbriano, Raffaela M. and Traller, Jesse C. and Davis, Aubrey and Trentacoste, Emily and Vernet, Maria and Allen, Andrew E. and Hildebrand, Mark},
abstractNote = {Diatoms are one of the most productive and successful photosynthetic taxa on Earth and possess attributes such as rapid growth rates and production of lipids, making them candidate sources of renewable fuels. Despite their significance, few details of the mechanisms used to regulate growth and carbon metabolism are currently known, hindering metabolic engineering approaches to enhance productivity. To characterize the transcript level component of metabolic regulation, genome-wide changes in transcript abundance were documented in the model diatom Thalassiosira pseudonana on a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of coregulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes. Coordinated transcript level responses to silicon starvation are probably driven by signals linked to cell cycle progression and shifts in photophysiology. A mechanistic understanding of how this is accomplished will aid efforts to engineer metabolism for development of algal-derived biofuels.},
doi = {10.1111/nph.13843},
journal = {New Phytologist},
number = 3,
volume = 210,
place = {United States},
year = {Thu Feb 04 00:00:00 EST 2016},
month = {Thu Feb 04 00:00:00 EST 2016}
}
Web of Science
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