Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii
Abstract
Microalgae-based biofuels are promising sources of alternative energy, but improvements throughout the production process are required to establish them as economically feasible. One of the most influential improvements would be a significant increase in lipid yields, which could be achieved by altering the regulation of lipid biosynthesis and accumulation. Chlamydomonas reinhardtii accumulates oil (triacylglycerols, TAG) in response to nitrogen (N) deprivation. Although a few important regulatory genes have been identified that are involved in controlling this process, a global understanding of the larger regulatory network has not been developed. In order to uncover this network in this species, a combined omics (transcriptomic, proteomic and metabolomic) analysis was applied to cells grown in a time course experiment after a shift from N-replete to N-depleted conditions. Changes in transcript and protein levels of 414 predicted transcription factors (TFs) and transcriptional regulators (TRs) were monitored relative to other genes. The TF and TR genes were thus classified by two separate measures: up-regulated versus down-regulated and early response versus late response relative to two phases of polar lipid synthesis (before and after TAG biosynthesis initiation). Lipidomic and primary metabolite profiling generated compound accumulation levels that were integrated with the transcript dataset and TF profilingmore »
- Authors:
-
- Washington State Univ., Pullman, WA (United States)
- New Mexico State Univ., Las Cruces, NM (United States)
- Donald Danforth Plant Science Center, St. Louis, MO (United States); National Center of Biomedical Analysis, Beijing (China)
- Michigan State Univ., East Lansing, MI (United States)
- Donald Danforth Plant Science Center, St. Louis, MO (United States); Univ. of North Carolina, Chapel Hill, NC (United States)
- Publication Date:
- Research Org.:
- Energy Frontier Research Centers (EFRC) (United States). Center for Advanced Biofuel Systems (CABS); Washington State Univ., Pullman, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1343282
- Grant/Contract Number:
- SC0001295
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Experimental Botany
- Additional Journal Information:
- Journal Volume: 66; Journal Issue: 15; Journal ID: ISSN 0022-0957
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; biofuel; Chlamydomonas reinhardtii; metabolomics; network analysis; proteomics; regulatory hubs; RNA-seq; transcription factors; transcriptional regulators
Citation Formats
Gargouri, Mahmoud, Park, Jeong -Jin, Holguin, F. Omar, Kim, Min -Jeong, Wang, Hongxia, Deshpande, Rahul R., Shachar-Hill, Yair, Hicks, Leslie M., and Gang, David R. Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii. United States: N. p., 2015.
Web. doi:10.1093/jxb/erv217.
Gargouri, Mahmoud, Park, Jeong -Jin, Holguin, F. Omar, Kim, Min -Jeong, Wang, Hongxia, Deshpande, Rahul R., Shachar-Hill, Yair, Hicks, Leslie M., & Gang, David R. Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii. United States. https://doi.org/10.1093/jxb/erv217
Gargouri, Mahmoud, Park, Jeong -Jin, Holguin, F. Omar, Kim, Min -Jeong, Wang, Hongxia, Deshpande, Rahul R., Shachar-Hill, Yair, Hicks, Leslie M., and Gang, David R. Thu .
"Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii". United States. https://doi.org/10.1093/jxb/erv217. https://www.osti.gov/servlets/purl/1343282.
@article{osti_1343282,
title = {Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii},
author = {Gargouri, Mahmoud and Park, Jeong -Jin and Holguin, F. Omar and Kim, Min -Jeong and Wang, Hongxia and Deshpande, Rahul R. and Shachar-Hill, Yair and Hicks, Leslie M. and Gang, David R.},
abstractNote = {Microalgae-based biofuels are promising sources of alternative energy, but improvements throughout the production process are required to establish them as economically feasible. One of the most influential improvements would be a significant increase in lipid yields, which could be achieved by altering the regulation of lipid biosynthesis and accumulation. Chlamydomonas reinhardtii accumulates oil (triacylglycerols, TAG) in response to nitrogen (N) deprivation. Although a few important regulatory genes have been identified that are involved in controlling this process, a global understanding of the larger regulatory network has not been developed. In order to uncover this network in this species, a combined omics (transcriptomic, proteomic and metabolomic) analysis was applied to cells grown in a time course experiment after a shift from N-replete to N-depleted conditions. Changes in transcript and protein levels of 414 predicted transcription factors (TFs) and transcriptional regulators (TRs) were monitored relative to other genes. The TF and TR genes were thus classified by two separate measures: up-regulated versus down-regulated and early response versus late response relative to two phases of polar lipid synthesis (before and after TAG biosynthesis initiation). Lipidomic and primary metabolite profiling generated compound accumulation levels that were integrated with the transcript dataset and TF profiling to produce a transcriptional regulatory network. In conclusion, evaluation of this proposed regulatory network led to the identification of several regulatory hubs that control many aspects of cellular metabolism, from N assimilation and metabolism, to central metabolism, photosynthesis and lipid metabolism.},
doi = {10.1093/jxb/erv217},
journal = {Journal of Experimental Botany},
number = 15,
volume = 66,
place = {United States},
year = {Thu May 28 00:00:00 EDT 2015},
month = {Thu May 28 00:00:00 EDT 2015}
}
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Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response
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The Evolutionary Origin of an Altruistic Gene
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Phytozome: a comparative platform for green plant genomics
journal, November 2011
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- Nucleic Acids Research, Vol. 40, Issue D1
Oil accumulation is controlled by carbon precursor supply for fatty acid synthesis in Chlamydomonas reinhardtii
journal, May 2012
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- Plant and Cell Physiology, Vol. 53, Issue 8
Overlapping Photoprotective Function of Vitamin E and Carotenoids in Chlamydomonas
journal, November 2011
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- Plant Physiology, Vol. 158, Issue 1
The Regulation of Photosynthetic Structure and Function during Nitrogen Deprivation in Chlamydomonas reinhardtii
journal, December 2014
- Juergens, Matthew T.; Deshpande, Rahul R.; Lucker, Ben F.
- Plant Physiology, Vol. 167, Issue 2
Zeaxanthin Accumulation in the Absence of a Functional Xanthophyll Cycle Protects Chlamydomonas reinhardtii from Photooxidative Stress
journal, March 2003
- Baroli, Irene; Do, An D.; Yamane, Tomoko
- The Plant Cell, Vol. 15, Issue 4
Etioplast Differentiation in Arabidopsis: Both PORA and PORB Restore the Prolamellar Body and Photoactive Protochlorophyllide–F655 to the cop1 Photomorphogenic Mutant
journal, February 1998
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