A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses
Abstract
Microalgae have reemerged as organisms of prime biotechnological interest due to their ability to synthesize a suite of valuable chemicals. To harness the capabilities of these organisms, we need a comprehensive systems-level understanding of their metabolism, which can be fundamentally achieved through large-scale mechanistic models of metabolism. In this study, we present a revised and significantly improved genome-scale metabolic model for the widely-studied microalga, Chlamydomonas reinhardtii. The model, iCre1355, represents a major advance over previous models, both in content and predictive power. iCre1355 encompasses a broad range of metabolic functions encoded across the nuclear, chloroplast and mitochondrial genomes accounting for 1355 genes (1460 transcripts), 2394 and 1133 metabolites. We found improved performance over the previous metabolic model based on comparisons of predictive accuracy across 306 phenotypes (from 81 mutants), lipid yield analysis and growth rates derived from chemostat-grown cells (under three conditions). Measurement of macronutrient uptake revealed carbon and phosphate to be good predictors of growth rate, while nitrogen consumption appeared to be in excess. We analyzed high-resolution time series transcriptomics data using iCre1355 to uncover dynamic pathway-level changes that occur in response to nitrogen starvation and changes in light intensity. This approach enabled accurate prediction of growth rates, themore »
- Authors:
-
- Institute for Systems Biology, Seattle, WA (United States)
- Institute for Systems Biology, Seattle, WA (United States); Friedrich-Schiller-Univ. Jena, Jena (Germany)
- Institute for Systems Biology, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States)
- Institute for Systems Biology, Seattle, WA (United States); Univ. of Washington, Seattle, WA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1378660
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The Plant Journal
- Additional Journal Information:
- Journal Volume: 84; Journal Issue: 6; Journal ID: ISSN 0960-7412
- Publisher:
- Society for Experimental Biology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; metabolic modeling; Chlamydomonas reinhardtii; constraint-based analysis; flux balance analysis; data integration; systems biology; biomass; lipid accumulation; photosynthesis
Citation Formats
Imam, Saheed, Schäuble, Sascha, Valenzuela, Jacob, Lopez Garcia de Lomana, Adrian, Carter, Warren, Price, Nathan D., and Baliga, Nitin S. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. United States: N. p., 2015.
Web. doi:10.1111/tpj.13059.
Imam, Saheed, Schäuble, Sascha, Valenzuela, Jacob, Lopez Garcia de Lomana, Adrian, Carter, Warren, Price, Nathan D., & Baliga, Nitin S. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. United States. https://doi.org/10.1111/tpj.13059
Imam, Saheed, Schäuble, Sascha, Valenzuela, Jacob, Lopez Garcia de Lomana, Adrian, Carter, Warren, Price, Nathan D., and Baliga, Nitin S. Tue .
"A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses". United States. https://doi.org/10.1111/tpj.13059. https://www.osti.gov/servlets/purl/1378660.
@article{osti_1378660,
title = {A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses},
author = {Imam, Saheed and Schäuble, Sascha and Valenzuela, Jacob and Lopez Garcia de Lomana, Adrian and Carter, Warren and Price, Nathan D. and Baliga, Nitin S.},
abstractNote = {Microalgae have reemerged as organisms of prime biotechnological interest due to their ability to synthesize a suite of valuable chemicals. To harness the capabilities of these organisms, we need a comprehensive systems-level understanding of their metabolism, which can be fundamentally achieved through large-scale mechanistic models of metabolism. In this study, we present a revised and significantly improved genome-scale metabolic model for the widely-studied microalga, Chlamydomonas reinhardtii. The model, iCre1355, represents a major advance over previous models, both in content and predictive power. iCre1355 encompasses a broad range of metabolic functions encoded across the nuclear, chloroplast and mitochondrial genomes accounting for 1355 genes (1460 transcripts), 2394 and 1133 metabolites. We found improved performance over the previous metabolic model based on comparisons of predictive accuracy across 306 phenotypes (from 81 mutants), lipid yield analysis and growth rates derived from chemostat-grown cells (under three conditions). Measurement of macronutrient uptake revealed carbon and phosphate to be good predictors of growth rate, while nitrogen consumption appeared to be in excess. We analyzed high-resolution time series transcriptomics data using iCre1355 to uncover dynamic pathway-level changes that occur in response to nitrogen starvation and changes in light intensity. This approach enabled accurate prediction of growth rates, the cessation of growth and accumulation of triacylglycerols during nitrogen starvation, and the temporal response of different growth-associated pathways to increased light intensity. Thus, iCre1355 represents an experimentally validated genome-scale reconstruction of C. reinhardtii metabolism that should serve as a useful resource for studying the metabolic processes of this and related microalgae.},
doi = {10.1111/tpj.13059},
journal = {The Plant Journal},
number = 6,
volume = 84,
place = {United States},
year = {Tue Oct 20 00:00:00 EDT 2015},
month = {Tue Oct 20 00:00:00 EDT 2015}
}
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Works referenced in this record:
Three Acyltransferases and Nitrogen-responsive Regulator Are Implicated in Nitrogen Starvation-induced Triacylglycerol Accumulation in Chlamydomonas
journal, March 2012
- Boyle, Nanette R.; Page, Mark Dudley; Liu, Bensheng
- Journal of Biological Chemistry, Vol. 287, Issue 19
Powering the planet: Chemical challenges in solar energy utilization
journal, October 2006
- Lewis, N. S.; Nocera, D. G.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 43, p. 15729-15735
Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures
journal, January 2014
- Zwiener, Isabella; Frisch, Barbara; Binder, Harald
- PLoS ONE, Vol. 9, Issue 1
RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations
journal, January 2012
- Kim, Joonhoon; Reed, Jennifer L.
- Genome Biology, Vol. 13, Issue 9
The rotary mechanism of ATP synthase
journal, December 2000
- Stock, Daniela; Gibbons, Clyde; Arechaga, Ignacio
- Current Opinion in Structural Biology, Vol. 10, Issue 6
The geographical distribution of fossil fuels unused when limiting global warming to 2 °C
journal, January 2015
- McGlade, Christophe; Ekins, Paul
- Nature, Vol. 517, Issue 7533
Microalgal carbon-dioxide-concentrating mechanisms: Chlamydomonas inorganic carbon transporters
journal, June 2007
- Spalding, M. H.
- Journal of Experimental Botany, Vol. 59, Issue 7
Impact of Oxidative Stress on Ascorbate Biosynthesis in Chlamydomonas via Regulation of the VTC2 Gene Encoding a GDP-l-galactose Phosphorylase
journal, March 2012
- Urzica, Eugen I.; Adler, Lital N.; Page, M. Dudley
- Journal of Biological Chemistry, Vol. 287, Issue 17
Biodiesel from algae: challenges and prospects
journal, June 2010
- Scott, Stuart A.; Davey, Matthew P.; Dennis, John S.
- Current Opinion in Biotechnology, Vol. 21, Issue 3
The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features
journal, April 2011
- Terashima, Mia; Specht, Michael; Hippler, Michael
- Current Genetics, Vol. 57, Issue 3
Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
journal, August 2013
- Guo, Yan; Sheng, Quanhu; Li, Jiang
- PLoS ONE, Vol. 8, Issue 8
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology
journal, December 2009
- Milne, Caroline B.; Kim, Pan-Jun; Eddy, James A.
- Biotechnology Journal, Vol. 4, Issue 12
Substrate inhibition of Chlamydomonas reinhardtii by acetate in heterotrophic culture
journal, January 1994
- Chen, Feng; Johns, Michael R.
- Process Biochemistry, Vol. 29, Issue 4
Locating proteins in the cell using TargetP, SignalP and related tools
journal, April 2007
- Emanuelsson, Olof; Brunak, Søren; von Heijne, Gunnar
- Nature Protocols, Vol. 2, Issue 4
Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013
- Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
- Nucleic Acids Research, Vol. 42, Issue D1
Chlamydomonas , a model system for studying the assembly and dynamics of photosynthetic complexes
journal, August 2002
- Rochaix, Jean-David
- FEBS Letters, Vol. 529, Issue 1
Green genes: bioinformatics and systems-biology innovations drive algal biotechnology
journal, December 2014
- Reijnders, Maarten J. M. F.; van Heck, Ruben G. A.; Lam, Carolyn M. C.
- Trends in Biotechnology, Vol. 32, Issue 12
Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function
journal, July 2011
- Petti, A. A.; Crutchfield, C. A.; Rabinowitz, J. D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 45
Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks
journal, January 2012
- Krasensky, J.; Jonak, C.
- Journal of Experimental Botany, Vol. 63, Issue 4
Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii
journal, June 2014
- Mettler, Tabea; Mühlhaus, Timo; Hemme, Dorothea
- The Plant Cell, Vol. 26, Issue 6
Identification of Novel Mitochondrial Protein Components of Chlamydomonas reinhardtii . A Proteomic Approach
journal, April 2003
- van Lis, Robert; Atteia, Ariane; Mendoza-Hernández, Guillermo
- Plant Physiology, Vol. 132, Issue 1
Metabolite Profiling of Chlamydomonas reinhardtii under Nutrient Deprivation
journal, November 2005
- Bölling, Christian; Fiehn, Oliver
- Plant Physiology, Vol. 139, Issue 4
A chloroplast pathway for the de novo biosynthesis of triacylglycerol in Chlamydomonas reinhardtii
journal, May 2011
- Fan, Jilian; Andre, Carl; Xu, Changcheng
- FEBS Letters, Vol. 585, Issue 12, p. 1985-1991
The Geological Record of Ocean Acidification
journal, March 2012
- Honisch, B.; Ridgwell, A.; Schmidt, D. N.
- Science, Vol. 335, Issue 6072
Proteomic analysis of a eukaryotic cilium
journal, July 2005
- Pazour, Gregory J.; Agrin, Nathan; Leszyk, John
- The Journal of Cell Biology, Vol. 170, Issue 1
Metabolic network reconstruction of Chlamydomonas offers insight into light‐driven algal metabolism
journal, January 2011
- Chang, Roger L.; Ghamsari, Lila; Manichaikul, Ani
- Molecular Systems Biology, Vol. 7, Issue 1
Analysis of Chlamydomonas thiamin metabolism in vivo reveals riboswitch plasticity
journal, August 2013
- Moulin, Michael; Nguyen, Ginnie T. D. T.; Scaife, Mark A.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 36
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
journal, October 2003
- Mahadevan, R.; Schilling, C. H.
- Metabolic Engineering, Vol. 5, Issue 4
Carotenoid deficiency triggers autophagy in the model green alga Chlamydomonas reinhardtii
journal, March 2012
- Pérez-Pérez, María Esther; Couso, Inmaculada; Crespo, José L.
- Autophagy, Vol. 8, Issue 3
Zeaxanthin Deficiency Enhances the High Light Sensitivity of an Ascorbate-Deficient Mutant of Arabidopsis
journal, August 2003
- Müller-Moulé, Patricia; Havaux, Michel; Niyogi, Krishna K.
- Plant Physiology, Vol. 133, Issue 2
The Pfam protein families database
journal, January 2004
- Bateman, Alex; Coin, Lachlan; Durbin, Richard
- Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141
Network-based prediction of human tissue-specific metabolism
journal, August 2008
- Shlomi, Tomer; Cabili, Moran N.; Herrgård, Markus J.
- Nature Biotechnology, Vol. 26, Issue 9
Remodeling of Membrane Lipids in Iron-starved Chlamydomonas
journal, August 2013
- Urzica, Eugen I.; Vieler, Astrid; Hong-Hermesdorf, Anne
- Journal of Biological Chemistry, Vol. 288, Issue 42
Impact of Anthropogenic CO2 on the CaCO3 System in the Oceans
journal, July 2004
- Feely, R. A.
- Science, Vol. 305, Issue 5682
Metabolic acclimation to excess light intensity in Chlamydomonas reinhardtii : High-light metabolomics of
journal, February 2013
- Davis, Maria C.; Fiehn, Oliver; Durnford, Dion G.
- Plant, Cell & Environment, Vol. 36, Issue 7
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
journal, January 2009
- Henry, Christopher S.; Zinner, Jenifer F.; Cohoon, Matthew P.
- Genome Biology, Vol. 10, Issue 6
Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism
journal, October 2010
- Miller, Rachel; Wu, Guangxi; Deshpande, Rahul R.
- Plant Physiology, Vol. 154, Issue 4
Effect of nitrogen starvation on ammonium assimilation by Chlamydomonas reinhardtii
journal, February 1989
- Menacho, Alberto; Vega, Jose M.
- Physiologia Plantarum, Vol. 75, Issue 2
Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance
journal, April 2011
- Kliphuis, Anna M. J.; Klok, Anne J.; Martens, Dirk E.
- Journal of Applied Phycology, Vol. 24, Issue 2
Synthesizing and Salvaging NAD+: Lessons Learned from Chlamydomonas reinhardtii
journal, September 2010
- Lin, Huawen; Kwan, Alan L.; Dutcher, Susan K.
- PLoS Genetics, Vol. 6, Issue 9
The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis
journal, February 2015
- Park, Jeong-Jin; Wang, Hongxia; Gargouri, Mahmoud
- The Plant Journal, Vol. 81, Issue 4
An Outlook on Microalgal Biofuels
journal, August 2010
- Wijffels, R. H.; Barbosa, M. J.
- Science, Vol. 329, Issue 5993, p. 796-799
Nitric oxide controls nitrate and ammonium assimilation in Chlamydomonas reinhardtii
journal, July 2013
- Sanz-Luque, Emanuel; Ocaña-Calahorro, Francisco; Llamas, Angel
- Journal of Experimental Botany, Vol. 64, Issue 11
Microalgae: The Potential for Carbon Capture
journal, October 2010
- Sayre, Richard
- BioScience, Vol. 60, Issue 9
Characterizing the Anaerobic Response of Chlamydomonas reinhardtii by Quantitative Proteomics
journal, February 2010
- Terashima, Mia; Specht, Michael; Naumann, Bianca
- Molecular & Cellular Proteomics, Vol. 9, Issue 7
Arrangement of the Multicopy H + -translocating Subunit c in the Membrane Sector of the Escherichia coli F 1 F 0 ATP Synthase
journal, July 1998
- Jones, Phil C.; Jiang, Weiping; Fillingame, Robert H.
- Journal of Biological Chemistry, Vol. 273, Issue 27
Algae Need Their Vitamins
journal, August 2006
- Croft, Martin T.; Warren, Martin J.; Smith, Alison G.
- Eukaryotic Cell, Vol. 5, Issue 8
Enhancement of extraplastidic oil synthesis in Chlamydomonas reinhardtii using a type-2 diacylglycerol acyltransferase with a phosphorus starvation-inducible promoter
journal, June 2014
- Iwai, Masako; Ikeda, Keiko; Shimojima, Mie
- Plant Biotechnology Journal, Vol. 12, Issue 6
A protocol for generating a high-quality genome-scale metabolic reconstruction
journal, January 2010
- Thiele, Ines; Palsson, Bernhard Ø
- Nature Protocols, Vol. 5, Issue 1
The Chlamydomonas genome project: a decade on
journal, October 2014
- Blaby, Ian K.; Blaby-Haas, Crysten E.; Tourasse, Nicolas
- Trends in Plant Science, Vol. 19, Issue 10
C HLAMYDOMONAS AS A M ODEL O RGANISM
journal, June 2001
- Harris, Elizabeth H.
- Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 52, Issue 1
Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival
journal, January 2013
- Duanmu, Deqiang; Casero, David; Dent, Rachel M.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 9
Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant
journal, November 2013
- Blaby, I. K.; Glaesener, A. G.; Mettler, T.
- The Plant Cell, Vol. 25, Issue 11
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
journal, October 2007
- Merchant, S. S.; Prochnik, S. E.; Vallon, O.
- Science, Vol. 318, Issue 5848, p. 245-250
The challenges of in silico biology
journal, November 2000
- Palsson, Bernhard
- Nature Biotechnology, Vol. 18, Issue 11
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
journal, October 1994
- Varma, Amit; Palsson, Bernhard O.
- Bio/Technology, Vol. 12, Issue 10
A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the -Proteobacterial Mitochondrial Ancestor
journal, April 2009
- Atteia, A.; Adrait, A.; Brugiere, S.
- Molecular Biology and Evolution, Vol. 26, Issue 7
Chapter 1 Basal Bodies
book, January 2008
- Marshall, Wallace F.
- Ciliary Function in Mammalian Development
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii
journal, January 2009
- Boyle, Nanette R.; Morgan, John A.
- BMC Systems Biology, Vol. 3, Issue 1
Characterization of an internal type-II NADH dehydrogenase from Chlamydomonas reinhardtii mitochondria
journal, July 2012
- Lecler, Renaud; Vigeolas, Hélène; Emonds-Alt, Barbara
- Current Genetics, Vol. 58, Issue 4
The KEGG databases at GenomeNet
journal, January 2002
- Kanehisa, M.
- Nucleic Acids Research, Vol. 30, Issue 1
Biodiesel from microalgae
journal, May 2007
- Chisti, Yusuf
- Biotechnology Advances, Vol. 25, Issue 3, p. 294-306
Molecular analysis of the Chlamydomonas nuclear gene encoding PsbW and demonstration that PsbW is a subunit of photosystem II, but not photosystem I
journal, May 2003
- Bishop, Cleo L.
- Plant Molecular Biology, Vol. 52, Issue 2, p. 285-289
The Mitochondrial Oxidative Phosphorylation Proteome of Chlamydomonas reinhardtii Deduced from the Genome Sequencing Project: Table I.
journal, February 2005
- Cardol, Pierre; González-Halphen, Diego; Reyes-Prieto, Adrian
- Plant Physiology, Vol. 137, Issue 2
Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana
journal, December 2008
- Branco-Price, Cristina; Kaiser, Kayla A.; Jang, Charles J. H.
- The Plant Journal, Vol. 56, Issue 5
Oxidative stress, antioxidants and stress tolerance
journal, September 2002
- Mittler, Ron
- Trends in Plant Science, Vol. 7, Issue 9
Proton-powered turbine of a plant motor
journal, May 2000
- Seelert, Holger; Poetsch, Ansgar; Dencher, Norbert A.
- Nature, Vol. 405, Issue 6785
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
journal, May 2005
- Alper, Hal; Jin, Yong-Su; Moxley, J. F.
- Metabolic Engineering, Vol. 7, Issue 3
Hypoxic survival requires a 2-on-2 hemoglobin in a process involving nitric oxide
journal, June 2013
- Hemschemeier, A.; Duner, M.; Casero, D.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 26
Shrinking the Metabolic Solution Space Using Experimental Datasets
journal, August 2012
- Reed, Jennifer L.
- PLoS Computational Biology, Vol. 8, Issue 8
Metabolic and gene expression changes triggered by nitrogen deprivation in the photoautotrophically grown microalgae Chlamydomonas reinhardtii and Coccomyxa sp. C-169
journal, March 2012
- Msanne, Joseph; Xu, Di; Konda, Anji Reddy
- Phytochemistry, Vol. 75
Systems and Trans -System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage
journal, October 2012
- Urzica, Eugen I.; Casero, David; Yamasaki, Hiroaki
- The Plant Cell, Vol. 24, Issue 10
Applications of genome‐scale metabolic reconstructions
journal, January 2009
- Oberhardt, Matthew A.; Palsson, Bernhard Ø; Papin, Jason A.
- Molecular Systems Biology, Vol. 5, Issue 1
Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
journal, January 2013
- McCloskey, Douglas; Palsson, Bernhard Ø; Feist, Adam M.
- Molecular Systems Biology, Vol. 9, Issue 1
Defining functional DNA elements in the human genome
journal, April 2014
- Kellis, M.; Wold, B.; Snyder, M. P.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 17
iMAT: an integrative metabolic analysis tool
journal, November 2010
- Zur, Hadas; Ruppin, Eytan; Shlomi, Tomer
- Bioinformatics, Vol. 26, Issue 24
Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps
journal, April 2011
- Castruita, Madeli; Casero, David; Karpowicz, Steven J.
- The Plant Cell, Vol. 23, Issue 4
Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment
journal, February 2015
- Kleessen, Sabrina; Irgang, Susann; Klie, Sebastian
- The Plant Journal, Vol. 81, Issue 5
Predotar: A tool for rapidly screening proteomes forN-terminal targeting sequences
journal, June 2004
- Small, Ian; Peeters, Nemo; Legeai, Fabrice
- PROTEOMICS, Vol. 4, Issue 6
Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production
journal, August 2009
- Colijn, Caroline; Brandes, Aaron; Zucker, Jeremy
- PLoS Computational Biology, Vol. 5, Issue 8
From RNA-seq reads to differential expression results
journal, January 2010
- Oshlack, Alicia; Robinson, Mark D.; Young, Matthew D.
- Genome Biology, Vol. 11, Issue 12
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation
journal, April 2007
- Park, J. H.; Lee, K. H.; Kim, T. Y.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 19, p. 7797-7802
pkn22 ( alr2502 ) encoding a putative Ser/Thr kinase in the cyanobacterium Anabaena sp. PCC 7120 is induced by both iron starvation and oxidative stress and regulates the expression of isiA
journal, September 2003
- Xu, Wen-Liang; Jeanjean, Robert; Liu, Yong-Ding
- FEBS Letters, Vol. 553, Issue 1-2
Identification of the peroxisomal targeting signal for cottonseed catalase
journal, August 1997
- Mullen, Robert T.; Lee, Michael S.; Trelease, Richard N.
- The Plant Journal, Vol. 12, Issue 2
The Pfam Protein Families Database
journal, January 2002
- Bateman, A.
- Nucleic Acids Research, Vol. 30, Issue 1
Biodiesel from Microalgae
conference, January 2017
- Nagarajan, R.; Jain, Aatmesh; Vora, Kamalkishore
- Symposium on International Automotive Technology 2017, SAE Technical Paper Series
The oligomeric state of c rings from cyanobacterial F-ATP synthases varies from 13 to 15
text, January 2007
- Pogoryelov, D.; Reichen, C.; Klyszejko, A. L.
- American Society for Microbiology
The Geological Record of Ocean Acidification
text, January 2012
- Baerbel, Hoenisch,; Andy, Ridgwell,; N., Schmidt, Daniela
- Columbia University
The Pfam Protein Families Database
journal, January 2000
- Bateman, A.
- Nucleic Acids Research, Vol. 28, Issue 1
Accomplishments in Genome-Scale In Silico Modeling for Industrial and Medical Biotechnology
text, January 2009
- Milne, Caroline B.; Kim, Pan-Jun; Eddy, James A.
- arXiv
Works referencing / citing this record:
Metabolic modelling and simulation of the light and dark metabolism of Chlamydomonas reinhardtii
journal, October 2018
- Shene, Carolina; Asenjo, Juan A.; Chisti, Yusuf
- The Plant Journal, Vol. 96, Issue 5
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina
journal, January 2020
- Fachet, Melanie; Witte, Carina; Flassig, Robert J.
- BMC Bioinformatics, Vol. 21, Issue 1
Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production
journal, July 2017
- Loira, Nicolás; Mendoza, Sebastian; Paz Cortés, María
- BMC Systems Biology, Vol. 11, Issue 1
Current status and applications of genome-scale metabolic models
journal, June 2019
- Gu, Changdai; Kim, Gi Bae; Kim, Won Jun
- Genome Biology, Vol. 20, Issue 1
Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models
journal, May 2018
- Aite, Méziane; Chevallier, Marie; Frioux, Clémence
- PLOS Computational Biology, Vol. 14, Issue 5
Metabolic flux analysis of heterotrophic growth in Chlamydomonas reinhardtii
journal, May 2017
- Boyle, Nanette R.; Sengupta, Neelanjan; Morgan, John A.
- PLOS ONE, Vol. 12, Issue 5
Algal Cell Factories: Approaches, Applications, and Potentials
journal, December 2016
- Fu, Weiqi; Chaiboonchoe, Amphun; Khraiwesh, Basel
- Marine Drugs, Vol. 14, Issue 12
Development of a Chlamydomonas reinhardtii metabolic network dynamic model to describe distinct phenotypes occurring at different CO 2 levels
journal, January 2018
- Mora Salguero, Daniela Alejandra; Fernández-Niño, Miguel; Serrano-Bermúdez, Luis Miguel
- PeerJ, Vol. 6
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift
journal, February 2020
- Belcour, Arnaud; Girard, Jean; Aite, Méziane
- iScience, Vol. 23, Issue 2
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift
journal, February 2020
- Belcour, Arnaud; Girard, Jean; Aite, Méziane
- iScience, Vol. 23, Issue 2
Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production
journal, July 2017
- Loira, Nicolás; Mendoza, Sebastian; Paz Cortés, María
- BMC Systems Biology, Vol. 11, Issue 1
Advances in metabolic modeling of oleaginous microalgae
journal, September 2018
- Tibocha-Bonilla, Juan D.; Zuñiga, Cristal; Godoy-Silva, Rubén D.
- Biotechnology for Biofuels, Vol. 11, Issue 1
Metabolic flux analysis of heterotrophic growth in Chlamydomonas reinhardtii
journal, May 2017
- Boyle, Nanette R.; Sengupta, Neelanjan; Morgan, John A.
- PLOS ONE, Vol. 12, Issue 5
An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models
journal, February 2020
- Bjerkelund Røkke, Gunvor; Hohmann-Marriott, Martin Frank; Almaas, Eivind
- PLOS ONE, Vol. 15, Issue 2
Algal Cell Factories: Approaches, Applications, and Potentials
journal, December 2016
- Fu, Weiqi; Chaiboonchoe, Amphun; Khraiwesh, Basel
- Marine Drugs, Vol. 14, Issue 12