TY  - JOUR
A1  - Smith, Sarah R.
A1  - Dupont, Chris L.
A1  - McCarthy, James K.
A1  - Broddrick, Jared T.
A1  - Obornik, Miroslav
A1  - Horak, Ales
A1  - Füssy, Zoltán
A1  - Cihlar, Jaromir
A1  - Kleessen, Sabrina
A1  - Zheng, Hong
A1  - McCrow, John P.
A1  - Hixson, Kim K.
A1  - Araujo, Wagner L.
A1  - Nunes-Nesi, Adriano
A1  - Fernie, Alisdair R.
A1  - Nikoloski, Zoran
A1  - Palsson, Bernhard O.
A1  - Allen, Andrew E.
T1  - Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom
JF  - Nature Communications
N2  - Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.
KW  - Biochemistry
KW  - Computational biology and bioinformatics
KW  - Evolution
KW  - Microbiology
KW  - Molecular biology
Y1  - 2019
U6  - https://doi.org/10.1038/s41467-019-12407-y
SN  - 2041-1723
VL  - 10
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Kleessen, Sabrina
A1  - Araujo, Wagner L.
A1  - Fernie, Alisdair R.
A1  - Nikoloski, Zoran
T1  - Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain
JF  - The journal of biological chemistry
N2  - Background: There are alternative substrates to the mitochondrial respiration.
 Results: Data-driven model-based analysis renders predictions of alternative substrates to the mitochondrial respiration.
 Conclusion: Metabolomics data in conjunction with flux-based models can discriminate among hypotheses based on enzymology alone.
 Significance: This analysis provides a basic framework for in silico studies of alternative pathways in metabolism.
Y1  - 2012
U6  - https://doi.org/10.1074/jbc.M111.310383
SN  - 0021-9258
VL  - 287
IS  - 14
SP  - 11122
EP  - 11131
PB  - American Society for Biochemistry and Molecular Biology
CY  - Bethesda
ER  -