TY  - JOUR
A1  - Mettler, Tabea
A1  - Mühlhaus, Timo
A1  - Hemme, Dorothea
A1  - Schöttler, Mark Aurel
A1  - Rupprecht, Jens
A1  - Idoine, Adam
A1  - Veyel, Daniel
A1  - Pal, Sunil Kumar
A1  - Yaneva-Roder, Liliya
A1  - Winck, Flavia Vischi
A1  - Sommer, Frederik
A1  - Vosloh, Daniel
A1  - Seiwert, Bettina
A1  - Erban, Alexander
A1  - Burgos, Asdrubal
A1  - Arvidsson, Samuel Janne
A1  - Schoenfelder, Stephanie
A1  - Arnold, Anne
A1  - Guenther, Manuela
A1  - Krause, Ursula
A1  - Lohse, Marc
A1  - Kopka, Joachim
A1  - Nikoloski, Zoran
A1  - Müller-Röber, Bernd
A1  - Willmitzer, Lothar
A1  - Bock, Ralph
A1  - Schroda, Michael
A1  - Stitt, Mark
T1  - Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii
JF  - The plant cell
N2  - We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.
Y1  - 2014
U6  - https://doi.org/10.1105/tpc.114.124537
SN  - 1040-4651
SN  - 1532-298X
VL  - 26
IS  - 6
SP  - 2310
EP  - 2350
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - JOUR
A1  - Córdoba, Sandra Correa
A1  - Tong, Hao
A1  - Burgos, Asdrubal
A1  - Zhu, Feng
A1  - Alseekh, Saleh
A1  - Fernie, Alisdair R.
A1  - Nikoloski, Zoran
T1  - Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
JF  - Nature Communications
N2  - The use of automated tools to reconstruct lipid metabolic pathways is not warranted in plants. Here, the authors construct Plant Lipid Module for Arabidopsis rosette using constraint-based modeling, demonstrate its integration in other plant metabolic models, and use it to dissect the genetic architecture of lipid metabolism. 
Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.
KW  - Biochemical networks
KW  - Biochemical reaction networks
KW  - Genetic models
KW  - Plant molecular biology
Y1  - 2023
U6  - https://doi.org/10.1038/s41467-023-40644-9
SN  - 2041-1723
VL  - 14
IS  - 1
PB  - Springer Nature
CY  - London
ER  -