Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K. Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol. 2011;11(1):163.
Article
PubMed Central
PubMed
Google Scholar
Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 2012;158(1):2–22.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hannah MA, Wiese D, Freund S, Fiehn O, Heyer AG, Hincha DK. Natural genetic variation of freezing tolerance in Arabidopsis. Plant Physiol. 2006;142:98–112.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hannah MA, Heyer AG, Hincha DK. A global survey of gene regulation during cold acclimation in Arabidopsis thaliana. PLoS Genet. 2005;1:179–96.
Article
CAS
Google Scholar
Juenger TE. Natural variation and genetic constraints on drought tolerance. Curr Opin Plant Biol. 2013.
Ikram S, Bedu M, Daniel-Vedele F, Chaillou S, Chardon F. Natural variation of Arabidopsis response to nitrogen availability. J Exp Bot. 2012;63(1):91–105.
Article
CAS
PubMed
Google Scholar
Clauw P, Coppens F, De Beuf K, Dhondt S, Van Daele T, Maleux K, et al. Leaf Responses to Mild Drought Stress in Natural Variants of Arabidopsis thaliana. Plant Physiol. 2015.
Nägele T, Heyer AG. Approximating subcellular organisation of carbohydrate metabolism during cold acclimation in different natural accessions of Arabidopsis thaliana. New Phytol. 2013;198(3):777–87.
Article
PubMed
Google Scholar
Samis KE, Murren CJ, Bossdorf O, Donohue K, Fenster CB, Malmberg RL, et al. Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana. Ecol Evol. 2012;2(6):1162–80.
Article
PubMed Central
PubMed
Google Scholar
Xin Z, Browse J. Cold comfort farm: the acclimation of plants to freezing temperatures. Plant Cell Environ. 2000;23:893–902.
Article
Google Scholar
Kosova K, Vitamvas P, Prasil IT, Renaut J. Plant proteome changes under abiotic stress--contribution of proteomics studies to understanding plant stress response. J Proteome. 2011;74(8):1301–22.
Article
CAS
Google Scholar
Guy C, Kaplan F, Kopka J, Selbig J, Hincha DK. Metabolomics of temperature stress. Physiol Plant. 2008;132(2):220–35.
CAS
PubMed
Google Scholar
Stitt M, Hurry V. A plant for all seasons: alterations in photosynthetic carbon metabolism during cold acclimation in Arabidopsis. Curr Opin Plant Biol. 2002;5:199–206.
Article
CAS
PubMed
Google Scholar
Cook D, Fowler S, Fiehn O, Thomashow MF. A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. Proc Natl Acad Sci U S A. 2004;101(42):15243–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Maruyama K, Takeda M, Kidokoro S, Yamada K, Sakuma Y, Urano K, et al. Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol. 2009;150(4):1972–80.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mikkelsen MD, Thomashow MF. A role for circadian evening elements in cold-regulated gene expression in Arabidopsis. Plant J. 2009.
Davey MP, Woodward FI, Quick WP. Intraspecfic variation in cold-temperature metabolic phenotypes of Arabidopsis lyrata ssp. petraea. Metabolomics. 2009;5(1):138–49.
Article
CAS
Google Scholar
Scarth GW, Levitt J. The frost-hardening mechanism of plant cells. Plant Physiol. 1937;12(1):51–78.
Article
PubMed Central
CAS
PubMed
Google Scholar
Klotke J, Kopka J, Gatzke N, Heyer AG. Impact of soluble sugar concentrations on the acquisition of freezing tolerance in accessions of Arabidopsis thaliana with contrasting cold adaptation - evidence for a role of raffinose in cold acclimation. Plant Cell Environ. 2004;27:1395–404.
Article
CAS
Google Scholar
Hincha DK, Sonnewald U, Willmitzer L, Schmitt JM. The role of sugar accumulation in leaf frost hardiness: investigations with transgenic tobacco expressing a bacterial pyrophosphatase or a yeast invertase gene. J Plant Physiol. 1996;147:604–10.
Article
CAS
Google Scholar
Huner NPA, Öquist G, Sarhan F. Energy balance and acclimation to light and cold. Trends Plant Sci. 1998;3(6):224–30.
Article
Google Scholar
Nägele T, Kandel BA, Frana S, Meissner M, Heyer AG. A systems biology approach for the analysis of carbohydrate dynamics during acclimation to low temperature in Arabidopsis thaliana. FEBS J. 2011;278(3):506–18.
Article
PubMed
Google Scholar
Muller B, Pantin F, Genard M, Turc O, Freixes S, Piques M, et al. Water deficits uncouple growth from photosynthesis, increase C content, and modify the relationships between C and growth in sink organs. J Exp Bot. 2011;62(6):1715–29.
Article
CAS
PubMed
Google Scholar
Goldschmidt EE, Huber SC. Regulation of photosynthesis by End-product accumulation in leaves of plants storing starch, sucrose, and hexose sugars. Plant Physiol. 1992;99(4):1443–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sheen J. Feedback control of gene expression. Photosynth Res. 1994;39(3):427–38.
Article
CAS
PubMed
Google Scholar
Savitch LV, Barker-Astrom J, Ivanov AG, Hurry V, Oquist G, Huner NP, et al. Cold acclimation of Arabidopsis thaliana results in incomplete recovery of photosynthetic capacity, associated with an increased reduction of the chloroplast stroma. Planta. 2001;214(2):295–303.
Article
CAS
PubMed
Google Scholar
Strand A, Hurry V, Gustafsson P, Gardeström P. Development of Arabidopsis thaliana leaves at low temperatures releases the suppression of photosynthesis and photosynthetic gene expression despite the accumulation of soluble carbohydrates. Plant J. 1997;12(3):605–14.
Article
CAS
PubMed
Google Scholar
Masclaux-Daubresse C, Purdy S, Lemaitre T, Pourtau N, Taconnat L, Renou J-P, et al. Genetic variation suggests interaction between cold acclimation and metabolic regulation of leaf senescence. Plant Physiol. 2007;143(1):434–46.
Article
PubMed Central
CAS
PubMed
Google Scholar
Talts P, Parnik T, Gardestrom P, Keerberg O. Respiratory acclimation in Arabidopsis thaliana leaves at low temperature. J Plant Physiol. 2004;161(5):573–9.
Article
CAS
PubMed
Google Scholar
Weckwerth W. Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteomics. 2011;75(1):284–305.
Article
CAS
PubMed
Google Scholar
van Norman JM, Benfey PN. Arabidopsis thaliana as a model organism in systems biology. Wiley Interdiscip Rev Syst Biol Med. 2009;1(3):372–9.
Article
PubMed Central
PubMed
Google Scholar
Hoffmann MH. Biogeography of Arabidopsis thaliana (L.) heynh. (brassicaceae). J Biogeography. 2002;29:125–34.
Article
Google Scholar
Koornneef M, Alonso-Blanco C, Vreugdenhil D. Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol. 2004;55:141–72.
Article
CAS
PubMed
Google Scholar
Lawrence MJ. Variations in natural populations of Arabidopsis thaliana (L.) Heynh. 1976. p. 167–90.
Google Scholar
Mishra A, Mishra KB, Höermiller II, Heyer AG, Nedbal L. Chlorophyll fluorescence emission as a reporter on cold tolerance in Arabidopsis thaliana accessions. Plant Signal Behav. 2011;6(2):301–10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brunetti C, George RM, Tattini M, Field K, Davey MP. Metabolomics in plant environmental physiology. J Exp Bot. 2013;64(13):4011–20.
Article
CAS
PubMed
Google Scholar
Chen D, Neumann K, Friedel S, Kilian B, Chen M, Altmann T, et al. Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis. Plant Cell Online. 2014;26(12):4636–55.
Article
CAS
Google Scholar
Weckwerth W. Green systems biology—from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. J Proteome. 2011;75(1):284–305.
Article
CAS
Google Scholar
Beckers GJ, Hoehenwarter W, Rohrig H, Conrath U, Weckwerth W. Tandem metal-oxide affinity chromatography for enhanced depth of phosphoproteome analysis. Methods Mol Biol. 2014;1072:621–32.
Article
CAS
PubMed
Google Scholar
Chen Y, Hoehenwarter W, Weckwerth W. Comparative analysis of phytohormone responsive phosphoproteins in Arabidopsis thaliana using TiO2phosphopeptide enrichment and mass accuracy precursor alignment. Plant J. 2010;63(1):1–17.
CAS
PubMed
Google Scholar
Weckwerth W. Unpredictability of metabolism—the key role of metabolomics science in combination with next-generation genome sequencing. Anal Bioanal Chem. 2011;400(7):1967–78.
Article
PubMed Central
CAS
PubMed
Google Scholar
Weckwerth W, Wienkoop S, Hoehenwarter W, Egelhofer V, Sun X. From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform, Plant Proteomics. New York: Humana Press; 2014. p. 15–27.
Google Scholar
Morgenthal K, Wienkoop S, Scholz M, Selbig J, Weckwerth W. Correlative GC-TOF-MS-based metabolite profiling and LC-MS-based protein profiling reveal time-related systemic regulation of metabolite–protein networks and improve pattern recognition for multiple biomarker selection. Metabolomics. 2005;1(2):109–21.
Article
CAS
Google Scholar
Barrero-Gil J, Salinas J. Post-translational regulation of cold acclimation response. Plant Sci. 2013;205–206:48–54.
Article
PubMed
Google Scholar
Zhu J, Dong CH, Zhu JK. Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Curr Opin Plant Biol. 2007;10(3):290–5.
Article
CAS
PubMed
Google Scholar
Hincha DK, Zuther E. Plant cold acclimation and freezing tolerance. Methods Mol Biol. 2014;1166:1–6.
Article
CAS
PubMed
Google Scholar
Tomé FS, Nägele T, Adamo M, Garg A, Marco-llorca C, Nukarinen E, et al. The low energy signaling network. Front Plant Sci. 2014;5:353.
PubMed Central
PubMed
Google Scholar
Brauner K, Hormiller I, Nägele T, Heyer AG. Exaggerated root respiration accounts for growth retardation in a starchless mutant of Arabidopsis thaliana. Plant J. 2014;79(1):82–91.
Article
CAS
PubMed
Google Scholar
Nägele T, Stutz S, Hörmiller II, Heyer AG. Identification of a metabolic bottleneck for cold acclimation in Arabidopsis thaliana. Plant J. 2012;72(1):102–14.
Article
PubMed
Google Scholar
Pons T. Interaction of temperature and irradiance effects on photosynthetic acclimation in two accessions of Arabidopsis thaliana. Photosynth Res. 2012;113(1–3):207–19.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sulpice R, Pyl E-T, Ishihara H, Trenkamp S, Steinfath M, Witucka-Wall H, et al. Starch as a major integrator in the regulation of plant growth. Proc Natl Acad Sci U S A. 2009;106(25):10348–53.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smith AM, Zeeman SC, Smith SM. Starch degradation. Annu Rev Plant Biol. 2005;56:73–98.
Article
CAS
PubMed
Google Scholar
Zeeman SC, Smith SM, Smith AM. The diurnal metabolism of leaf starch. Biochem J. 2007;401(1):13–28.
Article
CAS
PubMed
Google Scholar
Streb S, Eicke S, Zeeman SC. The simultaneous abolition of three starch hydrolases blocks transient starch breakdown in Arabidopsis. J Biol Chem. 2012;287(50):41745–56.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yano R, Nakamura M, Yoneyama T, Nishida I. Starch-related alpha-glucan/water dikinase is involved in the cold-induced development of freezing tolerance in Arabidopsis. Plant Physiol. 2005;138(2):837–46.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sicher R. Carbon partitioning and the impact of starch deficiency on the initial response of Arabidopsis to chilling temperatures. Plant Sci. 2011;181(2):167–76.
Article
CAS
PubMed
Google Scholar
Fincher GB. Molecular and cellular biology associated with endosperm mobilization in germinating cereal grains. Annu Rev Plant Physiol Plant Mol Biol. 1989;40(1):305–46.
Article
CAS
Google Scholar
Yu TS, Zeeman SC, Thorneycroft D, Fulton DC, Dunstan H, Lue WL, et al. alpha-Amylase is not required for breakdown of transitory starch in Arabidopsis leaves. J Biol Chem. 2005;280(11):9773–9.
Article
CAS
PubMed
Google Scholar
Santelia D, Trost P, Sparla F. New insights into redox control of starch degradation. Curr Opin Plant Biol. 2015;25:1–9.
Article
CAS
PubMed
Google Scholar
Lao NT, Schoneveld O, Mould RM, Hibberd JM, Gray JC, Kavanagh TA. An Arabidopsis gene encoding a chloroplast-targeted beta-amylase. Plant J. 1999;20(5):519–27.
Article
CAS
PubMed
Google Scholar
Kaplan F, Guy CL. RNA interference of Arabidopsis beta-amylase8 prevents maltose accumulation upon cold shock and increases sensitivity of PSII photochemical efficiency to freezing stress. Plant J. 2005;44(5):730–43.
Article
CAS
PubMed
Google Scholar
Monroe JD, Storm AR, Badley EM, Lehman MD, Platt SM, Saunders LK, et al. Beta-Amylase1 and beta-amylase3 are plastidic starch hydrolases in Arabidopsis that seem to be adapted for different thermal, pH, and stress conditions. Plant Physiol. 2014;166(4):1748–63.
Article
PubMed Central
PubMed
Google Scholar
Wienkoop S, Morgenthal K, Wolschin F, Scholz M, Selbig J, Weckwerth W. Integration of metabolomic and proteomic phenotypes analysis of data covariance dissects starch and RFO metabolism from Low and high temperature compensation response in Arabidopsis thaliana. Mol Cell Proteomics. 2008;7(9):1725–36.
Article
PubMed Central
CAS
PubMed
Google Scholar
Thomashow MF. Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol. 2010;154(2):571–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 1998;16(4):433–42.
Article
CAS
PubMed
Google Scholar
Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, et al. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell. 1998;10(8):1391–406.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gilmour SJ, Fowler SG, Thomashow MF. Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities. Plant Mol Biol. 2004;54(5):767–81.
Article
CAS
PubMed
Google Scholar
Jaglo-Ottosen KR, Gilmour SJ, Zarka DK, Schabenberger O, Thomashow MF. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science. 1998;280:104–6.
Article
CAS
PubMed
Google Scholar
Rekarte-Cowie I, Ebshish OS, Mohamed KS, Pearce RS. Sucrose helps regulate cold acclimation of Arabidopsis thaliana. J Exp Bot. 2008;59(15):4205–17.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lastdrager J, Hanson J, Smeekens S. Sugar signals and the control of plant growth and development. J Exp Bot. 2014;65(3):799–807.
Article
CAS
PubMed
Google Scholar
Monfared MM, Simon MK, Meister RJ, Roig-Villanova I, Kooiker M, Colombo L, et al. Overlapping and antagonistic activities of BASIC PENTACYSTEINE genes affect a range of developmental processes in Arabidopsis. Plant J. 2011;66(6):1020–31.
Article
CAS
PubMed
Google Scholar
Lee SH, Chung GC, Jang JY, Ahn SJ, Zwiazek JJ. Overexpression of PIP2;5 aquaporin alleviates effects of Low root temperature on cell hydraulic conductivity and growth in Arabidopsis. Plant Physiol. 2012;159(1):479–88.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schulze WX, Schneider T, Starck S, Martinoia E, Trentmann O. Cold acclimation induces changes in Arabidopsis tonoplast protein abundance and activity and alters phosphorylation of tonoplast monosaccharide transporters. Plant J. 2012;69(3):529–41.
Article
CAS
PubMed
Google Scholar
Rampitsch C, Bykova NV. The beginnings of crop phosphoproteomics: exploring early warning systems of stress. Front Plant Sci. 2012;3:144.
Article
PubMed Central
PubMed
Google Scholar
Doerfler H, Lyon D, Nägele T, Sun X, Fragner L, Hadacek F, et al. Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism. Metabolomics. 2013;9(3):564–74.
Article
PubMed Central
CAS
PubMed
Google Scholar
Weckwerth W, Wenzel K, Fiehn O. Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co‐regulation in biochemical networks. Proteomics. 2004;4(1):78–83.
Article
CAS
PubMed
Google Scholar
Colby T, Röhrig H, Harzen A, Schmidt J. Modified metal-oxide affinity enrichment combined with 2D-PAGE and analysis of phosphoproteomes. Methods Mol Biol. 2011;779:273–86.
Article
CAS
PubMed
Google Scholar
Furuhashi T, Nukarinen E, Ota S, Weckwerth W. Boron nitride as desalting material in combination with phosphopeptide enrichment in shotgun proteomics. Anal Biochem. 2014;452:16–8.
Article
CAS
PubMed
Google Scholar
Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R. Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods. 2007;4(3):231–7.
Article
CAS
PubMed
Google Scholar
Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26(12):1367–72.
Article
CAS
PubMed
Google Scholar
Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res. 2011;10(4):1794–805.
Article
CAS
PubMed
Google Scholar
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006;127(3):635–48.
Article
CAS
PubMed
Google Scholar
R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2013.
Google Scholar
Sun X, Weckwerth W. COVAIN: a toolbox for uni-and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data. Metabolomics. 2012;8(1):81–93.
Article
CAS
Google Scholar
von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, et al. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 2005;33(Database issue):D433–7.
Article
Google Scholar