REFERENCES
Abraham, P. E., Yin, H., Borland, A. M., Weighill, D., Lim, S. D., De Paoli, H. C., . . . Yang, X. (2016). Transcript, protein and metabolite temporal dynamics in the CAM plant Agave. Nat Plants, 2 , 16178. doi:10.1038/nplants.2016.178
Adam, K., & Hunter, T. (2018). Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes. Lab Invest, 98 (2), 233-247. doi:10.1038/labinvest.2017.118
Annunziata, M. G., Apelt, F., Carillo, P., Krause, U., Feil, R., Koehl, K., . . . Stitt, M. (2018). Response of Arabidopsis primary metabolism and circadian clock to low night temperature in a natural light environment. J Exp Bot, 69 (20), 4881-4895. doi:10.1093/jxb/ery276
Arent, S., Christensen, C. E., Pye, V. E., Norgaard, A., & Henriksen, A. (2010). The multifunctional protein in peroxisomal beta-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. J Biol Chem, 285 (31), 24066-24077. doi:10.1074/jbc.M110.106005
Baerenfaller, K., Massonnet, C., Walsh, S., Baginsky, S., Buhlmann, P., Hennig, L., . . . Gruissem, W. (2012). Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Mol Syst Biol, 8 , 606. doi:10.1038/msb.2012.39
Barboza-Barquero, L., Nagel, K. A., Jansen, M., Klasen, J. R., Kastenholz, B., Braun, S., . . . Fiorani, F. (2015). Phenotype of Arabidopsis thaliana semi-dwarfs with deep roots and high growth rates under water-limiting conditions is independent of the GA5 loss-of-function alleles. Ann Bot, 116 (3), 321-331. doi:10.1093/aob/mcv099
Barnes, W. J., & Anderson, C. T. (2017). Release, Recycle, Rebuild: Cell wall remodeling, autodegradation, and sugar salvage for new wall biosynthesis during plant development. Mol Plant . doi:10.1016/j.molp.2017.08.011
Bischoff, V., Desprez, T., Mouille, G., Vernhettes, S., Gonneau, M., & Hofte, H. (2011). Phytochrome regulation of cellulose synthesis in Arabidopsis. Curr Biol, 21 (21), 1822-1827. doi:10.1016/j.cub.2011.09.026
Blasing, O. E., Gibon, Y., Gunther, M., Hohne, M., Morcuende, R., Osuna, D., . . . Stitt, M. (2005). Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell, 17 (12), 3257-3281. doi:10.1105/tpc.105.035261
Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., & Heck, A. J. (2009). Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat Protoc, 4 (4), 484-494. doi:10.1038/nprot.2009.21
Boex-Fontvieille, E., Daventure, M., Jossier, M., Zivy, M., Hodges, M., & Tcherkez, G. (2013). Photosynthetic control of Arabidopsis leaf cytoplasmic translation initiation by protein phosphorylation.PLoS One, 8 (7), e70692. doi:10.1371/journal.pone.0070692
Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem, 72 , 248-254.
Chou, M. F., & Schwartz, D. (2011). Biological sequence motif discovery using motif-x. Curr Protoc Bioinformatics, Chapter 13 , Unit 13 15-24. doi:10.1002/0471250953.bi1315s35
Choudhary, M. K., Nomura, Y., Wang, L., Nakagami, H., & Somers, D. E. (2015). Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways. Mol Cell Proteomics, 14 (8), 2243-2260. doi:10.1074/mcp.M114.047183
Cosgrove, D. J. (2005). Growth of the plant cell wall. Nat Rev Mol Cell Biol, 6 (11), 850-861. doi:10.1038/nrm1746
Covington, M. F., Maloof, J. N., Straume, M., Kay, S. A., & Harmer, S. L. (2008). Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol, 9 (8), R130. doi:10.1186/gb-2008-9-8-r130
Dai, M., Xue, Q., McCray, T., Margavage, K., Chen, F., Lee, J. H., . . . Wang, H. (2013). The PP6 phosphatase regulates ABI5 phosphorylation and abscisic acid signaling in Arabidopsis. Plant Cell, 25 (2), 517-534. doi:10.1105/tpc.112.105767
Delatte, T., Trevisan, M., Parker, M. L., & Zeeman, S. C. (2005). Arabidopsis mutants Atisa1 and Atisa2 have identical phenotypes and lack the same multimeric isoamylase, which influences the branch point distribution of amylopectin during starch synthesis. Plant J, 41 (6), 815-830. doi:10.1111/j.1365-313X.2005.02348.x
Delker, C., Zolman, B. K., Miersch, O., & Wasternack, C. (2007). Jasmonate biosynthesis in Arabidopsis thaliana requires peroxisomal beta-oxidation enzymes–additional proof by properties of pex6 and aim1. Phytochemistry, 68 (12), 1642-1650. doi:10.1016/j.phytochem.2007.04.024
Duby, G., & Boutry, M. (2009). The plant plasma membrane proton pump ATPase: a highly regulated P-type ATPase with multiple physiological roles. Pflugers Arch, 457 (3), 645-655. doi:10.1007/s00424-008-0457-x
Flis, A., Fernandez, A. P., Zielinski, T., Mengin, V., Sulpice, R., Stratford, K., . . . Millar, A. J. (2015). Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. Open Biol, 5 (10). doi:10.1098/rsob.150042
Gibon, Y., Pyl, E. T., Sulpice, R., Lunn, J. E., Hohne, M., Gunther, M., & Stitt, M. (2009). Adjustment of growth, starch turnover, protein content and central metabolism to a decrease of the carbon supply when Arabidopsis is grown in very short photoperiods. Plant Cell and Environment, 32 (7), 859-874. doi:10.1111/j.1365-3040.2009.01965.x
Gibon, Y., Usadel, B., Blaesing, O. E., Kamlage, B., Hoehne, M., Trethewey, R., & Stitt, M. (2006). Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol, 7 (8), R76. doi:10.1186/gb-2006-7-8-R76
Graf, A., Coman, D., Uhrig, R. G., Walsh, S., Flis, A., Stitt, M., & Gruissem, W. (2017). Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation. Open Biol, 7 (3). doi:10.1098/rsob.160333
Grossmann, J., Roschitzki, B., Panse, C., Fortes, C., Barkow-Oesterreicher, S., Rutishauser, D., & Schlapbach, R. (2010). Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods. J Proteomics, 73 (9), 1740-1746. doi:10.1016/j.jprot.2010.05.011
Guan, P. (2017). Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis. Front Plant Sci, 8 , 1697. doi:10.3389/fpls.2017.01697
Heazlewood, J. L., Durek, P., Hummel, J., Selbig, J., Weckwerth, W., Walther, D., & Schulze, W. X. (2008). PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res, 36 (Database issue), D1015-1021. doi:10.1093/nar/gkm812
Hughes, M. E., Hogenesch, J. B., & Kornacker, K. (2010). JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms, 25 (5), 372-380. doi:10.1177/0748730410379711
Hsiao, A. S., Haslam, R. P., Michaelson, L. V., Liao, P., Napier, J. A., & Chye, M. L. (2014). Gene expression in plant lipid metabolism in Arabidopsis seedlings. PLoS One, 9(9), e107372. doi:10.1371/journal.pone.0107372
Ivakov, A., Flis, A., Apelt, F., Funfgeld, M., Scherer, U., Stitt, M., . . . Suslov, D. (2017). Cellulose Synthesis and Cell Expansion Are Regulated by Different Mechanisms in Growing Arabidopsis Hypocotyls.Plant Cell, 29 (6), 1305-1315. doi:10.1105/tpc.16.00782
Jackson, R. J., Hellen, C. U., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation.Nat Rev Mol Cell Biol, 11 (2), 113-127. doi:10.1038/nrm2838
Jiang, T., Zhang, X. F., Wang, X. F., & Zhang, D. P. (2011). Arabidopsis 3-ketoacyl-CoA thiolase-2 (KAT2), an enzyme of fatty acid beta-oxidation, is involved in ABA signal transduction. Plant Cell Physiol, 52 (3), 528-538. doi:10.1093/pcp/pcr008
Julkowska, M. M., McLoughlin, F., Galvan-Ampudia, C. S., Rankenberg, J. M., Kawa, D., Klimecka, M., . . . Testerink, C. (2015). Identification and functional characterization of the Arabidopsis Snf1-related protein kinase SnRK2.4 phosphatidic acid-binding domain. Plant Cell Environ, 38 (3), 614-624. doi:10.1111/pce.12421
Kanekatsu, M., Saito, H., Motohashi, K., & Hisabori, T. (1998). The beta subunit of chloroplast ATP synthase (CF0CF1-ATPase) is phosphorylated by casein kinase II. Biochemistry and Molecular Biology International, 46 (1), 99-105.
Kerk, D., Templeton, G., & Moorhead, G. B. (2008). Evolutionary radiation pattern of novel protein phosphatases revealed by analysis of protein data from the completely sequenced genomes of humans, green algae, and higher plants. Plant Physiol, 146 (2), 351-367. doi:10.1104/pp.107.111393
Kim, S. C., Nusinow, D. A., Sorkin, M. L., Pruneda-Paz, J., & Wang, X. (2019). Interaction and Regulation Between Lipid Mediator Phosphatidic Acid and Circadian Clock Regulators. Plant Cell, 31(2), 399-416. doi:10.1105/tpc.18.00675
Kotting, O., Kossmann, J., Zeeman, S. C., & Lloyd, J. R. (2010). Regulation of starch metabolism: the age of enlightenment? Curr Opin Plant Biol, 13 (3), 321-329. doi:10.1016/j.pbi.2010.01.003
Krahmer, J., Hindle, M., Perby, L., Nielson, T. H., VanOoijen, G., Halliday, K. J., . . . Millar, A. J. (2019). Circadian protein regulation in the green lineage II. The clock gene circuit controls a phospho-dawn in Arabidopsis thaliana. bioRXiv . doi:10.1101/760892
Kusakina, J., & Dodd, A. N. (2012). Phosphorylation in the plant circadian system. Trends Plant Sci, 17 (10), 575-583. doi:10.1016/j.tplants.2012.06.008
Le, H., Browning, K. S., & Gallie, D. R. (2000). The phosphorylation state of poly(A)-binding protein specifies its binding to poly(A) RNA and its interaction with eukaryotic initiation factor (eIF) 4F, eIFiso4F, and eIF4B. J Biol Chem, 275 (23), 17452-17462. doi:10.1074/jbc.M001186200
Lehti-Shiu, M. D., & Shiu, S. H. (2012). Diversity, classification and function of the plant protein kinase superfamily. Philos Trans R Soc Lond B Biol Sci, 367 (1602), 2619-2639. doi:10.1098/rstb.2012.0003
Li, F., Li, M., Wang, P., Cox, K. L., Jr., Duan, L., Dever, J. K., . . . He, P. (2017). Regulation of cotton (Gossypium hirsutum) drought responses by mitogen-activated protein (MAP) kinase cascade-mediated phosphorylation of GhWRKY59. New Phytol, 215 (4), 1462-1475. doi:10.1111/nph.14680
Li, G., Zhang, L., Wang, M., Di, D., Kronzucker, H. J., & Shi, W. (2019). The Arabidopsis AMOT1/EIN3 gene plays an important role in the amelioration of ammonium toxicity. J Exp Bot, 70 (4), 1375-1388. doi:10.1093/jxb/ery457
Li, L., Nelson, C. J., Trosch, J., Castleden, I., Huang, S., & Millar, A. H. (2017). Protein Degradation Rate in Arabidopsis thaliana Leaf Growth and Development. Plant Cell, 29 (2), 207-228. doi:10.1105/tpc.16.00768
Lillo, C. (2008). Signalling cascades integrating light-enhanced nitrate metabolism. Biochem J, 415 (1), 11-19. doi:10.1042/BJ20081115
Lillo, C., Meyer, C., Lea, U. S., Provan, F., & Oltedal, S. (2004). Mechanism and importance of post-translational regulation of nitrate reductase. J Exp Bot, 55 (401), 1275-1282. doi:10.1093/jxb/erh132
Lin, D., Nagawa, S., Chen, J., Cao, L., Chen, X., Xu, T., . . . Yang, Z. (2012). A ROP GTPase-dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Curr Biol, 22 (14), 1319-1325. doi:10.1016/j.cub.2012.05.019
Lu, S. X., Liu, H., Knowles, S. M., Li, J., Ma, L., Tobin, E. M., & Lin, C. (2011). A role for protein kinase casein kinase2 alpha-subunits in the Arabidopsis circadian clock. Plant Physiol, 157 (3), 1537-1545. doi:10.1104/pp.111.179846
Ma, C., Haslbeck, M., Babujee, L., Jahn, O., & Reumann, S. (2006). Identification and characterization of a stress-inducible and a constitutive small heat-shock protein targeted to the matrix of plant peroxisomes. Plant Physiol, 141 (1), 47-60. doi:10.1104/pp.105.073841
Manning, G., Whyte, D. B., Martinez, R., Hunter, T., & Sudarsanam, S. (2002). The protein kinase complement of the human genome.Science, 298 (5600), 1912-1934. doi:10.1126/science.1075762
Marti Ruiz, M. C., Hubbard, K. E., Gardner, M. J., Jung, H. J., Aubry, S., Hotta, C. T., . . . Webb, A. A. R. (2018). Circadian oscillations of cytosolic free calcium regulate the Arabidopsis circadian clock.Nat Plants, 4 (9), 690-698. doi:10.1038/s41477-018-0224-8
Martin-Perez, M., & Villen, J. (2017). Determinants and Regulation of Protein Turnover in Yeast. Cell Systems, 5 (3), 283-294 e285. doi:10.1016/j.cels.2017.08.008
Mockler, T. C., Michael, T. P., Priest, H. D., Shen, R., Sullivan, C. M., Givan, S. A., . . . Chory, J. (2007). The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol, 72 , 353-363. doi:10.1101/sqb.2007.72.006
Moorhead, G., Douglas, P., Cotelle, V., Harthill, J., Morrice, N., Meek, S., . . . MacKintosh, C. (1999). Phosphorylation-dependent interactions between enzymes of plant metabolism and 14-3-3 proteins. Plant J, 18 (1), 1-12. doi:10.1046/j.1365-313x.1999.00417.x
Moorhead, G. B., Trinkle-Mulcahy, L., Nimick, M., De Wever, V., Campbell, D. G., Gourlay, R., . . . Lamond, A. I. (2008). Displacement affinity chromatography of protein phosphatase one (PP1) complexes.BMC Biochem, 9 , 28. doi:10.1186/1471-2091-9-28
Muench, D. G., Zhang, C., & Dahodwala, M. (2012). Control of cytoplasmic translation in plants. Wiley Interdiscip Rev RNA, 3 (2), 178-194. doi:10.1002/wrna.1104
Munnik, T., Ligterink, W., Meskiene, I. I., Calderini, O., Beyerly, J., Musgrave, A., & Hirt, H. (1999). Distinct osmo-sensing protein kinase pathways are involved in signalling moderate and severe hyper-osmotic stress. Plant J, 20 (4), 381-388. doi:10.1046/j.1365-313x.1999.00610.x
Nakagami, H., Sugiyama, N., Mochida, K., Daudi, A., Yoshida, Y., Toyoda, T., . . . Shirasu, K. (2010). Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol, 153 (3), 1161-1174. doi:10.1104/pp.110.157347
Nakamura, M., Claes, A. R., Grebe, T., Hermkes, R., Viotti, C., Ikeda, Y., & Grebe, M. (2018). Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol, 176 (1), 378-391. doi:10.1104/pp.17.00713
Nakamura, Y. (2018). Membrane Lipid Oscillation: An Emerging System of Molecular Dynamics in the Plant Membrane. Plant Cell Physiol, 59 (3), 441-447. doi:10.1093/pcp/pcy023
Nakamura, Y., Andres, F., Kanehara, K., Liu, Y. C., Coupland, G., & Dormann, P. (2014). Diurnal and circadian expression profiles of glycerolipid biosynthetic genes in Arabidopsis. Plant Signal Behav, 9 (9), e29715. doi:10.4161/psb.29715
Nohales, M. A., & Kay, S. A. (2016). Molecular mechanisms at the core of the plant circadian oscillator. Nat Struct Mol Biol, 23 (12), 1061-1069. doi:10.1038/nsmb.3327
Oakenfull, R. J., & Davis, S. J. (2017). Shining a light on the Arabidopsis circadian clock. Plant Cell Environ . doi:10.1111/pce.13033
Olas, J. J., Van Dingenen, J., Abel, C., Dzialo, M. A., Feil, R., Krapp, A., . . . Wahl, V. (2019). Nitrate acts at the Arabidopsis thaliana shoot apical meristem to regulate flowering time. New Phytol, 223 (2), 814-827. doi:10.1111/nph.15812
Olas, J. J., & Wahl, V. (2019). Tissue-specific NIA1 and NIA2 expression in Arabidopsis thaliana. Plant Signal Behav, 14 (11), 1656035. doi:10.1080/15592324.2019.1656035
Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., & Mann, M. (2006). Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell, 127 (3), 635-648. doi:10.1016/j.cell.2006.09.026
Pal, S. K., Liput, M., Piques, M., Ishihara, H., Obata, T., Martins, M. C., . . . Stitt, M. (2013). Diurnal changes of polysome loading track sucrose content in the rosette of wild-type arabidopsis and the starchless pgm mutant. Plant Physiol, 162 (3), 1246-1265. doi:10.1104/pp.112.212258
Pan, R., Reumann, S., Lisik, P., Tietz, S., Olsen, L. J., & Hu, J. (2018). Proteome analysis of peroxisomes from dark-treated senescent Arabidopsis leaves. J Integr Plant Biol, 60 (11), 1028-1050. doi:10.1111/jipb.12670
Pinfield-Wells, H., Rylott, E. L., Gilday, A. D., Graham, S., Job, K., Larson, T. R., & Graham, I. A. (2005). Sucrose rescues seedling establishment but not germination of Arabidopsis mutants disrupted in peroxisomal fatty acid catabolism. Plant J, 43 (6), 861-872. doi:10.1111/j.1365-313X.2005.02498.x
Piques, M., Schulze, W. X., Hohne, M., Usadel, B., Gibon, Y., Rohwer, J., & Stitt, M. (2009). Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol, 5 , 314. doi:10.1038/msb.2009.68
Qin, Q., Wang, W., Guo, X., Yue, J., Huang, Y., Xu, X., . . . Hou, S. (2014). Arabidopsis DELLA protein degradation is controlled by a type-one protein phosphatase, TOPP4. PLoS Genet, 10 (7), e1004464. doi:10.1371/journal.pgen.1004464
Rao, R. S., Thelen, J. J., & Miernyk, J. A. (2014). In silico analysis of protein Lys-N()-acetylation in plants. Front Plant Sci, 5 , 381. doi:10.3389/fpls.2014.00381
Reiland, S., Messerli, G., Baerenfaller, K., Gerrits, B., Endler, A., Grossmann, J., . . . Baginsky, S. (2009). Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol, 150 (2), 889-903. doi:10.1104/pp.109.138677
Rigbolt, K. T., Vanselow, J. T., & Blagoev, B. (2011). GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data. Mol Cell Proteomics, 10 (8), O110 007450. doi:10.1074/mcp.O110.007450
Robles, M. S., Humphrey, S. J., & Mann, M. (2017). Phosphorylation Is a Central Mechanism for Circadian Control of Metabolism and Physiology.Cell Metab, 25 (1), 118-127. doi:10.1016/j.cmet.2016.10.004
Schwartz, D., & Gygi, S. P. (2005). An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol, 23(11), 1391-1398. doi:10.1038/nbt1146
Seaton, D. D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A. J., & Gruissem, W. (2018). Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol, 14 (3), e7962. doi:10.15252/msb.20177962
Seluzicki, A., Burko, Y., & Chory, J. (2017). Dancing in the dark: darkness as a signal in plants. Plant Cell Environ . doi:10.1111/pce.12900
Simillion, C., Liechti, R., Lischer, H. E., Ioannidis, V., & Bruggmann, R. (2017). Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC Bioinformatics, 18 (1), 151. doi:10.1186/s12859-017-1571-6
Sondergaard, T. E., Schulz, A., & Palmgren, M. G. (2004). Energization of transport processes in plants. roles of the plasma membrane H+-ATPase. Plant Physiol, 136 (1), 2475-2482. doi:10.1104/pp.104.048231
Staiger, D., Shin, J., Johansson, M., & Davis, S. J. (2013). The circadian clock goes genomic. Genome Biol, 14 (6), 208. doi:10.1186/gb-2013-14-6-208
Sugiyama, N., Nakagami, H., Mochida, K., Daudi, A., Tomita, M., Shirasu, K., & Ishihama, Y. (2008). Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol, 4 , 193. doi:10.1038/msb.2008.32
Sullivan, S., Thomson, C. E., Kaiserli, E., & Christie, J. M. (2009). Interaction specificity of Arabidopsis 14-3-3 proteins with phototropin receptor kinases. FEBS Lett, 583 (13), 2187-2193. doi:10.1016/j.febslet.2009.06.011
Sullivan, S., Thomson, C. E., Lamont, D. J., Jones, M. A., & Christie, J. M. (2008). In vivo phosphorylation site mapping and functional characterization of Arabidopsis phototropin 1. Mol Plant, 1 (1), 178-194. doi:10.1093/mp/ssm017
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., . . . von Mering, C. (2017). The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Research, 45 (D1), D362-D368. doi:10.1093/nar/gkw937
Szydlowski, N., Ragel, P., Hennen-Bierwagen, T. A., Planchot, V., Myers, A. M., Merida, A., . . . Wattebled, F. (2011). Integrated functions among multiple starch synthases determine both amylopectin chain length and branch linkage location in Arabidopsis leaf starch. J Exp Bot, 62 (13), 4547-4559. doi:10.1093/jxb/err172
Tanz, S. K., Castleden, I., Hooper, C. M., Vacher, M., Small, I., & Millar, H. A. (2013). SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res, 41 (Database issue), D1185-1191. doi:10.1093/nar/gks1151
Türker, C., Akal, F., Joho, D., Panse, C., Barkow-Oesterreicher, S., Rehrauer, H., & Schlapbach, R. (2010). B-Fabric: the Swiss Army Knife for life sciences. 10: Proceedings of the 13th International Conference on Extending Database Technology . doi:10.1145/1739041.1739135
Turkina, M. V., Klang Arstrand, H., & Vener, A. V. (2011). Differential phosphorylation of ribosomal proteins in Arabidopsis thaliana plants during day and night. PLoS One, 6 (12), e29307. doi:10.1371/journal.pone.0029307
Uehara, T. N., Mizutani, Y., Kuwata, K., Hirota, T., Sato, A., Mizoi, J., . . . Nakamichi, N. (2019). Casein kinase 1 family regulates PRR5 and TOC1 in the Arabidopsis circadian clock. Proc Natl Acad Sci U S A, 116 (23), 11528-11536. doi:10.1073/pnas.1903357116
Uhrig, R. G., Labandera, A. M., & Moorhead, G. B. (2013). Arabidopsis PPP family of serine/threonine protein phosphatases: many targets but few engines. Trends Plant Sci, 18 (9), 505-513. doi:10.1016/j.tplants.2013.05.004
Uhrig, R. G., Schlapfer, P., Roschitzki, B., Hirsch-Hoffmann, M., & Gruissem, W. (2019). Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings.Plant J, 99 (1), 176-194. doi:10.1111/tpj.14315
Usadel, B., Blasing, O. E., Gibon, Y., Retzlaff, K., Hohne, M., Gunther, M., & Stitt, M. (2008). Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes. Plant Physiol, 146 (4), 1834-1861. doi:10.1104/pp.107.115592
Vu, L. D., Gevaert, K., & De Smet, I. (2018). Protein Language: Post-Translational Modifications Talking to Each Other. Trends Plant Sci, 23 (12), 1068-1080. doi:10.1016/j.tplants.2018.09.004
Wang, L., Wang, C., Liu, X., Cheng, J., Li, S., Zhu, J. K., & Gong, Z. (2019). Peroxisomal beta-oxidation regulates histone acetylation and DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A, 116 (21), 10576-10585. doi:10.1073/pnas.1904143116
Wang, P., Du, Y., & Song, C. P. (2011). Phosphorylation by MPK6: a conserved transcriptional modification mediates nitrate reductase activation and NO production? Plant Signal Behav, 6(6), 889-891. doi:10.4161/psb.6.6.15308
Wisniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009). Universal sample preparation method for proteome analysis. Nat Meth, 6 (5), 359-362. doi:http://www.nature.com/nmeth/journal/v6/n5/suppinfo/nmeth.1322_S1.html
Wurzinger, B., Nukarinen, E., Nagele, T., Weckwerth, W., & Teige, M. (2018). The SnRK1 Kinase as Central Mediator of Energy Signaling between Different Organelles. Plant Physiol, 176(2), 1085-1094. doi:10.1104/pp.17.01404
Yu, Y., Wang, J., Li, S., Kakan, X., Zhou, Y., Miao, Y., . . . Huang, R. (2019). Ascorbic Acid Integrates the Antagonistic Modulation of Ethylene and Abscisic Acid in the Accumulation of Reactive Oxygen Species.Plant Physiol, 179 (4), 1861-1875. doi:10.1104/pp.18.01250
Zanella, M., Borghi, G. L., Pirone, C., Thalmann, M., Pazmino, D., Costa, A., . . . Sparla, F. (2016). beta-amylase 1 (BAM1) degrades transitory starch to sustain proline biosynthesis during drought stress.J Exp Bot, 67 (6), 1819-1826. doi:10.1093/jxb/erv572
Zhang, B., Jia, J., Yang, M., Yan, C., & Han, Y. (2012). Overexpression of a LAM domain containing RNA-binding protein LARP1c induces precocious leaf senescence in Arabidopsis. Mol Cells, 34 (4), 367-374. doi:10.1007/s10059-012-0111-5
Zhang, S., Feng, M., Chen, W., Zhou, X., Lu, J., Wang, Y., . . . Gao, J. (2019). In rose, transcription factor PTM balances growth and drought survival via PIP2;1 aquaporin. Nat Plants, 5 (3), 290-299. doi:10.1038/s41477-019-0376-1
Zhao, C., Wang, P., Si, T., Hsu, C. C., Wang, L., Zayed, O., . . . Zhu, J. K. (2017). MAP Kinase Cascades Regulate the Cold Response by Modulating ICE1 Protein Stability. Dev Cell, 43 (5), 618-629 e615. doi:10.1016/j.devcel.2017.09.024
Zhou, H., Low, T. Y., Hennrich, M. L., van der Toorn, H., Schwend, T., Zou, H., . . . Heck, A. J. (2011). Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment. Mol Cell Proteomics, 10 (10), M110 006452. doi:10.1074/mcp.M110.006452