Abstract
Because of their fixed lifestyle, plants must acclimate to environmental changes by orchestrating several responses ranging from protective measures to growth control. Growth arrest is observed upon abiotic stress and can cause penalties to plant production. But, the molecular interface between stress perception and cell cycle control is poorly understood. The rice protein RSS1 is required at G1/S transition ensuring normal dividing activity of proliferative cells during salt stress. The role of RSS1 in meristem maintenance together with its flexible protein structure implies its key function as molecular integrator of stress signaling for cell cycle control. To study further the relevance of RSS1 and its related proteins in cereals, we isolated the durum wheat homolog, TdRL1, from Tunisian durum wheat varieties and extended our analyses to RSS1-like proteins from Poaceae. Our results show that the primary sequences of TdRL1 and the Graminae RSS1-like family members are highly conserved. In silico analyses predict that TdRL1 and other RSS1-like proteins share flexible 3-D structures and have features of intrinsically disordered/unstructured proteins (IDP). The disordered structure of TdRL1 is well illustrated by an electrophoretical mobility shift of the purified protein. Moreover, heterologous expression of TdRL1 in yeast improves its tolerance to salt and heat stresses strongly suggesting its involvement in abiotic stress tolerance mechanisms. Such finding adds new knowledge to our understanding of how IDPs may contribute as central molecular integrators of stress signaling into improving plant tolerance to abiotic stresses.
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References
Achard P, Cheng H, De Grauwe L, Decat J, Schoutteten H, Moritz T, Van Der Straeten D, Peng J, Harberd NP (2006) Integration of plant responses to environmentally activated phytohormonal signals. Science 311:91–94
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, pp 28–36
Baker SH, Frederick DL, Bloecher A, Tatchell K (1997) Alanine-scanning mutagenesis of protein phosphatase type 1 in the yeast Saccharomyces cerevisiae. Genetics 145:615–626
Bollen M, Peti W, Ragusa MJ, Beullens M (2010) The extended PP1 toolkit: designed to create specificity. Trends Biochem Sci 35:450–458
Burssens S, Himanen K, van de Cotte B, Beeckman T, Van Montagu M, Inzé D, Verbruggen N (2000) Expression of cell cycle regulatory genes and morphological alterations in response to salt stress in Arabidopsis thaliana. Planta 211:632–640
Cromer L, Jolivet S, Horlow C, Chelysheva L, Heyman J, De Jaeger G, Koncz C, De Veylder L, Mercier R (2013) Centromeric cohesion is protected twice at meiosis, by SHUGOSHINs at anaphase I and by PATRONUS at interkinesis. Curr Biol 23:2090–2099
Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA (2012) PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Res 40:D1194–D1201
De Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34(Web Server issue):W362–W365
De Veylder L, Beeckman T, Inzé D (2007) The ins and outs of the plant cell cycle. Nat Rev Mol Cell Biol 8:655–665
Drira M, Saibi W, Brini F, Gargouri A, Masmoudi K, Hanin M (2013) The K-segments of the wheat dehydrin DHN-5 are essential for the protection of lactate dehydrogenase and β-glucosidase activities in vitro. Mol Biotechnol 54:643–650
Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang C, Kissinger CR, Bailey RW, Griswold MD, Chiu W, Garner EC, Obradovic ZJ (2001) Intrinsically disordered protein. Mol Graph Model 19:26–59
Durfee T, Becherer K, Chen PL, Yeh SH, Yang Y, Kilburn AE, Lee WH, Elledge SJ (1993) The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit. Genes Dev 7:555–569
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M (2014) The Pfam protein families database. Nucleic Acids Res Database Issue 42:D222–D230
Gietz D, St Jean A, Woods RA, Schiestl RH (1992) Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res 20:1425
Hasan MM, Brocca S, Sacco E, Spinelli M, Papaleo E, Lambrughi M, Alberghina L, Vanoni M (2014) A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks. Front Physiol 4:315
Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM (2006) Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol 2:e100
Heroes E, Lesage B, Görnemann J, Beullens M, Van Meervelt L, Bollen M (2013) The PP1 binding code: a molecular-lego strategy that governs specificity. FEBS J 280:584–595
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P (2008) GENEVESTIGATOR V3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008:420747
Iakoucheva LM, Brown CJ, Lawson JD, Obradović Z, Dunker AK (2002) Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 323:573–584
Iakoucheva LM, Radivojac P, Brown CJ, O’Connor TR, Sikes JG, Obradovic Z, Dunker AK (2004) Intrinsic disorder and protein phosphorylation. Nucleic Acids Res 32:1037–1049
Juraniec M, Lequeux H, Hermans C, Willems G, Nordborg M, Schneeberger K, Salis P, Vromant M, Lutts S, Verbruggen N (2014) Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. New Phytol 201:810–824
Kitsios G, Doonan JH (2011) Cyclin dependent protein kinases and stress responses in plants. Plant Signal Behav 6:204–209
Komaki S, Sugimoto K (2012) Control of the plant cell cycle by developmental and environmental cues. Plant Cell Physiol 53:953–964
Ludlow JW, Glendening CL, Livingston DM, DeCarprio JA (1993) Specific enzymatic dephosphorylation of the retinoblastoma protein. Mol Cell Biol 13:367–372
Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK (2005) Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 61(Suppl 7):176–182
Ogawa D, Abe K, Miyao A, Kojima M, Sakakibara H, Mizutani M, Morita H, Toda Y, Hobo T, Sato Y, Hattori T, Hirochika H, Takeda S (2011) RSS1 regulates the cell cycle and maintains meristematic activity under stress conditions in rice. Nat Commun 2:278
Ogawa D, Morita H, Hattori T, Takeda S (2012) Molecular characterization of the rice protein RSS1 required for meristematic activity under stressful conditions. Plant Physiol Biochem 61:54–60
Peres A, Churchman ML, Hariharan S, Himanen K, Verkest A, Vandepoele K, Magyar Z, Hatzfeld Y, Van Der Schueren E, Beemster GT, Frankard V, Larkin JC, Inzé D, De Veylder L (2007) Novel plant-specific cyclin-dependent kinase inhibitors induced by biotic and abiotic stresses. J Biol Chem 282:25588–25596
Pietrosemoli N, García-Martín JA, Solano R, Pazos F (2013) Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation. PLoS One 8(2):e55524. doi:10.1371/journal.pone.0055524
Posas F, Bollen M, Stalmans W, Arino J (1995) Biochemical characterization of recombinant yeast PPZ1, a protein phosphatase involved in salt tolerance. FEBS Lett 368:39–44
Prilusky J, Felder CE, Zeev-Ben-Mordehai T, Rydberg E, Man O, Beckmann JS, Silman I, Sussman JL (2005) FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21:3435–3438
Ren J, Wen L, Gao X, Jin C, Xue Y, Yao X (2009) DOG 1.0: illustrator of protein domain structures. Cell Res 19:271–273
Schuppler U, He PH, John PC, Munns R (1998) Effect of water stress on cell division and cell-division-cycle 2-like cell-cycle kinase activity in wheat leaves. Plant Physiol 117:667–678
Skirycz A, Claeys H, De Bodt S, Oikawa A, Shinoda S, Andriankaja M, Maleux K, Eloy NB, Coppens F, Yoo SD, Saito K, Inzé D (2011) Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest. Plant Cell 23:1876–1888
Stuart JS, Frederick DL, Varner CM, Tatchell K (1994) The mutant type 1 protein phosphatase encoded by glc7-1 from Saccharomyces cerevisiae fails to interact productively with the GAC1-encoded regulatory subunit. Mol Cell Biol 14:896–905
Tamura K, Stecher G, Perterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–2729
Tompa P (2005) The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett 579:3346–3354
Uhrig RG, Kerk D, Moorhead GB (2013) Evolution of bacterial-like phosphoprotein phosphatases in photosynthetic eukaryotes features ancestral mitochondrial or archaeal origin and possible lateral gene transfer. Plant Physiol 163:1829–1843
Venturi GM, Bloecher A, Williams-Hart T, Tatchell K (2000) Genetic interactions between GLC7, PPZ1 and PPZ2 in Saccharomyces cerevisiae. Genetics 155:69–83
West G, Inzé D, Beemster GT (2004) Cell cycle modulation in the response of the primary root of Arabidopsis to salt stress. Plant Physiol 135:1050–1058
Wu X, Tatchell K (2001) Mutations in yeast protein phosphatase type 1 that affect targeting subunit binding. Biochemistry 40:7410–7420
Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN, Obradovic Z (2007) Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res 6:1882–1898
Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN (2010) PONDR-Fit: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta 1804:996–1010
Zamariola L, De Storme N, Vannerum K, Vandepoele K, Armstrong SJ, Franklin FC, Geelen D (2014) SHUGOSHINs and PATRONUS protect meiotic centromere cohesion in Arabidopsis thaliana. Plant J 77:782–794
Acknowledgments
We are very grateful to Prof. J Ariño from the Institute of Biotechnology and Biomedicine of the Universidad Autonoma of Barcelona, for providing the yeast strains. This work was supported by grants provided by the Ministry of Higher Education and Scientific Research (Tunisia).
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The authors declare that they have no conflict of interest.
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Habib Mahjoubi and Chantal Ebel contributed equally to this work.
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Fig. 1a
Sequence comparison between Bread wheat RSS1-like EST (TA75750_4565) and durum wheat cDNA of TdRL1. Alignment was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/) with default settings SFig. 1b Percentage in Amino acid composition of TdRL1. The percentage in aminoacid composition was obtained using protparam and the chart was established in excel. (PPTX 180 kb)
Fig. 2
Genomic organization of Graminae RSS1-like genes. The different cDNA and genomic sequences were downloaded from EnsemblPlant and the genomic organization was depicted using FancyGene (http://bio.ieo.eu/fancygene/). (PPTX 126 kb)
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Mahjoubi, H., Ebel, C. & Hanin, M. Molecular and functional characterization of the durum wheat TdRL1, a member of the conserved Poaceae RSS1-like family that exhibits features of intrinsically disordered proteins and confers stress tolerance in yeast. Funct Integr Genomics 15, 717–728 (2015). https://doi.org/10.1007/s10142-015-0448-x
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DOI: https://doi.org/10.1007/s10142-015-0448-x