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Dissecting the transcriptional networks underlying the gibberellin response in Nicotiana tabacum

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Biologia Plantarum

Abstract

The present work examines global transcriptional and limited metabolic profiling to dissect the signalling pathways associated with gibberellin A3 (GA3) induced alterations in tobacco (Nicotiana tabacum L.) under field conditions. Our microarray analysis revealed that GA3 foliar application elicited 7 032 differentially expressed genes (DEGs) with 3 507 and 3 525 genes displaying up- and down-regulation, respectively. These DEGs broadly belong to diverse metabolic pathways: GA signalling and homeostasis, ethylene and auxin biosyntheses, saccharide metabolism, glycolysistricarboxylic acid cycle, terpenoid biosynthesis, shikimate-phenylpropanoid pathway, S-adenosyl methionine cycle, fatty acid biosynthesis, cell wall metabolism, oxidative stress, DNA repair, and stress responses. Transcription validation of representative DEGs was confirmed by real-time quantitative PCR. A relative enhancement in cellular acetyl-CoA pool corroborated with a concomitant increase and decrease in transcriptions as well as activities of histone acetyltransferases and histone deacetylases, respectively. Phytochemical analysis shows an enhanced content of total sugars, reducing sugars, total flavonoids, and phenolics with a concomitant decrease of the content of starch, chlorophylls a and b, and carotenoids. Gas chromatography with mass spectrometry analysis revealed the presence of 30 differential metabolites, mostly belonging to terpenoid biosynthesis pathway.

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Abbreviations

ABA:

abscisic acid

BRs:

brassinosteroids

CDP-ME:

4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol

CK:

cytokinin

DEG:

differentially expressed gene

DDR:

DNA damage response

DOX:

1-deoxy-D-xylulose-5-phosphate

ET:

ethylene

GA:

gibberellin

GC-MS:

gas chromatography with mass spectrometry

GO:

gene ontology

HAT:

histone acetyltransferase

HDAC:

histone deacetylase

HPLC:

high-performance liquid chromatography

IAA:

indoleacetic acid

JA:

jasmonic acid

MEP:

2-methyl-D-erythritol-4-phosphate

MVA:

mevalonate

NtDNMT:

N. tabacum DNA methyltransferase

RT-qPCR:

quantitative real time PCR

PEPC:

phosphoenolpyruvate carboxylase

PFK:

phosphofructokinase

PGK:

phosphoglycerate kinase

PGM:

phosphoglyceromutase

PK:

pyruvate kinase

PTM:

post-translational modification

RFC:

relative fold-change

ROS:

reactive oxygen species

SA:

salicylic acid

SAM:

S-adenosyl methionine

SL:

strigolactone

TCA:

tricarboxylic acid cycle

TF:

transcription factor

TFC:

total flavonoid content

TPC:

total phenolic content

References

  • Achard, P., Cheng, H., De Grauwe, L., Decat, J., Schoutteten, H., Moritz, T., Van Der Straeten, D., Peng, J., Harberd, N.P.: Integration of plant responses to environmentally activated phytohormonal signals. - Science 311: 91–94, 2006.

    Article  CAS  PubMed  Google Scholar 

  • Achard, P., Gong, F., Cheminant, S., Alioua, M., Hedden, P., Genschik, P.: The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism. - Plant Cell 20: 2117–2129, 2008a.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Achard, P., Renou, J., Berthomé, R., Harberd, N.P., Genschik, P.: Plant DELLAs restrain growth and promote survival of adversity by reducing the levels of reactive oxygen species. - Curr. Biol. 18: 656–660, 2008b.

    Article  CAS  PubMed  Google Scholar 

  • Agius, F., Kapoor, A., Zhu, J.K.: Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. - Proc. nat. Acad. Sci. USA 103: 11796–11801, 2006.

    Article  CAS  PubMed  Google Scholar 

  • Baenas, N., García-Viguera, C., Moreno, D.A.: Elicitation: a tool for enriching the bioactive composition of foods. - Molecules 19: 13541–13563. 2014.

    Article  CAS  PubMed  Google Scholar 

  • Bailey-Serres, J., Mittler, R.: The roles of reactive oxygen species in plant cells. - Plant Physiol. 141: 311–311, 2006.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Banerjee, A., Wu, Y., Banerjee, R., Li, Y., Yan, H., Sharkey, T.D.: Feedback inhibition of deoxy-D-xylulose-5-phosphate synthase regulates the methylerythritol-4-phosphate pathway. - J. biol. Chem. 288: 16926–16936. 2013.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Colebrook, E.H., Thomas, S.G., Phillips, A.L., Hedden, P.: The role of gibberellin signalling in plant responses to abiotic stress. - J. exp. Biol. 217: 67–75. 2014.

    Article  CAS  PubMed  Google Scholar 

  • Corbineau, F., Xia, Q., Bailly, C., El-Maarouf-Bouteau, H.: Ethylene, a key factor in the regulation of seed dormancy. - Front. Plant. Sci. 5: 1–13, 2014.

    Article  Google Scholar 

  • Cordoba, E., Salmi, M., León, P.: Unravelling the regulatory mechanisms that modulate the MEP pathway in higher plants. - J. exp. Bot. 60: 2933–2943, 2009.

    Article  CAS  PubMed  Google Scholar 

  • Dennis, D.T., Greyson, M.F.: Fructose 6-phosphate metabolism in plants. - Physiol. Plant. 69: 395–404, 1987.

    Article  CAS  Google Scholar 

  • Disch, A., Hemmerlin, A., Rohmer, M.: Mevalonate-derived isopentenyl diphosphate is the biosynthetic precursor of ubiquinone prenyl side chain in tobacco BY-2 cells. - Biochem. J. 331: 615–621, 1998.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Dubois, M., Skirycz, A., Claeys, H., Maleux, K., Dhondt, S., De Bodt, S., Bossche, R.V., De Milde, L., Yoshizumi, T., Matsui, M.: ETHYLENE RESPONSE FACTOR6 acts as a central regulator of leaf growth under water-limiting conditions in Arabidopsis. - Plant Physiol. 162: 319–332, 2013.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Dugardeyn, J., Van den Bussche, F., Van der Straeten, D.: To grow or not to grow: what can we learn on ethylenegibberellin cross-talk by In silico gene expression analysis?. - J. exp. Bot. 59: 1–16, 2008.

    Article  CAS  PubMed  Google Scholar 

  • Fatland, B.L., Nikolau, B.J., Wurtele, E.S.: Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-citrate lyase in Arabidopsis. - Plant Cell 17: 182–203, 2005.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Finnegan, E.J., Kovac, K.A.: Plant DNA methyltransferases. - Plant mol. Biol. 43: 189–201, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Frigerio, M., Alabadi, D., Pérez-Gómez, J., García-Cárcel, L., Phillips, A.L., Hedden, P., Blázquez, M.A.: Transcriptional regulation of gibberellin metabolism genes by auxin signaling in Arabidopsis. - Plant Physiol. 142: 553–563, 2006.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Fujita, M., Fujita, Y., Maruyama, K., Seki, M., Hiratsu, K., Ohme-Takagi, M., Tran, L.P., Yamaguchi-Shinozaki, K., Shinozaki, K.: A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. - Plant J. 39: 863–876, 2004.

    Article  CAS  PubMed  Google Scholar 

  • Fuks, F.: DNA methylation and histone modifications: teaming up to silence genes. - Curr. Opin. Genet. Dev. 15: 490–495, 2005.

    Article  CAS  PubMed  Google Scholar 

  • Galdieri, L., Vancura, A.: Acetyl-CoA carboxylase regulates global histone acetylation. - J. biol. Chem. 287: 23865–23876, 2012.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Guevara-García, A., San Román, C., Arroyo, A., Cortés, M.E., De la Luz Gutiérrez-Nava, M., León, P.: Characterization of the Arabidopsis clb6 mutant illustrates the importance of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate pathway. - Plant Cell 17: 628–643, 2005.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gupta, R., Chakrabarty, S.K.: Gibberellic acid in plant: still a mystery unresolved. - Plant Signal. Behav. 8: e25504. 2013.

    Article  PubMed Central  PubMed  Google Scholar 

  • Hansen, J., Møller, I.: Percolation of starch and soluble carbohydrates from plant tissue for quantitative determination with anthrone. - Anal. Biochem. 68: 87–94, 1975.

    Article  CAS  PubMed  Google Scholar 

  • Hauvermale, A.L., Ariizumi, T., Steber, C.M.: Gibberellin signaling: a theme and variations on DELLA repression. - Plant Physiol. 160: 83–92. 2012.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hedden, P., Phillips, A.L.: Gibberellin metabolism: new insights revealed by the genes. - Trends Plant Sci. 5: 523–530, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Herrmann, K.M.: The shikimate pathway: early steps in the biosynthesis of aromatic compounds. - Plant Cell 7: 907, 1995.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Inaba, Y., Brotherton, J.E., Ulanov, A., Widholm, J.M.: Expression of a feedback insensitive anthranilate synthase gene from tobacco increases free tryptophan in soybean plants. - Plant Cell Rep. 26: 1763–1771, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Kant, M., Jonckheere, W., Knegt, B., Lemos, F., Liu, J., Schimmel, B., Villarroel, C., Ataide, L., Dermauw, W., Glas, J.: Mechanisms and ecological consequences of plant defence induction and suppression in herbivore communities. - Ann. Bot. 115: 1015–1051. 2015.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kasote, D.M., Katyare, S.S., Hegde, M.V., Bae, H.: Significance of antioxidant potential of plants and its relevance to therapeutic applications. - Int. J. biol. Sci. 11: 982–991. 2015.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kawaguchi, A., Bloch, K.: Inhibition of glucose 6-phosphatedehydrogenase by palmitoyl coenzyme A. - J. biol. Chem. 249: 5793–5800, 1974.

    CAS  PubMed  Google Scholar 

  • Keyes, G., Sorrells, M.E., Setter, T.L.: Gibberellic acid regulates cell wall extensibility in wheat (Triticum aestivum L.). - Plant Physiol. 92: 242–245, 1990.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kim, D., Jeong, S.W., Lee, C.Y.: Antioxidant capacity of phenolic phytochemicals from various cultivars of plums. - Food Chem. 81: 321–326, 2003.

    Article  CAS  Google Scholar 

  • Kim, D.S., Hwang, B.K.: An important role of the pepper phenylalanine ammonia-lyase gene (PAL1) in salicylic aciddependent signalling of the defence response to microbial pathogens. - J. exp. Bot. 65: 2295–2306. 2014.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kolbe, A., Tiessen, A., Schluepmann, H., Paul, M., Ulrich, S., Geigenberger, P.: Trehalose 6-phosphate regulates starch synthesis via posttranslational redox activation of ADPglucose pyrophosphorylase. - Proc. nat. Acad. Sci. USA 102: 11118–11123, 2005.

    Article  CAS  PubMed  Google Scholar 

  • Lange, B.M., Rujan, T., Martin, W., Croteau, R.: Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. - Proc. nat. Acad. Sci. USA 97: 13172–13177, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Lata, C., Prasad, M.: Role of DREBs in regulation of abiotic stress responses in plants. - J. exp. Bot. 62: 4731–4748. 2011.

    Article  CAS  PubMed  Google Scholar 

  • Laule, O., Fürholz, A., Chang, H., Zhu, T., Wang, X., Heifetz, P.B., Gruissem, W., Lange, M.: Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana. - Proc. nat. Acad. Sci. USA 100: 6866–6871, 2003.

    Article  CAS  PubMed  Google Scholar 

  • Laware, S.L.: Sequential extraction of plant metabolites. - Int. J. Curr. Microbiol. appl. Sci. 4: 33–38, 2015.

    CAS  Google Scholar 

  • Li, Z., Niu, S., Yuan, H., Li, W.: Gibberellins affect tobacco growth and development in a dose dependent manner through genes involved in metabolic processes. - Plant mol. Biol. Rep. 33: 1259–1269. 2015.

    Article  CAS  Google Scholar 

  • Lichtenthaler, H.K., Wellburn, A.R.: Determinations of total carotenoids and chlorophylls a and b of leaf extracts in different solvents. - Biochem. Soc. Trans. 11: 591–592, 1983.

    Article  CAS  Google Scholar 

  • Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., Jacobsen, S.E.: Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. - Science 292: 2077–2080, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Mabiki, F.P., Magadula, J.J., Mdegela, R.H., Mosha, R.D.: Optimization of extraction conditions and phytochemical screening of root extract of Synadenium glaucescens Pax. - Int. J. Chem. 5: 103, 2013.

    Article  CAS  Google Scholar 

  • Magome, H., Yamaguchi, S., Hanada, A., Kamiya, Y., Oda, K.: The DDF1 transcriptional activator upregulates expression of a gibberellin-activating gene, GA2ox7, under highsalinity stress in Arabidopsis. - Plant J. 56: 613–626, 2008.

    Article  CAS  PubMed  Google Scholar 

  • Manoharlal, R., Saiprasad, G.V.S., Ullagaddi, C., Kovarík, A.: Gibberellin A3 (GA3) as an epigenetic determinant of global DNA hypo-methylation in tobacco. - Biol. Plant. 62: 11–23, 2018.

    Article  CAS  Google Scholar 

  • Manova, V., Gruszka, D.: DNA damage and repair in plantsfrom models to crops. - Front. Plant. Sci. 6: 1–26, 2015.

    Article  Google Scholar 

  • Mansouri, H., Asrar, Z., Amarowicz, R.: The response of terpenoids to exogenous gibberellic acid in Cannabis sativa L. at vegetative stage. - Acta Physiol. Plant. 33: 1085–1091. 2011.

    Article  CAS  Google Scholar 

  • Miller, G., Shulaev, V., Mittler, R.: Reactive oxygen signaling and abiotic stress. - Physiol. Plant. 133: 481–489, 2008.

    Article  CAS  PubMed  Google Scholar 

  • Miller, G.L.: Use of dinitrosalicylic acid reagent for determination of reducing sugar. - Anal. Chem. 31: 426–428, 1959.

    Article  CAS  Google Scholar 

  • Mustroph, A., Sonnewald, U., Biemelt, S.: Characterisation of the ATP-dependent phosphofructokinase gene family from Arabidopsis thaliana. - FEBS Lett. 581: 2401–2410, 2007.

    Article  CAS  PubMed  Google Scholar 

  • Nemhauser, J.L., Hong, F., Chory, J.: Different plant hormones regulate similar processes through largely non overlapping transcriptional responses. - Cell 126: 467–475, 2006.

    Article  CAS  PubMed  Google Scholar 

  • Nishiuchi, S., Yamauchi, T., Takahashi, H., Kotula, L., Nakazono, M.: Mechanisms for coping with submergence and waterlogging in rice. - Rice 5: 2, 2012.

    Article  PubMed Central  PubMed  Google Scholar 

  • O'Neill, D.P., Ross, J.J.: Auxin regulation of the gibberellin pathway in pea. - Plant Physiol. 130: 1974–1982, 2002.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Phukan, U.J., Jeena, G.S., Shukla, R.K.: WRKY transcription factors: molecular regulation and stress responses in plants. - Front. Plant. Sci. 7: 760, 2016.

    Article  PubMed Central  PubMed  Google Scholar 

  • Poirier, Y., Antonenkov, V.D., Glumoff, T., Hiltunen, J.K.: Peroxisomal β-oxidation-A metabolic pathway with multiple functions. - Biochim. biophys Acta 1763: 1413–1426, 2006.

    Article  CAS  PubMed  Google Scholar 

  • Richard, O., Paquet, N., Haudecoeur, E., Charrier, B.: Organization and expression of the GSK3/Shaggy kinase gene family in the moss Physcomitrella patens suggest early gene multiplication in land plants and an ancestral response to osmotic stress. - J. mol. EVol. 61: 99–113, 2005.

    Article  CAS  PubMed  Google Scholar 

  • Richards, D.E., King, K.E., Ait-Ali, T., Harberd, N.P.: How gibberellin regulates plant growth and development: a molecular genetic analysis of gibberellin signaling. - Annu. Rev. Plant Physiol. Plant mol. Biol. 52: 67–88, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Rodwell, V.W., Beach, M.J., Bischoff, K.M., Bochar, D.A., Darnay, B.G., Friesen, J.A., Gill, J.F., Hedl, M., Jordan-Starck, T., Kennelly, P.J.: 3-Hydroxy-3-methylglutaryl-CoA reductase. - Meth. Enzymol. 324: 259, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Rohmer, M.: The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. - Nat. Prod. Rep. 16: 565–574, 1999.

    Article  CAS  PubMed  Google Scholar 

  • Ross, J.J., O'Neill, D.P., Smith, J.J., Kerckhoffs, L.H.J., Elliott, R.C.: Evidence that auxin promotes gibberellin A1 biosynthesis in pea. - Plant J. 21: 547–552, 2000.

    Article  CAS  PubMed  Google Scholar 

  • Sauter, M., Moffatt, B., Saechao, M.C., Hell, R., Wirtz, M.: Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. - Biochem. J. 451: 145–154, 2013.

    Article  CAS  PubMed  Google Scholar 

  • Silva, L., Pezzini, B.R., Soares, L.: Spectrophotometric determination of the total flavonoid content in Ocimum basilicum L. (Lamiaceae) leaves. - Pharmacogn. Mag. 11: 96,2015.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Speranzini, V., Pilotto, S., Sixma, T.K., Mattevi, A.: Touch, act and go: landing and operating on nucleosomes. - EMBO J. 35: 376–388, 2016.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sun, T.P., Gubler, F.: Molecular mechanism of gibberellin signaling in plants. - Annu. Rev. Plant Biol. 55: 197–223, 2004.

    Article  CAS  PubMed  Google Scholar 

  • Tamang, B.G., Fukao, T.: Plant adaptation to multiple stresses during submergence and following desubmergence. - Int. J. mol. Sci. 16: 30164–30180,F 2015.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Thomas, S.G., Sun, T.P.: Update on gibberellin signaling. A tale of the tall and the short. - Plant Physiol. 135: 668–676, 2004.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tumaney, A.W., Ohlrogge, J.B., Pollard, M.: Acetyl coenzyme A concentration in plant tissues. - J. Plant Physiol. 161: 485–488, 2004.

    Article  CAS  PubMed  Google Scholar 

  • Verma, V., Ravindran, P., Kumar, P.P.: Plant hormonemediated regulation of stress responses. - BMC Plant Biol. 16: 1, 2016.

    Article  CAS  Google Scholar 

  • Wang, G., Que, F., Xu, Z., Wang, F., Xiong, A.: Exogenous gibberellin altered morphology, anatomic and transcriptional regulatory networks of hormones in carrot root and shoot. - BMC Plant Biol. 15: 1, 2015.

    Article  CAS  Google Scholar 

  • Wolbang, C.M., Ross, J.J.: Auxin promotes gibberellin biosynthesis in decapitated tobacco plants. - Planta 214: 153–157, 2001.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, J., Jia, W., Yang, J., Ismail, A.M.: Role of ABA in integrating plant responses to drought and salt stresses. - Field Crops Res. 97: 111–119, 2006.

    Article  Google Scholar 

  • Zhao, Y.: The roles of YUCCA genes in local auxin biosynthesis and plant development. - In: Pua, E., Davey, M. (ed.): Plant Developmental Biology ? Biotechnological Perspectives. Vol. 2. Pp. 227–235. Springer, Berlin - Heidelberg 2010.

    Article  Google Scholar 

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Authors and Affiliations

  1. ITC Life Science and Technology Centre, Peenya Industrial Area, Bengaluru, Karnataka, 560058, India

    R. Manoharlal, G. V. S. Saiprasad, A. Thambrahalli & K. Madhavakrishna

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  1. R. Manoharlal
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  2. G. V. S. Saiprasad
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  3. A. Thambrahalli
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  4. K. Madhavakrishna
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Correspondence to R. Manoharlal.

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Acknowledgment: We would like to acknowledge Dr. C.C. Lakshmanan (the head of the ITC Life Science and Technology Centre) for his consistent support. Genotypic Technology, Bengaluru, India is acknowledged for performing microarray processing and data analysis. We also acknowledge field-workers at Northern Light Soil region, Rajahmundry, Andhra Pradesh, India, for providing their consistent help and support during field experiment and sample collection.

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Manoharlal, R., Saiprasad, G.V.S., Thambrahalli, A. et al. Dissecting the transcriptional networks underlying the gibberellin response in Nicotiana tabacum. Biol Plant 62, 647–662 (2018). https://doi.org/10.1007/s10535-018-0809-0

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