Abstract
Key message
This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes.
Abstract
Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Asai T, Tena G, Plotnikova J, Willmann MR, Chiu W-L, Gomez-Gomez L, Boller T, Ausubel FM, Sheen J (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415:977–983. https://doi.org/10.1038/415977a
Bellincampi D, Cervone F, Lionetti V (2014) Plant cell wall dynamics and wall-related susceptibility in plant–pathogen interactions. Front Plant Sci 5:1–8. https://doi.org/10.3389/fpls.2014.00228
Boller T, He SY (2009) Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens. Science 324:742–744. https://doi.org/10.1126/science.1171647
Brutus A, Sicilia F, Macone A, Cervone F, Lorenzo G, De (2010) A domain swap approach reveals a role of the plant wall-associated kinase 1 (WAK1) as a receptor of oligogalacturonides. Proc Natl Acad Sci USA. https://doi.org/10.1073/pnas.1000675107. http://www.pnas.org/cgi
Consonni C, Bednarek P, Humphry M, Francocci F, Ferrari S, Harzen A, van Themaat EVL, Panstruga R (2010) Tryptophan-derived metabolites are required for antifungal defense in the Arabidopsis mlo2 mutant. Plant Physiol 152:1544–1561. https://doi.org/10.1104/pp.109.147660
De Vos M, Denekamp M, Dicke M, Vuylsteke M, Van Loon L, Smeekens SC, Pieterse CM (2006) The Arabidopsis thaliana transcription factor AtMYB102 functions in defense against the insect herbivore Pieris rapae. Plant Signal Behav 1:305–311
De Lorenzo G, Brutus A, Savatin DV, Sicilia F, Cervone F (2011) Engineering plant resistance by constructing chimeric receptors that recognize damage-associated molecular patterns (DAMPs). FEBS Lett 585:1521–1528. https://doi.org/10.1016/j.febslet.2011.04.043
de Jonge R, van Esse HP, Maruthachalam K, Bolton MD, Santhanam P, Saber MK, Zhang Z, Usami T, Lievens B, Subbarao KV, Thomma BPHJ (2012) Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing. Proc Natl Acad Sci USA 109:5110–5115. https://doi.org/10.1073/pnas.1119623109
De Cremer K, Mathys J, Vos C, Froenicke L, Michelmore RW, Cammue BPA, De Coninck B (2013) RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea. Plant Cell Environ 36:1992–2007. https://doi.org/10.1111/pce.12106
Denekamp M, Smeekens SC (2003) Integration of wounding and osmotic stress signals determines the expression of the AtMYB102 transcription factor gene. Plant Physiol 132:1415–1423. https://doi.org/10.1104/PP.102.019273
Ehlting J, Chowrira SG, Mattheus N, Aeschliman DS, Arimura G-I, Bohlmann J (2008) Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling. BMC Genom 9:154. https://doi.org/10.1186/1471-2164-9-154
Engelsdorf T, Hamann T (2014) An update on receptor-like kinase involvement in the maintenance of plant cell wall integrity. Ann Bot 114:1339–1347. https://doi.org/10.1093/aob/mcu043
Ferrari S, Savatin DV, Sicilia F, Gramegna G, Cervone F, De Lorenzo G (2013) Oligogalacturonides: plant damage-associated molecular patterns and regulators of growth and development. Front Plant Sci 4:49. https://doi.org/10.3389/fpls.2013.00049
Field B, Cardon G, Traka M, Botterman J, Vancanneyt G, Mithen R (2004) Glucosinolate and amino acid biosynthesis. Plant Physiol 135:828–839. https://doi.org/10.1104/pp.104.039347.828
Godfrey D, Rathjen JP (2012) Recognition and response in plant PAMP-triggered immunity. Wiley, Chichester
Gou J, Yu X, Liu C (2009) A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis. Proc Natl Acad Sci USA 106:18855–18860
Gramegna G, Modesti V, Savatin DV, Sicilia F, Cervone F, De Lorenzo G (2016) GRP-3 and KAPP, encoding interactors of WAK1, negatively affect defense responses induced by oligogalacturonides and local response to wounding. J Exp Bot 67:1715–1729. https://doi.org/10.1093/jxb/erv563
Grubb CD, Abel S (2006) Glucosinolate metabolism and its control. Trends Plant Sci 11:89–100. https://doi.org/10.1016/j.tplants.2005.12.006
Guo H, Li L, Ye H, Yu X, Algreen A, Yin Y (2009) Three related receptor-like kinases are required for optimal cell elongation in Arabidopsis thaliana. Proc Natl Acad Sci USA 106:7648–7653. https://doi.org/10.1073/pnas.0812346106
Hamann T (2012) Plant cell wall integrity maintenance as an essential component of biotic stress response mechanisms. Front Plant Sci 3:77. https://doi.org/10.3389/fpls.2012.00077
Hamann T, Denness L (2011) Cell wall integrity maintenance in plants: lessons to be learned from yeast? Plant Signal Behav 6:1706–1709. https://doi.org/10.4161/psb.6.11.17782
Hamann T, Bennett M, Mansfield J, Somerville C (2009) Identification of cell-wall stress as a hexose-dependent and osmosensitive regulator of plant responses. Plant J 57:1015–1026. https://doi.org/10.1111/j.1365-313X.2008.03744.x
Hématy K, Sado P, Van Tuinen A, Rochange S, Desnos T, Balzergue S, Pelletier S, Renou J, Höfte H (2007) A receptor-like kinase mediates the response of Arabidopsis cells to the inhibition of cellulose synthesis. Curr Biol 17:922–931. https://doi.org/10.1016/j.cub.2007.05.018
Hur M, Campbell AA, Almeida-de-Macedo M, Li L, Ransom N, Jose A, Crispin M, Nikolau BJ, Wurtele ES (2013) A global approach to analysis and interpretation of metabolic data for plant natural product discovery. Nat Prod Rep 30:565. https://doi.org/10.1039/c3np20111b
Kim K-C, Lai Z, Fan B, Chen Z (2008) Arabidopsis WRKY38 and WRKY62 transcription factors interact with histone deacetylase 19 in basal defense. Plant Cell 20:2357–2371. https://doi.org/10.1105/tpc.107.055566
Kohorn BD (2016) Cell wall-associated kinases and pectin perception. J Exp Bot 67:489–494
Kohorn BD, Kohorn SL, Saba NJ, Martinez VM (2014) Requirement for pectin methyl esterase and preference for fragmented over native pectins for wall-associated kinase-activated, EDS1/PAD4-dependent stress response in Arabidopsis. J Biol Chem 289:18978–18986. https://doi.org/10.1074/jbc.M114.567545
Kohorn BD, Hoon D, Minkoff BB, Sussman MR, Kohorn SL (2016) Rapid oligo-galacturonide induced changes in protein phosphorylation in Arabidopsis. Mol Cell Proteom 15:1351–1359. https://doi.org/10.1074/mcp.M115.055368
Kubicek CP, Starr TL, Glass NL (2014) Plant cell wall-degrading enzymes and their secretion in plant–pathogenic fungi. Annu Rev Phytopathol. https://doi.org/10.1146/annurev-phyto-102313-045831
Laluk K, Mengiste T (2010) Necrotroph attacks on plants: wanton destruction or covert extortion? Arab B 8:e0136. https://doi.org/10.1199/tab.0136
Lamport DTa, Kieliszewski MJ, Chen Y, Cannon MC (2011) Role of the extensin superfamily in primary cell wall architecture. Plant Physiol 156:11–19. https://doi.org/10.1104/pp.110.169011
Li L, Zheng W, Zhu Y, Ye H, Tang B, Arendsee ZW, Jones D, Li R, Ortiz D, Zhao X, Du C, Nettleton D, Scott MP, Salas-Fernandez MG, Yin Y, Wurtele ES (2015) QQS orphan gene regulates carbon and nitrogen partitioning across species via NF–YC interactions. Proc Natl Acad Sci USA 112:14734–14739. https://doi.org/10.1073/pnas.1514670112
Lionetti V, Raiola A, Cervone F, Bellincampi D (2014) Transgenic expression of pectin methylesterase inhibitors limits tobamovirus spread in tobacco and Arabidopsis. Mol Plant Pathol 15:265–274. https://doi.org/10.1111/mpp.12090
Liu Q, Wang X, Tzin V, Romeis J, Peng Y, Li Y (2016) Combined transcriptome and metabolome analyses to understand the dynamic responses of rice plants to attack by the rice stem borer Chilo suppressalis (Lepidoptera: Crambidae). BMC Plant Biol 16:259. https://doi.org/10.1186/s12870-016-0946-6
Lund SP, Division SE, Mccarthy DJ, Smyth GK, Hall E, Nettleton D (2012) Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Stat Appl Genet Mol Biol. https://doi.org/10.1515/1544-6115.1826
Ma Y, Walker RK, Zhao Y, Berkowitz GA (2012) Linking ligand perception by PEPR pattern recognition receptors to cytosolic Ca2+ elevation and downstream immune signaling in plants. Proc Natl Acad Sci USA 109:19852–19857. https://doi.org/10.1073/pnas.1205448109
Mikulic Petkovšek M, Stampar F, Veberic R (2008) Increased phenolic content in apple leaves infected with the apple scab pathogen. J Plant Pathol 90:49–55
Molina I, Li-beisson Y, Beisson F, Ohlrogge JB, Pollard M (2009) Identification of an Arabidopsis feruloyl-coenzyme A transferase required for suberin synthesis. Plant Physiol 151:1317–1328. https://doi.org/10.1104/pp.109.144907
Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497. https://doi.org/10.1111/j.1399-3054.1962.tb08052.x
Nafisi M, Stranne M, Fimognari L, Atwell S, Martens HJ, Pedas PR, Hansen SF, Nawrath C, Scheller HV, Kliebenstein DJ, Sakuragi Y (2015) Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses. Front Plant Sci 6:1–13. https://doi.org/10.3389/fpls.2015.00550
Navarro L, Zipfel C, Rowland O, Keller I, Robatzek S, Boller T, Jones JDG (2004) The transcriptional innate immune response to flg22. Interplay and overlap with Avr gene-dependent defense responses and bacterial pathogenesis. Plant Physiol 135:1113–1128. https://doi.org/10.1104/pp.103.036749
Nettleton D, Hwang JTG, Caldo RA, Wise RP (2006) Estimating the number of true null hypotheses from a histogram of p values. J Agric Biol Environ Stat 11:337–356. https://doi.org/10.1198/108571106X129135
Penninckx IA, Thomma BP, Buchala A, Métraux JP, Broekaert WF (1998) Concomitant activation of jasmonate and ethylene response pathways is required for induction of a plant defensin gene in Arabidopsis. Plant Cell 10:2103–2113. https://doi.org/10.1105/TPC.10.12.2103
Pogorelko G, Fursova O, Lin M, Pyle E, Jass J, Zabotina OA (2011) Post-synthetic modification of plant cell walls by expression of microbial hydrolases in the apoplast. Plant Mol Biol 77:433–445. https://doi.org/10.1007/s11103-011-9822-9
Pogorelko G, Lionetti V, Fursova O, Sundaram RM, Qi M, Whitham SA, Bogdanove AJ, Bellincampi D, Zabotina OA (2013) Arabidopsis and Brachypodium distachyon transgenic plants expressing Aspergillus nidulans Acetylesterases have decreased degree of polysaccharide acetylation and increased resistance to pathogens. Plant Physiol 162:9–23. https://doi.org/10.1104/pp.113.214460
Popper ZA, Fry SC (2003) Primary cell wall composition of bryophytes and charophytes. Ann Bot 91:1–12. https://doi.org/10.1093/aob/mcg013
Pré M, Atallah M, Champion A, De Vos M, Pieterse CMJ, Memelink J (2008) The AP2/ERF domain transcription factor ORA59 integrates jasmonic acid and ethylene signals in plant defense. Plant Physiol 147:1347–1357. https://doi.org/10.1104/pp.108.117523
Qi X, Behrens BX, West PR, Mort AJ (1995) Solubilization and partial characterization of extensin fragments from cell walls of cotton suspension cultures. Evidence for a covalent cross-link between extensin and pectin. Plant Physiol 108:1691–1701. https://doi.org/10.1104/pp.108.4.1691
Rasmussen S, Barah P, Suarez-rodriguez MC, Bressendorff S, Friis P, Costantino P, Bones AM, Nielsen HB, Mundy J (2013) Transcriptome responses to combinations of stresses in Arabidopsis. Plant Physiol 161:1783–1794. https://doi.org/10.1104/pp.112.210773
Reem NT, Pogorelko G, Lionetti V, Chambers L, Held MA, Bellincampi D, Zabotina OA (2016) Decreased polysaccharide feruloylation compromises plant cell wall integrity and increases susceptibility to necrotrophic fungal pathogens. Front Plant Sci 7:1–21. https://doi.org/10.3389/fpls.2016.00630
Ringli C (2010) Monitoring the outside: cell wall-sensing mechanisms. Plant Physiol 153:1445–1452. https://doi.org/10.1104/pp.110.154518
Rodicio R, Heinisch JJ (2010) Together we are strong-cell wall integrity sensors in yeasts. Yeast 27:531–540. https://doi.org/10.1002/yea.1785
Savatin DV, Gramegna G, Modesti V, Cervone F (2014) Wounding in the plant tissue: the defense of a dangerous passage. Front Plant Sci 5:470. https://doi.org/10.3389/fpls.2014.00470
Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative CT method. Nat Protoc 3:1101–1108. https://doi.org/10.1038/nprot.2008.73
Shen X, Wang Z, Song X, Xu J, Jiang C, Zhao Y, Ma C, Zhang H (2014) Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis. Plant Mol Biol 86:303–317. https://doi.org/10.1007/s11103-014-0230-9
Strauch RC, Svedin E, Dilkes B, Chapple C, Li X (2015) Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana. Proc Natl Acad Sci USA 112:11726–11731. https://doi.org/10.1073/pnas.1503272112
Takenaka Y, Nakano S, Tamoi M, Sakuda S, Fukamizo T (2009) Chitinase gene expression in response to environmental stresses in Arabidopsis thaliana: chitinase inhibitor allosamidin enhances stress tolerance. Biosci Biotechnol Biochem 73:1066–1071. https://doi.org/10.1271/bbb.80837
Tang W, Kim T-W, Oses-Prieto JA, Sun Y, Deng Z, Zhu S, Wang R, Burlingame AL, Wang Z-Y (2008) BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis. Science 321:557–560. https://doi.org/10.1126/science.1156973
Thomma BPHJ, Bruno A, Cammue PA, Thevissen K (2002) Plant defensins. Planta 216:193–202. https://doi.org/10.1007/s00425-002-0902-6
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-SEq. Bioinformatics 25:1105–1111. https://doi.org/10.1093/bioinformatics/btp120
Trépanier M, Bécard G, Moutoglis P, Willemot C, Gagné S, Avis TJ, Rioux J-A (2005) Dependence of arbuscular-mycorrhizal fungi on their plant host for palmitic acid synthesis. Appl Environ Microbiol 71:5341–5347. https://doi.org/10.1128/AEM.71.9.5341-5347.2005
Tsai AYL, Chan K, Ho CY, Canam T, Capron R, Master ER, Bräutigam K (2017) Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response. PLoS ONE 12:e0173094. https://doi.org/10.1371/journal.pone.0173094
Underwood W (2012) The plant cell wall: a dynamic barrier against pathogen invasion. Front Plant Sci 3:85. https://doi.org/10.3389/fpls.2012.00085
Voxeur A, Hofte H (2016) Cell wall integrity signaling in plants: “to grow or not to grow that’s the question”. Glycobiology 1:1–11. https://doi.org/10.1093/glycob/cww029
Wagner TA, Kohorn BD (2001) Wall-associated kinases are expressed throughout plant development and are required for cell expansion. Plant Cell 13:303–318. https://doi.org/10.1105/TPC.13.2.303
Walley JW, Kliebenstein DJ, Bostock RM, Dehesh K (2013) Fatty acids and early detection of pathogens. Curr Opin Plant Biol 16:520–526. https://doi.org/10.1016/j.pbi.2013.06.011
Wasternack C (2007) Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann Bot 100:681–697. https://doi.org/10.1093/aob/mcm079
Wolf S, Hématy K, Höfte H (2012) Growth control and cell wall signaling in plants. Annu Rev Plant Biol 63:381–407. https://doi.org/10.1146/annurev-arplant-042811-105449
Wu S, Shan L, He P (2014) Microbial signature-triggered plant defense responses and early signaling mechanisms. Plant Sci 228:118–126. https://doi.org/10.1016/j.plantsci.2014.03.001
Xing J, Chin C-K (2000) Modification of fatty acids in eggplant affects its resistance to Verticilliumdahliae. Physiol Mol Plant Pathol 56:217–225. https://doi.org/10.1006/pmpp.2000.0268
Xu Z, Wang M, Shi D, Zhou G, Niu T, Hahn MG, O’Neill MA, Kong Y (2017) DGE-seq analysis of MUR3-related Arabidopsis mutants provides insight into how dysfunctional xyloglucan affects cell elongation. Plant Sci 258:156–169. https://doi.org/10.1016/j.plantsci.2017.01.005
Yang S, Hoffman N (1984) Ethylene biosynthesis and its regulation in higher plants. Annu Rev Plant Physiol 35:155–189. https://doi.org/10.1146/annurev.pp.35.060184.001103
Acknowledgements
This research was in part supported by the NSF-MCB (National Science Foundation) (Grant #1121163 to OAZ) and USDA-NIFA (National Institute of Food and Agriculture) (Grant #2015-07802 to OAZ). The authors thank Zebulun Arendsee (Iowa State University) for his assistance in bioinformatics analysis.
Author information
Authors and Affiliations
Contributions
NTR conducted all analyses of transcriptome and metabolome datasets, and wrote the paper. OZ and LL designed the experiments and wrote the paper. XZ cleaned and mapped reads, and applied statistical analysis to transcriptome data. HC and XL conducted metabolite analysis. MH and ESW developed and maintain the PMR database and statistical analyses and contributed to the paper.
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
11103_2018_714_MOESM1_ESM.pptx
Supp. Fig. 1 p-value distribution of RNAseq data from AnAXE, AnRAE, and AnFAE plants. Supp. Fig. 2 Molecular functions of DE genes upregulated (top) and downregulated (bottom) as determined by Panther Gene Ontology Database. Supp. Fig. 3 Visualization of pathway cutoffs. Supp. Fig. 4 Total lignin content in wild-type Col-0 and AnFAE Arabidopsis plants as determined by acetyl bromide quantification. Supplementary material 1 (PPTX 79 KB)
11103_2018_714_MOESM4_ESM.xlsx
Supp. Table 3 Full RNAseq dataset showing p-value, q-value, and log2-fold change. Supplementary material 4 (XLSX 2966 KB)
Rights and permissions
About this article
Cite this article
Reem, N.T., Chen, HY., Hur, M. et al. Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations. Plant Mol Biol 96, 509–529 (2018). https://doi.org/10.1007/s11103-018-0714-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11103-018-0714-0