title: Distinct and conserved transcriptomic changes during nematode-induced giant cell development in tomato compared with Arabidopsis: a functional role for gene repression.
abstract: Root-knot nematodes (RKNs) induce giant cells (GCs) from root vascular cells inside the galls. Accompanying molecular changes as a function of infection time and across different species, and their functional impact, are still poorly understood. Thus, the transcriptomes of tomato galls and laser capture microdissected (LCM) GCs over the course of parasitism were compared with those of Arabidopsis, and functional analysis of a repressed gene was performed. Microarray hybridization with RNA from galls and LCM GCs, infection-reproduction tests and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) transcriptional profiles in susceptible and resistant (Mi-1) lines were performed in tomato. Tomato GC-induced genes include some possibly contributing to the epigenetic control of GC identity. GC-repressed genes are conserved between tomato and Arabidopsis, notably those involved in lignin deposition. However, genes related to the regulation of gene expression diverge, suggesting that diverse transcriptional regulators mediate common responses leading to GC formation in different plant species. TPX1, a cell wall peroxidase specifically involved in lignification, was strongly repressed in GCs/galls, but induced in a nearly isogenic Mi-1 resistant line on nematode infection. TPX1 overexpression in susceptible plants hindered nematode reproduction and GC expansion. Time-course and cross-species comparisons of gall and GC transcriptomes provide novel insights pointing to the relevance of gene repression during RKN establishment.
authors: Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avenida de Carlos III s/n, 45071, Toledo, Spain.
authors: Mary
authors: M
authors: Portillo
authors: Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avenida de Carlos III s/n, 45071, Toledo, Spain.
authors: Javier
authors: J
authors: Cabrera
authors: Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK.
authors: Keith
authors: K
authors: Lindsey
authors: Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK.
authors: Jen
authors: J
authors: Topping
authors: ICA CSIC, Protección Vegetal, Serrano 115 dpdo, 28006, Madrid, Spain.
authors: Maria Fe
authors: MF
authors: Andrés
authors: ICA CSIC, Protección Vegetal, Serrano 115 dpdo, 28006, Madrid, Spain.
authors: Mariana
authors: M
authors: Emiliozzi
authors: Centro Nacional de Biotecnología CSIC, Darwin3, Campus Universidad Autónoma de Madrid, 28049, Spain.
authors: Juan C
authors: JC
authors: Oliveros
authors: Centro Nacional de Biotecnología CSIC, Darwin3, Campus Universidad Autónoma de Madrid, 28049, Spain.
authors: Gloria
authors: G
authors: García-Casado
authors: Centro Nacional de Biotecnología CSIC, Darwin3, Campus Universidad Autónoma de Madrid, 28049, Spain.
authors: Roberto
authors: R
authors: Solano
authors: Institute of Plant Sciences ARO, Volcani Center, 50250, Bet-Dagan, Israel.
authors: Hinanit
authors: H
authors: Koltai
authors: Institute of Plant Sciences ARO, Volcani Center, 50250, Bet-Dagan, Israel.
authors: Nathalie
authors: N
authors: Resnick
authors: Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avenida de Carlos III s/n, 45071, Toledo, Spain.
authors: Carmen
authors: C
authors: Fenoll
authors: Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avenida de Carlos III s/n, 45071, Toledo, Spain.
authors: Carolina
authors: C
authors: Escobar
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics* / Q000469:parasitology; D018506:Gene Expression Regulation, Plant; D006790:Host-Parasite Interactions / Q000235:genetics; D018551:Solanum lycopersicum / Q000235:genetics* / Q000469:parasitology; D020411:Oligonucleotide Array Sequence Analysis; D009195:Peroxidase / Q000235:genetics / Q000378:metabolism; D059828:Plant Cells; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D059467:Transcriptome; D014431:Tylenchoidea / Q000502:physiology*
chemical_list: D010940:Plant Proteins; D009195:Peroxidase
references: Adie BA, Pérez-Pérez MM, Godoy MP, Sánchez-Serrano JJ, Schmelz EA, Solano R. 2007. ABA is an essential signal for plant resistance to pathogens affecting JA biosynthesis and the activation of defenses in Arabidopsis. Plant Cell 19: 1665-1681.
references: Almagro L, Gómez Ros LV, Belchi-Navarro S, Bru R, Ros Barceló A, Pedreño MA. 2009. Class III peroxidases in plant defence reactions. Journal of Experimental Botany 60: 377-390.
references: Aslam SN, Newman MA, Erbs G, Morrissey KL, Chinchilla D, Boller T, Jensen TT, De Castro C, Ierano T, Molinaro A et al. 2008. Bacterial polysaccharides suppress induced innate immunity by calcium chelation. Current Biology 18: 1078-1083.
references: Barcala M, Garcia A, Cabrera J, Casson S, Lindsey K, Favery B, Garcia-Casado G, Solano R, Fenoll C, Escobar C. 2010. Early transcriptomic events in microdissected Arabidopsis nematode-induced giant cells. The Plant Journal 61: 698-712.
references: Bar-Or C, Kapulnik Y, Koltai H. 2005. A broad characterization of the transcriptional profile of the compatible tomato response to the plant parasitic root knot nematode Meloidogyne javanica. European Journal of Plant Pathology 111: 181-192.
references: Bellafiore S, Shen Z, Rosso MN, Abad P, Shih P, Briggs SP. 2008. Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential. PLoS Pathogens 4: e1000192.
references: Benjamini Y, Hochberg Y. 1995. Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society 57: 289-300.
references: Bhattarai KK, Xie QG, Mantelin S, Bishnoi U, Girke T, Navarre DA, Kaloshian I. 2008. Tomato susceptibility to root-knot nematodes requires an intact jasmonic acid signaling pathway. Molecular Plant-Microbe Interactions 21: 1205-1214.
references: Bhattarai KK, Atamian HS, Kaloshian I, Eulgem T. 2010. WRKY72-type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene-for-gene resistance mediated by the tomato R gene Mi-1. The Plant Journal 63: 229-240.
references: Bird AF. 1961. The ultrastructure and histochemistry of a nematode-induced giant cell. Journal of Biophysical and Biochemical Cytology 11: 701-715.
references: Bird DM. 1996. Manipulation of host gene expression by root-knot nematodes. Journal of Parasitology 82: 881-888.
references: Bird DM, Wilson MA. 1994. DNA sequence and expression analysis of root-knot nematode-elicited giant cell transcripts. Molecular Plant-Microbe Interactions 7: 419-424.
references: Caillaud MC, Dubreuil G, Quentin M, Perfus-Barbeoch L, Lecomte P, de Almeida Engler J, Abad P, Rosso MN, Favery B. 2008b. Root-knot nematodes manipulate plant cell functions during a compatible interaction. Journal of Physiology 165: 104-113.
references: Caillaud MC, Lecomte P, Jammes F, Quentin M, Pagnotta S, Andrio E, de Almeida Engler J, Marfaing N, Gounon P, Abad P et al. 2008a. MAP65-3 microtubule-associated protein is essential for nematode-induced giant cell ontogenesis in Arabidopsis. The Plant Cell 20: 423-437.
references: Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas R. 2012. TrakEM2 software for neural circuit reconstruction. PLoS ONE 7: 1-8.
references: Casson S, Spencer M, Walker K, Lindsey K. 2005. Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis. The Plant Journal 42: 111-123.
references: Chen Z, Zheng Z, Huang J, Lai Z, Fan B. 2009. Biosynthesis of salicylic acid in plants. Plant Signaling & Behavior 4: 493-496.
references: Cooper AJ, Latunde-Dada AO, Woods-Tor A, Lynn J, Lucas JA, Crute IR, Holub EB. 2008. Basic compatibility of Albugo candida in Arabidopsis thaliana and Brassica juncea causes broad-spectrum suppression of innate immunity. Molecular Plant-Microbe Interactions 21: 745-756.
references: Damiani I, Baldacci-Cresp F, Hopkins J, Andrio E, Balzergue S, Lecomte P, Puppo A, Abad P, Favery B, Hérouart D. 2012. Plant genes involved in harbouring symbiotic rhizobia or pathogenic nematodes. New Phytologist 194: 511-522.
references: De Almeida J, Favery B. 2011. Unravelling the plant cell cycle in nematode induced feeding sites. In: Jones J, Gheysen G, Fenoll C, eds. Genomics and molecular genetics of plant-nematode interactions. Dordrecht, the Netherlands: Springer, 349-368.
references: El Mansouri I, Mercado JA, Santiago-Domenech N, Pliego-Alfaro F, Valpuesta V, Quesada MA. 1999. Biochemical and phenotypical characterization of transgenic tomato plants over-expressing a basic peroxidase. Physiologia Plantarum 106: 355-362.
references: Escobar C, Sigal B, Mitchum M. 2011. Transcriptomic and proteomic analysis of the plant response to nematode infection. In: Jones J, Gheysen G, Fenoll C, eds. Genomics and molecular genetics of plant-nematode interactions. Dordrecht, the Netherlands: Springer, 157-176.
references: Eulgem T, Somssich IE. 2007. Networks of WRKY transcription factors in defense signaling. Current Opinion in Plant Biology 10: 366-371.
references: Fei Z, Joung JG, Tang X, Zheng Y, Huang M, Lee JM, McQuinn R, Tieman DM, Alba R, Klee HJ et al. 2011. Tomato functional genomics database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Research 39: D1156-D1163.
references: Fosu-Nyarko J, Jones MG, Wang Z. 2009. Functional characterization of transcripts expressed in early-stage Meloidogyne javanica-induced giant cells isolated by laser microdissection. Molecular Plant Pathology 10: 237-248.
references: Fraser CM, Chapple C. 2011. The phenylpropanoid pathway in Arabidopsis. The Arabidopsis Book 9: e0152.
references: Gal TZ, Aussenberg ER, Burdman S, Kapulnik Y, Koltai H. 2006. Expression of a plant expansin is involved in the establishment of root knot nematode parasitism in tomato. Planta 224: 155-162.
references: Gamborg OL, Miller RA, Ojima K. 1968. Nutrient requirements of suspension cultures of soybean root cells. Experimental Cell Research 50: 151-158.
references: Gheysen G, Fenoll C. 2002. Gene expression in nematode feeding sites. Annual Review of Phytopathology 40: 191-219.
references: Gheysen G, Fenoll C. 2011. Arabidopsis as a tool for the study of plant-nematode interactions. In: Jones J, Gheysen G, Fenoll C, eds. Genomics and molecular genetics of plant-nematode interactions. Dordrecht, the Netherlands: Springer, 139-156.
references: Hammes UZ, Schachtman DP, Berg RH, Nielsen E, Koch W, McIntyre LM, Taylor CG. 2005. Nematode-induced changes of transporter gene expression in Arabidopsis roots. Molecular Plant-Microbe Interactions 18: 1247-1257.
references: Hewezi T, Howe PJ, Maier TR, Hussey RS, Mitchum MG, Davis EL, Baum TJ. 2010. Arabidopsis spermidine synthase is targeted by an effector protein of the cyst nematode Heterodera schachtii. Plant Physiology 152: 968-984.
references: Hewezi T, Maier T, Nettleton D, Baum T. 2012. The Arabidopsis MicroRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection. Plant Physiology 159: 321-335.
references: Hollender C, Liu Z. 2008. Histone deacetylase genes in Arabidopsis development. Journal of Integrative Plant Biology 50: 875-885.
references: Huang GR, Dong AR, Davis EL, Baum TJ, Hussey RS. 2006. A root-knot nematode secretory peptide functions as a ligand for a plant transcription factor. Molecular Plant-Microbe Interactions 19: 463-470.
references: Huang X, Springer PS, Kaloshian I. 2003. Expression of the Arabidopsis MCM gene PROLIFERA during root-knot and cyst nematode infection. Phytopathology 93: 35-41.
references: Ithal N, Recknor J, Nettleton D, Maier T, Baum TJ, Mitchum MG. 2007. Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Molecular Plant-Microbe Interactions 20: 510-525.
references: Ito T, Sun B. 2009. Epigenetic regulation of developmental timing in floral stem cells. Epigenetics 4: 564-567.
references: Jammes F, Lecomte P, de Almeida-Engler J, Bitton F, Martin-Magniette ML, Renou JP, Abad P, Favery B. 2005. Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis. The Plant Journal 44: 447-458.
references: Jaouannet M, Perfus-Barbeoch L, Deleury E, Magliano M, Engler G, Vieira P, Danchin EGJ, Rocha MD, Coquillard P, Abad P et al. 2012. A root-knot nematode-secreted protein is injected into giant cells and targeted to the nuclei. New Phytologist 194: 924-931.
references: Klink VP, Alkharouf N, MacDonald M, Matthews B. 2005. Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogen Heterodera glycines (soybean cyst nematode). Plant Molecular Biology 59: 965-979.
references: Klink VP, Hosseini P, Alkharouf N, Matthews B. 2009. A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). Plant Molecular Biology 71: 525-567.
references: Klink VP, Overall C, Alkharouf N, MacDonald M, Matthews B. 2007. Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). Planta 226: 1389-1409.
references: Klink VP, Overall C, Alkharouf N, MacDonald M, Matthews B. 2010. Microarray detection call methodology as a means to identify and compare transcripts expressed within syncytial cells from soybean (Glycine max) roots undergoing resistant and susceptible reactions to the soybean cyst nematode (Heterodera glycines). Journal of Biomedicine and Biotechnology 2010: 1-30.
references: Knizewski L, Ginalski K, Jerzmanowski A. 2008. Snf2 proteins in plants: gene silencing and beyond. Trends in Plant Science 13: 557-565.
references: Kohler C, Hennig L, Bouveret R, Gheyselinck J, Grossniklaus U, Gruissem W. 2003. Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development. The Embo Journal 22: 4804-4814.
references: Koltai H, Bird DM. 2000. Epistatic repression of PHANTASTICA and class 1 KNOTTED genes is uncoupled in tomato. The Plant Journal 22: 455-459.
references: Koltai H, Dhandaydham M, Opperman C, Thomas J, Bird D. 2001. Overlapping plant signal transduction pathways induced by a parasitic nematode and a rhizobial endosymbiont. Molecular Plant-Microbe Interactions 14: 1168-1177.
references: Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080.
references: Lucena MA, Romero-Aranda R, Mercado JA, Cuarteros J, Valpuesta V, Quesada MA. 2003. Structural and physiological changes in the roots of tomato plants over-expressing a basic peroxidase. Physiologia Plantarum 118: 422-429.
references: Maunoury N, Redondo-Nieto M, Bourcy M, Van de Velde W, Alunni B, Laporte P, Durand P, Agier N, Marisa L, Vaubert D et al. 2010. Differentiation of symbiotic cells and endosymbionts in Medicago truncatula nodulation are coupled to two transcriptome-switches. PLoS ONE 5: e9519.
references: Moreau S, Verdenaud M, Ott T, Letort SB, de Billy FO, Niebel A, Gouzy JM, Carvalho-Niebel F, Gamas P. 2011. Transcription reprogramming during root 712 nodule development in Medicago truncatula. PLoS ONE 6: e16463.
references: Olsen AN, Ernst HA, Leggio LL, Skriver K. 2005. NAC transcription factors: structurally distinct, functionally diverse. Trends in Plant Science 10: 79-87.
references: Passardi F, Theiler G, Zamocky M, Cosio C, Rouhier N, Teixera F, Margis-Pinheiro M, Ioannidis V, Penel C, Falquet L et al. 2007. PeroxiBase: the peroxidase database. Phytochemistry 68: 1605-1611.
references: Portillo M, Fenoll C, Escobar C. 2006. Evaluation of different RNA extraction methods for small quantities of plant tissue: combined effects of reagent type and homogenization procedure on RNA quality-integrity and yield. Physiologia Plantarum 128: 1-7.
references: Portillo M, Lindsey K, Casson S, Garcia-Casado G, Solano R, Fenoll C, Escobar C. 2009. Isolation of RNA from laser-capture-microdissected giant cells at early differentiation stages suitable for differential transcriptome analysis. Molecular Plant Pathology 10: 523-535.
references: Rosso M-N, Grenier E. 2011. Other nematode effectors and evolutionary constraints. In: Jones J, Gheysen G, Fenoll C, eds. Genomics and molecular genetics of plant-nematode interactions. Dordrecht, the Netherlands: Springer, 287-307.
references: Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J. 2006. TM4 microarray software suite. Methods in Enzymology 411: 134-193.
references: Sanchez MdeL, Caro E, Desvoyes B, Ramirez-Parra E, Gutierrez C. 2008. Chromatin dynamics during the plant cell cycle. Seminars in Cell and Developmental Biology 19: 537-546.
references: Sawa S, Demura T, Horiguchi G, Kubo M, Fukuda H. 2005. The ATE genes are responsible for repression of transdifferentiation into xylem cells in Arabidopsis. Plant Physiology 137: 141-148.
references: Schaff JE, Nielsen DM, Smith CP, Scholl EH, Bird DM. 2007. Comprehensive transcriptome profiling in tomato reveals a role for glycosyltransferase in Mi-mediated nematode resistance. Plant Physiology 144: 1079-1092.
references: Schlink K. 2010. Down-regulation of defense genes and resource allocation into infected roots as factors for compatibility between Fagus sylvatica and Phytophthora citricola. Functional & Integrative Genomics 10: 253-264.
references: Shultz RW, Tatineni VM, Hanley-Bowdoin L, Thompson WF. 2007. Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice. Plant Physiology 144: 1697-1714.
references: Siefers N, Dang KK, Kumimoto RW, Bynum WE, Tayrose G, Holt BF. 2009. Tissue-specific expression patterns of Arabidopsis NF-Y transcription factors suggest potential for extensive combinatorial complexity. Plant Physiology 149: 625-641.
references: Smant G, Jones J. 2011. Suppression of plant defences by nematodes. In: Jones J, Gheysen G, Fenoll C, eds. Genomics and molecular genetics of plant-nematode interactions. Dordrecht, the Netherlands: Springer, 273-286.
references: Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC. 2007. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. The Plant Cell 19: 1507-1521.
references: Smyth GK. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3: 1-26.
references: Smyth GK, Speed T. 2003. Normalization of cDNA microarray data. Methods 31: 265-273.
references: Starr JL. 1993. Dynamics of the nuclear complement of giant cells induced by Meloidogyne incognita. Journal of Nematology 25: 416-421.
references: Szakasits D, Heinen P, Wieczorek K, Hofmann J, Wagner F, Kreil DP, Sykacek P, Grundler FM, Bohlmann H. 2009. The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots. The Plant Journal 57: 771-784.
references: Toledo-Ortiz G, Huq E, Quail PH. 2003. The Arabidopsis basic/helix-loop-helix transcription factor family. The Plant Cell 15: 1749-1770.
references: Truman W, de Zabala MT, Grant M. 2006. Type III effectors orchestrate a complex interplay between transcriptional networks to modify basal defence responses during pathogenesis and resistance. The Plant Journal 46: 14-33.
references: Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blasing O, Kowalczyk M, Weicht D, Polinceusz A et al. 2006. Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Molecular Biology 60: 773-792.
references: Wang Z, Potter RH, Jones MGK. 2001. A novel approach to extract and analyse cytoplasmic contents from individual giant cells in tomato roots induced by Meloidogyne javanica. International Journal of Nematology 11: 219-225.
references: Wang Z, Potter RH, Jones MGK. 2003. Differential display analysis of gene expression in the cytoplasm of giant cells induced in tomato roots by Meloidogyne javanica. Molecular Plant Pathology 4: 361-371.
references: Williamson VM, Hussey RS. 1996. Nematode pathogenesis and resistance in plants. The Plant Cell 8: 1735-1745.
references: Zhong R, Lee C, Zhou J, McCarthy RL, Ye ZH. 2008. A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. The Plant Cell 20: 2763-2782.