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Time-dependent effects of Pochonia chlamydosporia endophytism on gene expression profiles of colonized tomato roots

  • Genomics, transcriptomics, proteomics
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Abstract

A transcriptome analysis was produced from tomato roots inoculated with the hyphomycete Pochonia chlamydosporia at three different times. Gene expression data were also yielded from fungus grown in vitro or endophytic. A next-generation sequencing (NGS) and network analysis approach were applied. We identified 3.676 differentially expressed tomato genes (DEG), highlighting a core of 93 transcripts commonly down- or upregulated at every time point, shedding light on endophytism process. Functional categories related to plant information-processing system, which recognizes, percepts, and transmits signals, were associated with gene upregulated early in time, with higher representations in processes such as plant defense regulation later in time. Network analysis of a DEG subset showed dominance of MAP kinase hubs in the uninoculated control samples, replaced by an increased centrality of WRKY transcription factor and ETR—ethylene response factor genes in the colonized roots. Fungus genes expressed during progression of plant colonization, therefore related to the host colonization process or endophytism persistence, were also identified. Data provided a high-resolution insight on tomato transcriptome changes as induced by endophytism, highlighting a specific modulation of stress-responsive transcripts, related to a selective activation of defense pathways, likely required by the fungus to establish a persistent endophytic lifestyle.

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References

  • Bastian M, Heymann S, Jacomy M (2009) Gephi: An open source software for exploring and manipulating networks. In: Adar E, Hurst M, Finin T, Glance N, Nicolov N, Tseng B (eds) Proceedings of the Third International AAAI Conference on Weblogs and Social Media. San Jose, CA, 17-20 May 2009. AAAI Press, Menlo Park, pp 361–362

  • Behie SW, Zelisko PM, Bidochka MJ (2012) Endophytic insect-parasitic fungi translocate nitrogen directly from insects to plants. Science 336:1576–1577

    CAS  PubMed  Google Scholar 

  • 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. Mol Plant-Microbe Interact 21:1205–1214

    CAS  PubMed  Google Scholar 

  • Cao Y, Song F, Goodman RM, Zheng Z (2006) Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. J Plant Physiol 163:1167–1178

    CAS  PubMed  Google Scholar 

  • Casalongue CA, Fiol DF, París R, Godoy AV, D’Ippolito S, Terrile MC (2012) Auxin as part of the wounding response in plants. In: Khan NA, Nazar R, Iqbal N, Anjum NA (eds) Phytohormones and abiotic stress tolerance in plants. Springer, Berlin, pp 115–124

    Google Scholar 

  • Cheong YH (2002) Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis. Plant Physiol 129:661–677

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nürnberger T, Jones JD, Felix G, Boller T (2007) A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature 448:497–500. https://doi.org/10.1038/nature05999

    Article  CAS  PubMed  Google Scholar 

  • Conconi A, Miquel M, Browse JA, Ryan CA (1996) Intracellular levels of free linolenic and linoleic acids increase in tomato leaves in response to wounding. Plant Physiol 111:797–803

    CAS  PubMed  PubMed Central  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    CAS  PubMed  Google Scholar 

  • 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 U S A 109:5110–5115

    PubMed  PubMed Central  Google Scholar 

  • Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64–W70

    CAS  PubMed  PubMed Central  Google Scholar 

  • Escudero N, Lopez-Llorca LV (2013) Effects on plant growth and root-knot nematode infection of an endophytic GFP transformant of the nematophagous fungus Pochonia chlamydosporia. Symbiosis 57:33–42

    Google Scholar 

  • Foyer CH, Noctor G (2011) Ascorbate and glutathione: the heart of the redox hub. Plant Physiol 155:2–18

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fruchterman TMJ, Reingold EM (1991) Graph drawing by force-directed placement. SOFTWARE PRACT EXPER 21:1129–1164

    Google Scholar 

  • Harrell FE Jr (2018) Hmisc: Harrell Miscellaneous. R package version 4.1-1. https://CRAN.R-project.org/package=Hmisc

  • Hause B, Schaarschmidt S (2009) The role of jasmonates in mutualistic symbioses between plants and soil-born microorganisms. Phytochemistry 70:1589–1599. https://doi.org/10.1016/j.phytochem.2009.07.003 Epub 2009 Aug 21

    Article  CAS  PubMed  Google Scholar 

  • Heberle H, Meirelles GV, da Silva FR, Telles GP, Minghim R (2015) InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 16:169

    PubMed  PubMed Central  Google Scholar 

  • Hirsch PR, Mauchline TH (2012) Who’s who in the plant root microbiome? Nat Biotechnol 30:961–962

    CAS  PubMed  Google Scholar 

  • Hwang D, Rhee SH (1999) Receptor-mediated signaling pathways: potential targets of modulation by dietary fatty acids. Am J Clin Nutr 70:545–556

    CAS  PubMed  Google Scholar 

  • Iberkleid I, Sela N, Sigal Brown M (2015) Meloidogyne javanica fatty acid- and retinol-binding protein (Mj-FAR-1) regulates expression of lipid-, cell wall-, stress- and phenylpropanoid-related genes during nematode infection of tomato. BMC Genomics 16:272

    PubMed  PubMed Central  Google Scholar 

  • Kerry BR (2000) Rhizosphere interactions and the exploitation of microbial agents for the biological control of plant-parasitic nematodes. Annu Rev Phytopathol 38:423–424

    CAS  PubMed  Google Scholar 

  • Kuźniak E, Kopczewski T, Chojak-Koźniewska J (2017) Ascorbate-glutathione cycle and biotic stress tolerance in plants. In: Hossain M, Munné-Bosch S, Burritt D, Diaz-Vivancos P, Fujita M, Lorence A (eds) Ascorbic acid in plant growth, development and stress tolerance. Springer, Cham, pp 201–231. https://doi.org/10.1007/978-3-319-74057-7_8

    Chapter  Google Scholar 

  • Lahrmann U, Strehmel N, Langen G, Frerigmann H, Leson L, Ding Y, Scheel D, Herklotz S, Hilbert M, Zuccaro A (2015) Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a non compromised plant innate immunity. New Phytol 207:841–857

    CAS  PubMed  Google Scholar 

  • Larriba E, Jaime MD, Carbonell-Caballero J, Conesa A, Dopazo J, Nislow C, Martín-Nieto J, Lopez-Llorca LV (2014) Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. Fungal Genet Biol 65:69–80

    CAS  PubMed  Google Scholar 

  • Larriba E, Jaime MD, Nislow C, Martin-Nieto J, Lopez-Llorca LV (2015) Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response. J Plant Res 128:665–678

    CAS  PubMed  Google Scholar 

  • Lee HI, León J, Raskin I (1995) Biosynthesis and metabolism of salicylic acid. Proc Natl Acad Sci U S A 92:4076–4079

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li C, Liu G, Xu C, Lee GI, Bauer P, Ling HQ, Ganal MW, Howe GA (2003) The tomato suppressor of prosystemin-mediated responses gene encodes a fatty acid desaturase required for the biosynthesis of jasmonic acid and the production of a systemic wound signal for defense gene expression. Plant Cell 15:1646–1661. https://doi.org/10.1105/tpc.012237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li X, Wu Y, Liu Z, Zhang C (2017) The function and transcriptome analysis of a bZIP transcription factor CgAP1 in Colletotrichum gloeosporioides. Microbiol Res 197:39–48

    CAS  PubMed  Google Scholar 

  • Lin R, Qin F, Shen B, Shi Q, Liu C, Zhang X, Jiao Y, Lu J, Gao Y, Suarez-Fernandez M, Lopez-Moya F, Lopez-Llorca L, Wang G, Mao Z, Ling J, Yang Y, Cheng X, Bingyan X (2018) Genome and secretome analysis of Pochonia chlamydosporia provide new insight into egg-parasitic mechanisms. Sci Rep-UK 8:1123. https://doi.org/10.1038/s41598-018-19169-5

    Article  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−CT method. Methods 25:402–408

    CAS  PubMed  Google Scholar 

  • López-Bucio JS, Dubrovsky JG, Raya-González J, Ugartechea-Chirino Y, López-Bucio J, de Luna-Valdez LA, Ramos-Vega M, León P, Guevara-García AA (2013) Arabidopsis thaliana mitogen-activated protein kinase 6 is involved in seed formation and modulation of primary and lateral root development. J Exp Bot 65:169–183

    PubMed  PubMed Central  Google Scholar 

  • Maciá-Vicente JG, Rosso LC, Ciancio A, Jansson HB, Lopez-Llorca LV (2009) Colonization of barley roots by endophytic Fusarium equiseti and Pochonia chlamydosporia: effects on plant growth and disease. Ann Appl Biol 155:391–401

    Google Scholar 

  • Manzanilla-López RH, Esteves I, Finetti-Sialer MM, Hirsch PR, Ward E, Devonshire J, Hidalgo-Diaz L (2013) Pochonia chlamydosporia: advances and challenges to improve its performance as a biological control agent of sedentary endo-parasitic nematodes. J Nematol 45:1–7

    PubMed  PubMed Central  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5:621–628

    CAS  PubMed  Google Scholar 

  • Nahar K, Kyndt T, De Vleesschauwer D, Hofte M, Gheysen G (2011) The jasmonate pathway is a key player in systemically induced defense against root knot nematodes in rice. Plant Physiol 157:305–316

    CAS  PubMed  PubMed Central  Google Scholar 

  • Noctor G, Reichheld JP, Foyer CH (2017) ROS-related redox regulation and signalling in plants. Semin Cell Dev Biol 80:3–12. https://doi.org/10.1016/j.semcdb.2017.07.013

    Article  CAS  PubMed  Google Scholar 

  • Nombela G, Williamson VM, Muniz M (2003) The root-knot nematode resistance gene Mi-1.2 of tomato is responsible for resistance against the whitefly Bemisia tabaci. Mol Plant-Microbe Interact 16:645–649

    CAS  PubMed  Google Scholar 

  • Ozalvo R, Cabrera J, Escobar C, Christensen SA, Borrego EJ, Kolomiets MV, Castresana C, Iberkleid I, Horowitz SB (2014) Two closely related members of Arabidopsis 13-lipoxygenases (13-LOXs), LOX3 and LOX4, reveal distinct functions in response to plant-parasitic nematode infection. Mol Plant Pathol 15:319–332

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pentimone I, Lebrón R, Hackenberg M, Rosso LC, Colagiero M, Nigro F, Ciancio A (2018) Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia. Appl Microbiol Biotechnol 102(2):907–919. https://doi.org/10.1007/s00253-017-8608-7

    Article  CAS  PubMed  Google Scholar 

  • Pfaffl MW, Horgan GW, Dempfle L (2002) Relative expression software tool (REST©) for group-wise comparison and statis- tical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30:e36

    Google Scholar 

  • Pinchai N, Perfect BZ, Juvvadi PR, Fortwendel JR, Cramer RAJ, Asfaw YG, Heitman J, Perfect JR, Steinbach WJ (2009) Aspergillus fumigatus calcipressin CbpA is involved in hyphal growth and calcium homeostasis. Eukaryot Cell 8:511–519. https://doi.org/10.1128/EC.00336-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Plett JM, Daguerre Y, Wittulsky S, Vayssieres A, Deveau A, Melton SJ, Kohler A, Morrel-Falvey JL, Brun A, Veneault-Fourrey C, Martin F (2014) Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes. Proc Natl Acad Sci U S A 111:8299–8304

    CAS  PubMed  PubMed Central  Google Scholar 

  • Porta H, Rocha-Sosa M (2002) Plant lipoxygenases. Physiological and molecular features. Plant Physiol 130:15–21

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts PA, Thomason IJ (1986) Variability in reproduction of isolates of Meloidogyne incognita and M. javanica on resistant tomato genotypes. Plant Dis 70:547–551

    Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK (2010) edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    CAS  PubMed  Google Scholar 

  • Rossi M, Goggin FL, Milligan SB, Kaloshian I, Ullman DE, Williamson VM (1998) The nematode resistance gene Mi of tomato confers resistance against the potato aphid. Proc Natl Acad Sci U S A 95:9750–9754

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rosso LC, Finetti-Sialer MM, Hirsch PR, Ciancio A, Kerry BR, Clark IM (2011) Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia. Appl Microbiol Biotechnol 90:1981–1994. https://doi.org/10.1007/s00253-011-3282-7

    Article  CAS  PubMed  Google Scholar 

  • Rosso LC, Colagiero M, Salatino N, Ciancio A (2014) Observations on the effect of trophic conditions on Pochonia chlamydosporia gene expression. Ann Appl Biol 164:232–243

    CAS  Google Scholar 

  • Rouhier N, Lemaire SD, Jacquot JP (2008) The role of glutathione in photosynthetic organisms: emerging functions for glutaredoxins and glutathionylation. Annu Rev Plant Biol 59:143–166. https://doi.org/10.1146/annurev.arplant.59.032607.092811

    Article  CAS  PubMed  Google Scholar 

  • RStudio Team (2015) RStudio: integrated development for R. RStudio, Inc., Boston URL http://www.rstudio.com/

    Google Scholar 

  • Spyropoulou EA, Haring MA, Schuurink RC (2014) RNA sequencing on Solanum lycopersicum trichomes identifies transcription factors that activate terpene synthase promoters. BMC Genomics 15:402. https://doi.org/10.1186/1471-2164-15-402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taj G, Agarwal P, Grant M, Kumar A (2010) MAPK machinery in plants: recognition and response to different stresses through multiple signal transduction pathways. Plant Signal Behav 5:1370–1378

    CAS  PubMed  PubMed Central  Google Scholar 

  • Takahashi H (2013) Auxin biology in roots. Plant Roots 7:49–64

    CAS  Google Scholar 

  • Tejeda-Sartorius M, Martınez De La Vega O, Delano-Frier JP (2008) Jasmonic acid influences mycorrhizal colonization in tomato plants by modifying the expression of genes involved in carbohydrate partitioning. Physiol Plant 133:339–353

    CAS  PubMed  Google Scholar 

  • Vierheilig H (2004) Regulatory mechanisms during the plant–arbuscular mycorrhizal fungus interaction. Can J Bot 82:1166–1176

    CAS  Google Scholar 

  • Vogt T (2010) Phenylpropanoid biosynthesis) Phenylpropanoid Biosynthesis. Mol Plant 3:2–20

    CAS  PubMed  Google Scholar 

  • Vos P, Simons G, Jesse T, Wijbrandi J, Heinen L, Hogers R, Frijters A, Groenendijk J, Diergaarde P, Reijans M (1998) The tomato Mi-1 gene confers resistance to both root-knot nematodes and potato aphids. Nat Biotechnol 16:1365–1369

    CAS  PubMed  Google Scholar 

  • Wasternack C, Hause B (2013) Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 Review in Annals of Botany. Ann Bot 111:1021–1058

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zavala-Gonzalez EA, Rodrıguez-Cazorla E, Escudero N, Aranda-Martinez A, Martınez-Laborda A, Ramırez-Lepe M, Vera A, Lopez-Llorca LV (2017) Arabidopsis thaliana root colonization by the nematophagous fungus Pochonia chlamydosporia is modulated by jasmonate signaling and leads to accelerated flowering and improved yield. New Phytol 213:351–364

    CAS  PubMed  Google Scholar 

  • Zhou B, Mural RV, Chen X, Oates ME, Connor RA, Martin GB, Gough J, Zeng L (2017) A subset of ubiquitin-conjugating enzymes is essential for plant immunity. Plant Physiol 173:1371–1390. https://doi.org/10.1104/pp.16.01190

    Article  CAS  PubMed  Google Scholar 

  • Zuccaro A, Lahrmann U, Güldener U, Langen G, Pfiffi S, Biedenkopf D, Wong P, Samans B, Grimm C, Basiewicz M, Murat C, Martin F, Kogel KH (2011) Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Path 7:e1002290

    CAS  Google Scholar 

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Funding

This research was partially funded by projects Eureka!Eurostars E!7364 “Poch_art.”

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Authors and Affiliations

  1. Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126, Bari, Italy

    Isabella Pentimone, Mariantonietta Colagiero, Laura Cristina Rosso & Aurelio Ciancio

  2. Istituto di scienze delle produzioni alimentari, Via G. Amendola 122/D, 70126, Bari, Italy

    Massimo Ferrara

  3. Dipartimento di Biologia e Chimica Agro-Forestale e Ambientale, Università degli Studi “Aldo Moro”, Via G. Amendola 165/A, 70126, Bari, Italy

    Franco Nigro

Authors
  1. Isabella Pentimone
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  2. Mariantonietta Colagiero
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  3. Massimo Ferrara
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  4. Franco Nigro
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  5. Laura Cristina Rosso
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  6. Aurelio Ciancio
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Contributions

All authors designed the research; M.C., M.F., I.P., and L.C.R. performed the experiments; I.P., A.C., and L.C.R. analyzed the data; I.P. and L.C.R. identified and annotated the genes; all authors discussed the results; A.C., I.P., and L.C.R. wrote the article.

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Correspondence to Isabella Pentimone.

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Pentimone, I., Colagiero, M., Ferrara, M. et al. Time-dependent effects of Pochonia chlamydosporia endophytism on gene expression profiles of colonized tomato roots. Appl Microbiol Biotechnol 103, 8511–8527 (2019). https://doi.org/10.1007/s00253-019-10058-z

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