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Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea

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Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea may contribute to find biomarkers of the early detection of this devastating pathogen.

Abstract

Recent studies have linked epigenetic modifications with plant responses to biotic stresses. Information about specific histone marks upon necrotrophic pathogens is scarce. Here we wondered whether the altered responsiveness of specific genes in plants infected with Botrytis cinerea was associated with changes in chromatin structure. We performed a chromatin immunoprecipitation analysis that obtained differential epigenetic signature of activating marks H3K4me3, H3K9ac, and the repressor one H3K27me3 on both the promoter and the body of the highly induced PR1 in Arabidopsis plants infected with B. cinerea at 24 and 33 h after inoculation. We also determined the histone marks’ profile in two differentially expressed genes in response to B. cinerea, as well as to oxidative stress, given its relevance in this infection. These are both the induced CYP71A13, which encodes a cytochrome P450 involved in camalexin synthesis, and is essential against this necrotroph and the repressed EXL7 (Exordium-like 1). We also adapted our protocol in tomato plants infected with B. cinerea. At 24 hpi, H3K4me3 level increased on the promoter and at different locations of the body of the genes induced upon B. cinerea, including DES (divinyl ethyl synthase), LoxD (lipoxygenase D), DOX1 (α-dioxygenase 1), PR2 (pathogenesis-related protein2), WRKY53 and WRKY33. The histone modifications determined herein will allow future studies on epigenetic marks and their transgenerational inheritance in plants infected with B. cinerea. In addition, the analyzed genes are potential biomarkers of B. cinerea infection that could contribute to its early detection in tomato and related crops.

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References

  • AbuQamar S, Chen X, Dhawan R, Bluhm B, Salmeron J, Lam S, Dietrich RA, Mengiste T (2006) Expression profiling and mutant analysis reveals complex regulatory networks involved in Arabidopsis response to Botrytis infection. Plant J Cell Mol Biol 48:28–44

    Article  CAS  Google Scholar 

  • AbuQamar S, Moustafa K, Tran LS (2017) Mechanisms and strategies of plant defense against Botrytis cinerea. Crit Rev Biotechnol 37:262–274

    Article  CAS  PubMed  Google Scholar 

  • Ahuja I, Kissen R, Bones AM (2012) Phytoalexins in defense against pathogens. Trends Plant Sci 17:73–90

    Article  CAS  PubMed  Google Scholar 

  • Alvarez ME, Nota F, Cambiagno DA (2010) Epigenetic control of plant immunity. Mol Plant Pathol 11:563–576

    Article  CAS  PubMed  Google Scholar 

  • Amselem et al (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7:1–27

  • Angulo C, de la OLM, Finiti, Lopez-Cruz I, Fernandez-Crespo J, Garcia-Agustin E, Gonzalez-Bosch P C (2015) Role of dioxygenase alpha-DOX2 and SA in basal response and in hexanoic acid-induced resistance of tomato (Solanum lycopersicum) plants against Botrytis cinerea. J Plant Physiol 175:163–173

    Article  CAS  PubMed  Google Scholar 

  • Aranega-Bou P, de la OLM, Finiti, Garcia-Agustin I, Gonzalez-Bosch P C (2014) Priming of plant resistance by natural compounds. Hexanoic acid as a model. Front Plant Sci 5:488

    Article  PubMed  PubMed Central  Google Scholar 

  • Avramova Z (2015) Transcriptional ‘memory’ of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes. Plant J Cell Mol Biol 83:149–159

    Article  CAS  Google Scholar 

  • Avramova Z (2017) The jasmonic acid-signalling and abscisic acid-signalling pathways cross talk during one, but not repeated, dehydration stress: a non-specific ‘panicky’ or a meaningful response? Plant Cell Environ 40:1704–1710

  • Berr A, McCallum EJ, Alioua A, Heintz D, Heitz T, Shen WH (2010) Arabidopsis histone methyltransferase SET DOMAIN GROUP8 mediates induction of the jasmonate/ethylene pathway genes in plant defense response to necrotrophic fungi. Plant Physiol 154:1403–1414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Birkenbihl RP, Diezel C, Somssich IE (2012) Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic responses toward Botrytis cinerea infection. Plant Physiol 159:266–285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Camañes G, Scalschi L, Vicedo B, Gonzalez-Bosch C, Garcia-Agustin P (2015) An untargeted global metabolomic analysis reveals the biochemical changes underlying basal resistance and priming in Solanum lycopersicum, and identifies 1-methyltryptophan as a metabolite involved in plant responses to Botrytis cinerea and Pseudomonas syringae. Plant J Cell Mol Biol 84:125–139

    Article  Google Scholar 

  • Chen X, Liu X, Zhao Y, Zhou DX (2015) Histone H3K4me3 and H3K27me3 regulatory genes control stable transmission of an epimutation in rice. Sci Rep 5:13251

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conrath U, Beckers GJ, Langenbach CJ, Jaskiewicz MR (2015) Priming for enhanced defense. Annu Rev Phytopathol 53:97–119

    Article  CAS  PubMed  Google Scholar 

  • De Leon IP, Sanz A, Hamberg M, Castresana C (2002) Involvement of the Arabidopsis alpha-DOX1 fatty acid dioxygenase in protection against oxidative stress and cell death. Plant J Cell Mol Biol 29:61–62

    Article  Google Scholar 

  • Dean R, Van Kan JA, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD (2012) The top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414–430

    Article  PubMed  Google Scholar 

  • Dhawan R, Luo H, Foerster AM, Abuqamar S, Du HN, Briggs SD, Mittelsten Scheid O, Mengiste T (2009) HISTONE MONOUBIQUITINATION1 interacts with a subunit of the mediator complex and regulates defense against necrotrophic fungal pathogens in Arabidopsis. Plant Cell 21:1000–1019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding B, Wang GL (2015) Chromatin versus pathogens: the function of epigenetics in plant immunity. Front Plant Sci 6:675

    PubMed  PubMed Central  Google Scholar 

  • Ding Y, Fromm M, Avramova Z (2012) Multiple exposures to drought ‘train’ transcriptional responses in Arabidopsis. Nat Commun 3:740

    Article  PubMed  Google Scholar 

  • Eberharter A, Becker PB (2002) Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep 3:224–229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Espinas NA, Saze H, Saijo Y (2016) Epigenetic control of defense signaling and priming in plants. Front Plant Sci 7:1201

    PubMed  PubMed Central  Google Scholar 

  • Finiti I, Leyva MO, Lopez-Cruz J, Calderan Rodrigues B, Vicedo B, Angulo C, Bennett AB, Grant M, Garcia-Agustin P, Gonzalez-Bosch C (2013) Functional analysis of endo-1,4-beta-glucanases in response to Botrytis cinerea and Pseudomonas syringae reveals their involvement in plant-pathogen interactions. Plant Biol 15:819–831

    Article  CAS  PubMed  Google Scholar 

  • Finiti I, de la OLM, Vicedo, Gomez-Pastor B, Lopez-Cruz R, Garcia-Agustin J, Real P, Gonzalez-Bosch MD C (2014) Hexanoic acid protects tomato plants against Botrytis cinerea by priming defence responses and reducing oxidative stress. Mol Plant Pathol 15:550–562

    Article  CAS  PubMed  Google Scholar 

  • Gachon C, Saindrenan P (2004) Real-time PCR monitoring of fungal development in Arabidopsis thaliana infected by Alternaria brassicicola and Botrytis cinerea. PPB 42:367–371

    CAS  PubMed  Google Scholar 

  • Gonzalez RM, Ricardi MM, Iusem ND (2013) Epigenetic marks in an adaptive water stress-responsive gene in tomato roots under normal and drought conditions. Epigenetics 8:864–872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hahn M, Viaud M, van Kan J (2014) The Genome of Botrytis cinerea, a ubiquitous broad host range necrotroph. pp 19–44

  • Haring M, Offermann S, Danker T, Horst I, Peterhansel C, Stam M (2007) Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. Plant Methods 3:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Heller J, Tudzynski P (2011) Reactive oxygen species in phytopathogenic fungi: signaling, development, and disease. Annu Rev Phytopathol 49:369–390

    Article  CAS  PubMed  Google Scholar 

  • Hemsley PA, Hurst CH, Kaliyadasa E, Lamb R, Knight MR, De Cothi EA, Steele JF, Knight H (2014) The Arabidopsis mediator complex subunits MED16, MED14, and MED2 regulate mediator and RNA polymerase II recruitment to CBF-responsive cold-regulated genes. Plant Cell 26:465–484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jaskiewicz M, Conrath U, Peterhansel C (2011a) Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response. EMBO Rep 12:50–55

    Article  CAS  PubMed  Google Scholar 

  • Jaskiewicz M, Peterhansel C, Conrath U (2011b) Detection of histone modifications in plant leaves. J Vis Exp 23(55)pii:3096. https://doi.org/10.3791/3096

  • Jones JD, Dangl JL (2006) The plant immune system. Nature 444:323–329

    Article  CAS  PubMed  Google Scholar 

  • Kaufmann K, Muino JM, Osteras M, Farinelli L, Krajewski P, Angenent GC (2010) Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protoc 5:457–472

    Article  CAS  PubMed  Google Scholar 

  • Kidd BN, Cahill DM, Manners JM, Schenk PM, Kazan K (2011) Diverse roles of the mediator complex in plants. Semin Cell Dev Biol 22:741–748

    Article  CAS  PubMed  Google Scholar 

  • Lai Z, Schluttenhofer CM, Bhide K, Shreve J, Thimmapuram J, Lee SY, Yun DJ, Mengiste T (2014) MED18 interaction with distinct transcription factors regulates multiple plant functions. Nat Commun 5:3064

    Article  PubMed  Google Scholar 

  • Lee S, Fu F, Xu S, Lee SY, Yun DJ, Mengiste T (2016) Global regulation of plant immunity by histone lysine methyl transferases. Plant Cell 28:1640–1661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128:707–719

    Article  CAS  PubMed  Google Scholar 

  • Li W, Lin YC, Li Q, Shi R, Lin CY, Chen H, Chuang L, Qu GZ, Sederoff RR, Chiang VL (2014) A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue. Nat Protoc 9:2180–2193

    Article  CAS  PubMed  Google Scholar 

  • Liu N, Avramova Z (2016) Molecular mechanism of the priming by jasmonic acid of specific dehydration stress response genes in Arabidopsis. Epigenet Chromatin 9:8

    Article  Google Scholar 

  • Liu N, Fromm M, Avramova Z (2014) H3K27me3 and H3K4me3 chromatin environment at super-induced dehydration stress memory genes of Arabidopsis thaliana. Mol Plant 7:502–513

    Article  CAS  PubMed  Google Scholar 

  • Lopez-Cruz J, Oscar CS, Emma FC, Pilar GA, Carmen GB (2017) Absence of Cu-Zn superoxide dismutase BCSOD1 reduces Botrytis cinerea virulence in Arabidopsis and tomato plants, revealing interplay among reactive oxygen species, callose and signalling pathways. Mol Plant Pathol 18:16–31

    Article  CAS  PubMed  Google Scholar 

  • Luna E, Bruce TJ, Roberts MR, Flors V, Ton J (2012) Next-generation systemic acquired resistance. Plant Physiol 158:844–853

    Article  CAS  PubMed  Google Scholar 

  • Luna E, Lopez A, Kooiman J, Ton J (2014) Role of NPR1 and KYP in long-lasting induced resistance by beta-aminobutyric acid. Front Plant Sci 5:184

    Article  PubMed  PubMed Central  Google Scholar 

  • Martinez-Aguilar K, Ramirez-Carrasco G, Hernandez-Chavez JL, Barraza A, Alvarez-Venegas R (2016) Use of BABA and INA as activators of a primed state in the common bean (Phaseolus vulgaris L.). Front Plant Sci 7:653

    Article  PubMed  PubMed Central  Google Scholar 

  • Mbengue M, Navaud O, Peyraud R, Barascud M, Badet T, Vincent R, Barbacci A, Raffaele S (2016) Emerging trends in molecular interactions between plants and the broad host range fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum. Front Plant Sci 7:422

    Article  PubMed  PubMed Central  Google Scholar 

  • Oide S, Bejai S, Staal J, Guan N, Kaliff M, Dixelius C (2013) A novel role of PR2 in abscisic acid (ABA) mediated, pathogen-induced callose deposition in Arabidopsis thaliana. New Phytol 200:1187–1199

    Article  CAS  PubMed  Google Scholar 

  • Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Po-Wen C, Singh P, Zimmerli L (2013) Priming of the Arabidopsis pattern-triggered immunity response upon infection by necrotrophic Pectobacterium carotovorum bacteria. Mol Plant Pathol 14:58–70

    Article  PubMed  Google Scholar 

  • Ricardi MM, Gonzalez RM, Iusem ND (2010) Protocol: fine-tuning of a chromatin immunoprecipitation (ChIP) protocol in tomato. Plant Methods 6:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Saleh A, Alvarez-Venegas R, Avramova Z (2008) An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat Protoc 3:1018–1025

    Article  CAS  PubMed  Google Scholar 

  • Scalschi L, Sanmartin M, Camanes G, Troncho P, Sanchez-Serrano JJ, Garcia-Agustin P, Vicedo B (2015) Silencing of OPR3 in tomato reveals the role of OPDA in callose deposition during the activation of defense responses against Botrytis cinerea. Plant J Cell Mol Biol 81:304–315

    Article  CAS  Google Scholar 

  • Sham A, Al-Azzawi A, Al-Ameri S, Al-Mahmoud B, Awwad F, Al-Rawashdeh A, Iratni R, AbuQamar S (2014) Transcriptome analysis reveals genes commonly induced by Botrytis cinerea infection, cold, drought and oxidative stresses in Arabidopsis. PloS One 9:e113718

    Article  PubMed  PubMed Central  Google Scholar 

  • Temme N, Tudzynski P (2009) Does Botrytis cinerea Ignore H(2)O(2)-induced oxidative stress during infection? Characterization of botrytis activator protein 1. Molecular plant-microbe interactions. MPMI 22:987–998

    Article  CAS  PubMed  Google Scholar 

  • Thomma BP, Nelissen I, Eggermont K, Broekaert WF (1999) Deficiency in phytoalexin production causes enhanced susceptibility of Arabidopsis thaliana to the fungus Alternaria brassicicola. Plant J Cell Mol Biol 19:163–171

    Article  CAS  Google Scholar 

  • Tirajoh A, Aung TS, McKay AB, Plant AL (2005) Stress-responsive alpha-dioxygenase expression in tomato roots. J Exp Bot 56:713–723

    Article  CAS  PubMed  Google Scholar 

  • Van Eck L, Davidson RM, Wu S, Zhao BY, Botha AM, Leach JE, Lapitan NL (2014) The transcriptional network of WRKY53 in cereals links oxidative responses to biotic and abiotic stress inputs. Funct Integr Genom 14:351–362

    Article  Google Scholar 

  • Vicedo B, Flors V, de la OLM, Finiti, Kravchuk I, Real Z, Garcia-Agustin MD, Gonzalez-Bosch P C (2009) Hexanoic acid-induced resistance against Botrytis cinerea in tomato plants. MPMI 22:1455–1465

    Article  CAS  PubMed  Google Scholar 

  • Wang C, Ding Y, Yao J, Zhang Y, Sun Y, Colee J, Mou Z (2015) Arabidopsis Elongator subunit 2 positively contributes to resistance to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola. Plant J cell Mol Biol 83:1019–1033

    Article  CAS  Google Scholar 

  • Wang C, Du X, Mou Z (2016) The mediator complex subunits MED14, MED15, and MED16 are involved in defense signaling crosstalk in arabidopsis. Front Plant Sci 7:1947

    PubMed  PubMed Central  Google Scholar 

  • Williamson B, Tudzynski B, Tudzynski P, van Kan JA (2007) Botrytis cinerea: the cause of grey mould disease. Mol Plant Pathol 8:561–580

    Article  CAS  PubMed  Google Scholar 

  • Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ (2012) Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. Plant Cell 24:3530–3557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamaguchi N, Winter CM, Wu MF, Kwon CS, William DA, Wagner D (2014) PROTOCOLS: chromatin immunoprecipitation from arabidopsis tissues. Arabidopsis Book 12:e0170

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Li D, Zhang H, Hong Y, Huang L, Liu S, Li X, Ouyang Z, Song F (2015) Tomato histone H2B monoubiquitination enzymes SlHUB1 and SlHUB2 contribute to disease resistance against Botrytis cinerea through modulating the balance between SA- and JA/ET-mediated signaling pathways. BMC Plant Biol 15:252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou C, Zhang L, Duan J, Miki B, Wu K (2005) HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell 17:1196–1204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work has been supported by grants from the Spanish Ministry of Science and Innovation (AGL2010-22300-C03-01 and AGL2013-49023-C03-01), co-funded by European Regional Development Funds (ERDF), and by Generalitat Valenciana Grupos de Excelencia PROMETEO/2012/066. O. Crespo-Salvador was the recipient of a research contract from grant PROMETEO/2012/066 and from grant AGL2013-49023-C03-01. J. López-Cruz was the recipient of a research contract from grant AGL2013-49023-C03-01. We thank Dr. Paul Tudzynski for providing the B05.10 strain and the SCIE (University of Valencia) for technical support. We also thank Helen Warburton for proofreading the English.

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Authors and Affiliations

  1. Departamento de Bioquímica y Biología Molecular, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46980, Paterna, Valencia, Spain

    Óscar Crespo-Salvador, Mónica Escamilla-Aguilar, Jaime López-Cruz & Carmen González-Bosch

  2. Departamento de Bioquímica y Biología Molecular, Universitat de València, Dr. Moliner 50, Burjassot, Valencia, Spain

    Gerardo López-Rodas

  3. Institute of health research INCLIVA, Valencia, Spain

    Gerardo López-Rodas

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  1. Óscar Crespo-Salvador
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  2. Mónica Escamilla-Aguilar
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  3. Jaime López-Cruz
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  4. Gerardo López-Rodas
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  5. Carmen González-Bosch
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Correspondence to Carmen González-Bosch.

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Communicated by Tarek Hewezi.

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Crespo-Salvador, Ó., Escamilla-Aguilar, M., López-Cruz, J. et al. Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea . Plant Cell Rep 37, 153–166 (2018). https://doi.org/10.1007/s00299-017-2218-9

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