Skip to main content

Advertisement

SpringerLink
Log in

Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses

  • Original Article
  • Published:
Planta Aims and scope Submit manuscript

Abstract

The physiological and biochemical changes in fruit ripening produce key attributes of fruit quality including color, taste, aroma and texture. These changes are driven by the highly regulated and synchronized activation of a huge number of ripening-associated genes. In tomato (Solanum lycopersicum), a typical climacteric fruit, the MADS-box transcription factor RIN is one of the earliest-acting ripening regulators, required for both ethylene-dependent and ethylene-independent pathways. Although we previously identified several direct RIN targets, many additional targets remain unidentified, likely including key ripening-associated genes. Here, we report the identification of novel RIN targets by transcriptome and chromatin immunoprecipitation (ChIP) analyses. Transcriptome comparisons by microarray of wild-type and rin mutant tomatoes identified 342 positively regulated genes and 473 negatively regulated genes by RIN during ripening. Most of the positively regulated genes contained possible RIN-binding (CArG-box) sequences in their promoters. Subsequently, we selected six genes from the positively regulated genes and a ripening regulator gene, CNR, and assayed their promoters by quantitative ChIP-PCR to examine RIN binding. All of the seven genes, which are involved in cell wall modification, aroma and flavor development, pathogen defense and transcriptional regulation during ripening, are targets of RIN, suggesting that RIN may control multiple diverse ripening processes. In particular, RIN directly regulates the expression of the ripening-associated transcription factors, CNR, TDR4 and a GRAS family gene, providing an important clue to elucidate the complicated transcriptional cascade for fruit ripening.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Alba R, Payton P, Fei Z, McQuinn R, Debbie P, Martin GB, Tanksley SD, Giovannoni JJ (2005) Transcriptome and selected metabolite analyses reveal multiple points of ethylene control during tomato fruit development. Plant Cell 17:2954–2965

    Article  PubMed  CAS  Google Scholar 

  • Alexander L, Grierson D (2002) Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening. J Exp Bot 53:2039–2055

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Bolle C (2004) The role of GRAS proteins in plant signal transduction and development. Planta 218:683–692

    Article  PubMed  CAS  Google Scholar 

  • Busi MV, Bustamante C, D’Angelo C, Hidalgo-Cuevas M, Boggio SB, Valle EM, Zabaleta E (2003) MADS-box genes expressed during tomato seed and fruit development. Plant Mol Biol 52:801–815

    Article  PubMed  CAS  Google Scholar 

  • Cardon GH, Hohmann S, Nettesheim K, Saedler H, Huijser P (1997) Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J 12:367–377

    Article  PubMed  CAS  Google Scholar 

  • Chen G, Hackett R, Walker D, Taylor A, Lin Z, Grierson D (2004) Identification of a specific isoform of tomato lipoxygenase (TomloxC) involved in the generation of fatty acid-derived flavor compounds. Plant Physiol 136:2641–2651

    Article  PubMed  CAS  Google Scholar 

  • Chung MY, Vrebalov J, Alba R, Lee J, McQuinn R, Chung JD, Klein P, Giovannoni J (2010) A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant J 64:936–947

    Article  PubMed  CAS  Google Scholar 

  • Eriksson EM, Bovy A, Manning K, Harrison L, Andrews J, De Silva J, Tucker GA, Seymour GB (2004) Effect of the Colorless non-ripening mutation on cell wall biochemistry and gene expression during tomato fruit development and ripening. Plant Physiol 136:4184–4197

    Article  PubMed  CAS  Google Scholar 

  • Exposito-Rodriguez M, Borges AA, Borges-Perez A, Perez JA (2008) Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol 8:131

    Article  PubMed  Google Scholar 

  • Fan XT, Mattheis JP, Fellman JK (1998) A role for jasmonates in climacteric fruit ripening. Planta 204:444–449

    Article  CAS  Google Scholar 

  • Fei Z, Tang X, Alba RM, White JA, Ronning CM, Martin GB, Tanksley SD, Giovannoni JJ (2004) Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant J 40:47–59

    Article  PubMed  Google Scholar 

  • Fujisawa M, Nakano T, Ito Y (2011) Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation. BMC Plant Biol 11:26

    Article  PubMed  CAS  Google Scholar 

  • Gautier H, Diakou-Verdin V, Benard C, Reich M, Buret M, Bourgaud F, Poessel JL, Caris-Veyrat C, Genard M (2008) How does tomato quality (sugar, acid, and nutritional quality) vary with ripening stage, temperature, and irradiance? J Agric Food Chem 56:1241–1250

    Article  PubMed  CAS  Google Scholar 

  • Gimenez E, Pineda B, Capel J, Anton MT, Atares A, Perez-Martin F, Garcia-Sogo B, Angosto T, Moreno V, Lozano R (2010) Functional analysis of the Arlequin mutant corroborates the essential role of the Arlequin/TAGL1 gene during reproductive development of tomato. PLoS One 5:e14427

    Article  PubMed  CAS  Google Scholar 

  • Giovannoni JJ (2004) Genetic regulation of fruit development and ripening. Plant Cell 16(Suppl):S170–S180

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez-Bosch C, Brummell DA, Bennett AB (1996) Differential expression of two endo-1, 4-[beta]-Glucanase genes in pericarp and locules of wild-type and mutant tomato fruit. Plant Physiol 111:1313–1319

    PubMed  CAS  Google Scholar 

  • Greb T, Clarenz O, Schafer E, Muller D, Herrero R, Schmitz G, Theres K (2003) Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation. Genes Dev 17:1175–1187

    Article  PubMed  CAS  Google Scholar 

  • Grenier J, Potvin C, Trudel J, Asselin A (1999) Some thaumatin-like proteins hydrolyse polymeric beta-1,3-glucans. Plant J 19:473–480

    Article  PubMed  CAS  Google Scholar 

  • Griffiths A, Barry C, Alpuche-Solis AG, Grierson D (1999) Ethylene and developmental signals regulate expression of lipoxygenase genes during tomato fruit ripening. J Exp Bot 50:793–798

    CAS  Google Scholar 

  • Heitz T, Bergey DR, Ryan CA (1997) A gene encoding a chloroplast-targeted lipoxygenase in tomato leaves is transiently induced by wounding, systemin, and methyl jasmonate. Plant Physiol 114:1085–1093

    Article  PubMed  CAS  Google Scholar 

  • Hirsch S, Oldroyd GE (2009) GRAS-domain transcription factors that regulate plant development. Plant Signal Behav 4:698–700

    Article  PubMed  CAS  Google Scholar 

  • Hongxing Z, Benzhong Z, Bianyun Y, Yanling H, Daqi F, Wentao X, Yunbo L (2005) Cloning and DNA-binding properties of ethylene response factor, LeERF1 and LeERF2, in tomato. Biotechnol Lett 27:423–428

    Article  PubMed  Google Scholar 

  • Itai A, Ishihara K, Bewley JD (2003) Characterization of expression, and cloning, of beta-d-xylosidase and alpha-l-arabinofuranosidase in developing and ripening tomato (Lycopersicon esculentum Mill.) fruit. J Exp Bot 54:2615–2622

    Article  PubMed  CAS  Google Scholar 

  • Itkin M, Seybold H, Breitel D, Rogachev I, Meir S, Aharoni A (2009) TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network. Plant J 60:1081–1095

    Article  PubMed  CAS  Google Scholar 

  • Ito Y, Kitagawa M, Ihashi N, Yabe K, Kimbara J, Yasuda J, Ito H, Inakuma T, Hiroi S, Kasumi T (2008) DNA-binding specificity, transcriptional activation potential, and the rin mutation effect for the tomato fruit-ripening regulator RIN. Plant J 55:212–223

    Article  PubMed  CAS  Google Scholar 

  • Karlova R, Rosin FM, Busscher-Lange J, Parapunova V, Do PT, Fernie AR, Fraser PD, Baxter C, Angenent GC, de Maagd RA (2011) Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening. Plant Cell 23:923–941

    Article  PubMed  CAS  Google Scholar 

  • Kaufmann K, Muino JM, Jauregui R, Airoldi CA, Smaczniak C, Krajewski P, Angenent GC (2009) Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol 7:e1000090

    Article  PubMed  Google Scholar 

  • Kaufmann K, Wellmer F, Muino JM, Ferrier T, Wuest SE, Kumar V, Serrano-Mislata A, Madueno F, Krajewski P, Meyerowitz EM, Angenent GC, Riechmann JL (2010) Orchestration of floral initiation by APETALA1. Science 328:85–89

    Article  PubMed  CAS  Google Scholar 

  • Kitagawa M, Ito H, Shiina T, Nakamura N, Inakuma T, Kasumi T, Ishiguro Y, Yabe K, Ito Y (2005) Characterization of tomato fruit ripening and analysis of gene expression in F-1 hybrids of the ripening inhibitor (rin) mutant. Physiol Plantarum 123:331–338

    Article  CAS  Google Scholar 

  • Knapp J, Moureau P, Schuch W, Grierson D (1989) Organization and expression of polygalacturonase and other ripening related genes in Ailsa Craig Neverripe and Ripening inhibitor tomato mutants. Plant Mol Biol 12:105–116

    Article  CAS  Google Scholar 

  • Kononowicz AK, Nelson DE, Singh NK, Hasegawa PM, Bressan RA (1992) Regulation of the osmotin gene promoter. Plant Cell 4:513–524

    Article  PubMed  CAS  Google Scholar 

  • Kosugi S, Ohashi Y (2000) Cloning and DNA-binding properties of a tobacco Ethylene-Insensitive3 (EIN3) homolog. Nucleic Acids Res 28:960–967

    Article  PubMed  CAS  Google Scholar 

  • Kovacs K, Fray RG, Tikunov Y, Graham N, Bradley G, Seymour GB, Bovy AG, Grierson D (2009) Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis. Phytochemistry 70:1003–1008

    Article  PubMed  CAS  Google Scholar 

  • Larosa PC, Chen Z, Nelson DE, Singh NK, Hasegawa PM, Bressan RA (1992) Osmotin gene expression is posttranscriptionally regulated. Plant Physiol 100:409–415

    Article  PubMed  CAS  Google Scholar 

  • Lashbrook CC, Gonzalez-Bosch C, Bennett AB (1994) Two divergent endo-beta-1, 4-glucanase genes exhibit overlapping expression in ripening fruit and abscising flowers. Plant Cell 6:1485–1493

    Article  PubMed  CAS  Google Scholar 

  • Leseberg CH, Eissler CL, Wang X, Johns MA, Duvall MR, Mao L (2008) Interaction study of MADS-domain proteins in tomato. J Exp Bot 59:2253–2265

    Article  PubMed  CAS  Google Scholar 

  • Liang X, Nazarenus TJ, Stone JM (2008) Identification of a consensus DNA-binding site for the Arabidopsis thaliana SBP domain transcription factor, AtSPL14, and binding kinetics by surface plasmon resonance. Biochemistry 47:3645–3653

    Article  PubMed  CAS  Google Scholar 

  • Lichtenthaler HK (2007) Biosynthesis, accumulation and emission of carotenoids, alpha-tocopherol, plastoquinone, and isoprene in leaves under high photosynthetic irradiance. Photosynth Res 92:163–179

    Article  PubMed  CAS  Google Scholar 

  • Lin Z, Hong Y, Yin M, Li C, Zhang K, Grierson D (2008) A tomato HD-Zip homeobox protein, LeHB-1, plays an important role in floral organogenesis and ripening. Plant J 55:301–310

    Article  PubMed  CAS  Google Scholar 

  • Lincoln JE, Fischer RL (1988) Regulation of gene expression by ethylene in wild-type and rin tomato (Lycopersicon esculentum) fruit. Plant Physiol 88:370–374

    Article  PubMed  CAS  Google Scholar 

  • Litt A, Irish VF (2003) Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development. Genetics 165:821–833

    PubMed  CAS  Google Scholar 

  • Manning K, Tor M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ, Seymour GB (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38:948–952

    Article  PubMed  CAS  Google Scholar 

  • Mayrose M, Ekengren SK, Melech-Bonfil S, Martin GB, Sessa G (2006) A novel link between tomato GRAS genes, plant disease resistance and mechanical stress response. Mol Plant Pathol 7:593–604

    Article  PubMed  CAS  Google Scholar 

  • Nguyen-Quoc B, Foyer CH (2001) A role for ‘futile cycles’ involving invertase and sucrose synthase in sucrose metabolism of tomato fruit. J Exp Bot 52:881–889

    Article  PubMed  CAS  Google Scholar 

  • Ohme-Takagi M, Shinshi H (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7:173–182

    Article  PubMed  CAS  Google Scholar 

  • Ortiz-Serrano P, Gil JV (2010) Quantitative comparison of free and bound volatiles of two commercial tomato cultivars (Solanum lycopersicum L.) during ripening. J Agric Food Chem 58:1106–1114

    Article  PubMed  CAS  Google Scholar 

  • Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, Inai S, Bunsupa S, Yamazaki M, Shibata D, Aoki K (2010) Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res 17:105–116

    Article  PubMed  CAS  Google Scholar 

  • Pan IL, McQuinn R, Giovannoni JJ, Irish VF (2010) Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development. J Exp Bot 61:1795–1806

    Article  PubMed  CAS  Google Scholar 

  • Picton S, Gray J, Barton S, AbuBakar U, Lowe A, Grierson D (1993) cDNA cloning and characterisation of novel ripening-related mRNAs with altered patterns of accumulation in the ripening inhibitor (rin) tomato ripening mutant. Plant Mol Biol 23:193–207

    Article  PubMed  CAS  Google Scholar 

  • Pnueli L, Abu-Abeid M, Zamir D, Nacken W, Schwarz-Sommer Z, Lifschitz E (1991) The MADS box gene family in tomato: temporal expression during floral development, conserved secondary structures and homology with homeotic genes from Antirrhinum and Arabidopsis. Plant J 1:255–266

    Article  PubMed  CAS  Google Scholar 

  • Pressey R (1997) Two isoforms of NP24: a thaumatin-like protein in tomato fruit. Phytochemistry 44:1241–1245

    Article  PubMed  CAS  Google Scholar 

  • Raghothama KG, Maggio A, Narasimhan ML, Kononowicz AK, Wang G, D’Urzo MP, Hasegawa PM, Bressan RA (1997) Tissue-specific activation of the osmotin gene by ABA, C2H4 and NaCl involves the same promoter region. Plant Mol Biol 34:393–402

    Article  PubMed  CAS  Google Scholar 

  • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277

    Article  PubMed  CAS  Google Scholar 

  • Rodrigo I, Vera P, Frank R, Conejero V (1991) Identification of the viroid-induced tomato pathogenesis-related (PR) protein P23 as the thaumatin-like tomato protein NP24 associated with osmotic stress. Plant Mol Biol 16:931–934

    Article  PubMed  CAS  Google Scholar 

  • Seymour GB, Manning K, Eriksson EM, Popovich AH, King GJ (2002) Genetic identification and genomic organization of factors affecting fruit texture. J Exp Bot 53:2065–2071

    Article  PubMed  CAS  Google Scholar 

  • Seymour G, Poole M, Manning K, King GJ (2008) Genetics and epigenetics of fruit development and ripening. Curr Opin Plant Biol 11:58–63

    Article  PubMed  CAS  Google Scholar 

  • Seymour GB, Ryder CD, Cevik V, Hammond JP, Popovich A, King GJ, Vrebalov J, Giovannoni JJ, Manning K (2011) A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria x ananassa Duch.) fruit, a non-climacteric tissue. J Exp Bot 62:1179–1188

    Article  PubMed  CAS  Google Scholar 

  • Singh NK, Nelson DE, Kuhn D, Hasegawa PM, Bressan RA (1989) Molecular cloning of osmotin and regulation of its expression by ABA and adaptation to low water potential. Plant Physiol 90:1096–1101

    Article  PubMed  CAS  Google Scholar 

  • Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440–9445

    Article  PubMed  CAS  Google Scholar 

  • Thompson AJ, Tor M, Barry CS, Vrebalov J, Orfila C, Jarvis MC, Giovannoni JJ, Grierson D, Seymour GB (1999) Molecular and genetic characterization of a novel pleiotropic tomato-ripening mutant. Plant Physiol 120:383–390

    Article  PubMed  CAS  Google Scholar 

  • Tieman D, Taylor M, Schauer N, Fernie AR, Hanson AD, Klee HJ (2006) Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proc Natl Acad Sci USA 103:8287–8292

    Article  PubMed  CAS  Google Scholar 

  • Van Kan JA, Cozijnsen T, Danhash N, De Wit PJ (1995) Induction of tomato stress protein mRNAs by ethephon, 2, 6-dichloroisonicotinic acid and salicylate. Plant Mol Biol 27:1205–1213

    Article  PubMed  Google Scholar 

  • Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, Schuch W, Giovannoni J (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296:343–346

    Article  PubMed  CAS  Google Scholar 

  • Vrebalov J, Pan IL, Arroyo AJ, McQuinn R, Chung M, Poole M, Rose J, Seymour G, Grandillo S, Giovannoni J, Irish VF (2009) Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1. Plant Cell 21:3041–3062

    Article  PubMed  CAS  Google Scholar 

  • Winkel-Shirley B (2001) Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol 126:485–493

    Article  PubMed  CAS  Google Scholar 

  • Xu Y, Chang P, Liu D, Narasimhan ML, Raghothama KG, Hasegawa PM, Bressan RA (1994) Plant defense genes are synergistically induced by ethylene and methyl jasmonate. Plant Cell 6:1077–1085

    Article  PubMed  CAS  Google Scholar 

  • Yamaguchi A, Wu MF, Yang L, Wu G, Poethig RS, Wagner D (2009) The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Dev Cell 17:268–278

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, Huang Z, Xie B, Chen Q, Tian X, Zhang X, Lu X, Huang D, Huang R (2004) The ethylene-, jasmonate-, abscisic acid- and NaCl-responsive tomato transcription factor JERF1 modulates expression of GCC box-containing genes and salt tolerance in tobacco. Planta 220:262–270

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors express their sincere thanks to Drs. M. Kitagawa and J. Kimbara of the Research Institute of Kagome Co., Ltd (Tochigi, Japan) for the provision of tomato fruits. This work was supported in part by the Program for Promotion of Basic and Applied Researches for Innovations in the Bio-oriented Technology Research Advancement Institution (BRAIN) of Japan to Y.I.

Author information

Authors and Affiliations

  1. National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan

    Masaki Fujisawa, Yoko Shima & Toshitsugu Nakano

  2. Department of Agricultural and Biological Chemistry, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-8510, Japan

    Naoki Higuchi, Yoshiyuki Koyama & Takafumi Kasumi

  3. National Food Research Institute, NARO, 2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan

    Yasuhiro Ito

Authors
  1. Masaki Fujisawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yoko Shima
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Naoki Higuchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Toshitsugu Nakano
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yoshiyuki Koyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Takafumi Kasumi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yasuhiro Ito
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yasuhiro Ito.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fujisawa, M., Shima, Y., Higuchi, N. et al. Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses. Planta 235, 1107–1122 (2012). https://doi.org/10.1007/s00425-011-1561-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00425-011-1561-2

Keywords

Search

Navigation