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Journal of Plant Research

, Volume 132, Issue 2, pp 181–195 | Cite as

Transcriptome-wide effect of DE-ETIOLATED1 (DET1) suppression in embryogenic callus of Carica papaya

  • Nur Diyana Jamaluddin
  • Emelda Rosseleena Rohani
  • Normah Mohd Noor
  • Hoe-Han GohEmail author
JPR Symposium Regulatory networks in plant growth and development

Abstract

Papaya is one of the most nutritional fruits, rich in vitamins, carotenoids, flavonoids and other antioxidants. Previous studies showed phytonutrient improvement without affecting quality in tomato fruit and rapeseed through the suppression of DE-ETIOLATED-1 (DET1), a negative regulator in photomorphogenesis. This study is conducted to study the effects of DET1 gene suppression in papaya embryogenic callus. Immature zygotic embryos were transformed with constitutive expression of a hairpin DET1 construct (hpDET1). PCR screening of transformed calli and reverse transcription quantitative PCR (RT-qPCR) verified that DET1 gene downregulation in two of the positive transformants. High-throughput cDNA 3′ ends sequencing on DET1-suppressed and control calli for transcriptomic analysis of global gene expression identified a total of 452 significant (FDR < 0.05) differentially expressed genes (DEGs) upon DET1 suppression. The 123 upregulated DEGs were mainly involved in phenylpropanoid biosynthesis and stress responses, compared to 329 downregulated DEGs involved in developmental processes, lipid metabolism, and response to various stimuli. This is the first study to demonstrate transcriptome-wide relationship between light-regulated pathway and secondary metabolite biosynthetic pathways in papaya. This further supports that the manipulation of regulatory gene involved in light-regulated pathway is possible for phytonutrient improvement of tropical fruit crops.

Keywords

DE-ETIOLATED1 Embryogenic callus Photomorphogenesis HpRNAi RNA-seq 

Notes

Acknowledgements

The authors wish to thank research supports from the Malaysian Ministry of Science, Technology and Innovation (MOSTI) Sciencefund Grant 02-01-02-SF0907 and Universiti Kebangsaan Malaysia Research University Grant (GGPM-2011-053). We also thank the two anonymous reviewers and editor for their constructive comments in improving this manuscript.

Author contributions

Conceived the experiments: NDJ, NMN, HHG. Designed and performed the experiments: NDJ, ERR, HHG. Analysed the data: NDJ, HHG. Contributed reagents/materials/analysis tools: HHG. Wrote the paper: NDJ, HHG, ERR, NMN. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10265_2019_1086_MOESM1_ESM.xlsx (6.2 mb)
Supplementary material 1 (XLSX 6398 KB)
10265_2019_1086_MOESM2_ESM.pdf (951 kb)
Supplementary material 2 (PDF 950 KB)

References

  1. Allan AC, Hellens RP, Laing WA (2008) MYB transcription factors that colour our fruit. Trends Plant Sci 13:99–102.  https://doi.org/10.1016/j.tplants.2007.11.012 CrossRefGoogle Scholar
  2. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120CrossRefGoogle Scholar
  3. Carlos-Hilario LR, Christopher DA (2015) Improved Agrobacterium-mediated transformation of Carica papaya cultivar ‘Kapoho’from embryogenic cell suspension cultures. In Vitro Cel Dev Biol Plant 51:580–587CrossRefGoogle Scholar
  4. Chen M, Wang P, Maeda E (1987) Somatic embryogenesis and plant regeneration in Carica papaya L. tissue culture derived from root explants. Plant Cell Rep 6:348–351CrossRefGoogle Scholar
  5. Chory J, Peto C, Feinbaum R, Pratt L, Ausubel F (1989) Arabidopsis thaliana mutant that develops as a light-grown plant in the absence of light. Cell 58:991–999CrossRefGoogle Scholar
  6. Davuluri GR, van Tuinen A, Fraser PD, Manfredonia A, Newman R et al (2005) Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat Biotechnol 23:890–895CrossRefGoogle Scholar
  7. Elgadir MA, Salama M, Adam A (2014) Carica Papaya as a source of natural medicine and its utilization in selected pharmacetical applications. Int J Pharm Pharm Sci 6:868–871Google Scholar
  8. Enfissi EMA, Barneche F, Ahmed I, Lichtlé C, Gerrish C et al (2010) Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. Plant Cell 22:1190–1215CrossRefGoogle Scholar
  9. Fabi JP, Mendes LRBC, Lajolo FM, do Nascimento JRO (2010) Transcript profiling of papaya fruit reveals differentially expressed genes associated with fruit ripening. Plant Sci 179:225–233CrossRefGoogle Scholar
  10. Fabi JP, Broetto SG, da Silva SLGL, Zhong S, Lajolo FM, do Nascimento JRO (2014) Analysis of papaya cell wall-related genes during fruit ripening indicates a central role of polygalacturonases during pulp softening. PLoS One 9:e105685CrossRefGoogle Scholar
  11. Fitch MMM, Manshardt RM (1990) Somatic embryogenesis and plant regeneration from immature zygotic embryos of papaya (Carica papaya L.). Plant Cell Rep 9:320–324.  https://doi.org/10.1007/BF00232860 Google Scholar
  12. Fitch MM, Manshardt RM, Gonsalves D, Slightom JL (1993) Transgenic papaya plants from Agrobacterium-mediated transformation of somatic embryos. Plant Cell Rep 12:245–249CrossRefGoogle Scholar
  13. Helliwell C, Waterhouse P (2003) Constructs and methods for high-throughput gene silencing in plants. Methods 30:289–295.  https://doi.org/10.1016/S1046-2023(03)00036-7 CrossRefGoogle Scholar
  14. Jamaluddin D, Mohd Noor N, Goh HH (2017a) Transcriptome analysis of Carica papaya embryogenic callus upon De-etiolated 1 (DET1) gene suppression. Genom Data 12:120–121.  https://doi.org/10.1016/j.gdata.2017.05.004 CrossRefGoogle Scholar
  15. Jamaluddin ND, Mohd Noor N, Goh HH (2017b) Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus. Physiol Mol Biol Plants 23:357–368.  https://doi.org/10.1007/s12298-017-0429-8 CrossRefGoogle Scholar
  16. Kang M-Y, Yoo S-C, Kwon H-Y, Lee B-D, Cho J-N, Noh Y-S, Paek N-C (2015) Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis. Sci Rep 5:9728CrossRefGoogle Scholar
  17. Katavic V, Agrawal GK, Hajduch M, Harris SL, Thelen JJ (2006) Protein and lipid composition analysis of oil bodies from two Brassica napus cultivars. Proteomics 6:4586–4598CrossRefGoogle Scholar
  18. Keddie JS, Tsiantis M, Piffanelli P, Cella R, Hatzopoulos P, Murphy DJ (1994) A seed-specific Brassica napus oleosin promoter interacts with a G-box-specific protein and may be bi-directional. Plant Mol Biol 24:327–340.  https://doi.org/10.1007/BF00020171 CrossRefGoogle Scholar
  19. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefGoogle Scholar
  20. Lau OS, Deng XW (2012) The photomorphogenic repressors COP1 and DET1: 20 years later. Trends Plant Sci 17:584–593CrossRefGoogle Scholar
  21. Lewinsohn E, Schalechet F, Wilkinson J, Matsui K, Tadmor Y et al (2001) Enhanced levels of the aroma and flavor compound S-linalool by metabolic engineering of the terpenoid pathway in tomato fruits. Plant Physiol 127:1256–1265CrossRefGoogle Scholar
  22. Litz RE, Conover RA (1981) In vitro polyembryony in Carica papaya L. ovules. Zeitschr Pflanzenphysiol 104:285–288CrossRefGoogle Scholar
  23. 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.  https://doi.org/10.1006/meth.2001.1262 CrossRefGoogle Scholar
  24. Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448–3449CrossRefGoogle Scholar
  25. Mathias R, Mukasa C (1987) The effect of cefotaxime on the growth and regeneration of callus from four varieties of barley (Hordeum vulgare L.). Plant Cell Rep 6:454–457Google Scholar
  26. Moll P, Ante M, Seitz A, Reda T (2014) QuantSeq 3 [prime] mRNA sequencing for RNA quantification. Nat Methods 11Google Scholar
  27. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185CrossRefGoogle Scholar
  28. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497CrossRefGoogle Scholar
  29. Osterlund MT, Hardtke CS, Wei N, Deng XW (2000) Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405:462–466CrossRefGoogle Scholar
  30. Porter BW, Aizawa KS, Zhu YJ, Christopher DA (2008) Differentially expressed and new non-protein-coding genes from a Carica papaya root transcriptome survey. Plant Sci 174:38–50CrossRefGoogle Scholar
  31. Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10:71–73CrossRefGoogle Scholar
  32. Siloto RM, Findlay K, Lopez-Villalobos A, Yeung EC, Nykiforuk CL, Moloney MM (2006) The accumulation of oleosins determines the size of seed oilbodies in Arabidopsis. Plant Cell 18:1961–1974CrossRefGoogle Scholar
  33. Sun D-Q, Lu X-H, Liang G-L, Guo Q-G, Mo Y-W, Xie J-H (2011) Production of triploid plants of papaya by endosperm culture. Plant Cell Tissue Organ Cult 104:23–29CrossRefGoogle Scholar
  34. Urasaki N et al (2012) Digital transcriptome analysis of putative sex-determination genes in papaya (Carica papaya). PLoS One 7:e40904CrossRefGoogle Scholar
  35. Wall MM (2006) Ascorbic acid, vitamin A, and mineral composition of banana (Musa sp.) and papaya (Carica papaya) cultivars grown in Hawaii. J Food Comp Anal 19:434–445CrossRefGoogle Scholar
  36. Wei SHU, Xiang LI, Gruber MY, Rong LI, Zhou R, Zebarjadi A, Hannoufa A (2009) RNAi-Mediated suppression of DET1 alters the levels of carotenoids and sinapate esters in seeds of Brassica napus. J Agric Food Chem 57:5326–5333.  https://doi.org/10.1021/jf803983w CrossRefGoogle Scholar
  37. Wertz IE, O’rourke KM, Zhang Z, Dornan D, Arnott D, Deshaies RJ, Dixit VM (2004) Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase. Science 303:1371–1374CrossRefGoogle Scholar
  38. Xie C et al (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39:W316–W322CrossRefGoogle Scholar
  39. Ye X, Al-Babili S, Klöti A, Zhang J, Lucca P, Beyer P, Potrykus I (2000) Engineering the provitamin A (β-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science 287:303–305CrossRefGoogle Scholar
  40. Zhu YJ, Fitch MM, Moore PH (2007) Papaya (Carica papaya L.). In: Wang K (ed) Agrobacterium protocols, vol 2, 2nd edn. Humana Press, New York, pp 209–217Google Scholar

Copyright information

© The Botanical Society of Japan and Springer Japan KK, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Systems BiologyUniversiti Kebangsaan Malaysia, UKM BangiBangiMalaysia

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