The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening

Abstract

Fleshy fruit ripening is governed by multiple external and internal cues and accompanied by changes in color, texture, volatiles, and nutritional quality traits. While extended shelf-life and increased phytonutrients are desired, delaying ripening via genetic or postharvest means can be accompanied by reduced nutritional value. Here we report that the high pigment 1 (hp1) mutation at the UV-DAMAGED DNA BINDING PROTEIN 1 (DDB1) locus, previously shown to influence carotenoid and additional phytonutrient accumulation via altered light signal transduction, also results in delayed ripening and firmer texture, resulting at least in part from decreased ethylene evolution. Transcriptome analysis revealed multiple ethylene biosynthesis and signaling-associated genes downregulated in hp1. Furthermore, the hp1 mutation impedes softening of the pericarp, placenta, columella as well as the whole fruit, in addition to reduced expression of the FRUITFUL2 (FUL2) MADS-box transcription factor and xyloglucan endotransglucosylase/hydrolase 5 (XTH5). These results indicate that DDB1 influences a broader range of fruit development and ripening processes than previously thought and present an additional genetic target for increasing fruit quality and shelf-life.

References

[1] Klee, H. J. & Giovannoni, J. J. Genetics and control of tomato fruit ripening and quality attributes. Annu. Rev. Genet. 45, 41-59 (2011).

[2] Giovannoni, J., Nguyen, C., Ampofo, B., Zhong, S. & Fei, Z. The epigenome and transcriptional dynamics of fruit ripening. Annu. Rev. Plant Biol. 68, 61-84 (2017).

[3] Vrebalov, J. et al. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296, 343-346 (2002).

[4] Ito, Y. et al. Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening. Nat. Plants 3, 866-874 (2017).

[5] Li, S. et al. The RIN-MC fusion of MADS-box transcription factors has transcriptional activity. Plant Physiol. 176, 891-909 (2017).

[6] Seymour, G. B. et al. 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 (2011).

[7] Elitzur, T. et al. Banana MaMADS transcription factors are necessary for fruit ripening and molecular tools to promote shelf-life and food security. Plant Physiol. 171, 380-391 (2016).

[8] Itkin, M. et al. TOMATO AGAMOUS-LIKE 1 is a component of the fruit ripening regulatory network. Plant J. 60, 1081-1095 (2009).

[9] Vrebalov, J. et al. Fleshy fruit expansion and ripening are regulated by the Tomato SHATTERPROOF gene TAGL1. Plant Cell 21, 3041-3062 (2009).

[10] Martel, C., Vrebalov, J., Tafelmeyer, P. & Giovannoni, J. J. The tomato MADS-box transcription factor ripening inhibitor interacts with promoters involved in numerous ripening processes in a colorless nonripening-dependent manner. Plant Physiol. 157, 1568-1579 (2011).

[11] Bemer, M. et al. The tomato FRUITFULL homologs TDR4/FUL1 and MBP7/FUL2 regulate ethylene-independent aspects of fruit ripening. Plant Cell 24, 4437-4451 (2012).

[12] Fujisawa, M. et al. Transcriptional regulation of fruit ripening by tomato FRUITFULL homologs and associated MADS box proteins. Plant Cell 26, 89-101 (2014).

[13] Manning, K. et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38, 948-952 (2006).

[14] Lin, Z. et al. A tomato HD-Zip homeobox protein, LeHB-1, plays an important role in floral organogenesis and ripening. Plant J. 55, 301-310 (2008).

[15] Chung, M. Y. et al. A tomato (Solanum lycopersicum) APETALA2/ERF gene, SlAP2a, is a negative regulator of fruit ripening. Plant J. 64, 936-947 (2010).

[16] Karlova, R. et al. Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening. Plant Cell 23, 923-941 (2011).

[17] Dong, T. et al. A tomato MADS-box transcription factor, SlMADS1, acts as a negative regulator of fruit ripening. Plant Physiol. 163, 1026-1036 (2013).

[18] Davuluri, G. R. et al. Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nat. Biotechnol. 23, 890-895 (2005).

[19] Wang, S. et al. Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4. Plant J. 55, 89-103 (2008).

[20] Uluisik, S. et al. Genetic improvement of tomato by targeted control of fruit softening. Nat. Biotechnol. 34, 950-952 (2016).

[21] Fraser, P. D. et al. Manipulation of phytoene levels in tomato fruit: effects on isoprenoids, plastids, and intermediary metabolism. Plant Cell 19, 3194-3211 (2007).

[22] McQuinn, R. P., Giovannoni, J. J. & Pogson, B. J. More than meets the eye: from carotenoid biosynthesis, to new insights into apocarotenoid signaling. Curr. Opin. Plant. Biol. 27, 172-179 (2015).

[23] McQuinn, R., Wong, B. & Giovannoni, J. AtPDS overexpression in tomato: exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content. Plant Biotechnol. J. 16, 482-494 (2017).

[24] Rohrmann, J. et al. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. Plant J. 68, 999-1013 (2011).

[25] Kilambi, H. V., Kumar, R., Sharma, R. & Sreelakshmi, Y. Chromoplast-specific carotenoid-associated protein appears to be important for enhanced accumulation of carotenoids in hp1 tomato fruits. Plant Physiol. 161, 2085-2101 (2013).

[26] Lieberman, M., Segev, O., Gilboa, N., Lalazar, A. & Levin, I. The tomato homolog of the gene encoding UV-damaged DNA binding protein 1 (DDB1) underlined as the gene that causes the high pigment-1 mutant phenotype. Theor. Appl. Genet. 108, 1574-1581 (2004).

[27] Liu, Y. et al. Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc. Natl Acad. Sci. USA 101, 9897-9902 (2004).

[28] Tang, X. et al. Ubiquitin-conjugated degradation of golden 2-like transcription factor is mediated by CUL4-DDB1-based E3 ligase complex in tomato. New Phytol. 209, 1028-1039 (2016).

[29] Nadakuduti, S. S., Holdsworth, W. L., Klein, C. L. & Barry, C. S. KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN2-LIKE expression in tomato. Plant J. 78, 1022-1033 (2014).

[30] Nguyen, C. V. et al. Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. Plant Cell 26, 585-601 (2014).

[31] Lau, O. S. et al. Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock. Mol. Cell 43, 703-712 (2011).

[32] Cookson, P. J. et al. Increases in cell elongation, plastid compartment size and phytoene synthase activity underlie the phenotype of the high pigment-1 mutant of tomato. Planta 217, 896-903 (2003).

[33] McMurchie, E., McGlasson, W. & Eaks, I. Treatment of fruit with propylene gives information about the biogenesis of ethylene. Nature 237, 235-236 (1972).

[34] Tieman, D. M., Taylor, M. G., Ciardi, J. A. & Klee, H. J. The tomato ethylene receptors NR and LeETR4 are negative regulators of ethylene response and exhibit functional compensation within a multigene family. Proc. Natl Acad. Sci. USA 97, 5663-5668 (2000).

[35] Kevany, B. M., Tieman, D. M., Taylor, M. G., Cin, V. D. & Klee, H. J. Ethylene receptor degradation controls the timing of ripening in tomato fruit. Plant J. 51, 458-467 (2007).

[36] Smith, D. L., Abbott, J. A. & Gross, K. C. Down-regulation of tomato β-galactosidase 4 results in decreased fruit softening. Plant Physiol. 129, 1755-1762 (2002).

[37] Eda, M., Matsumoto, T., Ishimaru, M. & Tada, T. Structural and functional analysis of tomato β-galactosidase 4: insight into the substrate specificity of the fruit softening-related enzyme. Plant J. 86, 300-307 (2016).

[38] Mustilli, A. C., Fenzi, F., Ciliento, R., Alfano, F. & Bowler, C. Phenotype of the tomato high pigment-2 mutant is caused by a mutation in the tomato homolog of DEETIOLATED1. Plant Cell 11, 145-157 (1999).

[39] Barry, C. S. & Giovannoni, J. J. Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling. Proc. Natl Acad. Sci. USA 103, 7923-7928 (2006).

[40] Barry, C. S., McQuinn, R. P., Chung, M. Y., Besuden, A. & Giovannoni, J. J. Amino acid substitutions in homologs of the STAY-GREEN protein are responsible for the green-flesh and chlorophyll retainer mutations of tomato and pepper. Plant Physiol. 147, 179-187 (2008).

[41] Lee, J. M. et al. Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. Plant J. 70, 191-204 (2012).

[42] Fujisawa, M., Nakano, T., Shima, Y. & Ito, Y. A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening. Plant Cell 25, 371-386 (2013).

[43] Fujisawa, M. et al. Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses. Planta 235, 1107-1122 (2012).

[44] Yang, L. et al. Silencing of SlPL (Solyc03g111690), which encodes a pectate lyase in tomato, confers enhanced fruit firmness, prolonged shelf-life, and reduced susceptibility to gray mold. Plant Biotechnol. J. 15, 1544-1555 (2017).

[45] Li, Y. et al. Tomato MBD5, a methyl CpG binding domain protein, physically interacting with UV-damaged DNA binding protein-1, functions in multiple processes. New Phytol. 210, 208-226 (2015).

[46] Saladié, M., Rose, J. K., Cosgrove, D. J. & Catalá, C. Characterization of a new xyloglucan endotransglucosylase/hydrolase (XTH) from ripening tomato fruit and implications for the diverse modes of enzymic action. Plant J. 47, 282-295 (2006).

[47] Green, B. & Durnford, D. The chlorophyll-carotenoid proteins of oxygenic photosynthesis. Annu. Rev. Plant Biol. 47, 685-714 (1996).

[48] Demmig-Adams, B. & Adams, W. W. The role of xanthophyll cycle carotenoids in the protection of photosynthesis. Trends Plant Sci. 1, 21-26 (1996).

[49] Joung, J. G. et al. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol. 151, 1758-1768 (2009).

[50] Enfissi, E. M. A. et al. Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. Plant Cell 22, 1190-1215 (2010).

[51] Lytovchenko, A. et al. Tomato fruit photosynthesis is seemingly unimportant in primary metabolism and ripening but plays a considerable role in seed development. Plant Physiol. 157, 1650-1663 (2011).

[52] Ji, K. et al. SlNCED1 and SlCYP707A2: key genes involved in ABA metabolism during tomato fruit ripening. J. Exp. Bot. 65, 5243-5255 (2014).

[53] Leng, P., Yuan, B., Guo, Y. & Chen, P. The role of abscisic acid in fruit ripening and responses to abiotic stress. J. Exp. Bot. 65, 4577-4588 (2014).

[54] Chen, H. et al. Arabidopsis CULLIN4-damaged DNA binding protein 1 interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA complexes to regulate photomorphogenesis and flowering time. Plant Cell 22, 108-123 (2010).

[55] Shi, H. et al. Seedlings transduce the depth and mechanical pressure of covering soil using COP1 and ethylene to regulate EBF1/EBF2 for soil emergence. Curr. Biol. 26, 139-149 (2015).

[56] Wu, T. & Abbott, J. A. Firmness and force relaxation characteristics of tomatoes stored intact or as slices. Postharvest Biol. Technol. 24, 59-68 (2002).

[57] Expósito-Rodríguez, M., Borges, A. A., Borges-Pérez, A. & Pérez, J. A. Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol. 8, 131- 131 (2008).

[58] Zhong, S. et al. High-throughput illumina strand-specific RNA sequencing library preparation. Cold Spring Harb. Protoc. 2011, 940-949 (2011).

[59] Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357-360 (2015).

[60] Metsalu, T. & Vilo, J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 43, W566-W570 (2015).

[61] Hall, B. G. Building phylogenetic trees from molecular data with MEGA. Mol. Biol. Evol. 30, 1229-1235 (2013).