Abstract
Key message
Found a trans-splicing of PHYTOENE SYNTHASE 1 alters tomato fruit color by map-based cloning, functional complementation and RACE providing an insight into fruit color development.
Abstract
Color is an important fruit quality trait and a major determinant of the economic value of tomato (Solanum lycopersicum). Fruit color inheritance in a yellow-fruited cherry tomato (cv. No. 22), named yellow-fruited tomato 2 (yft2), was shown to be controlled by a single recessive gene, YFT2. The YFT2 gene was mapped in a 95.7 kb region on chromosome 3, and the candidate gene, PHYTOENE SYNTHASE 1 (PSY1), was confirmed by functional complementation analysis. Constitutive over expression of PSY1 in yft2 increased the accumulation of carotenoids and resulted in a red fruit color, while no causal mutation was detected in the YFT2 allele of yft2, compared with red-fruited SL1995 cherry tomato or cultivated variety (cv. M82). Expression of YFT2 3′ region in yft2 was significantly lower than in SL1995, and further studies revealed a difference in YFT2 post-transcriptional processing in yft2 compared with SL1995 and cv. M82, resulting in a longer YFT2 transcript. The alternatively trans-spliced allele of YFT2 in yft2 is predicted to encode a novel LT-YFT2 protein of 432 amino acid (AA) residues, compared to the 412 AA YFT2 protein of SL1995. The trans-spliced event also resulted in significantly down regulated expression of YFT2 in yft2 tomato, and the YFT2 allele suppressed expression of the downstream genes involved in the carotenoid biosynthesis pathway and carotenoids synthesis by a mechanism of the feed-forward regulation. In conclusion, we found that trans-splicing of YFT2 alters tomato fruit color, providing new insights into fruit color development.
Similar content being viewed by others
References
Ballester AR, Molthoff J, de Vos R, Hekkert BTL, Orzaez D, Fernandez-Moreno JP, Tripodi P, Grandillo S, Martin C, Heldens J et al (2010) Biochemical and molecular analysis of pink tomatoes: deregulated expression of the gene encoding transcription factor S1MYB12 leads to pink tomato fruit color. Plant Physiol 152:71–84
Banerjee A, Sharkey T (2014) Methylerythritol 4-phosphate (MEP) pathway metabolic regulation. Nat Prod Rep 31:1043–1055
Bedinger PA, Chetelat RT, McClure B, Moyle LC, Rose JK, Stack SM, van der Knaap E, Baek YS, Lopez-Casado G, Covey PA et al (2011) Interspecific reproductive barriers in the tomato clade: opportunities to decipher mechanisms of reproductive isolation. Sex Plant Reprod 24:171–187
Bird CR, Ray JA, Fletcher JD, Boniwell JM, Bird AS, Teulieres C, Blain I, Bramley P, Schuch W (1991) Using antisense RNA to study gene function: inhibition of carotenoid biosynthesis in transgenic tomatoes. Nat Biotechnol 9:635–639
Bramley P, Teulieres C, Blain I, Bird C, Schuch W (1992) Biochemical characterization of transgenic tomato plants in which carotenoid synthesis has been inhibited through the expression of antisense RNA to pTOM5. Plant J 2:343–349
Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890
Butelli E, Titta L, Giorgio M, Mock H-P, Matros A, Peterek S, Schijlen EG, Hall RD, Bovy AG, Luo J et al (2008) Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nat Biotechnol 26:1301
Chen Y, Wang A, Zhao L, Shen G, Cui L, Tang K (2009) Expression of thymosin α1 concatemer in transgenic tomato (Solanum lycopersicum) fruits. Biotechnol Appl Biochem 52:303–312
Cohen LA (2002) A review of animal model studies of tomato carotenoids, lycopene, and cancer chemoprevention. Exp Biol Med 227:864–868
Delgado-Vargas F, Jiménez A, Paredes-López O (2000) Natural pigments: carotenoids, anthocyanins, and betalains-characteristics, biosynthesis, processing, and stability. Crit Rev Food Sci Nutr 40:173–289
Dvinge H, Kim E, Abdel-Wahab O, Bradley RK (2016) RNA splicing factors as oncoproteins and tumour suppressors. Nat Rev Cancer 16:413–430
Egea I, Barsan C, Bian W, Purgatto E, Latché A, Chervin C, Bouzayen M, Pech JC (2010) Chromoplast differentiation: current status and perspectives. Plant Cell Physiol 51:1601–1611
Emmanuel E, Levy AA (2002) Tomato mutants as tools for functional genomics. Curr Opin Plant Biol 5:112–117
Enfissi EM, Nogueira M, Bramley PM, Fraser PD (2017) The regulation of carotenoid formation in tomato fruit. Plant J 89:774–788
Fraser PD, Pinto MES, Holloway DE, Bramley PM (2000) Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids. Plant J 24:551–558
Fray RG, Grierson D (1993) Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Plant Mol Biol 22:589–602
Fulton TM, Chunwongse J, Tanksley SD (1995) Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Rep 13:207–209
Galpaz N, Ronen G, Khalfa Z, Zamir D, Hirschberg J (2006) A chromoplast-specific carotenoid biosynthesis pathway is revealed by cloning of the tomato white-flower locus. Plant Cell 18:1947–1960
Galpaz N, Wang Q, Menda N, Zamir D, Hirschberg J (2008) Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. Plant J 53:717–730
Gao L, Zhao W, Qu H, Wang Q, Zhao L (2016) The yellow-fruited tomato 1 (yft1) mutant has altered fruit carotenoid accumulation and reduced ethylene production as a result of a genetic lesion in ETHYLENE INSENSITIVE2. Theor Appl Genet 129:717–728
Ghorbani R, Poozesh V, Khorramdel S (2012) Tomato production for human health, not only for food. Organic fertilisation, soil quality and human health. Springer, Dordrecht, pp 187–225
Giovannoni JJ (2007) Fruit ripening mutants yield insights into ripening control. Curr Opin Plant Biol 10:283–289
Hannoufa A, Hossain Z (2012) Regulation of carotenoid accumulation in plants. Biocatal Agric Biotechnol 1:198–202
Isaacson T, Ronen G, Zamir D, Hirschberg J (2002) Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of β-carotene and xanthophylls in plants. Plant Cell 14:333–342
Kachanovsky DE, Filler S, Isaacson T, Hirschberg J (2012) Epistasis in tomato color mutations involves regulation of phytoene synthase 1 expression by cis-carotenoids. Proc Nat Acad Sci USA 109:19021–19026
Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S (2013) Function of alternative splicing. Gene 514:1–30
Khachik F, Carvalho L, Bernstein PS, Muir GJ, Zhao D-Y, Katz NB (2002) Chemistry, distribution, and metabolism of tomato carotenoids and their impact on human health. Exp Biol Med 227:845–851
Kilambi HV, Kumar R, Sharma R, Sreelakshmi Y (2013) Chromoplast-specific carotenoid-associated protein appears to be important for enhanced accumulation of carotenoids in hp1 tomato fruits. Plant Physiol 161:2085–2101
Kong Y, Zhou H, Yu Y, Chen L, Hao P, Li X (2015) The evolutionary landscape of intergenic trans-splicing events in insects. Nat Commun 6:8734
Lanahan MB, Yen HC, Giovannoni JJ, Klee HJ (1994) The never ripe mutation blocks ethylene perception in tomato. Plant Cell 6:521–530
Levin I, Frankel P, Gilboa N, Tanny S, Lalazar A (2003) The tomato dark green mutation is a novel allele of the tomato homolog of the DEETIOLATED1 gene. Theor Appl Genet 106:454–460
Li H, Wang J, Mor G, Sklar J (2008) A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science 321:1357–1361
Lieberman M, Segev O, Gilboa N, Lalazar A, Levin I (2004) 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
Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X et al (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226
Manning K, Tör 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
Mao J, Zhang YC, Sang Y, Li QH, Yang HQ (2005) A role for Arabidopsis cryptochromes and COP1 in the regulation of stomatal opening. Proc Nat Acad Sci USA 102:12270–12275
Mustilli AC, Fenzi F, Ciliento R, Alfano F, Bowler C (1999) Phenotype of the tomato high pigment-2 mutant is caused by a mutation in the tomato homolog of DEETIOLATED1. Plant Cell 11:145–157
Ray J, Moureau P, Bird C, Bird A, Grierson D, Maunders M, Truesdale M, Bramley P, Schuch W (1992) Cloning and characterization of a gene involved in phytoene synthesis from tomato. Plant Mol Biol 19:401–404
Ronen G, Cohen M, Zamir D, Hirschberg J (1999) Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta. Plant J 17:341–351
Ronen G, Carmel-Goren L, Zamir D, Hirschberg J (2000) An alternative pathway to β-carotene formation in plant chromoplasts discovered by map-based cloning of Beta and old-gold color mutations in tomato. Proc Nat Acad Sci USA 97:11102–11107
Rosati C, Aquilani R, Dharmapuri S, Pallara P, Marusic C, Tavazza R, Bouvier F, Camara B, Giuliano G (2000) Metabolic engineering of beta-carotene and lycopene content in tomato fruit. Plant J 24:413–420
Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K et al (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641
Shinozaki Y, Nicolas P, Fernandez-Pozo N, Ma Q, Evanich DJ, Shi Y, Xu Y, Zheng Y, Snyder SI, Martin LB et al (2018) High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nat Commun 9:364
Spooner DM, Peralta IE, Knapp S (2005) Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes [Solanum L. section Lycopersicon (Mill.) Wettst.]. Taxon 54:43–61
Tan H-L, Thomas-Ahner JM, Moran NE, Cooperstone JL, Erdman JW, Young GS, Clinton SK (2017) β-carotene 9′, 10′ oxygenase modulates the anticancer activity of dietary tomato or lycopene on prostate carcinogenesis in the TRAMP model. Cancer Prev Res 10:161–169
Tanaka T, Shnimizu M, Moriwaki H (2012) Cancer chemoprevention by carotenoids. Molecules 17:3202–3242
Tanksley SD (2004) The genetic, developmental, and molecular bases of fruit size and shape variation in tomato. Plant Cell 16:S181–S189
Tieman D, Zhu G, Resende MF, Lin T, Nguyen C, Bies D, Rambla JL, Beltran KSO, Taylor M, Zhang B et al (2017) A chemical genetic roadmap to improved tomato flavor. Science 355:391–394
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
Weigel D, Glazebrook J (2006) Transformation of Agrobacterium using the freeze-thaw method. Cold Spring Harb Protoc 2006:1031–1036
Zhang H, Zhao L, Chen Y, Cui L, Ren W, Tang K (2007) Expression of human coagulation Factor IX in transgenic tomato (Lycopersicon esculentum). Biotechnol Appl Biochem 48:101–107
Zhu M, Chen G, Zhou S, Tu Y, Wang Y, Dong T, Hu Z (2013) A new tomato NAC (NAM/ATAF1/2/CUC2) transcription factor, SlNAC4, functions as a positive regulator of fruit ripening and carotenoid accumulation. Plant Cell Physiol 55:119–135
Acknowledgements
The authors are grateful to Dr. Dani Zamir and the TGRC (Tomato Genetic Resource Center, UC, Davis) for providing tomato seeds. We thank Dr. Pin Liu (Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University) for help with the carotenoid analysis. We thank PlantScribe (www.plantscribe.com) for editing this manuscript. This work was supported by a National Key Research and Development Project [2016YFD0100204-28]; the National Natural Science Foundation of China [31672158, 31872112]; the Key Technology Research and the Development Program of Shanghai Technology Committee [16391900900] and the Shanghai Jiao Tong University Agri-X Fund (2015).
Author information
Authors and Affiliations
Contributions
LXZ conceived and designed the research, and wrote the manuscript. LLC performed the main experimental work and wrote the manuscript; WZL and YPL participated in the mapping; XCF and KYD conducted HPLC analysis; GW participated in the ultrastructural analysis.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Chen, L., Li, W., Li, Y. et al. Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE. Plant Mol Biol 100, 647–658 (2019). https://doi.org/10.1007/s11103-019-00886-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11103-019-00886-y