The role of a class III gibberellin 2-oxidase in tomato internode elongation

Abstract

[EN] A network of environmental inputs and internal signaling controls plant growth, development and organ elongation. In particular, the growth-promoting hormone gibberellin (GA) has been shown to play a significant role in organ elongation. The use of tomato as a model organism to study elongation presents an opportunity to study the genetic control of internode-specific elongation in a eudicot species with a sympodial growth habit and substantial internodes that can and do respond to external stimuli. To investigate internode elongation, a mutant with an elongated hypocotyl and internodes but wild-type petioles was identified through a forward genetic screen. In addition to stem-specific elongation, this mutant, named tomato internode elongated -1 (tie-1) is more sensitive to the GA biosynthetic inhibitor paclobutrazol and has altered levels of intermediate and bioactive GAs compared with wild-type plants. The mutation responsible for the internode elongation phenotype was mapped to GA2oxidase 7, a class III GA 2-oxidase in the GA biosynthetic pathway, through a bulked segregant analysis and bioinformatic pipeline, and confirmed by transgenic complementation. Furthermore, bacterially expressed recombinant TIE protein was shown to have bona fide GA 2-oxidase activity. These results define a critical role for this gene in internode elongation and are significant because they further the understanding of the role of GA biosynthetic genes in organ-specific elongation.This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303. We thank the Tomato Genetics Resource Center for providing seed of the M82 and Heinz cultivars. The material was developed by and/or obtained from the UC Davis/C M Rick Tomato Genetics Resource Center and maintained by the Department of Plant Sciences, University of California, Davis, CA 95616, USA. We thank Anthony Bolger, Alisdair Fernie and Bjorn Usadel for providing us with access to pre-publication genomic reads of the S. lycopersicum cultivar M82, and Cristina Urbez and Noel Blanco-Tourinan (IBMCP, Spain) for technical help with in vitro production of TIE1. This work was supported in part by the Elsie Taylor Stocking Memorial Fellowship awarded to ASL in 2013, by NSF grant IOS-0820854, by USDA National Institute of Food and Agriculture project CA-D-PLB-2465-H, by internal UC Davis funds, and by Spanish Ministry of Economy and Competitiveness grant BFU2016-80621-P.Lavelle, A.; Gath, N.; Devisetty, U.; Carrera Bergua, E.; Lopez Diaz, I.; Blazquez Rodriguez, MA.; Maloof, J. (2018). The role of a class III gibberellin 2-oxidase in tomato internode elongation. The Plant Journal. https://doi.org/10.1111/tpj.14145SAndrés, F., Porri, A., Torti, S., Mateos, J., Romera-Branchat, M., García-Martínez, J. L., … Coupland, G. (2014). SHORT VEGETATIVE PHASE reduces gibberellin biosynthesis at theArabidopsisshoot apex to regulate the floral transition. Proceedings of the National Academy of Sciences, 111(26), E2760-E2769. doi:10.1073/pnas.1409567111Bolger, A., Scossa, F., Bolger, M. E., Lanz, C., Maumus, F., Tohge, T., … Fernie, A. R. (2014). The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics, 46(9), 1034-1038. doi:10.1038/ng.3046Bowen, M. E., Henke, K., Siegfried, K. R., Warman, M. L., & Harris, M. P. (2011). Efficient Mapping and Cloning of Mutations in Zebrafish by Low-Coverage Whole-Genome Sequencing. Genetics, 190(3), 1017-1024. doi:10.1534/genetics.111.136069Burset, M. (2000). Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Research, 28(21), 4364-4375. doi:10.1093/nar/28.21.4364Chen, W., Yao, J., Chu, L., Yuan, Z., Li, Y., & Zhang, Y. (2015). Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. Theoretical and Applied Genetics, 128(3), 539-547. doi:10.1007/s00122-014-2452-2Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., … Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly, 6(2), 80-92. doi:10.4161/fly.19695Cuperus, J. T., Montgomery, T. A., Fahlgren, N., Burke, R. T., Townsend, T., Sullivan, C. M., & Carrington, J. C. (2009). Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proceedings of the National Academy of Sciences, 107(1), 466-471. doi:10.1073/pnas.0913203107Curtis, M. D., & Grossniklaus, U. (2003). A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta. Plant Physiology, 133(2), 462-469. doi:10.1104/pp.103.027979Devisetty, U. K., Covington, M. F., Tat, A. V., Lekkala, S., & Maloof, J. N. (2014). Polymorphism Identification and Improved Genome Annotation ofBrassica rapaThrough Deep RNA Sequencing. G3: Genes|Genomes|Genetics, 4(11), 2065-2078. doi:10.1534/g3.114.012526Eckardt, N. A. (2007). GA Perception and Signal Transduction: Molecular Interactions of the GA Receptor GID1 with GA and the DELLA Protein SLR1 in Rice. The Plant Cell, 19(7), 2095-2097. doi:10.1105/tpc.107.054916Ernst, H. A., Lo Leggio, L., Willemoës, M., Leonard, G., Blum, P., & Larsen, S. (2006). Structure of the Sulfolobus solfataricus α-Glucosidase: Implications for Domain Conservation and Substrate Recognition in GH31. Journal of Molecular Biology, 358(4), 1106-1124. doi:10.1016/j.jmb.2006.02.056Fillatti, J. J., Kiser, J., Rose, R., & Comai, L. (1987). Efficient Transfer of a Glyphosate Tolerance Gene into Tomato Using a Binary Agrobacterium Tumefaciens Vector. Nature Biotechnology, 5(7), 726-730. doi:10.1038/nbt0787-726Garrison , E. Marth , G. 2012 Haplotype-based variant detection from short-read sequencingHedden, P., & Graebe, J. E. (1985). Inhibition of gibberellin biosynthesis by paclobutrazol in cell-free homogenates ofCucurbita maxima endosperm andMalus pumila embryos. Journal of Plant Growth Regulation, 4(1-4), 111-122. doi:10.1007/bf02266949Kimura, S., & Sinha, N. (2008). Tomato (Solanum lycopersicum): A Model Fruit-Bearing Crop. Cold Spring Harbor Protocols, 2008(12), pdb.emo105-pdb.emo105. doi:10.1101/pdb.emo105Koenig, D., Jimenez-Gomez, J. M., Kimura, S., Fulop, D., Chitwood, D. H., Headland, L. R., … Maloof, J. N. (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences, 110(28), E2655-E2662. doi:10.1073/pnas.1309606110Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760. doi:10.1093/bioinformatics/btp324Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352Li, J., Sima, W., Ouyang, B., Wang, T., Ziaf, K., Luo, Z., … Ye, Z. (2012). Tomato SlDREB gene restricts leaf expansion and internode elongation by downregulating key genes for gibberellin biosynthesis. Journal of Experimental Botany, 63(18), 6407-6420. doi:10.1093/jxb/ers295Lorrain, S., & Fankhauser, C. (2012). Plant Development: Should I Stop or Should I Grow? Current Biology, 22(16), R645-R647. doi:10.1016/j.cub.2012.06.054Menda, N., Semel, Y., Peled, D., Eshed, Y., & Zamir, D. (2004). In silicoscreening of a saturated mutation library of tomato. The Plant Journal, 38(5), 861-872. doi:10.1111/j.1365-313x.2004.02088.xMichelmore, R. W., Paran, I., & Kesseli, R. V. (1991). Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proceedings of the National Academy of Sciences, 88(21), 9828-9832. doi:10.1073/pnas.88.21.9828Pimenta Lange, M. J., Liebrandt, A., Arnold, L., Chmielewska, S.-M., Felsberger, A., Freier, E., … Lange, T. (2013). Functional characterization of gibberellin oxidases from cucumber, Cucumis sativus L. Phytochemistry, 90, 62-69. doi:10.1016/j.phytochem.2013.02.006Raskin, I., & Kende, H. (1984). Role of Gibberellin in the Growth Response of Submerged Deep Water Rice. Plant Physiology, 76(4), 947-950. doi:10.1104/pp.76.4.947Reinecke, D. M., Wickramarathna, A. D., Ozga, J. A., Kurepin, L. V., Jin, A. L., Good, A. G., & Pharis, R. P. (2013). Gibberellin 3-oxidase Gene Expression Patterns Influence Gibberellin Biosynthesis, Growth, and Development in Pea. PLANT PHYSIOLOGY, 163(2), 929-945. doi:10.1104/pp.113.225987Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3), R25. doi:10.1186/gb-2010-11-3-r25Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2009). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011). Integrative genomics viewer. Nature Biotechnology, 29(1), 24-26. doi:10.1038/nbt.1754Schneeberger, K., Ossowski, S., Lanz, C., Juul, T., Petersen, A. H., Nielsen, K. L., … Andersen, S. U. (2009). SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nature Methods, 6(8), 550-551. doi:10.1038/nmeth0809-550Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671-675. doi:10.1038/nmeth.2089Schomburg, F. M., Bizzell, C. M., Lee, D. J., Zeevaart, J. A. D., & Amasino, R. M. (2002). Overexpression of a Novel Class of Gibberellin 2-Oxidases Decreases Gibberellin Levels and Creates Dwarf Plants. The Plant Cell, 15(1), 151-163. doi:10.1105/tpc.005975Seo, M., Jikumaru, Y., & Kamiya, Y. (2011). Profiling of Hormones and Related Metabolites in Seed Dormancy and Germination Studies. Methods in Molecular Biology, 99-111. doi:10.1007/978-1-61779-231-1_7Sun, T. (2011). The Molecular Mechanism and Evolution of the GA–GID1–DELLA Signaling Module in Plants. Current Biology, 21(9), R338-R345. doi:10.1016/j.cub.2011.02.036Sun, T., & Gubler, F. (2004). MOLECULAR MECHANISM OF GIBBERELLIN SIGNALING IN PLANTS. Annual Review of Plant Biology, 55(1), 197-223. doi:10.1146/annurev.arplant.55.031903.141753Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2012). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics, 14(2), 178-192. doi:10.1093/bib/bbs017(2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635-641. doi:10.1038/nature11119Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9), 1105-1111. doi:10.1093/bioinformatics/btp120Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., … Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3), 562-578. doi:10.1038/nprot.2012.016Tsai, H., Howell, T., Nitcher, R., Missirian, V., Watson, B., Ngo, K. J., … Comai, L. (2011). Discovery of Rare Mutations in Populations: TILLING by Sequencing. Plant Physiology, 156(3), 1257-1268. doi:10.1104/pp.110.169748Ueguchi-Tanaka, M., Nakajima, M., Katoh, E., Ohmiya, H., Asano, K., Saji, S., … Matsuoka, M. (2007). Molecular Interactions of a Soluble Gibberellin Receptor, GID1, with a Rice DELLA Protein, SLR1, and Gibberellin. The Plant Cell, 19(7), 2140-2155. doi:10.1105/tpc.106.043729Wickham, H. (2016). ggplot2. Use R! doi:10.1007/978-3-319-24277-4Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G. V., & Provart, N. J. (2007). An «Electronic Fluorescent Pictograph» Browser for Exploring and Analyzing Large-Scale Biological Data Sets. PLoS ONE, 2(8), e718. doi:10.1371/journal.pone.0000718Xu, H., Liu, Q., Yao, T., & Fu, X. (2014). Shedding light on integrative GA signaling. Current Opinion in Plant Biology, 21, 89-95. doi:10.1016/j.pbi.2014.06.010Yamaguchi, S. (2008). Gibberellin Metabolism and its Regulation. Annual Review of Plant Biology, 59(1), 225-251. doi:10.1146/annurev.arplant.59.032607.09280