Abstract
Cytochrome P450s are among the largest protein coding gene families in plant genomes. However, majority of the genes remain uncharacterized. Here, we report the characterization of dss1, a rice mutant showing dwarfism and reduced grain size. The dss1 phenotype is caused by a non-synonymous point mutation we identified in DSS1, which is member of a P450 gene cluster located on rice chromosome 3 and corresponds to the previously reported CYP96B4/SD37 gene. Phenotypes of several dwarf mutants characterized in rice are associated with defects in the biosynthesis or perception of the phytohormones gibberellins (GAs) and brassinosteroids (BRs). However, both GA and BR failed to rescue the dss1 phenotype. Hormone profiling revealed the accumulation of abscisic acid (ABA) and ABA metabolites, as well as significant reductions in GA19 and GA53 levels, precursors of the bioactive GA1, in the mutant. The dss1 contents of cytokinin and auxins were not significantly different from wild-type plants. Consistent with the accumulation of ABA and metabolites, germination and early growth was delayed in dss1, which also exhibited an enhanced tolerance to drought. Additionally, expressions of members of the DSS1/CYP96B gene cluster were regulated by drought stress and exogenous ABA. RNA-seq-based transcriptome profiling revealed, among others, that cell wall-related genes and genes involved in lipid metabolism were up- and down-regulated in dss1, respectively. Taken together, these findings suggest that DSS1 mediates growth and stress responses in rice by fine-tuning GA-to-ABA balance, and might as well play a role in lipid metabolism.
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Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178
Asano K, Takashi T, Miura K, Qian Q, Kitano H, Matsuoka M, Ashikari M (2007) Genetic and molecular analysis of utility of sd1 alleles in rice breeding. Breed Sci 57:53–58
Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, Satoh H, Kitano H, Matsuoka M, Ashikari M (2009) Isolation and characterization of dominant dwarf mutants, Slr-d, in rice. Mol Genet Genom 281:223–231
Asano K, Miyao A, Hirochika H, Kitano H, Matsuoka M, Ashikari M (2010) SSD1, which encodes a plant-specific novel protein, controls plant elongation by regulating cell division in rice. Proc Jpn Acad Ser B 86:265–273
Bishop GJ, Koncz C (2002) Brassinosteroids and plant steroid hormone signaling. Plant Cell 14:97–110
Chiwocha SDS, Abrams SR, Ambrose SJ, Cutler AJ, Loewen M, Ross ARS, Kermode AR (2003) A method for profiling classes of plant hormones and their metabolites using liquid chromatography-electrospray ionization tandem mass spectrometry: analysis of hormone regulation of thermodormancy of lettuce (Lactuca sativa L.) seeds. Plant J 3:405–417
Chiwocha SDS, Cutler AJ, Abrams SR, Ambrose SJ, Yang J, Ross ARS, Kermode AR (2005) The etr1-2 mutation in Arabidopsis thaliana affects the abscisic acid, auxin, cytokinin and gibberellin metabolic pathways during maintenance of seed dormancy, moist-chilling and germination. Plant J 42:35–48
Chu HY, Wegel E, Osbourn A (2011) From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants. Plant J 66:66–79
de Saint Germain A, Ligerot A, Dun EA, Pillot JP, Ross JJ, Beveridge CA, Rameau C (2013) Strigolactones stimulate internode elongation independently of gibberellins. Plant Physiol 163:1012–1025
Feurtado JA, Huang D, Wicki-Stordeur L, Hemstock LE, Potentier MS, Tsang EWT, Cutler AJ (2011) The Arabidopsis C2H2 zinc Finger INDETERMINATE DOMAIN1/ENHYDROUS promotes the transition to germination by regulating light and hormonal signaling during seed maturation. Plant Cell 23:1772–1794
Field B, Osbourn AE (2008) Metabolic diversification-independent assembly of operon-like gene clusters in different plants. Science 320:543–547
Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and control of germination. New Phytol 171:501–523
Finkelstein R (2013) Abscisic acid synthesis and response. The Arabidopsis Book e0166. doi:10.1199/tab.0166
Gao Z, Qian Q, Liu X, Yan M, Feng Q, Dong G, Liu J, Bi Han (2009) Dwarf 88, a novel putative esterase gene affecting architecture of rice plant. Plant Mol Biol 71:265–276
Garg R, Jhanwar S, Tyagi AK, Jain M (2010) Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during development and response to various stimuli in rice. DNA Res 17:353–367
Greer S, Wen M, Bird D, Wu X, Samuels L, Kunst L, Jetter R (2007) The cytochrome P450 enzyme CYP96A15 is the mid chain alkane hydroxylase responsible for formation of secondary alcohols and ketones in stem cuticular wax of Arabidopsis. Plant Physiol 145:653–667
Hamberger B, Bak S (2013) Plant P450s as versatile drivers for evolution of species-specific chemical diversity. Phil Trans R Soc B 368:1476–2970
Hirano K, Ueguchi-Tanaka M, Matsuoka M (2008) GID1-mediated gibberellin signaling in plants. Trends Plant Sci 13:192–199
Hong Z, Ueguchi-Tanaka M, Matsuoka M (2004) Brassinosteroids and rice architecture. J Pestic Sci 29:184–188
Jain M, Ghanashyam C, Bhattacharjee A (2010) Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses. BMC Genomics 11:73
Kanwar P, Sanyal SK, Tokas I, Yadav AK, Pandey A, Kapoor S, Pandey GK (2014) Comprehensive structural, interaction and expression analysis of CBL and CIPK complement during abiotic stresses and development in rice. Cell Calcium 56:81–95
Kim GT, Tsukaya H (2002) Regulation of the biosynthesis of plant hormones by cytochrome P450s. Plant Res 115:169–177
Kojima M, Sakakibara H (2012) Highly sensitive high-throughput profiling of six phytohormones using MS-probe modification and liquid chromatography-tandem mass spectrometry. In: Normanly J (ed) High-throughput phenotyping in plants. Humana Press, New York, pp 151–164
Komorisono M, Ueguchi-Tanaka M, Aichi I, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M, Sazuka T (2005) Analysis of the rice mutant dwarf and gladius leaf 1. Aberrant katanin-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling. Plant Physiol 138:1982–1993
Koornneef M, Bentsink L, Hilhorst H (2002) Seed dormancy and germination. Curr Opin Plant Biol 5:33–36
Lee KW, Piao HL, Kim H-Y, Choi SM, Jiang F, Hartung W, Hwang I, Kwak JM, Lee I-L, Hwang I (2006) Activation of glucosidase via stress-induced polymerization rapidly increases active pools of abscisic acid. Cell 126:1109–1120
Li GW, Peng YH, Yu X, Zhang MH, Cai WM, Sun WN, Su WA (2008a) Transport functions and expression analysis of vacuolar membrane aquaporins in response to various stresses in rice. J Plant Physiol 165:1879–1888
Li H, Ruan J, Durbin R (2008b) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858
Li W, Wu J, Weng S, Zhang Y, Zhang D, Shi C (2010) Identification of dwarf 62, loss-of-function mutation in DLY/OsGRAS-32 affecting gibberellin metabolism in rice. Planta 232:1383–1396
Liu C, Mao B, Ou S, Wang W, Liu L, Wu Y, Chu C, Wang X (2014) OsbZIP71, a bZIP transcription factor, confers salinity and drought tolerance in rice. Plant Mol Biol 84:19–36
Lu G, Gao C, Zhneg X, Han B (2009) Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice. Planta 229:605–615
McCourt P, Creelman R (2008) The ABA receptors—we report you decide. Curr Opin Plant Biol 11:474–478
Michalak P (2008) Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes. Genomics 91:243–248
Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 4:490–495
Mizutani M, Ohata D (2010) Diversification of P450 genes during land plant evolution. Annu Rev Plant Biol 61:291–315
Mori M, Nomura T, Ooka H, Ishizaka M, Yokota T, Sugimoto K, Okabe K, Kajiwara H, Satoh K, Yamamoto K, Hirochika H, Kikuchi S (2002) Isolation and characterization of a rice dwarf mutant with a defect in brassinosteroid biosynthesis. Plant Physiol 130:1152–1161
Nakagawa T, Ishiguro S, Kimura T (2009) Gateway vectors for plant transformation. Plant Biotechnol 26:275–284
Nambara E, Marion-Poll A (2005) Abscisic acid biosynthesis and catabolism. Annu Rev Plant Biol 56:165–185
Nelson D, Werck-Reichhart D (2011) The plant genome: an evolutionary view on structure and function, a P450-centric view of plant evolution. Plant J 66:194–211
Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S (2004) Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiol 135:756–772
Nelson BK, Cai X, Nebenführ A (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J 51:1126–1136
Nützmann HW, Osbourn A (2014) Gene clustering in plant specialized metabolism. Curr Opin Biotechnol 26:91–99
Oh E, Yamaguchi S, Kamiya Y, Bae G, Chung WI, Choi G (2006) Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Plant J 47:124–139
Rakshit S, Kanzaki H, Matsumura H, Rakshit A, Fujibe T, Okuyama Y, Yoshida K, Tamiru MO, Shenton M et al (2010) Use of tilling for reverse and forward genetics of rice. In: Meksem K, Kahl G (eds) The handbook of plant mutation screening: mining of natural and induced alleles. Wiley-VCH, Weinheim, pp 187–197
Ramamoorthy R, Jiang SY, Ramachandran S (2011) Oryza sativa cytochrome P450 family member OsCYP96B4 reduces plant height in a transcript dosage dependent manner. PLoS ONE 6:1–14
Razem FA, Baron K, Hill RD (2006) Turning on gibberellin and abscisic acid signaling. Curr Opin Plant Biol 9:454–459
Reiter WD (2002) Biosynthesis and properties of the plant cell wall. Curr Opin Cell Biol 5:536–542
Richter R, Behringer C, Müller IK, Schwechheimer C (2010) The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS. Genes Dev 24:2093–2104
Ross ARS, Ambrose SJ, Cutler AJ, Feurtado JA, Kermode AR, Nelson K, Zhou R, Abrams SR (2004) Determination of endogenous and supplied deuterated abscisic acid in plant tissues by high performance liquid chromatography-electrospray ionization tandem mass spectrometry with multiple reaction monitoring. Anal Biochem 329:324–333
Sakamoto T, Miura K, Itoh H, Tatsumi T, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Agrawal GK, Takeda S, Abe K et al (2004) An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol 134:1642–1653
Sazuka T, Aichi I, Kawai T, Matsuo N, Kitano H, Matsuoka M (2005) The rice mutant dwarf bamboo shoot 1: a leaky mutant of the NACK-type kinesine like gene can initiate organ primordial but not organ development. Plant Cell Physiol 48:1934–1943
Schuler MA, Werck-Reichhart D (2003) Functional genomics of P450s. Annu Rev Plant Biol 54:629–667
Seo M, Hanada A, Kuwahara A, Endo A, Okamoto M, Yamauchi Y, North H, Marion-Poll A, Sun T-P, Koshiba T, Kamiya Y, Yamaguchi S, Nambara E (2006) Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism. Plant J 48:354–366
Seto M, Hanada A, Kuwahara A, Endo A, Okamoto M, Yamauchi Y, North H, Marion-Poll A, Sun T, Koshiba T, Kamiya Y, Yamaguchi S, Nambara E (2006) Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism. Plant J 48:354–366
Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A, Yaegashi H, Obara T, Oikawa K, Utsuchi H, Kanzaki E, Mitsuoka C, Natsuem S, Kosugi S, Kanzaki H, Matsumura H, Urasaki N, Kamoun S, Terauch (2015) MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol (in press)
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Toki S, Hara N, Ono K, Onodera H, Tagiri A, Oka S, Tanaka H (2006) Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. Plant J 47:969–976
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111
Weiss D, Ori N (2007) Mechanisms of crosstalk between gibberellin and other hormones. Plant Physiol 144:1240–1246
Wellesen K, Durst F, Pinot F, Benveniste I, Nettesheim K, Wismann E, Steiner-Lange S, Saedler H, Yephremov A (2001) Functional analysis of the LACERATA gene of Arabidopsis provide evidence for different roles of fatty acid ω-hydroxylation in development. Proc Natl Acad Sci USA 98:9694–9699
Werck-Reichhart D, Bak S, Paquette S (2002) Cytochrome P450. In: Somerville CR, Meyerowitz EM (eds) The Arabidopsis Book. American Society of Plant Biologists, Rockville, pp 1–28
Wu Y, Hillwig ML, Wang Q, Peters RJ (2011) Parsing a multifunctional biosynthetic gene cluster from rice: biochemical characterization of CYP71Z6 & 7. FEBS Lett 585:3446–3451
Xiang Y, Tang N, Du H, Ye H, Xiong L (2008) Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol 148:1938–1952
Xie X, Wang Y, Williamson Holroyd GH, Tagliavia C, Murchie E, Theobald J, Knight MR, Davies WJ, Ottoline Leyser HM, Hetherington AM (2006) The identification of genes involved in the stomatal response to reduced atmospheric relative humidity. Curr Biol 16:882–887
Xu MR, Huang LY, Zhang F, Zhu LH, Zhou YL, Li ZK (2013) Genome-wide phylogenetic analysis of stress-activated protein kinase genes in rice (OsSAPKs) and expression profiling in response to Xanthomonas oryzae pv. oryzicola infection. Plant Mol Biol Rep 31:877–885
Yang XC, Hwa CM (2008) Genetic modification of plant architecture and variety improvement in rice. Heredity 101:396–404
You J, Zong W, Hu H, Li X, Xiao J, Xiong L (2014) A SNAC1-regulated protein phosphatase gene OsPP18 modulates drought and oxidative stress tolerance through ABA-independent reactive oxygen species scavenging in rice. Plant Physiol. doi:10.1104/pp.114.251116 (Online first)
Zentella R, Zhang ZL, Park M, Thomas SG, Endo A, Murase K, Fleet CM, Jikumaru Y, Nambara E, Kamiya Y, Sun TP (2007) Global analysis of DELLA direct targets in early gibberellin signaling in Arabidopsis. Plant Cell 19:3037–3057
Zhang Y, Feng F, He C (2012) Downregulation of OsPK1 contributes to oxidative stress and variations in ABA/GA balance in rice. Plant Mol Biol Rep 30:1006–1013
Zhang J, Liu X, Li S, Cheng Z, Li C (2014) The rice semi-dwarf mutant d37, caused by a mutation in CYP96B4, plays an important role in the fine-tuning of plant growth. PLoS ONE 9:e88068
Zhou HL, He SJ, Cao YR, Chen T, Du BX, Chu CC, Zhang JS, Chen SY (2006) OsGLU1, a putative membrane-bound endo-1,4-β-d-glucanase from rice, affects plant internode elongation. Plant Mol Biol 60:137–151
Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273
Zhu Y, Nomura T, Xu Y, Zhang Y, Peng Y, Mao B, Hanada A, Zhou H, Wang R, Li P, Zhu X, Mander LN, Kamiya Y, Yamaguchi S, Hea Z (2006) ELONGATED UPPERMOST INTERNODE Encodes a cytochrome P450 monooxygenase that epoxidizes Gibberellins in a novel deactivation reaction in rice. Plant Cell 18:442–456
Acknowledgments
This work was partly supported by the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics for Agricultural Innovation PMI-0010), by the Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) Japan, by Grant-in-aid for Scientific Research from the Ministry of Education, Cultures, Sports and Technology, Japan (Grant-in-Aid for Scientific Research on Innovative Areas 23113009), and by Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research (KAKENHI) (Grant No. 24248004) to RT. JRU was supported by the Japanese Government Scholarship Grant for Foreign Students (Monbukagusho) for his Ph.D. study.
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Muluneh Tamiru and Jerwin R. Undan have contributed equally to this work.
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Tamiru, M., Undan, J.R., Takagi, H. et al. A cytochrome P450, OsDSS1, is involved in growth and drought stress responses in rice (Oryza sativa L.). Plant Mol Biol 88, 85–99 (2015). https://doi.org/10.1007/s11103-015-0310-5
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DOI: https://doi.org/10.1007/s11103-015-0310-5