Abstract
Major seed storage proteins in rice (Oryza sativa) are composed of glutelin, prolamin, and globulin. We previously generated four SSP-RNAi lines with reduced levels of globulin (Glb-RNAi); prolamin (Pro-RNAi); prolamin and globulin (PGb-RNAi); and glutelin, prolamin, and globulin (GPGb-RNAi). To identify the genes and molecular events associated with SSP deletion, we profiled the levels of seed transcripts in these four SSP-RNAi lines during seed development. We identified 2951 differentially expressed genes (DEGs) with a fold change of ≥ 2 or ≤ − 2 relative to the wild type (cv. Ilmi). Gene ontology (GO) analysis showed that most DEGs were associated with the functional categories “regulation of transcription, DNA-dependent”, “regulation of RNA metabolic process”, and “integral to membrane”. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the DEGs also functioned in “metabolism”, “folding, sorting and degradation”, and “transport and catabolism”. We identified 105 transcription factor (TF) genes and belonging to 25 TF gene families in our list of DEGs. Specifically, which are expected to affect expression of SSP-related genes, the expressions of TF genes, such as zinc finger protein, basic helix–loop–helix protein 008, and MYB transcription factor 55/61L, were decreased, and the expression levels of C2H2-type zinc finger protein, basic helix–loop–helix protein 073, and zinc finger protein were increased by RNA-Seq data and real-time quantitative PCR. Furthermore, it was confirmed in four SSP-RNAi lines that the expression levels of lipid transfer proteins were reduced. These results provide important information about the effect of SSPs-related genes on seed development.
Similar content being viewed by others
References
Amaratunga D, Cabrera J (2001) Analysis of data from viral DNA microchips. J Am Stat Assoc 96:1161–1170
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185–193
Boutrot F, Guirao A, Alary R, Joudrier P, Gautier MF (2005) Wheat non-specific lipid transfer protein genes display a complex pattern of expression in developing seeds. Biochim Biophys Acta 1730:114–125
Carvalho AO, Souza-Filho GA, Ferreira BS, Branco AT, Araujo IS, Fernandes KV, Retamal CA, Gomes VM (2006) Cloning and characterization of a cowpea seed lipid transfer protein cDNA: expression analysis during seed development and under fungal and cold stresses in seedlings’ tissues. Plant Physiol Biochem 44:732–742
Cho K, Lee HJ, Jo YM, Lim SH, Rakwal R, Lee JY, Km YM (2016) RNA interference-mediated simultaneous suppression of seed storage proteins in rice grains. Front Plant Sci 7:1624
Crofts AJ, Crofts N, Whitelegge JP, Okita TW (2010) Isolation and identification of cytoskeleton-associated prolamin mRNA binding proteins from developing rice seeds. Planta 231:1261–1276
Diaz I, Martinez M, Isabel-LaMoneda I, Rubio-Somoza I, Carbonero P (2005) The DOF protein, SAD, interacts with GAMYB in plant nuclei and activates transcription of endosperm-specific genes during barley seed development. Plant J 42:652–662
Doroshenk KA, Crofts AJ, Morris RT, Wyrick JJ, Okita TW (2009) Proteomic analysis of cytoskeleton-associated RNA binding proteins in developing rice seed. J Proteome Res 8:4641–4653
Doroshenk KA, Crofts AJ, Morris RT, Wyrick JJ, Okita TW (2012) RiceRBP: a resource for experimentally identified RNA binding proteins in Oryza sativa. Front Plant Sci 3:90
Doroshenk KA, Tian L, Crofts AJ, Kumamaru T, Okita TW (2014) Characterization of RNA binding protein RBP-P reveals a possible role in rice glutelin gene expression and RNA localization. Plant Mol Biol 85:381–394
Gao Y, Xu H, Shen Y, Wang J (2013) Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique. Plant Mol Bol 81:363–378
Hayashi G, Shibato J, Imanaka T, Cho K, Kubo A, Kikuchi S, Satoh K, Kimura S, Ozawa S, Fukutani S, Endo S, Ichikawa K, Agrawal GK, Shioda S, Fukumoto M, Rakwal R (2014) Unraveling low-level gamma radiation–responsive changes in expression of early and late genes in leaves of rice seedlings at litate village, Fukushima. J Hered 105:723–738
Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA (2007) The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol 8:R183
Izawa T, Foster R, Nakajima M, Shimamoto K, Chua NH (1994) The rice bZIP transcriptional activator RITA-1 is highly expressed during seed development. Plant Cell 6:1277–1287
Kawakatsu T, Yamamoto MP, Hirose S, Yano M, Takaiwa F (2008) Characterization of a new rice glutelin gene GluD-1 expressed in the starchy endosperm. J Exp Bot 59:4233–4245
Kim YM, Lee JY, Lee T, Lee YH, Kim SH, Kang SH, Yoon UH, Ha SH, Kim SH (2012) The suppression of the glutelin storage protein gene in transgenic rice seeds results in a higher yield of recombinant protein. Plant Biotechnol Rep 6:347–353
Kim HJ, Lee JY, Yoon UH, Lim SH, Kim YM (2013) Effects of reduced prolamin on seed storage protein composition and the nutritional quality of rice. Int J Mol Sci 14:17073–17084
Kovalchuk N, Smith J, Bazanova N, Pyvovarenko T, Singh R, Shirley N, Ismagul A, Johnson A, Milligan AS, Hrmova M, Langridge P, Lopato S (2012) Characterization of the wheat gene encoding a grain specific lipid transfer protein TdPR61, and promoter activity in wheat, barley and rice. J Exp Bot 63:2025–2040
Krishnan HB, Pueppke SG (1993) Nucleotide sequence of an abundant rice seed globulin: Homology with the high molecular weight glutelins of wheat, rye and triticale. Biochem Biophys Res Commun 193:460–466
Lee HJ, Jo YM, Lee JY, Lim SH, Kim YM (2015) Lack of globulin synthesis during seed development alters accumulation of seed storage proteins in rice. Int J Mol Sci 16:14717–14736
Mahto A, Mathew IE, Agarwal P (2017) Decoding the transcriptome of rice seed during development. IntechOpen 25–44
Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682
Mitsukawa N, Konishi R, Kidzu K, Ohtsuki K, Masumura T, Tanaka K (1999) Amino acid sequencing and cDNA cloning of rice seed storage proteins, the 13 kDa prolamins, extracted from type I protein bodies. Plant Biotechnol 16:103–113
Monnet FP, Dieryck W, Boutrot F, Joudrier P, Gautier MF (2001) Purification, characterization and cDNA cloning of a type 2 (7 kDa) lipid transfer protein from Triticum durum. Plant Sci 161:747–755
Nakase M, Hotta H, Adachi T, Aoki N, Nakamura R, Masumura T, Tanaka K, Matsuda T (1996) Cloning of the rice seed α-globulin-encoding gene: sequence similarity of the 5′-flanking region to those of the genes encoding wheat high-molecular-weight glutenin and barley D hordein. Gene 170:223–236
Nie DM, Ouyang YD, Wang X, Zhou W, Hu CG, Yao J (2013) Genome-wide analysis of endosperm-specific genes in rice. Gene 530:236–247
Onodera Y, Suzuki A, Wu CY, Washida H, Takaiwa F (2001) A rice functional transcriptional activator, RISBZ1, responsible for endosperm-specific expression of storage protein genes through GCN4 motif. J Biol Chem 276:14139–14152
Oono Y, Wakasa Y, Hirose S, Yang L, Sakuta C, Takaiwa F (2010) Analysis of ER stress in developing rice endosperm accumulating b-amyloid peptide. Plant Biotechnol J 8:691–718
Ranzani V, Rossetti G, Panzeri I, Arrigoni A, Bonnal RJ, Curti S, Gruarin P, Provasi E, Sugliano E, Marconi M, De Francesco R, Geginat J, Bodega B, Abrignani S, Pagani M (2015) The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. Nat Immunol 16:318–325
Saito Y, Shigemitsu T, Yamasaki R, Sasou A, Goto F, Kishida K, Kuroda M, Tanaka K, Morita S, Satoh S, Masumura T (2012) Formation mechanism of the internal structure of type I protein bodies in rice endosperm: relationship between the localization of prolamin species and the expression of individual genes. Plant J 70:1043–1055
Skirycz A, Reichelt M, Burow M, Birkemeyer C, Rolcik J, Kopka J, Zanor MI, Gershenzon J, Strnad M, Szopa J, Mueller-Roeber B, Witt I (2006) DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant J 47:10–24
Suzuki A, Wu CY, Washida H, Takaiwa F (1998) Rice MYB protein OSMYB5 specifically binds to the AACA motif conserved among promoters of genes for storage protein glutelin. Plant Cell Physiol 39:555–559
Takemoto Y, Coughlan SJ, Okita TW, Satoh H, Ogawa M, Kumamaru T (2002) The rice mutant esp2 greatly accumulates the glutelin precursor and deletes the protein disulfide isomerase. Plant Physiol 128:1212–1222
Tanaka K, Sugimoto T, Ogawa M, Kasai Z (1980) Isolation and characterization of two types of protein bodies in rice endosperm. Agric Biol Chem 44:1633–1639
Tian L, Xing Y, Fukuda M, Li R, Kumamaru T, Qian D, Dong X, Qu LQ (2018) A conserved motif is essential for the correct assembly of proglutelins and for their export from the endoplasmic reticulum in rice endosperm. J Exp Bot 69:5029–5043
Washida H, Sugino A, Doroshenk KA, Satoh-Cruz M, Nagamine A, Katsube-Tanaka T, Ogawa M, Kumamaru T, Satoh H, Okita TW (2012) RNA targeting to a specific ER sub-domain is required for efficient transport and packaging of α-globulins to the protein storage vacuole in developing rice endosperm. Plant J 70:471–479
Xu H, Gao Y, Wang J (2012) Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique. PLoS ONE 7:e30646
Yamagata H, Tanaka K (1986) The site of synthesis and accumulation of storage proteins. Plant Cell Physiol 27:135–145
Yamamoto MP, Onodera Y, Touno SM, Takaiwa F (2006) Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. Plant Physiol 141:1694–1707
Yanagisawa S (2002) The Dof family of plant transcription factors. Trends Plant Sci 7:555–560
Yang Y, Crofts AJ, Crofts N, Okita TW (2014) Multiple RNA binding protein complexes interact with the rice prolamine RNA cis-localization zipcode sequences. Plant Physiol 164:1271–1282
Acknowledgements
This work was supported by grants from the National Institute of Agricultural Science (RDA PJ014838) and the Next-Generation BioGreen 21 Program (RDA PJ013159 and RDA PJ013149), South Korea. This study was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2020R1I1A1A01069882) to KC.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Kim, S., Cho, K., Lim, SH. et al. Transcriptome profiling of transgenic rice seeds lacking seed storage proteins (globulin, prolamin, and glutelin) by RNA-Seq analysis. Plant Biotechnol Rep 15, 77–93 (2021). https://doi.org/10.1007/s11816-020-00655-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11816-020-00655-0