Dataset Information

Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds

ABSTRACT: Rice is a major component of the human diet and feeds more than 50 million people across the globe. Therefore, efforts are being made to improve the nutritional quality of rice seeds in order to make a super-rice cultivar rich in antioxidants and vitamins. We previously developed two rice cultivars, Super-hongmi (red seeds) and Super-jami (black seeds), that were highly rich in antioxidants and exhibited high levels of radical scavenging activities. However, the molecular mechanism underlying the color development and accumulation of different antioxidants in these rice cultivars remains largely elusive. Here, we report the proteome profiles of mature Super-hongmi, and Super-jami seeds and compared with the Hopum (white seeds) using a label-free quantitative proteomics approach. This approach led to the identification of 5127 rice seed proteins of which 1628 showed significant changes (ANOVA, Benjamini-Hochberg FDR ≤ 0.01, fold change ≥ 1.5). Functional annotation of the differentially modulated proteins led to the identification of a phytoene desaturase (PDS3) that was highly enriched in the red seeds and was decreased in the black seeds as compared to the control white seeds. PDS3 is involved in the conversion of phytoene to ζ-carotene which may be responsible for the accumulation of red color in red seeds. Moreover, black seeds seem to accumulate higher levels of anthocyanins because of the higher abundance of dihydroflavonol 4-reductase. In addition, proteins associated with lignin and tocopherol biosynthesis were found to be highly increased in both red and black cultivars. Taken together, these data report the seed proteome of three different colored rice seeds and identify novel components associated with pigment accumulation.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Sun Tae Kim

LAB HEAD: Sun Tae Kim

PROVIDER: PXD039588 | Pride | 2023-09-21

REPOSITORIES: Pride

ACCESS DATA

Publications

Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds.

Gupta Ravi R Min Cheol Woo CW Jung Ju-Young JY Ham Tae-Ho TH Jeon Jong-Seong JS Cho Lae-Hyeon LH Kwon Soon Wook SW Kim Sun Tae ST

Proteomics 20230414 12

Rice is a major component of the human diet and feeds more than 50 million people across the globe. We previously developed two pigmented rice cultivars, Super-hongmi (red seeds) and Super-jami (black seeds), that are highly rich in antioxidants and exhibit high levels of radical scavenging activities. However, the molecular mechanism underlying the accumulation of pigments and different antioxidants in these rice cultivars remains largely elusive. Here, we report the proteome profiles of mature ...[more]

PMID: 37058097

Similar Datasets

Project description:Treatment of the seeds. The Solanum lycopersicum var. Money Maker wild type (MM) and fri1-1 mutant seeds were incubated on distilled-water saturated cotton wool in clear plastic boxes wrapped in black plastic sheets in darkness during 3 hours at 25°C. After that, the seeds were treated as follows: a) 24 hr of continuous irradiation with far-red light, FRc; b) 24 hr of FRc follow by a 10 min red light pulse (Rp), FRc+Rp; and c) complete darkness. After the light treatments, the seeds were incubated in darkness (25°C) until sampling. Red light (35umol/m2sec) was provided by 40W fluorescent lamps (Phillips 40/15) in combination with a red translucid acrylic. FRc light (100 umol/m2sec) was provided by a set of 150W incandescent internal reflector lamps (Phillips) in combination with a red acetate filter, six 2mm thick blue acrylic filters Paolini 2031 and 10cm water filter. Total RNA isolation. The seeds were grinded in liquid nitrogen and extracted with two volumes of extraction buffer (1% SDS, 6% p-aminosalycilic acid, 1% NaCl, 6% water-saturated phenol and 2% 2-mercaptoethanol) and two volumes of acid phenol:chloroform solution. The aqueous phase was sequentially extracted with one volume of acid phenol:chloroform solution and one volume of chloroform. The nucleic acids in the aqueous phase were precipitated with 0.15 volumes of 3M NaCl and 2.5 volumes of 100% ethanol at –80°C for 20 minutes. After centrifugation, the pellet was washed with 70% ethanol, resuspended in RNase-free water and precipitated with one volume of 4M LiCl over night at 4°C. The LiCl was removed after centrifugation and the pellet was rinsed with 2M LiCl and resuspended in RNase-free water. The total RNA was treated with RNase-free DNase (Promega) and cleaned up with mini spin columns (RNeasy Plant Mini Kit, Qiagen). The mRNA was amplificated with Message Amp II aRNA Amplification Kit (Ambion) and concentrated by vacumm centrifugation. Keywords: Direct comparison 21 hybs total

Project description:Background: Weedy rice (Oryza sativa L.) is a worldwide problem in rice production, being highly tolerant to sub-optimal nutrient levels hence competitive in nutrient acquisition. To understand the function of genes that are potentially involved in the high nutrient acquisition ability of weedy rice, we compared the transcriptomes of strawhull weedy red rice (tolerant to N deficit) with the rice cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y (intolerant to N deficit), by examining profiles in flag leaves at panicle initiation under low and optimum N levels. Strawhull weedy red rice and cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y were grown in nutrient solution with NH4NO3 concentration manipulated to simulate optimum and deficient N conditions. Changes in gene expression in leaf tissues were analyzed at three conditions: N deficiency, and at 24- and 48-h NH4NO3 supplementation after N starvation. Differential gene expression on weedy red rice was evaluated using oligonucleotide arrays representing 44,974 rice gene models. Overall, comparative real-time PCR analysis of 21 candidate genes identified from the microarray data between weedy red rice and cultivar M-bM-^@M-^XWellsM-bM-^@M-^Y supported our hypothesis that key genes involved in N assimilation are expressed differentially at N- deficient conditions between the tolerant and intolerant strains. Results: Eight candidate genes showed significant differences in expression at one of the time points: N and starch metabolism-related [alanine aminotransferase (OsAlaAT) locus ID Os10g25140.1; soluble starch synthase 2-1(OsSSSII1), Os10g30156.1; and soluble starch synthase 2-3(OsSSSII3), Os06g12450.1]; cell structure-related [alpha-L-fucosidase 2 precursor (OsFUCA2), Os06g06250.1]; signal transduction [two-component response regulator-like(OsPRR1), Os02g40510.1 and EF hand family protein (OsPOLC2_JUNOX), Os02g50060.1]; and transcription factors [zinc finger, C2H2 type family protein(OsC2H2Znf), Os11g06840.1 and Myb-like DNA-binding domain (OsMYB), Os01g62660.1]. Genome-wide gene expression analysis of weedy rice showed that nitrite reductase (Os01g25484.1; Os01g25484.2; Os01g25484.3) was most highly induced at N starvation and was most deeply repressed at 24 h of N-stress recovery. A few other genes, namely SANT/MYB (Os01g47370.1), chaperonin (Os02g54060.1; Os02g54060.2), protein phosphatase (Os09g15670.1), polyamine transporter (Os01g61044.1), trehalose-6-phosphate synthase (Os02g54820.2), uracil phosphoribosyltransferase (Os05g38170.1), an MIKCc type-box transcription factor (Os02g52340.1), a cell homeostasis-related uncharacterized protein (Os02g16880.1), a protease inhibitor (Os07g18990.1), dehydrin (Os11g26760.1), and cytochrome P450 (Os11g05380.1) were also strong indicators of starvation and recovery. Conclusions: Weedy rice has N-stress adaptive mechanisms that are probably distinct to the mechanisms in most cultivars. This mechanism potentially contributes to its high vigor and competitive advantage over most rice cultivars under sub-optimal nutrient levels. Expression of key genes involved in nitrate assimilation, trehalose synthesis, and protein modification appeared to be critical for adaptation to N stress in weedy rice. N-stress tolerance of weedy red rice appeared to be due at least in part to the ability to sustain C fixation and starch synthesis during N starvation. Plants were subjected to four treatments: T1 M-bM-^@M-^S Full N; T2 M-bM-^@M-^S NH4NO3starvation until NSI <95%; T3 - 24-h NH4NO3 readdition post-starvation; and T4 M-bM-^@M-^S 48-h NH4NO3 readdition post-starvation. The 24- and 48-h time points for NH4NO3 supplementation were selected to assess both the early and late molecular responses. There were four replications, with three plants per replication per N treatment.

Dataset Information

Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds

Publications

Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure