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Transcriptome profiling identifies ABA mediated regulatory changes towards storage filling in developing seeds of castor bean (Ricinus communis L.).

Chandrasekaran U, Xu W, Liu A - Cell Biosci (2014)

Bottom Line: Exogenous ABA (10 μM) enhanced the accumulation of soluble sugar content (6.3%) followed by deposition of total lipid content (4.9 %).These genes were involved in sugar metabolism (such as glucose-6-phosphate, fructose 1,6 bis-phosphate, glycerol-3-phosphate, pyruvate kinase), lipid biosynthesis (such as ACS, ACBP, GPAT2, GPAT3, FAD2, FAD3, SAD1 and DGAT1), storage proteins synthesis (such as SGP1, zinc finger protein, RING H2 protein, nodulin 55 and cytochrome P450), and ABA biosynthesis (such as NCED1, NCED3 and beta carotene).Further, we confirmed the validation of RNA-Sequencing data by Semi-quantitative RT-PCR analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming 650223, China ; University of Chinese Academy of Sciences, Beijing 100049, China.

ABSTRACT

Background: The potential biodiesel plant castor bean (Ricinus communis) has been in the limelight for bioenergy research due to the availability of its genome which raises the bar for genome-wide studies claiming advances that impact the "genome-phenome challenge". Here we report the application of phytohormone ABA as an exogenous factor for the improvement of storage reserve accumulation with a focus on the complex interaction of pathways associated with seed filling.

Results: After the application of exogenous ABA treatments, we measured an increased ABA levels in the developing seeds cultured in vitro using the ELISA technique and quantified the content of major biomolecules (including total lipids, sugars and protein) in treated seeds. Exogenous ABA (10 μM) enhanced the accumulation of soluble sugar content (6.3%) followed by deposition of total lipid content (4.9 %). To elucidate the possible ABA signal transduction pathways towards overall seed filling, we studied the differential gene expression analysis using Illumina RNA-Sequencing technology, resulting in 2568 (1507-up/1061-down regulated) differentially expressed genes were identified. These genes were involved in sugar metabolism (such as glucose-6-phosphate, fructose 1,6 bis-phosphate, glycerol-3-phosphate, pyruvate kinase), lipid biosynthesis (such as ACS, ACBP, GPAT2, GPAT3, FAD2, FAD3, SAD1 and DGAT1), storage proteins synthesis (such as SGP1, zinc finger protein, RING H2 protein, nodulin 55 and cytochrome P450), and ABA biosynthesis (such as NCED1, NCED3 and beta carotene). Further, we confirmed the validation of RNA-Sequencing data by Semi-quantitative RT-PCR analysis.

Conclusions: Taken together, metabolite measurements supported by genes and pathway expression results indicated in this study provide new insights to understand the ABA signaling mechanism towards seed storage filling and also contribute useful information for facilitating oilseed crop functional genomics on an aim for utilizing castor bean agricultural and bioenergy use.

No MeSH data available.


Related in: MedlinePlus

Overall view of ABA signaling towards sucrose metabolism and lipid biosynthesis in castor developing seeds. This pathway describes major genes participating in sucrose and lipid metabolic pathways like Glucose-6-phopshate, fructose 1,6 bisphosphate, pyruvate kinase, glycerol-3-phosphate, ACS, GPAT, DGAT positively regulated to exogenous ABA signaling (Additional file 4: Table S1).
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Figure 4: Overall view of ABA signaling towards sucrose metabolism and lipid biosynthesis in castor developing seeds. This pathway describes major genes participating in sucrose and lipid metabolic pathways like Glucose-6-phopshate, fructose 1,6 bisphosphate, pyruvate kinase, glycerol-3-phosphate, ACS, GPAT, DGAT positively regulated to exogenous ABA signaling (Additional file 4: Table S1).

Mentions: In the total DEGs identified, several genes were found to be directly or indirectly involved in critical plant metabolic pathways related to seed filling like sucrose, starch, cellulose, lipid and protein metabolism apart from genes participating in other regulatory pathways. As shown in Additional file 4: Table S1, crucial enzymes like glucose 6 phosphate [30170.m014025], fructose 6 phosphate [30189.m001668], fructose 1,6-bisphosphate [29576.m000229], glycerol-3-phsophate [30131.m007256, 30147.m014220], 3- phosphoglycerate dehydrogenase [30074.m001363], polyethanolpyruvate [PEP] carboxynase [30170.m013617], pyruvate kinase [29815.m000503, 28842.m000927], pyruvate dioxygense [29993.m001037], pyruvate decarboxylase [29601.m000442, 29900.m001589], NAD(P)H dehydrogenase [29933.m001426], NADH dehydrogenase [53582.m000022], NADH oxidoreductase [48739.m000082], malate dehydrogenase [30138.m004069], glutamate decarboxylase [29780.m001375], acetyl CoA dehydrogense [30111.m000733], 3-OH acetyl CoA dehydrogenase [29912.m005496], acetyl CoA transferase [29844.m003188] participating in sucrose metabolic pathway i.e., breakdown of sucrose for synthesis of storage reserves (Figure 4). Sucrose synthase 3 (SS) [29986.m001646] a key enzyme in the conversion of sucrose in to starch was highly regulated by exogenous ABA signaling. In support, critical enzymes participating in cellulose synthesis like cellulose synthase [30073.m002256, 29603.m000538], UDP glucosyltransferase [29724.m000846, 29678.m000511, 30138.m003909, 30138.m003910], glucan endo 1,3 beta glucosidase [30170.m014027], glycosyl transferase [30138.m003935], xyloglucan [30179.m000573], beta 1,3 glucuronyltransferase [30170.m013621] were highly expressed. In addition, eight sugar transporter genes (STP) which play a nutritional role in supplying sugars to the cells for growth and development [29912.m005520, 30147.m014261, 29726.m003958, 29667.m000356, 29693.m001965, 29844.m003367, 29844.m003369, 29933.m001432] were found to be highly responsive supporting the high uptake of total sugars mediated by exogenous ABA signaling.


Transcriptome profiling identifies ABA mediated regulatory changes towards storage filling in developing seeds of castor bean (Ricinus communis L.).

Chandrasekaran U, Xu W, Liu A - Cell Biosci (2014)

Overall view of ABA signaling towards sucrose metabolism and lipid biosynthesis in castor developing seeds. This pathway describes major genes participating in sucrose and lipid metabolic pathways like Glucose-6-phopshate, fructose 1,6 bisphosphate, pyruvate kinase, glycerol-3-phosphate, ACS, GPAT, DGAT positively regulated to exogenous ABA signaling (Additional file 4: Table S1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4109380&req=5

Figure 4: Overall view of ABA signaling towards sucrose metabolism and lipid biosynthesis in castor developing seeds. This pathway describes major genes participating in sucrose and lipid metabolic pathways like Glucose-6-phopshate, fructose 1,6 bisphosphate, pyruvate kinase, glycerol-3-phosphate, ACS, GPAT, DGAT positively regulated to exogenous ABA signaling (Additional file 4: Table S1).
Mentions: In the total DEGs identified, several genes were found to be directly or indirectly involved in critical plant metabolic pathways related to seed filling like sucrose, starch, cellulose, lipid and protein metabolism apart from genes participating in other regulatory pathways. As shown in Additional file 4: Table S1, crucial enzymes like glucose 6 phosphate [30170.m014025], fructose 6 phosphate [30189.m001668], fructose 1,6-bisphosphate [29576.m000229], glycerol-3-phsophate [30131.m007256, 30147.m014220], 3- phosphoglycerate dehydrogenase [30074.m001363], polyethanolpyruvate [PEP] carboxynase [30170.m013617], pyruvate kinase [29815.m000503, 28842.m000927], pyruvate dioxygense [29993.m001037], pyruvate decarboxylase [29601.m000442, 29900.m001589], NAD(P)H dehydrogenase [29933.m001426], NADH dehydrogenase [53582.m000022], NADH oxidoreductase [48739.m000082], malate dehydrogenase [30138.m004069], glutamate decarboxylase [29780.m001375], acetyl CoA dehydrogense [30111.m000733], 3-OH acetyl CoA dehydrogenase [29912.m005496], acetyl CoA transferase [29844.m003188] participating in sucrose metabolic pathway i.e., breakdown of sucrose for synthesis of storage reserves (Figure 4). Sucrose synthase 3 (SS) [29986.m001646] a key enzyme in the conversion of sucrose in to starch was highly regulated by exogenous ABA signaling. In support, critical enzymes participating in cellulose synthesis like cellulose synthase [30073.m002256, 29603.m000538], UDP glucosyltransferase [29724.m000846, 29678.m000511, 30138.m003909, 30138.m003910], glucan endo 1,3 beta glucosidase [30170.m014027], glycosyl transferase [30138.m003935], xyloglucan [30179.m000573], beta 1,3 glucuronyltransferase [30170.m013621] were highly expressed. In addition, eight sugar transporter genes (STP) which play a nutritional role in supplying sugars to the cells for growth and development [29912.m005520, 30147.m014261, 29726.m003958, 29667.m000356, 29693.m001965, 29844.m003367, 29844.m003369, 29933.m001432] were found to be highly responsive supporting the high uptake of total sugars mediated by exogenous ABA signaling.

Bottom Line: Exogenous ABA (10 μM) enhanced the accumulation of soluble sugar content (6.3%) followed by deposition of total lipid content (4.9 %).These genes were involved in sugar metabolism (such as glucose-6-phosphate, fructose 1,6 bis-phosphate, glycerol-3-phosphate, pyruvate kinase), lipid biosynthesis (such as ACS, ACBP, GPAT2, GPAT3, FAD2, FAD3, SAD1 and DGAT1), storage proteins synthesis (such as SGP1, zinc finger protein, RING H2 protein, nodulin 55 and cytochrome P450), and ABA biosynthesis (such as NCED1, NCED3 and beta carotene).Further, we confirmed the validation of RNA-Sequencing data by Semi-quantitative RT-PCR analysis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming 650223, China ; University of Chinese Academy of Sciences, Beijing 100049, China.

ABSTRACT

Background: The potential biodiesel plant castor bean (Ricinus communis) has been in the limelight for bioenergy research due to the availability of its genome which raises the bar for genome-wide studies claiming advances that impact the "genome-phenome challenge". Here we report the application of phytohormone ABA as an exogenous factor for the improvement of storage reserve accumulation with a focus on the complex interaction of pathways associated with seed filling.

Results: After the application of exogenous ABA treatments, we measured an increased ABA levels in the developing seeds cultured in vitro using the ELISA technique and quantified the content of major biomolecules (including total lipids, sugars and protein) in treated seeds. Exogenous ABA (10 μM) enhanced the accumulation of soluble sugar content (6.3%) followed by deposition of total lipid content (4.9 %). To elucidate the possible ABA signal transduction pathways towards overall seed filling, we studied the differential gene expression analysis using Illumina RNA-Sequencing technology, resulting in 2568 (1507-up/1061-down regulated) differentially expressed genes were identified. These genes were involved in sugar metabolism (such as glucose-6-phosphate, fructose 1,6 bis-phosphate, glycerol-3-phosphate, pyruvate kinase), lipid biosynthesis (such as ACS, ACBP, GPAT2, GPAT3, FAD2, FAD3, SAD1 and DGAT1), storage proteins synthesis (such as SGP1, zinc finger protein, RING H2 protein, nodulin 55 and cytochrome P450), and ABA biosynthesis (such as NCED1, NCED3 and beta carotene). Further, we confirmed the validation of RNA-Sequencing data by Semi-quantitative RT-PCR analysis.

Conclusions: Taken together, metabolite measurements supported by genes and pathway expression results indicated in this study provide new insights to understand the ABA signaling mechanism towards seed storage filling and also contribute useful information for facilitating oilseed crop functional genomics on an aim for utilizing castor bean agricultural and bioenergy use.

No MeSH data available.


Related in: MedlinePlus