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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

Gene Ontology functional enrichment analysis of unigenes differentially expressed in control vs ABA treated seeds. Unigenes were assigned to three categories: (A) cellular components: 1-cell, 2-cell part, 3-envelope, 4-extracellular region, 5- extracellular region part, 6-macromolecular complex, 7-membrane enclosed lumen, 8-organelle, 9-organelle part; (B) molecular functions: 1-antioxidant, 2-binding, 3-catalytic, 4-electron carrier, 5-enzyme regulator, 6-molecular transducer, 7-structural molecule, 8-translation regulator, 9-transporter; and (C) biological processes: 1-anatomical structure formation, 2-biological adhesion, 3-biological regulation, 4-cellualar component biogenesis, 5-cellular component organization, 6-cellular process, 7-death, 8-developmental process, 9-establishment of localization, 10-growth, 11-immune system process, 12-localization, 13-locomotion, 14-metabolic process, 15-multi-organism process, 16-multicellular organism process, 17-pigmentation, 18-reproduction, 19-reproductive process, 20-response to stimulus, 21-rhythmic process, 22-viral reproduction.
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Figure 2: Gene Ontology functional enrichment analysis of unigenes differentially expressed in control vs ABA treated seeds. Unigenes were assigned to three categories: (A) cellular components: 1-cell, 2-cell part, 3-envelope, 4-extracellular region, 5- extracellular region part, 6-macromolecular complex, 7-membrane enclosed lumen, 8-organelle, 9-organelle part; (B) molecular functions: 1-antioxidant, 2-binding, 3-catalytic, 4-electron carrier, 5-enzyme regulator, 6-molecular transducer, 7-structural molecule, 8-translation regulator, 9-transporter; and (C) biological processes: 1-anatomical structure formation, 2-biological adhesion, 3-biological regulation, 4-cellualar component biogenesis, 5-cellular component organization, 6-cellular process, 7-death, 8-developmental process, 9-establishment of localization, 10-growth, 11-immune system process, 12-localization, 13-locomotion, 14-metabolic process, 15-multi-organism process, 16-multicellular organism process, 17-pigmentation, 18-reproduction, 19-reproductive process, 20-response to stimulus, 21-rhythmic process, 22-viral reproduction.

Mentions: To assess the transcriptional changes in ABA treated seeds; a stringent algorithm method was applied to identify differentially expressed genes from the normalized digital gene expression (DGE) library by comparing the ABA treated samples with control. The results showed that 2568 genes had P <0.05, false discovery rates (FDR) < 0.001, and fold-change ≥ 1 in the comparisons of ABA vs control which were identified as differentially expressed genes (Figure 1). Among these, 1507 genes were significantly up-regulated and 1061 genes were down-regulated in response to ABA treatment (Additional file 4: Table S1). Genes with differential expression responses included a wide variety of regulatory and metabolic processes and were classified into three categories based on their Gene Ontology (GO) terms (Figure 2). In each of the three categories (cellular component, molecular function and biological process) of the GO classification, ‘cell’, ‘cell part’, ‘binding’, ‘catalytic activity’, ‘cellular process’, ‘stimuli response’ and ‘metabolic process’, terms were dominant, respectively (Figure 2). We also noticed a high-percentage of genes from categories of, ‘developmental processes’, ‘cellular component’, ‘biological adhesion’, ‘immune system process’, ‘reproductive process’ and ‘growth’ and only a few genes from terms of ‘extra cellular part’, ‘electron carrier’, ‘locomotion’, and ‘rhythmic process’ (Figure 2). The GO analysis showed that the major functions of the identified genes were involved in various biological processes, suggesting that ABA have comprehensive impacts on seed development at this stage (21 DAP).Genes with similar expression patterns usually imply functional correlation. To evaluate our annotation process, the annotated unigenes were classified based on pathway analysis which can further help our understanding of the biological functions and interactions of genes (Figure 3). A total of 1437 unigenes were differentially expressed with pathway annotations assigned to 122 pathways in the KEGG database. The most represented pathways included “metabolic pathways” (containing 366 genes), “biosynthesis of secondary metabolites pathways” (containing 208 genes), “plant hormone signal transduction” (containing 87 genes), “protein processing” (containing 55 genes) and “starch metabolism” (containing 51 genes). Notably, main pathways were closely linked to changes in glycolysis pathway, sugar metabolism, lipid biosynthesis and hormone signal transduction (Figure 3). These identified genes would provide critical clues to clone and identify key ABA responsive genes which mediate sugar, lipid and protein biosynthesis in developing seeds of castor bean.


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)

Gene Ontology functional enrichment analysis of unigenes differentially expressed in control vs ABA treated seeds. Unigenes were assigned to three categories: (A) cellular components: 1-cell, 2-cell part, 3-envelope, 4-extracellular region, 5- extracellular region part, 6-macromolecular complex, 7-membrane enclosed lumen, 8-organelle, 9-organelle part; (B) molecular functions: 1-antioxidant, 2-binding, 3-catalytic, 4-electron carrier, 5-enzyme regulator, 6-molecular transducer, 7-structural molecule, 8-translation regulator, 9-transporter; and (C) biological processes: 1-anatomical structure formation, 2-biological adhesion, 3-biological regulation, 4-cellualar component biogenesis, 5-cellular component organization, 6-cellular process, 7-death, 8-developmental process, 9-establishment of localization, 10-growth, 11-immune system process, 12-localization, 13-locomotion, 14-metabolic process, 15-multi-organism process, 16-multicellular organism process, 17-pigmentation, 18-reproduction, 19-reproductive process, 20-response to stimulus, 21-rhythmic process, 22-viral reproduction.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4109380&req=5

Figure 2: Gene Ontology functional enrichment analysis of unigenes differentially expressed in control vs ABA treated seeds. Unigenes were assigned to three categories: (A) cellular components: 1-cell, 2-cell part, 3-envelope, 4-extracellular region, 5- extracellular region part, 6-macromolecular complex, 7-membrane enclosed lumen, 8-organelle, 9-organelle part; (B) molecular functions: 1-antioxidant, 2-binding, 3-catalytic, 4-electron carrier, 5-enzyme regulator, 6-molecular transducer, 7-structural molecule, 8-translation regulator, 9-transporter; and (C) biological processes: 1-anatomical structure formation, 2-biological adhesion, 3-biological regulation, 4-cellualar component biogenesis, 5-cellular component organization, 6-cellular process, 7-death, 8-developmental process, 9-establishment of localization, 10-growth, 11-immune system process, 12-localization, 13-locomotion, 14-metabolic process, 15-multi-organism process, 16-multicellular organism process, 17-pigmentation, 18-reproduction, 19-reproductive process, 20-response to stimulus, 21-rhythmic process, 22-viral reproduction.
Mentions: To assess the transcriptional changes in ABA treated seeds; a stringent algorithm method was applied to identify differentially expressed genes from the normalized digital gene expression (DGE) library by comparing the ABA treated samples with control. The results showed that 2568 genes had P <0.05, false discovery rates (FDR) < 0.001, and fold-change ≥ 1 in the comparisons of ABA vs control which were identified as differentially expressed genes (Figure 1). Among these, 1507 genes were significantly up-regulated and 1061 genes were down-regulated in response to ABA treatment (Additional file 4: Table S1). Genes with differential expression responses included a wide variety of regulatory and metabolic processes and were classified into three categories based on their Gene Ontology (GO) terms (Figure 2). In each of the three categories (cellular component, molecular function and biological process) of the GO classification, ‘cell’, ‘cell part’, ‘binding’, ‘catalytic activity’, ‘cellular process’, ‘stimuli response’ and ‘metabolic process’, terms were dominant, respectively (Figure 2). We also noticed a high-percentage of genes from categories of, ‘developmental processes’, ‘cellular component’, ‘biological adhesion’, ‘immune system process’, ‘reproductive process’ and ‘growth’ and only a few genes from terms of ‘extra cellular part’, ‘electron carrier’, ‘locomotion’, and ‘rhythmic process’ (Figure 2). The GO analysis showed that the major functions of the identified genes were involved in various biological processes, suggesting that ABA have comprehensive impacts on seed development at this stage (21 DAP).Genes with similar expression patterns usually imply functional correlation. To evaluate our annotation process, the annotated unigenes were classified based on pathway analysis which can further help our understanding of the biological functions and interactions of genes (Figure 3). A total of 1437 unigenes were differentially expressed with pathway annotations assigned to 122 pathways in the KEGG database. The most represented pathways included “metabolic pathways” (containing 366 genes), “biosynthesis of secondary metabolites pathways” (containing 208 genes), “plant hormone signal transduction” (containing 87 genes), “protein processing” (containing 55 genes) and “starch metabolism” (containing 51 genes). Notably, main pathways were closely linked to changes in glycolysis pathway, sugar metabolism, lipid biosynthesis and hormone signal transduction (Figure 3). These identified genes would provide critical clues to clone and identify key ABA responsive genes which mediate sugar, lipid and protein biosynthesis in developing seeds of castor bean.

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