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Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis.

Mata-Pérez C, Sánchez-Calvo B, Begara-Morales JC, Luque F, Jiménez-Ruiz J, Padilla MN, Fierro-Risco J, Valderrama R, Fernández-Ocaña A, Corpas FJ, Barroso JB - Front Plant Sci (2015)

Bottom Line: Thus, RNA-seq data analysis showed that an important set of these genes were associated with the jasmonic acid biosynthetic pathway including lypoxygenases (LOXs) and Allene oxide cyclases (AOCs).In this regard, we were able to identify new targets such as galactinol synthase 1 (GOLS1), methionine sulfoxide reductase (MSR) and alkenal reductase in ACSC.It is therefore possible to suggest that, in the absence of any oxidative stress, Ln is capable of modulating new sets of genes involved in the signaling mechanism mediated by additional abiotic stresses (salinity, UV and high light intensity) and especially in stresses mediated by ROS.

View Article: PubMed Central - PubMed

Affiliation: Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of Jaén Jaén, Spain.

ABSTRACT
Linolenic acid (Ln) released from chloroplast membrane galactolipids is a precursor of the phytohormone jasmonic acid (JA). The involvement of this hormone in different plant biological processes, such as responses to biotic stress conditions, has been extensively studied. However, the role of Ln in the regulation of gene expression during abiotic stress situations mediated by cellular redox changes and/or by oxidative stress processes remains poorly understood. An RNA-seq approach has increased our knowledge of the interplay among Ln, oxidative stress and ROS signaling that mediates abiotic stress conditions. Transcriptome analysis with the aid of RNA-seq in the absence of oxidative stress revealed that the incubation of Arabidopsis thaliana cell suspension cultures (ACSC) with Ln resulted in the modulation of 7525 genes, of which 3034 genes had a 2-fold-change, being 533 up- and 2501 down-regulated genes, respectively. Thus, RNA-seq data analysis showed that an important set of these genes were associated with the jasmonic acid biosynthetic pathway including lypoxygenases (LOXs) and Allene oxide cyclases (AOCs). In addition, several transcription factor families involved in the response to biotic stress conditions (pathogen attacks or herbivore feeding), such as WRKY, JAZ, MYC, and LRR were also modified in response to Ln. However, this study also shows that Ln has the capacity to modulate the expression of genes involved in the response to abiotic stress conditions, particularly those mediated by ROS signaling. In this regard, we were able to identify new targets such as galactinol synthase 1 (GOLS1), methionine sulfoxide reductase (MSR) and alkenal reductase in ACSC. It is therefore possible to suggest that, in the absence of any oxidative stress, Ln is capable of modulating new sets of genes involved in the signaling mechanism mediated by additional abiotic stresses (salinity, UV and high light intensity) and especially in stresses mediated by ROS.

No MeSH data available.


Related in: MedlinePlus

qRT–PCR validation of RNA-seq results. Sixteen genes identified previously as Ln-responsive genes by RNA-seq (white bar) in ACSC were randomly selected to analyze, by qRT–PCR the differential expression changes (red bars). Comparison of fold change of RNA-seq and qRT–PCR showed a correlation coefficient of 0.92, indicating that RNA-seq results were reliable. Results were average of two independent samples in triplicate. Standard deviations were less than 5% in all cases. NRT2.6 (AT3G45060), Arabidopsis thaliana high affinity nitrate transporter 2.6; XTH31 (AT3G44990), Arabidopsis thaliana xyloglucan endotransglycosylase/hydrolase 31; CHX17 (AT4G23700), Arabidopsis thaliana cation/H(+) antiporter 17; PTR3 (AT5G46050), Arabidopsis thaliana putative peptide transporter protein 3; CLV3 (AT2G27250), Arabidopsis thaliana protein CLAVATA 3; OZF1 (AT2G19810), Arabidopsis thaliana Oxidation-related Zinc Finger protein 1; HAC5 (AT3G12980), Arabidopsis thaliana histone acetyltransferase 5; JAZ1 (AT1G19180), Arabidopsis thaliana jasmonate-zim-domain protein 1; LHT7 (AT4G35180), Arabidopsis thaliana LYS/HIS transporter 7; GOLS1 (AT2G47180), Arabidopsis thaliana galactinol synthase 1; HSFB-2a (AT5G62020), Arabidopsis thaliana heat stress transcription factor B-2a; GSTU3 (AT2G29470), Arabidopsis thaliana glutathione S-transferase tau 3; EXP1 (AT1G69530), Arabidopsis thaliana Alpha-Expansin protein 1; MSRB7 (AT4G21830), Arabidopsis thaliana methionine sulfoxide reductase B7; LOX4 (AT1G72520), Arabidopsis thaliana lipoxygenase 4; RRTF1 (AT4G34410), Arabidopsis thaliana redox responsive transcription factor.
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Figure 6: qRT–PCR validation of RNA-seq results. Sixteen genes identified previously as Ln-responsive genes by RNA-seq (white bar) in ACSC were randomly selected to analyze, by qRT–PCR the differential expression changes (red bars). Comparison of fold change of RNA-seq and qRT–PCR showed a correlation coefficient of 0.92, indicating that RNA-seq results were reliable. Results were average of two independent samples in triplicate. Standard deviations were less than 5% in all cases. NRT2.6 (AT3G45060), Arabidopsis thaliana high affinity nitrate transporter 2.6; XTH31 (AT3G44990), Arabidopsis thaliana xyloglucan endotransglycosylase/hydrolase 31; CHX17 (AT4G23700), Arabidopsis thaliana cation/H(+) antiporter 17; PTR3 (AT5G46050), Arabidopsis thaliana putative peptide transporter protein 3; CLV3 (AT2G27250), Arabidopsis thaliana protein CLAVATA 3; OZF1 (AT2G19810), Arabidopsis thaliana Oxidation-related Zinc Finger protein 1; HAC5 (AT3G12980), Arabidopsis thaliana histone acetyltransferase 5; JAZ1 (AT1G19180), Arabidopsis thaliana jasmonate-zim-domain protein 1; LHT7 (AT4G35180), Arabidopsis thaliana LYS/HIS transporter 7; GOLS1 (AT2G47180), Arabidopsis thaliana galactinol synthase 1; HSFB-2a (AT5G62020), Arabidopsis thaliana heat stress transcription factor B-2a; GSTU3 (AT2G29470), Arabidopsis thaliana glutathione S-transferase tau 3; EXP1 (AT1G69530), Arabidopsis thaliana Alpha-Expansin protein 1; MSRB7 (AT4G21830), Arabidopsis thaliana methionine sulfoxide reductase B7; LOX4 (AT1G72520), Arabidopsis thaliana lipoxygenase 4; RRTF1 (AT4G34410), Arabidopsis thaliana redox responsive transcription factor.

Mentions: To validate RNA-seq results, we randomly assigned several Ln-responsive genes to conduct the expression analysis by qRT–PCR. Figure 6 shows the comparison between the qRT–PCR and RNA-seq analysis, showing that all the Ln-responsive genes tested and previously identified by RNA-seq were confirmed by qRT–PCR. The results showed a positive correlation between the two approaches (with a correlation coefficient of 0.92), indicating that the RNA-seq expression analysis performed is highly reliable.


Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis.

Mata-Pérez C, Sánchez-Calvo B, Begara-Morales JC, Luque F, Jiménez-Ruiz J, Padilla MN, Fierro-Risco J, Valderrama R, Fernández-Ocaña A, Corpas FJ, Barroso JB - Front Plant Sci (2015)

qRT–PCR validation of RNA-seq results. Sixteen genes identified previously as Ln-responsive genes by RNA-seq (white bar) in ACSC were randomly selected to analyze, by qRT–PCR the differential expression changes (red bars). Comparison of fold change of RNA-seq and qRT–PCR showed a correlation coefficient of 0.92, indicating that RNA-seq results were reliable. Results were average of two independent samples in triplicate. Standard deviations were less than 5% in all cases. NRT2.6 (AT3G45060), Arabidopsis thaliana high affinity nitrate transporter 2.6; XTH31 (AT3G44990), Arabidopsis thaliana xyloglucan endotransglycosylase/hydrolase 31; CHX17 (AT4G23700), Arabidopsis thaliana cation/H(+) antiporter 17; PTR3 (AT5G46050), Arabidopsis thaliana putative peptide transporter protein 3; CLV3 (AT2G27250), Arabidopsis thaliana protein CLAVATA 3; OZF1 (AT2G19810), Arabidopsis thaliana Oxidation-related Zinc Finger protein 1; HAC5 (AT3G12980), Arabidopsis thaliana histone acetyltransferase 5; JAZ1 (AT1G19180), Arabidopsis thaliana jasmonate-zim-domain protein 1; LHT7 (AT4G35180), Arabidopsis thaliana LYS/HIS transporter 7; GOLS1 (AT2G47180), Arabidopsis thaliana galactinol synthase 1; HSFB-2a (AT5G62020), Arabidopsis thaliana heat stress transcription factor B-2a; GSTU3 (AT2G29470), Arabidopsis thaliana glutathione S-transferase tau 3; EXP1 (AT1G69530), Arabidopsis thaliana Alpha-Expansin protein 1; MSRB7 (AT4G21830), Arabidopsis thaliana methionine sulfoxide reductase B7; LOX4 (AT1G72520), Arabidopsis thaliana lipoxygenase 4; RRTF1 (AT4G34410), Arabidopsis thaliana redox responsive transcription factor.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 6: qRT–PCR validation of RNA-seq results. Sixteen genes identified previously as Ln-responsive genes by RNA-seq (white bar) in ACSC were randomly selected to analyze, by qRT–PCR the differential expression changes (red bars). Comparison of fold change of RNA-seq and qRT–PCR showed a correlation coefficient of 0.92, indicating that RNA-seq results were reliable. Results were average of two independent samples in triplicate. Standard deviations were less than 5% in all cases. NRT2.6 (AT3G45060), Arabidopsis thaliana high affinity nitrate transporter 2.6; XTH31 (AT3G44990), Arabidopsis thaliana xyloglucan endotransglycosylase/hydrolase 31; CHX17 (AT4G23700), Arabidopsis thaliana cation/H(+) antiporter 17; PTR3 (AT5G46050), Arabidopsis thaliana putative peptide transporter protein 3; CLV3 (AT2G27250), Arabidopsis thaliana protein CLAVATA 3; OZF1 (AT2G19810), Arabidopsis thaliana Oxidation-related Zinc Finger protein 1; HAC5 (AT3G12980), Arabidopsis thaliana histone acetyltransferase 5; JAZ1 (AT1G19180), Arabidopsis thaliana jasmonate-zim-domain protein 1; LHT7 (AT4G35180), Arabidopsis thaliana LYS/HIS transporter 7; GOLS1 (AT2G47180), Arabidopsis thaliana galactinol synthase 1; HSFB-2a (AT5G62020), Arabidopsis thaliana heat stress transcription factor B-2a; GSTU3 (AT2G29470), Arabidopsis thaliana glutathione S-transferase tau 3; EXP1 (AT1G69530), Arabidopsis thaliana Alpha-Expansin protein 1; MSRB7 (AT4G21830), Arabidopsis thaliana methionine sulfoxide reductase B7; LOX4 (AT1G72520), Arabidopsis thaliana lipoxygenase 4; RRTF1 (AT4G34410), Arabidopsis thaliana redox responsive transcription factor.
Mentions: To validate RNA-seq results, we randomly assigned several Ln-responsive genes to conduct the expression analysis by qRT–PCR. Figure 6 shows the comparison between the qRT–PCR and RNA-seq analysis, showing that all the Ln-responsive genes tested and previously identified by RNA-seq were confirmed by qRT–PCR. The results showed a positive correlation between the two approaches (with a correlation coefficient of 0.92), indicating that the RNA-seq expression analysis performed is highly reliable.

Bottom Line: Thus, RNA-seq data analysis showed that an important set of these genes were associated with the jasmonic acid biosynthetic pathway including lypoxygenases (LOXs) and Allene oxide cyclases (AOCs).In this regard, we were able to identify new targets such as galactinol synthase 1 (GOLS1), methionine sulfoxide reductase (MSR) and alkenal reductase in ACSC.It is therefore possible to suggest that, in the absence of any oxidative stress, Ln is capable of modulating new sets of genes involved in the signaling mechanism mediated by additional abiotic stresses (salinity, UV and high light intensity) and especially in stresses mediated by ROS.

View Article: PubMed Central - PubMed

Affiliation: Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Area of Biochemistry and Molecular Biology, University of Jaén Jaén, Spain.

ABSTRACT
Linolenic acid (Ln) released from chloroplast membrane galactolipids is a precursor of the phytohormone jasmonic acid (JA). The involvement of this hormone in different plant biological processes, such as responses to biotic stress conditions, has been extensively studied. However, the role of Ln in the regulation of gene expression during abiotic stress situations mediated by cellular redox changes and/or by oxidative stress processes remains poorly understood. An RNA-seq approach has increased our knowledge of the interplay among Ln, oxidative stress and ROS signaling that mediates abiotic stress conditions. Transcriptome analysis with the aid of RNA-seq in the absence of oxidative stress revealed that the incubation of Arabidopsis thaliana cell suspension cultures (ACSC) with Ln resulted in the modulation of 7525 genes, of which 3034 genes had a 2-fold-change, being 533 up- and 2501 down-regulated genes, respectively. Thus, RNA-seq data analysis showed that an important set of these genes were associated with the jasmonic acid biosynthetic pathway including lypoxygenases (LOXs) and Allene oxide cyclases (AOCs). In addition, several transcription factor families involved in the response to biotic stress conditions (pathogen attacks or herbivore feeding), such as WRKY, JAZ, MYC, and LRR were also modified in response to Ln. However, this study also shows that Ln has the capacity to modulate the expression of genes involved in the response to abiotic stress conditions, particularly those mediated by ROS signaling. In this regard, we were able to identify new targets such as galactinol synthase 1 (GOLS1), methionine sulfoxide reductase (MSR) and alkenal reductase in ACSC. It is therefore possible to suggest that, in the absence of any oxidative stress, Ln is capable of modulating new sets of genes involved in the signaling mechanism mediated by additional abiotic stresses (salinity, UV and high light intensity) and especially in stresses mediated by ROS.

No MeSH data available.


Related in: MedlinePlus