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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

Scatter plot, line plot and heat map for 8-fold-change genes using DNAStar software. (A) Scatter plot of total Ln-responsive genes. (B) Line plot of overexpressed genes. (C) Heat map for overexpressed genes. (D) Line plot of repressed genes. (E) Heat map for repressed genes. Distilled water and methanol-responsive genes were used to filter the results of Ln treatment. All graphs show 8-fold-change genes with 95% significant differential expression obtained by t-student test from whole Ln-responsive genes.
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Figure 1: Scatter plot, line plot and heat map for 8-fold-change genes using DNAStar software. (A) Scatter plot of total Ln-responsive genes. (B) Line plot of overexpressed genes. (C) Heat map for overexpressed genes. (D) Line plot of repressed genes. (E) Heat map for repressed genes. Distilled water and methanol-responsive genes were used to filter the results of Ln treatment. All graphs show 8-fold-change genes with 95% significant differential expression obtained by t-student test from whole Ln-responsive genes.

Mentions: The gene-expression profile of two ACSC groups was firstly compared, one treated with distilled water and the other with 1 mM Ln (control vs. Ln). Importantly, to eliminate genes that respond to methanol, this comparison was filtered using vehicle-responsive genes, with control vs. vehicle comparison eliminating genes with a 1.5 FC due to methanol, henceforth referred to as control. RNA-seq analysis showed that Ln caused significant changes (95% of matches, p < 0.05) in the gene-expression levels of 8947 ACSC genes, 7525 genes with annotations and 1422 genes coding for hypothetical proteins not considered for the rest of this study. From these 7525 genes, we selected 2FC up and down Ln-responsive genes showing the modulation of 3034 genes, from which 533 were up- (Supplemental Table 7) and 2501 were down-regulated (Supplemental Table 8). Due to this large number of genes, we only show the trend for genes differentially expressed with 8FC up and down (Figure 1). In this sense, Figure 1A shows the scatter plot of total genes whose expression changes significantly in response to Ln. Panels 1B and 1C represent the line plot and heat map of 8FC over-expressed genes and panels 1D and 1E indicate the line plot and heat map of 8FC repressed genes.


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)

Scatter plot, line plot and heat map for 8-fold-change genes using DNAStar software. (A) Scatter plot of total Ln-responsive genes. (B) Line plot of overexpressed genes. (C) Heat map for overexpressed genes. (D) Line plot of repressed genes. (E) Heat map for repressed genes. Distilled water and methanol-responsive genes were used to filter the results of Ln treatment. All graphs show 8-fold-change genes with 95% significant differential expression obtained by t-student test from whole Ln-responsive genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4362301&req=5

Figure 1: Scatter plot, line plot and heat map for 8-fold-change genes using DNAStar software. (A) Scatter plot of total Ln-responsive genes. (B) Line plot of overexpressed genes. (C) Heat map for overexpressed genes. (D) Line plot of repressed genes. (E) Heat map for repressed genes. Distilled water and methanol-responsive genes were used to filter the results of Ln treatment. All graphs show 8-fold-change genes with 95% significant differential expression obtained by t-student test from whole Ln-responsive genes.
Mentions: The gene-expression profile of two ACSC groups was firstly compared, one treated with distilled water and the other with 1 mM Ln (control vs. Ln). Importantly, to eliminate genes that respond to methanol, this comparison was filtered using vehicle-responsive genes, with control vs. vehicle comparison eliminating genes with a 1.5 FC due to methanol, henceforth referred to as control. RNA-seq analysis showed that Ln caused significant changes (95% of matches, p < 0.05) in the gene-expression levels of 8947 ACSC genes, 7525 genes with annotations and 1422 genes coding for hypothetical proteins not considered for the rest of this study. From these 7525 genes, we selected 2FC up and down Ln-responsive genes showing the modulation of 3034 genes, from which 533 were up- (Supplemental Table 7) and 2501 were down-regulated (Supplemental Table 8). Due to this large number of genes, we only show the trend for genes differentially expressed with 8FC up and down (Figure 1). In this sense, Figure 1A shows the scatter plot of total genes whose expression changes significantly in response to Ln. Panels 1B and 1C represent the line plot and heat map of 8FC over-expressed genes and panels 1D and 1E indicate the line plot and heat map of 8FC repressed genes.

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