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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).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.

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

Functional classification of Ln-responsive genes in ACSC. Genes were classified by functional categories under the following gene ontology terms: cellular component (A,D), molecular function (B,E), biological process (C,F), up-regulated genes (A–C) and down-regulated genes (D–F). The number of genes assigned to each functional category is expressed as a percentage (%).
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Figure 2: Functional classification of Ln-responsive genes in ACSC. Genes were classified by functional categories under the following gene ontology terms: cellular component (A,D), molecular function (B,E), biological process (C,F), up-regulated genes (A–C) and down-regulated genes (D–F). The number of genes assigned to each functional category is expressed as a percentage (%).

Mentions: Functional classification of 2FC-Ln-induced genes shows that their products were mostly located in the nucleus, chloroplast and plasma membrane (Figure 2A). Furthermore, they were mostly characterized by nucleotide-, protein- and DNA/RNA-binding, transferase and hydrolase activity (Figure 2B). They were also predicted to be involved in the response to stress, biotic or abiotic stimuli and protein-metabolism processes (Figure 2C). On the other hand, the most abundant categories of 2FC-Ln-repressed genes in ACSC were also located in the nucleus, chloroplast, plasma membrane and mitochondria (Figure 2D). These genes showed hydrolase-, transferase-, nucleotide-, and protein-binding activity (Figure 2E) and were associated with the protein metabolism, developmental processes and stress responses (Figure 2F).


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)

Functional classification of Ln-responsive genes in ACSC. Genes were classified by functional categories under the following gene ontology terms: cellular component (A,D), molecular function (B,E), biological process (C,F), up-regulated genes (A–C) and down-regulated genes (D–F). The number of genes assigned to each functional category is expressed as a percentage (%).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Functional classification of Ln-responsive genes in ACSC. Genes were classified by functional categories under the following gene ontology terms: cellular component (A,D), molecular function (B,E), biological process (C,F), up-regulated genes (A–C) and down-regulated genes (D–F). The number of genes assigned to each functional category is expressed as a percentage (%).
Mentions: Functional classification of 2FC-Ln-induced genes shows that their products were mostly located in the nucleus, chloroplast and plasma membrane (Figure 2A). Furthermore, they were mostly characterized by nucleotide-, protein- and DNA/RNA-binding, transferase and hydrolase activity (Figure 2B). They were also predicted to be involved in the response to stress, biotic or abiotic stimuli and protein-metabolism processes (Figure 2C). On the other hand, the most abundant categories of 2FC-Ln-repressed genes in ACSC were also located in the nucleus, chloroplast, plasma membrane and mitochondria (Figure 2D). These genes showed hydrolase-, transferase-, nucleotide-, and protein-binding activity (Figure 2E) and were associated with the protein metabolism, developmental processes and stress responses (Figure 2F).

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).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.

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