Limits...
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

GO-term-enriched graph of biological processes of Ln-responsive genes. (A) Up-regulated genes. Node filter was set at FDR < 1e-5. (B) Down-regulated genes. Node filter was set at FDR < 0.001. Bars for up- and down-regulated genes are labeled with their corresponding P-values in Fisher's exact test against expressed control ACSC genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4362301&req=5

Figure 3: GO-term-enriched graph of biological processes of Ln-responsive genes. (A) Up-regulated genes. Node filter was set at FDR < 1e-5. (B) Down-regulated genes. Node filter was set at FDR < 0.001. Bars for up- and down-regulated genes are labeled with their corresponding P-values in Fisher's exact test against expressed control ACSC genes.

Mentions: On the basis of these results, we decided to carry out a more detailed analysis of biological processes involved in Ln treatments. To do this, the GO terms obtained by the analysis were loaded in Blast2GO suite V.2.7.2 to statistically analyze GO-term enrichment. The unchecked two-tail box was used to analyze only positive enrichment. The test was carried out using a filter cut-off value of FDR < 1e−5 for up-regulated genes and an FDR < 0.001 for down-regulated genes. The results are shown in Figure 3 as the percentage of sequences annotated for each biological process GO term for both ACSC and Ln-responsive genes. Bars are labeled with their corresponding P-values in Fisher's exact test. Ln treatment of ACSC produced a significant response in the GO terms of up-regulated genes (Figure 3A). The GO terms of these genes were closely associated with biotic stress-related processes such as responses to chitin and wounding and were closely connected with biosynthesis and the JA signaling pathway. GO enrichment analysis also highlighted the over-representation of processes associated with other important phytohormones such as abscisic acid, auxin, ethylene, salicylic acid and brassinosteroids. With regard to abiotic stress, Ln treatment affected hyperosmotic salinity responses and heat acclimation, specifically in responses to oxidative stress through the response to hydrogen peroxide. With regard to the GO terms of down-regulated genes (Figure 3B), we found that the level of over-representation of biological processes was lower than in up-regulated genes. These processes were mostly associated with the synthesis of cell wall depicted by a (1-> 3)-beta-D-glucan biosynthetic process and callose deposition in cell wall together with the transport of potassium, oligopeptides and nitrate. Finally, mitotic- and meiotic-related processes such as sister chromatid cohesion, chromosome organization regulation, reciprocal meiotic recombination and meiotic chromosome segregation were observed.


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)

GO-term-enriched graph of biological processes of Ln-responsive genes. (A) Up-regulated genes. Node filter was set at FDR < 1e-5. (B) Down-regulated genes. Node filter was set at FDR < 0.001. Bars for up- and down-regulated genes are labeled with their corresponding P-values in Fisher's exact test against expressed control ACSC genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: GO-term-enriched graph of biological processes of Ln-responsive genes. (A) Up-regulated genes. Node filter was set at FDR < 1e-5. (B) Down-regulated genes. Node filter was set at FDR < 0.001. Bars for up- and down-regulated genes are labeled with their corresponding P-values in Fisher's exact test against expressed control ACSC genes.
Mentions: On the basis of these results, we decided to carry out a more detailed analysis of biological processes involved in Ln treatments. To do this, the GO terms obtained by the analysis were loaded in Blast2GO suite V.2.7.2 to statistically analyze GO-term enrichment. The unchecked two-tail box was used to analyze only positive enrichment. The test was carried out using a filter cut-off value of FDR < 1e−5 for up-regulated genes and an FDR < 0.001 for down-regulated genes. The results are shown in Figure 3 as the percentage of sequences annotated for each biological process GO term for both ACSC and Ln-responsive genes. Bars are labeled with their corresponding P-values in Fisher's exact test. Ln treatment of ACSC produced a significant response in the GO terms of up-regulated genes (Figure 3A). The GO terms of these genes were closely associated with biotic stress-related processes such as responses to chitin and wounding and were closely connected with biosynthesis and the JA signaling pathway. GO enrichment analysis also highlighted the over-representation of processes associated with other important phytohormones such as abscisic acid, auxin, ethylene, salicylic acid and brassinosteroids. With regard to abiotic stress, Ln treatment affected hyperosmotic salinity responses and heat acclimation, specifically in responses to oxidative stress through the response to hydrogen peroxide. With regard to the GO terms of down-regulated genes (Figure 3B), we found that the level of over-representation of biological processes was lower than in up-regulated genes. These processes were mostly associated with the synthesis of cell wall depicted by a (1-> 3)-beta-D-glucan biosynthetic process and callose deposition in cell wall together with the transport of potassium, oligopeptides and nitrate. Finally, mitotic- and meiotic-related processes such as sister chromatid cohesion, chromosome organization regulation, reciprocal meiotic recombination and meiotic chromosome segregation were observed.

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