Limits...
RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

Lei X, Xiao Y, Xia W, Mason AS, Yang Y, Ma Z, Peng M - PLoS ONE (2014)

Bottom Line: Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide.CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice.Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs.

View Article: PubMed Central - PubMed

Affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, P. R. China.

ABSTRACT
Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated) samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors) of COG (Cluster of Orthologous Group) annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family) may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR). CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

Show MeSH

Related in: MedlinePlus

The expression profile of 15 unigenes putatively involved in the CBF-mediated signal transduction pathway at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment.Gene expression levels at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment are indicated with colored bars. The number within the color bar indicates the average value of the relative expression level and the standard deviation (average value ± standard deviation) at that time point.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4257668&req=5

pone-0114482-g004: The expression profile of 15 unigenes putatively involved in the CBF-mediated signal transduction pathway at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment.Gene expression levels at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment are indicated with colored bars. The number within the color bar indicates the average value of the relative expression level and the standard deviation (average value ± standard deviation) at that time point.

Mentions: In order to examine gene expression patterns involving the CBF-mediated pathway, quantitative real-time PCR (qRT-PCR) was used to detect expression changes in 14 unigenes (5 cbf orthologs, 2 ice1 orthologs, 3 siz1 orthologs, 2 zat10 orthologs, 1 hos1 ortholog, and 1 myb15 ortholog) at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment (Figure 4). At 0 h after cold treatment, all unigenes showed low expression levels except for Unigene615_ICE1 and Unigene6283_MYB15. It is possible that a large amount of MYB15 protein at this stage could hinder the expression of the cbf gene under warm conditions (27°C). Moreover, although Unigene615_ICE1 had a high expression level at this stage, the ICE1 protein cannot be sumoylated to avoid activation of the cbf gene due to low SIZ1 gene expression levels at this stage. At the following two time points (0.5 h and 1 h after cold treatment), all unigenes showed low expression levels. However, the expression levels of ICE1 (Unigene615_ICE1 (0.87±0.13) and Unigene5046-2_ ICE1 (0.75±0.25)) and SIZ1 (CL1094.Contig3_SIZ1 (1), Unigene2502-1_SIZ1 (0.75±0.25), and CL1094.Contig1_SIZ1 (0.9±0.1)) genes were sharply increased at 4 h after cold treatment. Obviously, the expression of ICE1 and SIZ1 can lead to the sumoylation of the ICE1 protein so as to activate CBF gene expression at this stage. The expression of CL1890.Contig1_CBF (0.98±0.02), CL4.Contig1_CBF (0.72±0.07) and CL83.Contig3_CBF (0.92±0.04) was intensively induced at this stage according to quantitative real-time PCR results. Meanwhile, Unigene6283_MYB15, a repressor of CBF gene expression, also showed increasing expression level at this stage, and may have reached highest expression level between 4 h and 8 h. The accumulation of CBF protein can activate the expression of the downstream ZAT10 genes. In fact, two ZAT10 genes (Unigene713-1_ZAT10 (0.94±0.06) and CL1971.Contig2-1_ZAT10 (1)) were intensively induced at this stage based on the quantitative real-time PCR results. Subsequently, the expression of almost all genes decreased at the following time point (8 h after cold treatment). However, at the last two time points (1 day and 7 days after cold treatment), the expression of ICE1 genes and SIZ1 genes had gradually increased, which resulted in high expression levels of CBF genes at 7 days after cold treatment. At this stage, high expression levels of the HOS1 gene ortholog (Unigene8210 (1)) were also detected, which would play a positive role in hindering the expression of the CBF gene by degrading the ICE1 protein. In brief, different to in Arabidopsis and rice, the expression of CBFs in Elaeis guineensis reaches a maximum level both at medium (4 h) and long (7 day) periods after cold treatment.


RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

Lei X, Xiao Y, Xia W, Mason AS, Yang Y, Ma Z, Peng M - PLoS ONE (2014)

The expression profile of 15 unigenes putatively involved in the CBF-mediated signal transduction pathway at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment.Gene expression levels at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment are indicated with colored bars. The number within the color bar indicates the average value of the relative expression level and the standard deviation (average value ± standard deviation) at that time point.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257668&req=5

pone-0114482-g004: The expression profile of 15 unigenes putatively involved in the CBF-mediated signal transduction pathway at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment.Gene expression levels at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment are indicated with colored bars. The number within the color bar indicates the average value of the relative expression level and the standard deviation (average value ± standard deviation) at that time point.
Mentions: In order to examine gene expression patterns involving the CBF-mediated pathway, quantitative real-time PCR (qRT-PCR) was used to detect expression changes in 14 unigenes (5 cbf orthologs, 2 ice1 orthologs, 3 siz1 orthologs, 2 zat10 orthologs, 1 hos1 ortholog, and 1 myb15 ortholog) at 0 h, 0.5 h, 1 h, 4 h, 8 h, 1 day and 7 days after cold treatment (Figure 4). At 0 h after cold treatment, all unigenes showed low expression levels except for Unigene615_ICE1 and Unigene6283_MYB15. It is possible that a large amount of MYB15 protein at this stage could hinder the expression of the cbf gene under warm conditions (27°C). Moreover, although Unigene615_ICE1 had a high expression level at this stage, the ICE1 protein cannot be sumoylated to avoid activation of the cbf gene due to low SIZ1 gene expression levels at this stage. At the following two time points (0.5 h and 1 h after cold treatment), all unigenes showed low expression levels. However, the expression levels of ICE1 (Unigene615_ICE1 (0.87±0.13) and Unigene5046-2_ ICE1 (0.75±0.25)) and SIZ1 (CL1094.Contig3_SIZ1 (1), Unigene2502-1_SIZ1 (0.75±0.25), and CL1094.Contig1_SIZ1 (0.9±0.1)) genes were sharply increased at 4 h after cold treatment. Obviously, the expression of ICE1 and SIZ1 can lead to the sumoylation of the ICE1 protein so as to activate CBF gene expression at this stage. The expression of CL1890.Contig1_CBF (0.98±0.02), CL4.Contig1_CBF (0.72±0.07) and CL83.Contig3_CBF (0.92±0.04) was intensively induced at this stage according to quantitative real-time PCR results. Meanwhile, Unigene6283_MYB15, a repressor of CBF gene expression, also showed increasing expression level at this stage, and may have reached highest expression level between 4 h and 8 h. The accumulation of CBF protein can activate the expression of the downstream ZAT10 genes. In fact, two ZAT10 genes (Unigene713-1_ZAT10 (0.94±0.06) and CL1971.Contig2-1_ZAT10 (1)) were intensively induced at this stage based on the quantitative real-time PCR results. Subsequently, the expression of almost all genes decreased at the following time point (8 h after cold treatment). However, at the last two time points (1 day and 7 days after cold treatment), the expression of ICE1 genes and SIZ1 genes had gradually increased, which resulted in high expression levels of CBF genes at 7 days after cold treatment. At this stage, high expression levels of the HOS1 gene ortholog (Unigene8210 (1)) were also detected, which would play a positive role in hindering the expression of the CBF gene by degrading the ICE1 protein. In brief, different to in Arabidopsis and rice, the expression of CBFs in Elaeis guineensis reaches a maximum level both at medium (4 h) and long (7 day) periods after cold treatment.

Bottom Line: Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide.CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice.Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs.

View Article: PubMed Central - PubMed

Affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, P. R. China.

ABSTRACT
Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated) samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors) of COG (Cluster of Orthologous Group) annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family) may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR). CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

Show MeSH
Related in: MedlinePlus