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Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

Nah G, Lee M, Kim DS, Rayburn AL, Voigt T, Lee DK - PLoS ONE (2016)

Bottom Line: The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins.Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression.Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea.

ABSTRACT
Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

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Comparison of DEGs belonging to acute and follow-up responses under freezing stress with the components of known abiotic signal transduction.
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pone.0152294.g005: Comparison of DEGs belonging to acute and follow-up responses under freezing stress with the components of known abiotic signal transduction.

Mentions: Based on GO categories of DEGs in six groups (Fig 2), several of the biological process groups (response to stress, signal transduction, transcription, metabolic process, and DNA and RNA metabolism) were extensively analyzed (S4 Table). The expression patterns of the majority of these genes featured (1) acute response (up-regulated within 5 min; Group I and II), and (2) follow-up response (up-regulated from 5 min to 30 min; Group III and V). The annotation data showed that genes belonging to the these groups were very diverse and included those that encode abiotic stress- responsive TFs, receptor kinases, stress proteins, ubiquitin-mediated proteases, hormone-responsive proteins, metabolism-related proteins, and chromatin modification-related proteins. Interestingly, the expression dynamics of these groups based on time-course reflected a logical overview of freezing signal transduction cascade: initiation of lipid metabolic and osmotic responsive genes, calmodulin, MYB TF (which affects ABA-signaling), WRKY (which affects AFP-expression), β-glucosidase at initial stage (0–5 min), followed by heat-shock protein (HSP), proteasome-related, PR protein, and cell/DNA damage repair gene expression at the following stage (5–30 min). We also detected chromatin-modification genes and circadian clock genes with dynamic expression pattern. Based on our result, we displayed a tentative gene expression order and reported genes involved in early response to freezing exposure (Fig 5).


Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

Nah G, Lee M, Kim DS, Rayburn AL, Voigt T, Lee DK - PLoS ONE (2016)

Comparison of DEGs belonging to acute and follow-up responses under freezing stress with the components of known abiotic signal transduction.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4816275&req=5

pone.0152294.g005: Comparison of DEGs belonging to acute and follow-up responses under freezing stress with the components of known abiotic signal transduction.
Mentions: Based on GO categories of DEGs in six groups (Fig 2), several of the biological process groups (response to stress, signal transduction, transcription, metabolic process, and DNA and RNA metabolism) were extensively analyzed (S4 Table). The expression patterns of the majority of these genes featured (1) acute response (up-regulated within 5 min; Group I and II), and (2) follow-up response (up-regulated from 5 min to 30 min; Group III and V). The annotation data showed that genes belonging to the these groups were very diverse and included those that encode abiotic stress- responsive TFs, receptor kinases, stress proteins, ubiquitin-mediated proteases, hormone-responsive proteins, metabolism-related proteins, and chromatin modification-related proteins. Interestingly, the expression dynamics of these groups based on time-course reflected a logical overview of freezing signal transduction cascade: initiation of lipid metabolic and osmotic responsive genes, calmodulin, MYB TF (which affects ABA-signaling), WRKY (which affects AFP-expression), β-glucosidase at initial stage (0–5 min), followed by heat-shock protein (HSP), proteasome-related, PR protein, and cell/DNA damage repair gene expression at the following stage (5–30 min). We also detected chromatin-modification genes and circadian clock genes with dynamic expression pattern. Based on our result, we displayed a tentative gene expression order and reported genes involved in early response to freezing exposure (Fig 5).

Bottom Line: The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins.Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression.Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 599 Gwanangno, Gwanakgu, Seoul 08826, Republic of Korea.

ABSTRACT
Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

Show MeSH