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Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters.

Anderson K, Taylor DA, Thompson EL, Melwani AR, Nair SV, Raftos DA - PLoS ONE (2015)

Bottom Line: To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters.We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress.In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

View Article: PubMed Central - PubMed

Affiliation: Sydney Institute of Marine Science, Chowder Bay, NSW, Australia; Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia.

ABSTRACT
Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

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The number of differentially expressed genes from all environmental treatments that fell into discrete intracellular process categories.
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pone.0118839.g002: The number of differentially expressed genes from all environmental treatments that fell into discrete intracellular process categories.

Mentions: Genes associated with metabolism were the most frequently identified (Fig. 2; 28%). These included genes involved in the mitochondiral electron transport chain (10%) and in glycolysis and the tricarboxylic acid (TCA/Krebs) cycle (2%). Genes associated with translation and post translational processing were the next most abundant category, comprising 26% of the differential transcriptome. Most of these genes encoded ribosomal proteins or rRNA (18%). Stress response genes, including molecular chaperones (2%) and enzymes involved in antioxidant responses (including superoxide dismutase, SOD, and peroxiredoxin, 2%), accounted for 11% of differential transcripts. Communication, the cytoskeleton, transcription, the cell cycle and protein regulation each represented approximately 10% of the differential transcriptome. Genes involved in immune responses and membrane transport each accounted for approximately 7% of differentially expressed transcripts. Nucleic acid regulation and the extracellular matrix were the least represented functional catgories (3% or less of the differential transcriptome). The most frequently identified genes in each functional group are shown in Table 4.


Meta-analysis of studies using suppression subtractive hybridization and microarrays to investigate the effects of environmental stress on gene transcription in oysters.

Anderson K, Taylor DA, Thompson EL, Melwani AR, Nair SV, Raftos DA - PLoS ONE (2015)

The number of differentially expressed genes from all environmental treatments that fell into discrete intracellular process categories.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358831&req=5

pone.0118839.g002: The number of differentially expressed genes from all environmental treatments that fell into discrete intracellular process categories.
Mentions: Genes associated with metabolism were the most frequently identified (Fig. 2; 28%). These included genes involved in the mitochondiral electron transport chain (10%) and in glycolysis and the tricarboxylic acid (TCA/Krebs) cycle (2%). Genes associated with translation and post translational processing were the next most abundant category, comprising 26% of the differential transcriptome. Most of these genes encoded ribosomal proteins or rRNA (18%). Stress response genes, including molecular chaperones (2%) and enzymes involved in antioxidant responses (including superoxide dismutase, SOD, and peroxiredoxin, 2%), accounted for 11% of differential transcripts. Communication, the cytoskeleton, transcription, the cell cycle and protein regulation each represented approximately 10% of the differential transcriptome. Genes involved in immune responses and membrane transport each accounted for approximately 7% of differentially expressed transcripts. Nucleic acid regulation and the extracellular matrix were the least represented functional catgories (3% or less of the differential transcriptome). The most frequently identified genes in each functional group are shown in Table 4.

Bottom Line: To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters.We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress.In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

View Article: PubMed Central - PubMed

Affiliation: Sydney Institute of Marine Science, Chowder Bay, NSW, Australia; Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia.

ABSTRACT
Many microarray and suppression subtractive hybridization (SSH) studies have analyzed the effects of environmental stress on gene transcription in marine species. However, there have been no unifying analyses of these data to identify common stress response pathways. To address this shortfall, we conducted a meta-analysis of 14 studies that investigated the effects of different environmental stressors on gene expression in oysters. The stressors tested included chemical contamination, hypoxia and infection, as well as extremes of temperature, pH and turbidity. We found that the expression of over 400 genes in a range of oyster species changed significantly after exposure to environmental stress. A repeating pattern was evident in these transcriptional responses, regardless of the type of stress applied. Many of the genes that responded to environmental stress encoded proteins involved in translation and protein processing (including molecular chaperones), the mitochondrial electron transport chain, anti-oxidant activity and the cytoskeleton. In light of these findings, we put forward a consensus model of sub-cellular stress responses in oysters.

Show MeSH
Related in: MedlinePlus