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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 ten most common differentially expressed genes identified by “name” (comprising more than one accession number) in oysters exposed to 10 different types of environmental stressors.Numbers in brackets represent the number of times this gene name appeared as differentially expressed in all of the different stress treatments. These data do not include genes encoding ribosomal proteins.
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pone.0118839.g005: The ten most common differentially expressed genes identified by “name” (comprising more than one accession number) in oysters exposed to 10 different types of environmental stressors.Numbers in brackets represent the number of times this gene name appeared as differentially expressed in all of the different stress treatments. These data do not include genes encoding ribosomal proteins.

Mentions: Fig. 5 shows the 10 most common differentially expressed genes (excluding ribosomes) across all stress treatments identified by name rather than accession number. These “names” represented groups of genes that encoded either different polypeptides of the same protein (for instance NADH dehydrogenase subunits), functionally related homologues in the same gene family (for example HSP70s), or synonyms for the same protein (for instance NADH dehydrogenase and NADH oxidoreductase). This pooling meant that the same “name” could occur more than once in the same stress treatment. Together, the top ten “names” accounted for 31% of the 586 differentially expressed genes identified across the 10 stress treatments. NADH dehydrogenases were by far the most commonly identified differential transcripts. By themselves, they accounted for 7% of the differential transcriptome. Their transcript abundance was significantly affected by all stressors. Among the top 10 gene names, those associated with the mitochondrial electron transport chain (NADH dehydrogenases, cytochrome c’s and ATP synthases) represented 16% of the entire differential transcriptome, whilst cytoskeletal (actin and tubulin) and stress response (metallothioneins, GSTs, HSP70s, and the antioxidant enzyme SOD) genes each comprised 6% of all differential transcripts.


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 ten most common differentially expressed genes identified by “name” (comprising more than one accession number) in oysters exposed to 10 different types of environmental stressors.Numbers in brackets represent the number of times this gene name appeared as differentially expressed in all of the different stress treatments. These data do not include genes encoding ribosomal proteins.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0118839.g005: The ten most common differentially expressed genes identified by “name” (comprising more than one accession number) in oysters exposed to 10 different types of environmental stressors.Numbers in brackets represent the number of times this gene name appeared as differentially expressed in all of the different stress treatments. These data do not include genes encoding ribosomal proteins.
Mentions: Fig. 5 shows the 10 most common differentially expressed genes (excluding ribosomes) across all stress treatments identified by name rather than accession number. These “names” represented groups of genes that encoded either different polypeptides of the same protein (for instance NADH dehydrogenase subunits), functionally related homologues in the same gene family (for example HSP70s), or synonyms for the same protein (for instance NADH dehydrogenase and NADH oxidoreductase). This pooling meant that the same “name” could occur more than once in the same stress treatment. Together, the top ten “names” accounted for 31% of the 586 differentially expressed genes identified across the 10 stress treatments. NADH dehydrogenases were by far the most commonly identified differential transcripts. By themselves, they accounted for 7% of the differential transcriptome. Their transcript abundance was significantly affected by all stressors. Among the top 10 gene names, those associated with the mitochondrial electron transport chain (NADH dehydrogenases, cytochrome c’s and ATP synthases) represented 16% of the entire differential transcriptome, whilst cytoskeletal (actin and tubulin) and stress response (metallothioneins, GSTs, HSP70s, and the antioxidant enzyme SOD) genes each comprised 6% of all differential transcripts.

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