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Transcriptome Profiling and Molecular Pathway Analysis of Genes in Association with Salinity Adaptation in Nile Tilapia Oreochromis niloticus.

Xu Z, Gan L, Li T, Xu C, Chen K, Wang X, Qin JG, Chen L, Li E - PLoS ONE (2015)

Bottom Line: In the constant change category (1), steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were significantly affected by salinity indicating the pivotal roles of sterol-related pathways in response to salinity stress.In the change-then-stable category (2), ribosomes, oxidative phosphorylation, signaling pathways for peroxisome proliferator activated receptors, and fat digestion and absorption changed significantly with increasing salinity, showing sensitivity to salinity variation in the environment and a responding threshold to salinity change.In the stable-then-change category (3), protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis-keratan sulfate were the significantly changed pathways, suggesting that these pathways were less sensitive to salinity variation.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, 500 Dongchuan Rd., Shanghai 200241, China.

ABSTRACT
Nile tilapia Oreochromis niloticus is a freshwater fish but can tolerate a wide range of salinities. The mechanism of salinity adaptation at the molecular level was studied using RNA-Seq to explore the molecular pathways in fish exposed to 0, 8, or 16 (practical salinity unit, psu). Based on the change of gene expressions, the differential genes unions from freshwater to saline water were classified into three categories. In the constant change category (1), steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were significantly affected by salinity indicating the pivotal roles of sterol-related pathways in response to salinity stress. In the change-then-stable category (2), ribosomes, oxidative phosphorylation, signaling pathways for peroxisome proliferator activated receptors, and fat digestion and absorption changed significantly with increasing salinity, showing sensitivity to salinity variation in the environment and a responding threshold to salinity change. In the stable-then-change category (3), protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis-keratan sulfate were the significantly changed pathways, suggesting that these pathways were less sensitive to salinity variation. This study reveals fundamental mechanism of the molecular response to salinity adaptation in O. niloticus, and provides a general guidance to understand saline acclimation in O. niloticus.

No MeSH data available.


Related in: MedlinePlus

Gene act subnetworks in the 8 vs 16 psu categories.(A): cytoskeleton; (B): PI3K signaling pathways; (C): endoplasmic reticulum activity; (D): lipid and glycerophospholipid metabolism; (E): carbohydrates and pyruvate metabolism; and (F): steroid hormone metabolism and oxidative stress. The red balls represent up-regulated genes, while the green balls represent down-regulated genes. The connections of genes were generated from the data analysis consist of GO analysis and KEGG pathway. The solid lines represent the relationships between the genes. The dashed lines represent the genes that have an indirect effect. The arrow represents activation. The flathead represents suppression. ‘a’ represents activation; ‘b’ represents binding; and ‘c’ represents compound. The abbreviation ‘dep’ represents phosphorylation; ‘dis’ represents dissociation; and ‘inh’ represents inhibition.
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pone.0136506.g004: Gene act subnetworks in the 8 vs 16 psu categories.(A): cytoskeleton; (B): PI3K signaling pathways; (C): endoplasmic reticulum activity; (D): lipid and glycerophospholipid metabolism; (E): carbohydrates and pyruvate metabolism; and (F): steroid hormone metabolism and oxidative stress. The red balls represent up-regulated genes, while the green balls represent down-regulated genes. The connections of genes were generated from the data analysis consist of GO analysis and KEGG pathway. The solid lines represent the relationships between the genes. The dashed lines represent the genes that have an indirect effect. The arrow represents activation. The flathead represents suppression. ‘a’ represents activation; ‘b’ represents binding; and ‘c’ represents compound. The abbreviation ‘dep’ represents phosphorylation; ‘dis’ represents dissociation; and ‘inh’ represents inhibition.

Mentions: A total of 101 differentially expressed genes composed the stable-then-change category, with 20 down-regulated genes and 81 up-regulated genes. The chief sub-networks which contained in this category were the signaling pathway of PI3K and p53, steroid hormone synthesis and oxidative stress, fat synthesis and glycerophospholipid metabolism, cytoskeleton, endoplasmic reticulum activity, sugar utilization and pyruvate metabolism (Fig 4A–4F).


Transcriptome Profiling and Molecular Pathway Analysis of Genes in Association with Salinity Adaptation in Nile Tilapia Oreochromis niloticus.

Xu Z, Gan L, Li T, Xu C, Chen K, Wang X, Qin JG, Chen L, Li E - PLoS ONE (2015)

Gene act subnetworks in the 8 vs 16 psu categories.(A): cytoskeleton; (B): PI3K signaling pathways; (C): endoplasmic reticulum activity; (D): lipid and glycerophospholipid metabolism; (E): carbohydrates and pyruvate metabolism; and (F): steroid hormone metabolism and oxidative stress. The red balls represent up-regulated genes, while the green balls represent down-regulated genes. The connections of genes were generated from the data analysis consist of GO analysis and KEGG pathway. The solid lines represent the relationships between the genes. The dashed lines represent the genes that have an indirect effect. The arrow represents activation. The flathead represents suppression. ‘a’ represents activation; ‘b’ represents binding; and ‘c’ represents compound. The abbreviation ‘dep’ represents phosphorylation; ‘dis’ represents dissociation; and ‘inh’ represents inhibition.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4548949&req=5

pone.0136506.g004: Gene act subnetworks in the 8 vs 16 psu categories.(A): cytoskeleton; (B): PI3K signaling pathways; (C): endoplasmic reticulum activity; (D): lipid and glycerophospholipid metabolism; (E): carbohydrates and pyruvate metabolism; and (F): steroid hormone metabolism and oxidative stress. The red balls represent up-regulated genes, while the green balls represent down-regulated genes. The connections of genes were generated from the data analysis consist of GO analysis and KEGG pathway. The solid lines represent the relationships between the genes. The dashed lines represent the genes that have an indirect effect. The arrow represents activation. The flathead represents suppression. ‘a’ represents activation; ‘b’ represents binding; and ‘c’ represents compound. The abbreviation ‘dep’ represents phosphorylation; ‘dis’ represents dissociation; and ‘inh’ represents inhibition.
Mentions: A total of 101 differentially expressed genes composed the stable-then-change category, with 20 down-regulated genes and 81 up-regulated genes. The chief sub-networks which contained in this category were the signaling pathway of PI3K and p53, steroid hormone synthesis and oxidative stress, fat synthesis and glycerophospholipid metabolism, cytoskeleton, endoplasmic reticulum activity, sugar utilization and pyruvate metabolism (Fig 4A–4F).

Bottom Line: In the constant change category (1), steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were significantly affected by salinity indicating the pivotal roles of sterol-related pathways in response to salinity stress.In the change-then-stable category (2), ribosomes, oxidative phosphorylation, signaling pathways for peroxisome proliferator activated receptors, and fat digestion and absorption changed significantly with increasing salinity, showing sensitivity to salinity variation in the environment and a responding threshold to salinity change.In the stable-then-change category (3), protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis-keratan sulfate were the significantly changed pathways, suggesting that these pathways were less sensitive to salinity variation.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, 500 Dongchuan Rd., Shanghai 200241, China.

ABSTRACT
Nile tilapia Oreochromis niloticus is a freshwater fish but can tolerate a wide range of salinities. The mechanism of salinity adaptation at the molecular level was studied using RNA-Seq to explore the molecular pathways in fish exposed to 0, 8, or 16 (practical salinity unit, psu). Based on the change of gene expressions, the differential genes unions from freshwater to saline water were classified into three categories. In the constant change category (1), steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were significantly affected by salinity indicating the pivotal roles of sterol-related pathways in response to salinity stress. In the change-then-stable category (2), ribosomes, oxidative phosphorylation, signaling pathways for peroxisome proliferator activated receptors, and fat digestion and absorption changed significantly with increasing salinity, showing sensitivity to salinity variation in the environment and a responding threshold to salinity change. In the stable-then-change category (3), protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis-keratan sulfate were the significantly changed pathways, suggesting that these pathways were less sensitive to salinity variation. This study reveals fundamental mechanism of the molecular response to salinity adaptation in O. niloticus, and provides a general guidance to understand saline acclimation in O. niloticus.

No MeSH data available.


Related in: MedlinePlus