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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: Based on the change of gene expressions, the differential genes unions from freshwater to saline water were classified into three categories.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.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.

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 0 vs 8 psu categories.(A): glucose utilization; (B): nucleotide metabolism; (C): protein and amino acid metabolism; (D): cytoskeleton; (E): oxidative stress; (F): PI3K signaling pathways; (G): lipid and glycerophospholipid metabolism. The red ball represents the up-regulated genes, while the green ball represents the down-regulated genes. The connections of genes were generated from the data analysis consisting of GO analysis and KEGG pathway. The solid lines represent the relationships between 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.g003: Gene act subnetworks in the 0 vs 8 psu categories.(A): glucose utilization; (B): nucleotide metabolism; (C): protein and amino acid metabolism; (D): cytoskeleton; (E): oxidative stress; (F): PI3K signaling pathways; (G): lipid and glycerophospholipid metabolism. The red ball represents the up-regulated genes, while the green ball represents the down-regulated genes. The connections of genes were generated from the data analysis consisting of GO analysis and KEGG pathway. The solid lines represent the relationships between 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: The gene-act network profile of the change-then-stable category was composed of 113 differentially expressed genes with 36 up-regulated genes and 77 down-regulated genes. The major subnetworks contained lipid and glycerophospholipid metabolism, glucose utilization, protein and amino acid metabolism, PI3K signaling pathways, nucleotide metabolism, oxidative stress and cytoskeleton (Fig 3A–3G).


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 0 vs 8 psu categories.(A): glucose utilization; (B): nucleotide metabolism; (C): protein and amino acid metabolism; (D): cytoskeleton; (E): oxidative stress; (F): PI3K signaling pathways; (G): lipid and glycerophospholipid metabolism. The red ball represents the up-regulated genes, while the green ball represents the down-regulated genes. The connections of genes were generated from the data analysis consisting of GO analysis and KEGG pathway. The solid lines represent the relationships between 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.g003: Gene act subnetworks in the 0 vs 8 psu categories.(A): glucose utilization; (B): nucleotide metabolism; (C): protein and amino acid metabolism; (D): cytoskeleton; (E): oxidative stress; (F): PI3K signaling pathways; (G): lipid and glycerophospholipid metabolism. The red ball represents the up-regulated genes, while the green ball represents the down-regulated genes. The connections of genes were generated from the data analysis consisting of GO analysis and KEGG pathway. The solid lines represent the relationships between 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: The gene-act network profile of the change-then-stable category was composed of 113 differentially expressed genes with 36 up-regulated genes and 77 down-regulated genes. The major subnetworks contained lipid and glycerophospholipid metabolism, glucose utilization, protein and amino acid metabolism, PI3K signaling pathways, nucleotide metabolism, oxidative stress and cytoskeleton (Fig 3A–3G).

Bottom Line: Based on the change of gene expressions, the differential genes unions from freshwater to saline water were classified into three categories.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.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.

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