Dataset Information

The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis.

ABSTRACT: BACKGROUND: The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway identification and prediction of protein functions. Eriocheir sinensis is a highly-commercial aquaculture species with an unclear proteome background which hinders the construction and development of PIN for E. sinensis. However, in recent years, the development of next-generation deep-sequencing techniques makes it possible to get high throughput data of E. sinensis tanscriptome and subsequently obtain a systematic overview of the protein-protein interaction system. RESULTS: In this work we sequenced the transcriptional RNA of eyestalk, Y-organ and hepatopancreas in E. sinensis and generated a PIN of E. sinensis which included 3,223 proteins and 35,787 interactions. Each protein-protein interaction in the network was scored according to the homology and genetic relationship. The signaling sub-network, representing the signal transduction pathways in E. sinensis, was extracted from the global network, which depicted a global view of the signaling systems in E. sinensis. Seven basic signal transduction pathways were identified in E. sinensis. By investigating the evolution paths of the seven pathways, we found that these pathways got mature in different evolutionary stages. Moreover, the functions of unclassified proteins and unigenes in the PIN of E. sinensis were predicted. Specifically, the functions of 549 unclassified proteins related to 864 unclassified unigenes were assigned, which respectively covered 76% and 73% of all the unclassified proteins and unigenes in the network. CONCLUSIONS: The PIN generated in this work is the first large-scale PIN of aquatic crustacean, thereby providing a paradigmatic blueprint of the aquatic crustacean interactome. Signaling sub-network extracted from the global PIN depicts the interaction of different signaling proteins and the evolutionary paths of the identified signal transduction pathways. Furthermore, the function assignment of unclassified proteins based on the PIN offers a new reference in protein function exploration. More importantly, the construction of the E. sinensis PIN provides necessary experience for the exploration of PINs in other aquatic crustacean species.

SUBMITTER: Hao T

PROVIDER: S-EPMC3986667 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis.

Hao Tong T Zeng Zheng Z Wang Bin B Zhang Yichen Y Liu Yichen Y Geng Xuyun X Sun Jinsheng J

BMC systems biology 20140327

<h4>Background</h4>The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway identification and prediction of protein functions. Eriocheir sinensis is a highly-commercial aquaculture species with an unclear proteome background which hinders the construction and development of PIN for E. sinensis. However, in recent years, the development of next-g ...[more]

PMID: 24674293

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Project description:BackgroundTo understand the regulation mechanism of eyestalk ablation on the activities of hepatopancreas, Illumina RNA-Seq and digital gene expression (DGE) analyses were performed to investigate the transcriptome of the eyestalk, Y-organ, and hepatopancreas of E. sinensis and to identify the genes associated with the hepatopancreas metabolism that are differentially expressed under eyestalk ablation conditions.ResultsA total of 58,582 unigenes were constructed from 157,168 contigs with SOAPdenovo. A BlastX search against the NCBI Nr database identified 21,678 unigenes with an E-value higher than 10⁻⁵. Using the BLAST2Go and BlastAll software programs, 6,883 unigenes (11.75% of the total) were annotated to the Gene Ontology (GO) database, 7,386 (12.6%) unigenes were classified into 25 Clusters of Orthologous Groups of Proteins (COGs), 16,200 (27.7%) unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 1,846 unigenes were matched to "metabolism pathways". The DGE analysis revealed that 1,416 unigenes were significantly differentially expressed in the hepatopancreas, of which 890 unigenes were up-regulated and 526 unigenes were down-regulated. Of the differentially expressed genes, 382 unigenes were annotated and 63 were classified into metabolism pathways. The results of the real-time polymerase chain reaction (PCR) analysis of four unigenes related to carbohydrate metabolism were consistent with those obtained from the DGE analysis, which demonstrates that the sequencing data were satisfactory for further gene expression analyses.ConclusionThis paper reported the transcriptom of the eyestalk, Y-organ, and hepatopancreas from E. sinensis. DGE analysis provided the different expressed genes of the metabolism processes in hepatopancreas that are affected by eyestalk ablation. These findings will facilitate further investigations on the mechanisms of the metabolism of organic substances during development and reproduction in crustaceans.

Project description:Environmental hypoxia represents a major physiological challenge for Eriocheir sinensis and Palaemonetes sinensis and is a severe problem in aquaculture. Therefore, understanding the metabolic response mechanisms of E. sinensis and P. sinensis, which are economically important species, to environmental hypoxia and reoxygenation is essential. However, little is known about the intrinsic mechanisms by which E. sinensis and P. sinensis cope with environmental hypoxia at the metabolic level. Hypoxia-reoxygenation represents an important physiological challenge for their culture. In this study, respiratory metabolism and respiratory metabolic enzymes of E. sinensis and P. sinensis were evaluated after different hypoxia and reoxygenation times. The results showed that environmental hypoxia had a dramatic influence on the respiratory metabolism and activities of related enzymes. The oxygen consumption rates (OCR) significantly increased as hypoxia time increased, while the ammonia excretion rate (AER) was significantly lower than that in the control group after 8 h hypoxia. The oxygen to nitrogen ratio (O:N) in the control group was <16, indicating that all the energy substrates were proteins. After environmental hypoxia, the O:N significantly increased, and the energy substrate shifted from protein to a protein-lipid mixture. The OCR, AER, and O:N did not restore to initial levels after 2 h or 12 h reoxygenation and was still the same as after 8 h hypoxia. As environmental hypoxia time increased, succinate dehydrogenase (SDH) gradually decreased and lactate dehydrogenase (LDH) gradually increased. Both SDH and LDH were gradually restored to normal levels after reoxygenation. Therefore, environmental hypoxia should be avoided as much as possible during aquaculture breeding of E. sinensis and P. sinensis. Further, since OCR will significantly increase after a short period of reoxygenation, secondary environmental hypoxia due to rapid consumption of oxygen should also be avoided in aquaculture.

Dataset Information

The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis.

Publications

The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis.

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