RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses

Shi, Minjun; Huang, Rong; Du, Fukuan; Pei, Yongyan; Liao, Lanjie; Zhang, Zhu; Wang, Yaping

doi:10.1016/j.molimm.2014.05.004

Cited by 67 publications

(26 citation statements)

References 66 publications

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“…This was a similar amount as identified in the same tissue 48 h after a reovirus infection42 and less than the amount found in both spleen and kidney tissues in a study aimed to identify miRNA targets using A. hydrophila -susceptible and/or resistant grass carp36. It is difficult to determine a precise number of inflammation-related genes among the 549 DEGs, since certain genes (such as IL-8) may participate in multiple KEGG pathways.…”

Section: Discussionmentioning

confidence: 64%

A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila

Song

Sun

et al. 2017

Sci Rep

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Inflammation is a protective response that is implicated in bacterial enteritis and other fish diseases.The inflammatory mechanisms behind Aeromonas hydrophila infections in fish remain poorly understood. In this study, we performed a de novo grass carp transcriptome assembly using Illumina's Solexa sequencing technique. On this basis we carried out a comparative analysis of intestinal transcriptomes from A. hydrophila-challenged and physiological saline solution (PSS/mock) -challenged fish, and 315 genes were up-regulated and 234 were down-regulated in the intestines infected with A. hydrophila. The GO enrichment analysis indicated that the differentially expressed genes were enriched to 12, 4, and 8 GO terms in biological process, molecular function, and cellular component, respectively. A KEGG analysis showed that 549 DEGs were involved in 165 pathways. Moreover, 15 DEGs were selected for quantitative real-time PCR analysis to validate the RNA-seq data. The results confirmed the consistency of the expression levels between RNA-seq and qPCR data. In addition, a time-course analysis of the mRNA expression of 12 inflammatory genes further demonstrated that the intestinal inflammatory responses to A. hydrophila infection simultaneously modulated gene expression variations. The present study provides intestine-specific transcriptome data, allowing us to unravel the mechanisms of intestinal inflammation triggered by bacterial pathogens.The grass carp (Ctenopharyngodon idella) is an intensively cultured and economically important herbivorous fish species in China. In grass carp aquaculture, the fish are often infected by bacterial, viral and parasitic pathogens. Aeromonas hydrophila, a Gram-negative aquatic bacterium, is regarded as the major bacterial pathogen causing intestinal inflammation in animal taxa, including farmed fish 1-4 . A. hydrophila-induced enteritis is probably the most widespread disease in grass carp, especially under intensive rearing conditions, which results in huge economic losses annually due to reduced growth and high mortality rates [5][6][7] . The molecular mechanisms and pathways that regulate bacterial-induced inflammatory processes in humans and other mammalian species are relatively well understood [8][9][10] . In fish, several inflammation-related genes, including chemokine (C-X-C motif) ligand 2 (CXCL2) 11 , CXCL10 12 , cyclooxygenase-2 (COX-2) 13 , interleukin-1β (IL-1β ) 4,13,14 , IL-8 15,16 , IL-17A/F2 17 , and tumor necrosis factor (TNF)-α 13,18 , have already been identified and characterized with regard to their involvement in inflammatory responses to bacterial infections. However, the definitive mechanisms responsible for the bacterial-induced intestinal inflammation in fish are still unclear. Therefore, further studies are required to identify more molecular components that mediate inflammatory reactions in fish.In the past few years, transcriptome sequencing technology has found broad applications in gene discovery and gene expression profiling. Recently, a number of studi...

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Section: Discussionmentioning

confidence: 64%

A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila

Song

Sun

et al. 2017

Sci Rep

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“…The mechanisms underlying the capability of a variety of viruses to trigger Bax may be dependent on antiviral innate immunity pathways (Berens and Tylcr 2011). In the GCRV-infected grass carp, the immune responses are elicited in the gill, liver, spleen, and intestine (Shi et al 2014). Furthermore, a higher number of viral RNA copies could be detected in liver, spleen, kidney, intestine, and muscle after infection with GCRV (Liang et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Cloning and characterization of Bax1 and Bax2 genes of Ctenopharyngodon idellus and evaluation of transcript expression in response to grass carp reovirus infection

Wang

Pei

et al. 2016

Fish Physiol Biochem

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Multidomain proapoptotic Bcl-2-associated X (Bax) protein is an essential effector responsible for mitochondrial outer membrane permeabilization, resulting in cell death via apoptosis. In this study, two Bax genes of grass carp (Ctenopharyngodon idellus), designated as CiBax1 and CiBax2, were isolated and analyzed. The obtained CiBax1 cDNA is 2058 bp long, with a 579 bp open reading frame (ORF) coding a protein of 192 amino acid residues. The full-length cDNA of CiBax2 is 1161 bp, with a 618 bp ORF coding 205 amino acids. Both CiBax1 and CiBax2 are typical members of Bcl-2 family containing conserved Bcl and C-terminal domains, and they share conserved synteny with zebrafish Bax genes despite the grass carp Bax mapping to different linkage groups. Phylogenetic analysis showed that CiBax1 was clustered with Bax from most teleost fish, and CiBax2 was close to Bax2 from teleost fish but far separated from that of Salmo salar. Quantitative real-time PCR analysis revealed broad expression of CiBax1 and CiBax2 in tissues from healthy grass carp, but the relative expression level differed. The mRNA expression of CiBax1 and CiBax2 was both upregulated significantly and peaked in all examined tissues at days 5 or 6 post-infection with grass carp reovirus. Subcellular localization indicated that CiBax1 protein was localized in both nucleus and cytosol, while CiBax2 protein only in cytosol. Moreover, CiBax2, but not CiBax1 was colocalized with mitochondrion under normal condition. Taken together, the findings would be helpful for further understanding of the function of Bax in teleost fish.

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“…Thus, transcriptomic signatures may be useful in identifying genes that play crucial roles during infection process. We obtained RNA-seq data from four diseased grass carp tissues (gill, intestine, liver, head kidney) with three replicates at four times after (0 h, 1 h, 3 h, 5 h) GCRV challenge [36], and investigated the expression pattern of host proteins targeted by virus during various stages of GCRV infection. We identified DEGs compared with the profile of 0 h time point independently.…”

Section: Resultsmentioning

confidence: 99%

Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions

Zhang

Wang

2017

BMC Bioinformatics

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BackgroundGrass carp hemorrhagic disease, caused by grass carp reovirus (GCRV), is the most fatal causative agent in grass carp aquaculture. Protein-protein interactions between virus and host are one avenue through which GCRV can trigger infection and induce disease. Experimental approaches for the detection of host-virus interactome have many inherent limitations, and studies on protein-protein interactions between GCRV and its host remain rare.ResultsIn this study, based on known motif-domain interaction information, we systematically predicted the GCRV virus-host protein interactome by using motif-domain interaction pair searching strategy. These proteins derived from different domain families and were predicted to interact with different motif patterns in GCRV. JAM-A protein was successfully predicted to interact with motifs of GCRV Sigma1-like protein, and shared the similar binding mode compared with orthoreovirus. Differentially expressed genes during GCRV infection process were extracted and mapped to our predicted interactome, the overlapped genes displayed different tissue expression distributions on the whole, the overall expression level in intestinal is higher than that of other three tissues, which may suggest that the functions of these genes are more active in intestinal. Function annotation and pathway enrichment analysis revealed that the host targets were largely involved in signaling pathway and immune pathway, such as interferon-gamma signaling pathway, VEGF signaling pathway, EGF receptor signaling pathway, B cell activation, and T cell activation.ConclusionsAlthough the predicted PPIs may contain some false positives due to limited data resource and poor research background in non-model species, the computational method still provide reasonable amount of interactions, which can be further validated by high throughput experiments. The findings of this work will contribute to the development of system biology for GCRV infectious diseases, and help guide the identification of novel receptors of GCRV in its host.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1500-8) contains supplementary material, which is available to authorized users.

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RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses

Cited by 67 publications

References 66 publications

A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila

A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila

Cloning and characterization of Bax1 and Bax2 genes of Ctenopharyngodon idellus and evaluation of transcript expression in response to grass carp reovirus infection

Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions

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