Project description:Tilapia Lake Virus (TiLV) poses a significant threat to global tilapia aquaculture, causing high mortality rates and severe economic losses. Despite its impact, the molecular mechanisms of TiLV-host interactions remain poorly understood. This study investigates the proteomic and phosphoproteomic changes in two piscine cell lines, E-11 and RHTiB, following TiLV infection.
Project description:Viral interfering RNA (viRNA) has been identified from several viral genomes via directly deep RNA sequencing of the virus-infected cells, including zika virus (ZIKV). Once produced by endoribonuclease Dicer, viRNAs, similar to microRNAs, are loaded onto Argonaute (AGO) family proteins of the RNA-induced silencing complexes (RISCs) to pair with their RNA targets and then initiate cleavage of the target genes. However, identities of functional ZIKV viRNAs and their viral RNA targets remain largely unknown. By combining AGO-associated RNA sequencing, deep sequencing analysis in ZIKV-infected neural stem cells (NSCs), and miRanda target scanning, we have defined 29 ZIKV derived viRNA profiles in NSCs, and established the complex interaction networks between the viRNAs and their viral targets. Our recent study has shown that ZIKV capsid protein interacted with Dicer and antagonized its endoribonuclease activity depending on its histidine (H) at the 41st amino acid. Accordingly, the rescued ZIKV-H41R mutant virus, compared to wild-type ZIKV, no longer suppressed Dicer enzymatic activity and consequently failed to inhibit miRNA biogenesis in NSCs. As a result, much higher levels of viRNAs generated from the ZIKV-H41R virus-infected NSCs, suggesting Dicer-dependent viRNA production. Knockdown of individual RNAi machinery in ZIKV-infected NSCs suggests that viRNA is a limiting factor of ZIKV infection in NSCs. The mapping of viRNAs to their RNA targets is paving a way to further investigate how viRNAs play the role in anti-viral mechanisms or even other unknown biological functions.
Project description:Innate antiviral immune responses are driven by virus-induced changes in host gene expression. In this study, RNA-sequencing of mock-infected and Sendai virus-infected cells was performed to characterize the virus-inducible transcriptome and identify novel virus-inducible RNAs in human cells.
Project description:SILAC labeled human kidney cells (293 cells) or bat kidney cells (PakiT03cells)were infected with Hendra virus for 8 or 24 hours and compared to uninfected control cells. Protein identification and quantitation relied on a combination of Uniprot lists of proteins and Proteomics Informed by Transcriptomics (PIT) analysis whereby RNA extracted from the same samples was deep sequenced and the sequencing data was used to construct mRNA from which possible ORFS were inferred and used as a search space by MaxQuant.
2016-06-17 | MSV000079832 | MassIVE
Project description:Tilapia lake virus isolate BD-2017 from Bangladesh
Project description:Purpose: The goal of this study was to compare NGS-derived mRNA transcriptome and miRNA expression profiles between Zika virus-infected A549 cells and control A549 cells to identify differentially expressed mRNAs and miRNAs. Methods: Zika virus-infected A549 cells and control A549 cells were subjected to mRNA sequencing and small RNA sequencing in biological triplicates using the Illumina HiSeq 4000 platform. For mRNA sequencing analysis, transcriptome profiles were generated by deep sequencing. The mapped reads of each sample were assembled by StringTie (v1.3.1) using a reference-based approach to assemble and quantify full-length transcripts representing multiple splice variants for each gene locus. For small RNA sequencing analysis, miRNA expression profiles were generated from small RNA sequencing data. Raw small RNA sequencing reads were filtered to obtain clean reads, which were aligned to the human reference genome using Bowtie. The DESeq R package (version 1.8.3) was used to identify differentially expressed miRNAs between Zika virus-infected and control A549 cells. Results: Sequencing analysis identified differentially expressed mRNAs and miRNAs between Zika virus-infected and control A549 cells. The sequencing data provide comprehensive mRNA and miRNA expression profiles for further analysis of host responses following Zika virus infection. Conclusions: This study provides a comprehensive characterization of the transcriptome and miRNA expression profiles of A549 cells following Zika virus infection using next-generation sequencing approaches. These sequencing data will facilitate further studies of host responses associated with Zika virus infection.
Project description:We investigated expression and localisation of all predicted proteins of Tilapia Lake Virus (TiLV) using in vitro translation, cell expression systems, and mass spectrometry, confirming major polypeptides from each segment and discovering an additional 11th protein, S9-F3, from an alternative reading frame. GFP-tagged constructs showed S2 and S10 localised mainly to the nucleus, while S1, S3, S5, S8 and S9-F3 were cytoplasmic, with S5 and S6 forming perinuclear foci. Bioinformatics and inhibitor assays revealed CRM1-dependent nuclear export of S9-F3. Evolutionary analyses indicated selective pressure on S9 and S9-F3 and identified an S9-F3 homologue in a TiLV-like guppy virus. These results reveal a novel protein and regulated nuclear export mechanism, offering new insights into TiLV biology and host interactions.