Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1289158 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Usutu virus (USUV) is an emerging orthoflavivirus, which mainly affects birds but in rare cases can cause severe neuroinvasive disease in humans. Due to the limited size of the orthoflavivirus genome the virus relies on the host machinery for replication. In addition, it must subvert the host antiviral response for successful replication in the cell. Studying this complex network of virus-host protein interactions by proteomics approaches can provide us new insights in the replication cycle of viruses and can help us better understand the viral pathogenesis. We have previously shown that the USUV protein NS4A acts as an antagonist of the interferon response, and here we further map the host interaction partners of USUV NS4A using proximity labeling coupled to mass spectrometry. The resulting NS4A interactome revealed many host proteins involved in the autophagy pathway. We showed that both USUV infection and overexpression of USUV NS4A can induce the autophagy pathway. However, stimulation or inhibition of the autophagy pathway did not affect USUV replication in general. Therefore, we decided to look specifically at the role of the selective autophagy receptor sequestosome 1 (p62/SQSTM1), which was identified as an interaction partner of USUV NS4A. We found that p62 is involved in the degradation of USUV NS4A. Furthermore, the knockdown of p62 enhanced replication of USUV in A549 cells, which means p62 functions to restrict USUV replication. In conclusion, this study showed that USUV NS4A induced autophagy and was then targeted by p62 for degradation by the autophagic machinery, uncovering a new role of p62 in the antiviral defense against USUV.
2025-05-07 | PXD057492 | Pride
Project description:Flavivirus infection is tightly connected to host lipid metabolism. Here, we performed shotgun lipidomics of cells infected with neurotropic Zika, West Nile, and tick-borne encephalitis viruses, as well as dengue and yellow fever virus. Early in infection specific lipids accumulated, e.g., neutral lipids in Zika and some lyso-phospholipids in all infections. Ceramide levels increased following infection with viruses that cause a cytopathic effect. In addition, fatty acid desaturation as well as glycerophospholipid metabolism were significantly altered. Importantly, depletion of enzymes involved in phosphatidylserine metabolism as well as phosphatidylinositol biosynthesis reduced orthoflavivirus titers and cytopathic effects while inhibition of fatty acid monounsaturation only rescued from virus-induced cell death. Interestingly, interfering with ceramide synthesis had opposing effects on virus replication and cytotoxicity depending on the targeted enzyme. Thus, lipid remodeling by orthoflaviviruses includes distinct changes but also common patterns shared by several viruses that are needed for efficient infection and replication.
2024-09-03 | GSE264306 | GEO
Project description:Orthoflavivirus denguei Genome sequencing
| PRJNA1348690 | ENA
Project description:Orthoflavivirus nilense Genome sequencing
| PRJNA1320692 | ENA
Project description:Ongoing genomic monitoring of Usutu virus in the Netherlands since 2016
| PRJEB83966 | ENA
Project description:Co-Infection: Simultaneous Detection of West Nile Virus and Usutu Virus in Birds from Germany
| PRJEB41417 | ENA
Project description:We applied the solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of 1 million CpGs in more than 21,408 CGIs and 15,946 transcriptional regulatory regions. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. In this study, we generated genome-wide, single-base resolution DNA methylation maps in three of the most commonly used breast cancer cell lines.Differentially methylated regions (DMRs) were identified in the 5?-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X chromosome among the three cell lines. The single CpG resolution methylation maps of many known tumor suppressor genes were also established in the three cell lines. Here we present a novel approach that combines solution-phase hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in targeted CGI and promoter regions. We designed 51,466 single strand DNA oligonucleotides (160-mer) which target 23,441 CGIs and the transcription start sites of 19,369 known genes in the human genome. The synthetic long DNA oligonucleotides were converted into biotinylated RNA probes for solution-phase hybridization capture of target DNA. The captured genomic DNA was treated with sodium bisulfite, amplified by PCR and sequenced using Illumina GA IIx sequencer.
2011-08-01 | E-GEOD-26826 | biostudies-arrayexpress