PXD058232

PXD058232 is an original dataset announced via ProteomeXchange.

Title	The translational landscape of HIV-1 infected cells reveals novel gene regulatory principles
Description	Human Immunodeficiency Virus-1 (HIV-1) uses a number of strategies to modulate viral and host gene expression during its lifecycle. To characterize the transcriptional and translational landscape of HIV-1 infected cells, we used a combination of ribosome profiling, disome sequencing and RNA sequencing. We found that the initial host response to viral infection is translationally regulated, and subsequently gives way to transcriptomic changes as the infection progresses. We show that HIV-1 mRNAs are efficiently translated at all stages of infection, despite evidence for a substantial decrease in translational efficiency of host genes that are implicated in host cell translation. Our data also reveal novel upstream open reading frames (uORFs) within the HIV-1 5'UTR as well as internal ORFs (iORFs) within the Vif and Pol coding domains. We observed ribosomal collisions in Gag-Pol upstream of the ribosome frameshift site that we attributed to a novel RNA structural fold using RNA structural probing and single molecule optical tweezers. Antisense oligos designed to break this structure decreased frameshifting efficiency. Overall, our data highlight the complexity of HIV-1 gene regulation and provide a key resource for decoding of host-pathogen interactions upon HIV-1 infection. Furthermore, we provide evidence for a novel RNA structural fold including the frameshift site that might be promising as target for antiviral therapy.
HostingRepository	PRIDE
AnnounceDate	2025-05-26
AnnouncementXML	Submission_2025-05-25_16:08:59.854.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Schlosser
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-25 06:40:55	ID requested
⏵ 1	2025-05-25 16:09:00	announced

Kibe A, Buck S, Gribling-Burrer AS, Gilmer O, Bohn P, Koch T, Mireisz CN, Schlosser A, Erhard F, Smyth RP, Caliskan N, The translational landscape of HIV-1 infected cells reveals key gene regulatory principles. Nat Struct Mol Biol, 32(5):841-852(2025) [pubmed]

10.1038/s41594-024-01468-3;

submitter keyword: HIV-1, ribosome profiling, disome profiling, RNA sequencing, LC-MS/MS

Andreas Schlosser
contact affiliation	Rudolf-Virchow-Zentrum Center for Integrative and Translational Bioimaging Universität Würzburg
contact email	andreas.schlosser@uni-wuerzburg.de
lab head
Andreas Schlosser
contact affiliation	Mass Spectrometry and Proteomics
contact email	andreas.schlosser@virchow.uni-wuerzburg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD058232

PRIDE project URI

• PRIDE
  1. PXD058232
     1. Label: PRIDE project
     2. Name: The translational landscape of HIV-1 infected cells reveals novel gene regulatory principles