PXD024716-1

PXD024716 is an original dataset announced via ProteomeXchange.

Title	Proteomic Organellar Mapping Identifies Modulation of Peroxisomes by HIV-1
Description	The interaction between HIV-1 and the host cell has been studied at many levels, but cell-wide organellar changes caused by the virus have not been defined. Here, we aimed to detail perturbations to the host cell spatial proteome following HIV protein expression. Subcellular fractionation followed by mass spectrometric analysis of Jurkat T cells, in which HIV-expression was uniformly induced, identified thousands of cytoplasmic and membrane-bound proteins and enable their placement within a multi-dimensional analytic space based on the 7 fractions. Spatial proteomic data were analyzed via a support vector machine bagging classifier to assess the movement of proteins between compartments. The proteins were also examined for absolute movement within 7-dimensional Euclidean space. We found that while some proteins moved between organelles, others remained classified within the same organelle but moved as a group relative to other organelles. The expression of HIV-1 affected the distribution of peroxisomal proteins, causing them to move closer to proteins of the endoplasmic reticulum and lysosomes, but only when the viral protein Nef was expressed. These data identify Nef-dependent changes in peroxisomes as a novel perturbation of the host cell by HIV-1.
HostingRepository	PRIDE
AnnounceDate	2022-01-28
AnnouncementXML	Submission_2022-01-28_01:44:37.820.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alicia Richards
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-14 23:44:02	ID requested
⏵ 1	2022-01-28 01:44:38	announced

Dataset with its publication pending

submitter keyword: LC-MS/MS, Proteomics, HIV-1, organelle mapping

Nevan J. Krogan
contact affiliation	Department of Cellular and Molecular Pathology, UCSF, San Francisco, CA
contact email	nevan.krogan@ucsf.edu
lab head
Alicia Richards
contact affiliation	Krogan lab
contact email	alicia.richards@ucsf.edu
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/2022/01/PXD024716

PRIDE project URI

• PRIDE
  1. PXD024716
     1. Label: PRIDE project
     2. Name: Proteomic Organellar Mapping Identifies Modulation of Peroxisomes by HIV-1