PXD007634

PXD007634 is an original dataset announced via ProteomeXchange.

Title	A comparative analysis of the interactomes of viral accessory proteins exploiting DDB1 and Cullin Ubiquitin ligases
Description	Viruses have an ambivalent relationship with the host proteome. While several host proteins are indispensable for replication, detrimental restriction factors need to be antagonized. This process is frequently catalysed by viral accessory proteins which exploit the ubiquitin proteasome pathway, DDB1, and Cullin Ubiquitin ligases for the degradation of restriction factors, like in the case of the mouse cytomegalovirus encoded interferon antagonist pM27 which exploits DDB1 for STAT2 degradation. pM27 homologous proteins are conserved in betaherpesviruses. DDB1 and Cullins also serve as essential co-factor for accessory proteins encoded by other virus families like Vpr (HIV-1- and -2-encoded), Vpx (HIV-2-encoded), HBx (HBV-encoded) and its woodchuck hepatitis virus homolog (WHx). To establish a comprehensive understanding of the complexes assembled by viral DDB1-interacting proteins and their targets, we performed immuno-affinity precipitations for a panel of viral proteins known or suspected to interact with DDB1 and/or Cullins. For each protein, we conducted four biological replicates and identified and quantified all co-precipitating proteins by mass spectrometry. Empty plasmids and the HCMV-encoded protein pUL42, which binds the unrelated ubiquitin ligase Itch, served as negative controls and outside group, respectively. This analysis confirmed previously described interactions (pM27 with STAT2), extended known interactions to paralogous proteins (e.g. HBx and WHx with different Spindlin proteins), and documented anticipated interactions for the first time (e.g. Vpr with Bax). The comparison revealed considerable differences concerning the interaction with DDB1 and Cullin 4A/B in terms of the general ability as well as the strength of interaction. On global level, the correlation of the interactomes fitted well with the phylogenetic relationship of the proteins but also highlighted a considerable overlap between the DDB1 interactors of non-related viruses (e.g. herpesviral and hepadnaviral).
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:31:42.659.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD007634
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Dominik Andre Meger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	residues isobaric at 113.084064 Da; Propionamide; Oxidation
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-04 01:26:35	ID requested
1	2019-01-14 01:03:18	announced
⏵ 2	2024-10-22 04:31:50	announced	2024-10-22: Updated project metadata.

10.3389/fimmu.2018.02978;

Landsberg CD, Megger DA, Hotter D, R, ü, ckborn MU, Eilbrecht M, Rashidi-Alavijeh J, Howe S, Heinrichs S, Sauter D, Sitek B, Le-Trilling VTK, Trilling M, B Inhibitory Activity of the HIV-2-Encoded Vpx. Front Immunol, 9():2978(2018) [pubmed]

10.6019/PXD007634;

curator keyword: Biological, Biomedical

submitter keyword: Proteomics, Mass spectrometry, Cullin Ubiquitin ligases, DDB1, Viral Interactome analysis

Dominik A. Megger
contact affiliation	Medizinisches Proteom-Center Ruhr-University Bochum Bochum, Germany
contact email	dominik.megger@rub.de
lab head
Dominik Andre Meger
contact affiliation	Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Germany
contact email	dominik.megger@rub.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007634
     1. Label: PRIDE project
     2. Name: A comparative analysis of the interactomes of viral accessory proteins exploiting DDB1 and Cullin Ubiquitin ligases