The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types

Michael E. Linde, David R. Colquhoun, Ceereena Ubaida Mohien, Thomas Kole, Veronica Aquino, Robert J. Cotter, Nathan Edwards, James E K Hildreth, David Graham

Research output: Contribution to journalArticle

Abstract

HIV-1 incorporates a large array of host proteins into virions. Determining the host protein composition in HIV virions has technical difficulties, including copurification of microvesicles. We developed an alternative purification technique using cholesterol that differentially modulates the density of virions and microvesicles (density modification, DM) allowing for high-yield virion purification that is essential for tandem mass spectrometric and quantitative proteomic (iTRAQ) analysis. DM purified virions were analyzed using iTRAQ and validated against Optiprep (60% iodixanol) purified virions. We were able to characterize host protein incorporation in DM-purified HIV particles derived from CD4+ T-cell lines; we compared this data set to a reprocessed data set of monocyte-derived macrophages (MDM) derived HIV-1 using the same bioinformatics pipeline. Seventy-nine clustered proteins were shared between the MDM derived and T-cell derived data set. These clusters included an extensive collection of actin isoforms, HLA proteins, chaperones, and a handful of other proteins, many of which have previously been documented to interact with viral proteins. Other proteins of note were ERM proteins, the dynamin domain containing protein EH4, a phosphodiesterase, and cyclophilin A. As these proteins are incorporated in virions produced in both cell types, we hypothesize that these proteins may have direct interactions with viral proteins or may be important in the viral life cycle. Additionally, identified common set proteins are predicted to interact with >1000 related human proteins. Many of these secondary interacting proteins are reported to be incorporated into virions, including ERM proteins and adhesion molecules. Thus, only a few direct interactions between host and viral proteins may dictate the host protein composition in virions. Ultimately, interaction and expression differences in host proteins between cell types may drive virion phenotypic diversity, despite conserved viral protein-host protein interactions between cell types.

Original languageEnglish (US)
Pages (from-to)2045-2054
Number of pages10
JournalJournal of Proteome Research
Volume12
Issue number5
DOIs
StatePublished - May 3 2013

Fingerprint

Virion
HIV-1
Proteins
Viral Proteins
T-cells
Macrophages
Purification
Cyclophilin A
HIV
Dynamins
T-Lymphocytes
Protein Array Analysis
Phosphoric Diester Hydrolases
Life Cycle Stages
Computational Biology
Cell Communication
Proteomics
Bioinformatics
Actins
Chemical analysis

Keywords

  • budding
  • envelope
  • HIV
  • host protein
  • iTRAQ
  • macrophage
  • mass spectrometry
  • T-cell

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

Cite this

The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types. / Linde, Michael E.; Colquhoun, David R.; Mohien, Ceereena Ubaida; Kole, Thomas; Aquino, Veronica; Cotter, Robert J.; Edwards, Nathan; Hildreth, James E K; Graham, David.

In: Journal of Proteome Research, Vol. 12, No. 5, 03.05.2013, p. 2045-2054.

Research output: Contribution to journalArticle

Linde, Michael E. ; Colquhoun, David R. ; Mohien, Ceereena Ubaida ; Kole, Thomas ; Aquino, Veronica ; Cotter, Robert J. ; Edwards, Nathan ; Hildreth, James E K ; Graham, David. / The conserved set of host proteins incorporated into HIV-1 virions suggests a common egress pathway in multiple cell types. In: Journal of Proteome Research. 2013 ; Vol. 12, No. 5. pp. 2045-2054.
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AU - Kole, Thomas

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AU - Graham, David

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AB - HIV-1 incorporates a large array of host proteins into virions. Determining the host protein composition in HIV virions has technical difficulties, including copurification of microvesicles. We developed an alternative purification technique using cholesterol that differentially modulates the density of virions and microvesicles (density modification, DM) allowing for high-yield virion purification that is essential for tandem mass spectrometric and quantitative proteomic (iTRAQ) analysis. DM purified virions were analyzed using iTRAQ and validated against Optiprep (60% iodixanol) purified virions. We were able to characterize host protein incorporation in DM-purified HIV particles derived from CD4+ T-cell lines; we compared this data set to a reprocessed data set of monocyte-derived macrophages (MDM) derived HIV-1 using the same bioinformatics pipeline. Seventy-nine clustered proteins were shared between the MDM derived and T-cell derived data set. These clusters included an extensive collection of actin isoforms, HLA proteins, chaperones, and a handful of other proteins, many of which have previously been documented to interact with viral proteins. Other proteins of note were ERM proteins, the dynamin domain containing protein EH4, a phosphodiesterase, and cyclophilin A. As these proteins are incorporated in virions produced in both cell types, we hypothesize that these proteins may have direct interactions with viral proteins or may be important in the viral life cycle. Additionally, identified common set proteins are predicted to interact with >1000 related human proteins. Many of these secondary interacting proteins are reported to be incorporated into virions, including ERM proteins and adhesion molecules. Thus, only a few direct interactions between host and viral proteins may dictate the host protein composition in virions. Ultimately, interaction and expression differences in host proteins between cell types may drive virion phenotypic diversity, despite conserved viral protein-host protein interactions between cell types.

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