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Cited by 54HIV Research and TreatmentAdvanced Proteomics Techniques and ApplicationsHIV/AIDS drug development and treatment

Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry

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Knoener, Rachel A., Becker, Jordan T., Scalf, Mark, Sherer, Nathan M., Smith, Lloyd M.·2017·Scientific Reports
DOI 10.1038/s41598-017-16793-5PMC PMC5717263
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Abstract

HIV-1 replication requires myriad interactions between cellular proteins and the viral unspliced RNA. These interactions are important in archetypal RNA processes such as transcription and translation as well as for more specialized functions including alternative splicing and packaging of unspliced genomic RNA into virions. We present here a hybridization capture strategy for purification of unspliced full-length HIV RNA-protein complexes preserved in vivo by formaldehyde crosslinking, and coupled with mass spectrometry to identify HIV RNA-protein interactors in HIV-1 infected cells. One hundred eighty-nine proteins were identified to interact with unspliced HIV RNA including Rev and Gag/Gag-Pol, 24 host proteins previously shown to bind segments of HIV RNA, and over 90 proteins previously shown to impact HIV replication. Further analysis using siRNA knockdown techniques against several of these proteins revealed significant changes to HIV expression. These results demonstrate the utility of the approach for the discovery of host proteins involved in HIV replication. Additionally, because this strategy only requires availability of 30 nucleotides of the HIV-RNA for hybridization with a capture oligonucleotide, it is readily applicable to any HIV system of interest regardless of cell type, HIV-1 virus strain, or experimental perturbation.

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  • Cellular factors interacting with HIV-1 proteins and RNAs have been identified using proteomic approaches.

    “In recent years, cellular factors interacting with HIV-1 proteins and RNAs have been identified using proteomic approaches (122-124).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [124]

  • LeuRS is among the factors identified interacting with unspliced full-length HIV-1 RNA.

    “Interestingly, LeuRS is among the factors identified, and future studies are required to understand the significance of this finding (124).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [124]

    The Results and Discussion section ('HyPR-MS identifies proteins involved in cytoplasmic RNA processes'; page unavailable) reports identifying tRNA ligases among proteins associated with unspliced HIV RNA, but does not name LeuRS. Searches for LeuRS, LARS, and leucyl-tRNA synthetase found no passage identifying that specific factor. (LLM, conf=0.74)

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Cited by

Sorted by citations

Authors
Knoener, R. A., Becker, J. T., Scalf, M., Sherer, N. M., & Smith, L. M.
Affiliations
University of Wisconsin–Madison (US)
Corresponding author
Smith, Lloyd M.
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2017-12-05
Volume
7
Issue
1
Pages
16965-16965
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-017-16793-5
PMC
PMC5717263
OpenAlex
W2769941852
Cited by
54
References
6
Citations by year
2026: 6 · 2025: 3 · 2024: 7 · 2023: 7 · 2022: 2 · 2021: 10 · 2020: 7 · 2019: 6 · 2018: 6
FWCI
2.83
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Cancer Institute (R01CA193481)
  • National Institute of Allergy and Infectious Diseases (R01AI110221)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
Keywords
HIV-1, RNA-protein interactions, unspliced viral RNA, hybridization capture, formaldehyde crosslinking, Rev, Gag-Pol, host factors, HIV replication, siRNA knockdown, viral RNA packaging, alternative splicing
MeSH terms
Cytoplasm, Humans, Microscopy, Fluorescence, Nucleic Acid Hybridization, Proteins, RNA Splicing, RNA, Viral, Mass Spectrometry, Viral Proteins, Reproducibility of Results, HIV-1, HIV Infections, RNA-Binding Proteins, RNA, Small Interfering, Gene Knockdown Techniques, HEK293 Cells

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