Proteomic analysis of HIV-1 Gag interacting partners using proximity-dependent biotinylation

Sage, Valerie Le; Cinti, Alessandro; Valiente-Echeverría, Fernando; Mouland, Andrew J.

doi:10.1186/s12985-015-0365-6

Cited by 41 publications

(40 citation statements)

References 25 publications

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“…Around 50 proteins were found to be biotinylated in cells expressing the wild-type BirA*-Gag protein and/or the MA-BirA*-Gag version, including translation factors, cytoskeletal proteins, membrane proteins, and RNA-processing factors, over half of which has previously been demonstrated or implied to interact with HIV-1. Comparison with the data of Le Sage et al [66] reveals that only one protein (Lyric/ AEG-1) was found in both screens, presumably reflecting the different experimental setups.…”

Section: Viral Infectionmentioning

confidence: 71%

“…Comparison with the data of Le Sage et al. reveals that only one protein (Lyric/AEG‐1) was found in both screens, presumably reflecting the different experimental setups.…”

Section: Wider Applications Of Bioidmentioning

confidence: 77%

“…This led to the identification of ∼50 proteins proximal to Myc‐BirA*‐Gag, including proteins involved in translation and innate immunity. For two of these proteins (DEAD‐box RNA helicase DDX17 and ribosomal protein S6), interactions were confirmed by coimmunoprecipitation .…”

Section: Wider Applications Of Bioidmentioning

confidence: 85%

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Meet the neighbors: Mapping local protein interactomes by proximity‐dependent labeling with BioID

2016

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Proximity‐dependent biotin identification (BioID) is a recently developed method that allows the identification of proteins in the close vicinity of a protein of interest in living cells. BioID relies on fusion of the protein of interest with a mutant form of the biotin ligase enzyme BirA (BirA*) that is capable of promiscuously biotinylating proximal proteins irrespective of whether these interact directly or indirectly with the fusion protein or are merely located in the same subcellular neighborhood. The covalent addition of biotin allows the labeled proteins to be purified from cell extracts on the basis of their affinity for streptavidin and identified by mass spectrometry. To date, BioID has been successfully applied to study a variety of proteins and processes in mammalian cells and unicellular eukaryotes and has been shown to be particularly suited to the study of insoluble or inaccessible cellular structures and for detecting weak or transient protein associations. Here, we provide an introduction to BioID, together with a detailed summary of where and how the method has been applied to date, and briefly discuss technical aspects involved in the planning and execution of a BioID study.

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Section: Viral Infectionmentioning

confidence: 71%

“…Comparison with the data of Le Sage et al. reveals that only one protein (Lyric/AEG‐1) was found in both screens, presumably reflecting the different experimental setups.…”

Section: Wider Applications Of Bioidmentioning

confidence: 77%

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Meet the neighbors: Mapping local protein interactomes by proximity‐dependent labeling with BioID

2016

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“…Few more studies also tried BioID on some virus proteins critical for their infections such as the Gag of HIV, LMP1 of EBV, etc. and some novel interacting proteins were identified in each case .…”

Section: Bioid: How Widely Is It Applied?mentioning

confidence: 99%

Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool

Wang

et al. 2017

Proteomics

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Proteins perform biochemical functions by forming complexes, or protein-protein interactions (PPIs). Many different approaches such as phage display, yeast hybridization, etc. were developed to illustrate the PPIs, and disclose the composition and organization of protein complexes. However, none of these approaches are based on the real-time and in vivo PPI analysis. Proximity-dependent labeling (PDL) of interacting proteins has recently been proposed by taking advantage of several enzymes, which are capable of attaching the known reactive groups to the nearby proteins covalently. Among the PDL methods, BioID is the earliest and the most widely used one and has been upgraded from its prototype, making it an extremely convenient research tool. In this review, we describe the BioID technology development, its potential applications according to the nature of the target protein, and some recent efforts to circumvent the technical limitations. Moreover, some comparable PDL methods are introduced, including selective proteomic proximity labeling assay using tyramide, enzyme-mediated activation of radical sources, Proximity Labeling with Ascorbate Peroxidase, in vivo proximal labeling, etc., and we propose that systematic comparison of the working radius of these methods may be helpful to develop a tool box, from which the right method can be selected for a given target protein for PPI research.

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“…A number of HIV-specific studies include analyses of the proteome of infected T cells [7], macrophages [8], intact HIV particles, purified HIV cores and HIV reverse transcription and pre-integration complexes [9]. Viral and host protein interaction has also been studied, including the viral proteins Gag [10], Nef [11], Tat [12], and Rev [13], as well as a comprehensive study of all HIV proteins.…”

Section: Introductionmentioning

confidence: 99%

HIV-1 induced differential expression of cell surface proteins in SupT1 cell lines

Sridevi¹,

SL²,

Gupta³

2018

biomedicalresearch

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Objective: HIV-1 infection to cluster of differentiation 4 (CD4)+ T cells alters many cellular pathways in host genome by protein-protein interactions. Methods: To better understand these events of infection and change in host protein expression, we opted an approach of differential protein expression profiling of CD4+ T cell; SupT1 cells. We studied the change in expression of surface proteome after HIV-1 induction in SupT1 cell line, after 4 d post infection. The level of protein expression was checked by isolating the surface proteins from SupT1 cell culture by biotinylating and immunoprecipitation followed by gradient SDS-PAGE (2%-20%). Results: A protein of 120kDa found to express in the infected cell line when compared with the control. Protein extracted was further subjected to 2D gel electrophoresis, three proteins were found to be differentially expressing in HIV-1 infected cells. Conclusion: Further analysis of these newly expressed proteins, not only helps in understanding the altered expression of surface proteins in CD4+ T cells after HIV infection but also in identification of potential molecules to be used in targeted drug delivery.

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Proteomic analysis of HIV-1 Gag interacting partners using proximity-dependent biotinylation

Cited by 41 publications

References 25 publications

Meet the neighbors: Mapping local protein interactomes by proximity‐dependent labeling with BioID

Meet the neighbors: Mapping local protein interactomes by proximity‐dependent labeling with BioID

Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool

HIV-1 induced differential expression of cell surface proteins in SupT1 cell lines

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