In planta proximity-dependent biotin identification (BioID) identifies a TMV replication co-chaperone NbSGT1 in the vicinity of 126 kDa replicase

Das, Prem Prakash; Macharia, Mercy; Lin, Qingsong; Wong, Sek‐Man

doi:10.1016/j.jprot.2019.103402

Cited by 22 publications

(12 citation statements)

References 66 publications

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“…While BioID/BioID2 have been applied successfully in many model systems including in live cultured cells, yeast [16,17], parasites [18][19][20][21][22][23][24], plants [25,26], and mice [27][28][29][30], most experiments have been performed utilizing a 12-24 h labeling period, with few exceptions labeling for 1 h or 3 h [31,32]. Experiments requiring shorter labeling periods require a faster version of BioID and one that would work well at temperatures well below 37 • C. Two groups have reported versions of BioID that address some or all of these limitations.…”

Section: Introductionmentioning

confidence: 99%

Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation

May

Scott

Campos

et al. 2020

Cells

137

120

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BioID is a well-established method for identifying protein–protein interactions and has been utilized within live cells and several animal models. However, the conventional labeling period requires 15–18 h for robust biotinylation which may not be ideal for some applications. Recently, two new ligases termed TurboID and miniTurbo were developed using directed evolution of the BioID ligase and were able to produce robust biotinylation following a 10 min incubation with excess biotin. However, there is reported concern about inducibility of biotinylation, cellular toxicity, and ligase stability. To further investigate the practical applications of TurboID and ascertain strengths and weaknesses compared to BioID, we developed several stable cell lines expressing BioID and TurboID fusion proteins and analyzed them via immunoblot, immunofluorescence, and biotin-affinity purification-based proteomics. For TurboID we observed signs of protein instability, persistent biotinylation in the absence of exogenous biotin, and an increase in the practical labeling radius. However, TurboID enabled robust biotinylation in the endoplasmic reticulum lumen compared to BioID. Induction of biotinylation could be achieved by combining doxycycline-inducible expression with growth in biotin depleted culture media. These studies should help inform investigators utilizing BioID-based methods as to the appropriate ligase and experimental protocol for their particular needs.

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Section: Introductionmentioning

confidence: 99%

Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation

May

Scott

Campos

et al. 2020

Cells

137

120

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“…On the contrary, with proximity labelling methods, there is no need to preserve PPIs during lysis and extraction. Proximity-dependent biotin identification (BioID) allows the spatial conditions of PPIs to be preserved and is particularly useful for identifying low-affinity and transient interactions (Roux et al, 2012), including in plants (Arora et al, 2020;Branon et al, 2018;Conlan et al, 2018;Das et al, 2019;Khan et al, 2018;Lin et al, 2017;Mair et al, 2019;Zhang et al, 2019). The downside of the above techniques is that they do not provide any information about the binary interactions occurring between bait and prey proteins.…”

Section: Introductionmentioning

confidence: 99%

Visualizing protein–protein interactions in plants by rapamycin-dependent delocalization

et al. 2021

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Identifying protein-protein interactions (PPI) is crucial for understanding biological processes. Many PPI tools are available, yet only some function within the context of a plant cell. Narrowing down even further, only a few tools allow complex multi-protein interactions to be visualized. Here, we present a conditional in vivo PPI tool for plant research that meets these criteria. Knocksideways in plants (KSP) is based on the ability of rapamycin to alter the localization of a bait protein and its interactors via the heterodimerization of FKBP and FRB domains. KSP is inherently free from many limitations of other PPI systems. This in vivo tool does not require spatial proximity of the bait and prey fluorophores and it is compatible with a broad range of fluorophores. KSP is also a conditional tool and therefore the visualization of the proteins in the absence of rapamycin acts as an internal control. We used KSP to confirm previously identified interactions in Nicotiana benthamiana leaf epidermal cells. Furthermore, the scripts that we generated allow the interactions to be quantified at high throughput. Finally, we demonstrate that KSP can easily be used to visualize complex multi-protein interactions. KSP is therefore a versatile tool with unique characteristics and applications that complements other plant PPI methods.

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“…Pioneering early work ( Lin et al, 2017 ), used the maize ( Zea mays ) UBQ promoter to express rice ( Oryza sativa ) FD transcription factors 1 and 2 (OsFD1 and OsFD2), fused to BirA* with a cryptic splice site removed (BirAG), in rice protoplasts and identified several putative interactors. Later studies used BioID to gain insight into plant–pathogen interactions using transient expression with the 35S promoter in Nicotiana benthamiana ( Conlan et al, 2018 ; Das et al, 2019 ; Macharia et al, 2019 ) or dexamethasone-inducible overexpression in stable Arabidopsis lines ( Khan et al, 2018 ). Recently, Tang et al (2020) and Huang et al (2020) tagged multiple proteins of the nuclear membrane and nuclear pore complex with BioID2, under the 35S promoter in stable Arabidopsis lines and identified (trans)membrane proteins specific for the outer and inner nuclear membrane, as well as components of the inner nuclear membrane protein degradation machinery.…”

Section: A Brief History Of Using Pl Techniques In Plantsmentioning

confidence: 99%

Advances in enzyme-mediated proximity labeling and its potential for plant research

Mair

Bergmann

2021

Plant Physiology

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Cellular processes rely on the intimate interplay of different molecules, including DNA, RNA, proteins and metabolites. Obtaining and integrating data on their abundance and dynamics at high temporal and spatial resolution is essential for our understanding of plant growth and development. In the past decade, enzymatic proximity labeling (PL) has emerged as a powerful tool to study local protein and nucleotide ensembles, discover protein-protein and -nucleotide interactions and resolve questions about protein localization and membrane topology. An ever-growing number and continuous improvement of enzymes and methods keeps broadening the spectrum of possible applications for PL and makes it more accessible to different organisms, including plants. While initial PL experiments in plants required high expression levels and long labeling times, recently developed faster enzymes now enable PL of proteins on a cell type-specific level, even with low-abundant baits, and in different plant species. Moreover, expanding the use of PL for additional purposes, such as identification of locus-specific gene regulators or high-resolution electron microscopy may now be in reach. In this review, we give an overview of currently available PL enzymes and their applications in mammalian cell culture and plants. We discuss challenges and limitations of PL methods and highlight open questions and possible future directions for PL in plants.

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In planta proximity-dependent biotin identification (BioID) identifies a TMV replication co-chaperone NbSGT1 in the vicinity of 126 kDa replicase

Cited by 22 publications

References 66 publications

Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation

Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation

Visualizing protein–protein interactions in plants by rapamycin-dependent delocalization

Advances in enzyme-mediated proximity labeling and its potential for plant research

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In planta proximity-dependent biotin identification (BioID) identifies a TMV replication co-chaperone NbSGT1 in the vicinity of 126 kDa replicase

Cited by 22 publications

References 66 publications

Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation

Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation

Visualizing protein–protein interactions in plants by rapamycin-dependent delocalization

Advances in enzyme-mediated proximity labeling and its potential for plant research

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In planta proximity-dependent biotin identification (BioID) identifies a TMV replication co-chaperone NbSGT1 in the vicinity of 126 kDa replicase