Identifying the Cardiac Dyad Proteome In Vivo by a BioID2 Knock-In Strategy

Feng, Wei; Liu, Canzhao; Spinozzi, Simone; Wang, Li; Evans, Sylvia M.; Chen, Ju

doi:10.1161/circulationaha.119.043434

Cited by 38 publications

(38 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The biotinylated proteome is isolated by streptavidin affinity, and proteins are identified by quantitative mass spectrometry. Most studies have applied proximity labeling to in vitro tissue culture systems, whereas many fewer have explored in vivo networks in mice or Drosophila ( Spence et al, 2019 ; Feng et al, 2020 ; Rudolph et al, 2020 ; Mannix et al, 2019 ; Cho et al, 2020 ). In the latter studies, proximity labeling captured the proteome within interneuron–neuron interactions, within muscle sarcomeres, and in the ring canal of Drosophila oocytes, producing new insights into protein network assemblies and signaling.…”

Section: Introductionmentioning

confidence: 99%

In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

Pronobis

Zheng

Singh

et al. 2021

eLife

View full text Add to dashboard Cite

Strategies have not been available until recently to uncover interacting protein networks specific to key cell types, their subcellular compartments, and their major regulators during complex in vivo events. Here we apply BioID2 proximity labeling to capture protein networks acting within cardiomyocytes during a key model of innate heart regeneration in zebrafish. Transgenic zebrafish expressing a promiscuous BirA2 localized to the entire myocardial cell or membrane compartment were generated, each identifying distinct proteomes in adult cardiomyocytes that became altered during regeneration. BioID2 profiling for interactors with ErbB2, a co-receptor for the cardiomyocyte mitogen Nrg1, implicated Rho A as a target of ErbB2 signaling in cardiomyocytes. Blockade of Rho A during heart regeneration, or during cardiogenic stimulation by the mitogenic influences Nrg1, Vegfaa or Vitamin D, disrupted muscle creation. Our findings reveal proximity labeling as a useful resource to interrogate cell proteomes and signaling networks during tissue regeneration in zebrafish.

show abstract

Section: Introductionmentioning

confidence: 99%

In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

Pronobis

Zheng

Singh

et al. 2021

eLife

View full text Add to dashboard Cite

show abstract

“…More recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) knock-in technique has made it possible to tag the target gene at its endogenous locus. Junctophilin-2 (JPH2) interactome was studied with knock-in of BioID2 ( Feng et al, 2020 ); the endogenous interaction networks of breast cancer type 1 susceptibility protein (BRCA1), tumor suppressor p53-binding protein 1 (TP53BP1), and mediator of DNA damage checkpoint protein 1 (MDC1) were also studied using knock-in of APEX2 ( Gupta et al, 2018 ). The endogenous tagging technique avoids the overexpression of an exogenous fusion protein.…”

Section: Strategies For Studying Interactomes With Mass Spectrometrmentioning

confidence: 99%

Mass spectrometry-based protein-protein interaction techniques and their applications in studies of DNA damage repair

Chen

2021

J. Zhejiang Univ. Sci. B

View full text Add to dashboard Cite

Proteins are major functional units that are tightly connected to form complex and dynamic networks. These networks enable cells and organisms to operate properly and respond efficiently to environmental cues. Over the past decades, many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected. At the same time, rapid development in proteomics and mass spectrometry (MS) techniques makes it possible to identify interacting proteins and build comprehensive protein-protein interaction networks. The resulting interactomes and networks have proven informative in the investigation of biological functions, such as in the field of DNA damage repair. In recent years, a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein-protein interaction studies. As the technologies for enriching associated proteins and MS become more sophisticated, the studies of protein-protein interactions are entering a new era. In this review, we summarize the strategies and recent developments for exploring protein -protein interaction. In addition, we discuss the application of these tools in the investigation of protein-protein interaction networks involved in DNA damage response and DNA repair.

show abstract

“…Furthermore, the proteomic investigation of heart and quadriceps muscle at ages extending from neonatal to adult has linked neonatal signaling pathways to the sarcomere [ 48 ]. Another BioID knock-in mouse line with BioID2 fused to the endogenous JPH2 coding sequence was developed to profile the cardiac dyad proteome [ 64 ]. This BioID2 knock-in strategy leads to expression levels of JPH2-BioID2 fusion protein comparable to that of the endogenous protein, but still reveals novel potential dyadic proteins that were not discovered using JPH2-HA overexpression transgenic mouse line [ 65 ].…”

Section: Introductionmentioning

confidence: 99%

“…Virus-mediated or transgenic overexpression of the PL enzyme-tagged POI may generate PPIs in vivo that are either not physiological or not specific, burdening the secondary validation procedure. This problem may be solved through CRISPR/Cas9-mediated knock-in to tag the PL enzyme to the endogenous POI at a physiological level [ 48 , 64 ]. If the endogenous level of PL enzyme-POI yields insufficient biotinylated material for subsequent analysis, the procedure for retrieval of biotinylated peptides may require modification, such as by using cryo-fractured tissue powder digested with trypsin as an input and anti-bio tin antibody [ 62 , 63 ].…”

Section: Introductionmentioning

confidence: 99%

In vivo interactome profiling by enzyme‐catalyzed proximity labeling

Fan

2021

Cell Biosci

View full text Add to dashboard Cite

Enzyme-catalyzed proximity labeling (PL) combined with mass spectrometry (MS) has emerged as a revolutionary approach to reveal the protein-protein interaction networks, dissect complex biological processes, and characterize the subcellular proteome in a more physiological setting than before. The enzymatic tags are being upgraded to improve temporal and spatial resolution and obtain faster catalytic dynamics and higher catalytic efficiency. In vivo application of PL integrated with other state of the art techniques has recently been adapted in live animals and plants, allowing questions to be addressed that were previously inaccessible. It is timely to summarize the current state of PL-dependent interactome studies and their potential applications. We will focus on in vivo uses of newer versions of PL and highlight critical considerations for successful in vivo PL experiments that will provide novel insights into the protein interactome in the context of human diseases.

show abstract

Identifying the Cardiac Dyad Proteome In Vivo by a BioID2 Knock-In Strategy

Cited by 38 publications

References 5 publications

In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

Mass spectrometry-based protein-protein interaction techniques and their applications in studies of DNA damage repair

In vivo interactome profiling by enzyme‐catalyzed proximity labeling

Contact Info

Product

Resources

About