How Are Genes And Proteins Related Apex

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How Are Genes And Proteins Related Apex

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Proteomic Technologies For Deciphering Local And Global Protein Interactions: Trends In Biochemical Sciences

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Center de Référence Maladies Rares Mucoviscidose et Maldies de CFTR, Hôpital Necker Enfants Malades, European Reference National (ERN) Lung Center, 75015 Paris, France

Whole Genome Association Study Of The Plasma Metabolome Identifies Metabolites Linked To Cardiometabolic Disease In Black Individuals

Received: July 12, 2022 / Revised: August 5, 2022 / Accepted: August 8, 2022 / Published: August 11, 2022

Proteins that interact with CFTR and its mutants have been intensively studied using a variety of experimental approaches. These studies have provided information on the cellular processes that lead to proper protein folding, plasma membrane routing, recycling, activation and degradation. Recently, new techniques have been developed based on the proximity labeling of protein partners or proteins in close proximity and their subsequent identification using mass spectrometry. In this study, we analyzed WT CFTR proximity labeling based on TurboID and APEX2 and compared the resulting data with data presented in databases. The interaction with CFTR-WT was compared with the interaction of two CFTR mutants (G551D and W1282X) and the structurally unrelated KCNK3 potassium channel. Both proximity labeling approaches have identified both known and additional protein partners of CFTR, including multiple SLC transporters. The proximity labeling approach provided a more complete picture of the CFTR interactome and improved our knowledge of the CFTR environment.

Cystic fibrosis (CF), the most common monogenic life-threatening disease, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene [1], which encodes a chloride channel located in the apical membrane of the respiratory epithelial cells [1] ]. 2].

The partner proteins of CFTR have been extensively studied, leading to a better understanding of the cellular processes that lead to proper protein folding, transport to the plasma membrane, recycling, and degradation. Several partner proteins involved in these various steps have been identified (reviewed in this special issue [3]). They are often identified based on comparisons between WT-CFTR and CFTR-F508del mutant [4, 5], the most common CF-causing mutation, or other misfolded mutants [6, 7]. These interactions occur in different cellular compartments corresponding to different stages in the CFTR biogenesis pathway. The first set of partner proteins is found within the endoplasmic reticulum and is mainly involved in the synthesis and replication of CFTR (rev. Refs. [8, 9]). Some of them are involved in ER quality control (ERQC) of CFTR, which recognizes misfolded channels and directs them to proteasomal degradation. ERQC includes various checkpoints, including both chaperones, such as calnexin, calreticulin, Hsp70 and their co-chaperones, and specific motifs found in CFTR, such as RXR motifs involved in maintaining ER, and the two-acid exit code (DAD), involved in the recruitment of CFTR cargo to vesicles budding from the ER exit site [10]. It has been suggested that proper folding of CFTR reduces the presence of RXR motifs, facilitating the release of properly folded channels from the ER [10, 11, 12]. After complex glycosylation in the Golgi apparatus, CFTR is exported to the plasma membrane, where it binds to a variety of proteins, such as membrane-anchoring proteins that connect the channel to the cytoskeleton, or endosomal proteins involved in vesicular recycling of CFTR [ 3 ]. , 13]. As in the ER, the peripheral quality control system monitors protein quality and targets altered channels for lysosomal degradation [ 14 , 15 ]. Finally, at the cell surface, the activity of the CFTR channel is mainly regulated by the phosphorylation of its regulatory domain [16]. Several kinases are involved in this regulation, mainly PKA [17, 18] and, to a lesser extent, PKC [19, 20] and tyrosine kinases [21]. Recently Mihai et al. showed that the association of CFTR with PKA initiates conformational changes leading to channel activation, while phosphorylation of specific residues is required to maintain the effect over time [22]. Similarly, a specific protein-protein interaction between CFTR and WNK1 was recently shown to alter the channel’s selectivity for bicarbonate over chloride ions [23], an effect independent of the kinase activity of WNK1. .

Spatiotemporal Resolved Protein Networks Profiling With Photoactivation Dependent Proximity Labeling

CFTR has also been shown to modulate the activity of other channels and transporters on the cell surface, such as ENaC [24], ORCC [25], SLC26A9 [26, 27, 28], SLC26A3 [29], or SLC26A6 [30]. ] . Coactivation of CFTR and SLC26 transporters is associated with a direct interaction between the STAS domain of SLC26 transporters and the R domain of CFTR [27, 29]. The CFTR PDZ C-terminal domain also plays an important role in protein-protein interactions at the plasma membrane, anchoring CFTR to the cytoskeleton and mediating interactions with other proteins that contain PDZ through PDZ-binding proteins such as NHERF1 [9].

The CFTR interactome appears to be location-specific and highly dynamic, influencing several steps in CFTR biogenesis, turnover, and activity. Several techniques have been used to identify CFTR partners, such as yeast two-hybrid screening and CFTR immunoprecipitation combined with mass spectrometry. These strategies have provided detailed maps of the CFTR interactome and continue to be improved. While the yeast two-hybrid screen remains difficult for transmembrane proteins. These strategies have provided detailed maps of the CFTR interactome and continue to be improved. While yeast two-hybrid screening for transmembrane proteins remains difficult, leading to the use of CFTR fragments as baits, technological advances now allow screening of full-length CFTR in mammalian cells [31]. compared to interactions occurring in a living cell [32, 33, 34, 35]. In addition, the specificity of the resulting interactions depends on the availability and specificity of the antibodies, as well as the experimental conditions.

To address these limiting aspects, new methods have recently been developed to label partner proteins in native environments. These include, among others, the proximity-marking enzymes BioID, TurboID, and APEX2 [32, 33, 34, 35], which bind to the protein of interest. BioID is an Escherichia coli biotin ligase that biotinylates proteins at lysine residues within a radius of approximately 10 nm. While the low activity of BioID usually requires 18 to 24 hours of labeling, optimization of the enzyme sequence led to the creation of a mutant ligase called TurboID, characterized by increased enzymatic activity, which reduced the labeling time to 10 minutes [33]. Another approach is based on APEX2, a peroxidase that allows the labeling of electron-rich amino acid residues of protein partners with biotin derivatives (biotin-phenol) with a spatial resolution of approx. about 20 nm [33, 35]. The labeling reaction is driven by the addition of H

For a short time in live cells (1 min), providing a picture of the proximal interactome.

Characterization Of Huntingtin Interactomes And Their Dynamic Responses In Living Cells By Proximity Proteomics

In this study, we investigated and compared CFTR interactions using three proximity labeling strategies, namely, APEX2, BioID, and TurboID. Experiments were performed in transiently transfected HEK293 cells to achieve high levels of fusion protein expression and facilitate identification by mass spectrometry.

The BioID, TurboID and APEX2 coding sequences were subcloned upstream of the CFTR coding sequence to produce fusion proteins containing enzymes at the N-terminus of CFTR. A linker region consisting of five glycine-serine repeat (GS5) motifs was introduced between BioID/APEX2/TurboID and CFTR to increase flexibility and reduce CFTR near-end crowding. The activity of these hybrid proteins made it possible to label proteins that interact with CFTR, or proximal proteins within a radius of 10-20 nm, while distal proteins or proteins separated by a membrane is not

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