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ANXA6 proximity-dependent biotinylation assay using ultraID in HeLa cells

ABSTRACT: Analysis of ANXA6 proximity interactome using ultraID (birA* derived biotin ligase) in HeLa ANXA6ko cells. We performed a proximity-dependent biotinylation assay (UltraID) followed by streptavidin enrichment using Dynabeads and LC-MS/MS.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Carles Rentero Alfonso

LAB HEAD: Carles Rentero

PROVIDER: PXD078364 | Pride | 2026-06-29

REPOSITORIES: Pride

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	2023LB019_CARE_001_01_45pto.raw	Raw
	2023LB019_CARE_002_01_45pto.raw	Raw
	2023LB019_CARE_003_01_45pto.raw	Raw
	2023LB019_CARE_004_01_45pto.raw	Raw
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Publications

Annexin A6 controls multi-organelle contact site formation and endolysosomal positioning, and remodels the STARD3 interactome.

Bernaus-Esqué Marc M Liu Yangjing Y Prats Eva E Estanyol Josep M JM Martin Gemma G Calvo Maria M Gigourtsi Panagiota Areti PA Nguyen Mai Khanh Linh MKL Álvarez Alejandra R AR Zanlungo Silvana S Agell Neus N Lu Albert A Tebar Francesc F Enrich Carlos C Grewal Thomas T Rentero Carles C

iScience 20260615 7

Annexin A6 (ANXA6) regulates cholesterol transfer across membrane contact sites (MCSs) between late endosomes/lysosomes (LE/Lys) and the endoplasmic reticulum (ER) via the late endosomal StAR-related lipid transfer domain-3 (STARD3) transporter. Here, we describe a significant reduction of MCSs in ANXA6-depleted HeLa cells, which could be rescued by restoration of ANXA6 expression. Using AnxA6 as bait in BioID-based assays, we demonstrate that ANXA6 interacts with various tethers and bona fide M ...[more]

PMID: 42338474

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Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells.

Project description: Not available

| S-EPMC9253107 | biostudies-literature

RNA-Immunoprecipitation Sequencing of Actinin-BirA* vs. Control iPSC-CMs

Project description:We found an enrichment of metabolic transcripts in proximity to actinin-BirA*, with sarcomere transcripts being depleted.

2021-08-10 | GSE144806 | GEO

BirA*-RAB18 proximity biotinylation in HeLa cells

Project description:Proximity labelling using transient expression of the same exogenous BirA*-RAB18 construct in wild-type HeLa cells and in otherwise isogenic RAB3GAP1-, RAB3GAP2- and TRAPPC9-null HeLa cell lines.

2024-01-26 | PXD016336 | Pride

Tbx1 binding site in whole mouse embryo at E9.5 from in vivo ChIP-seq

Project description:We generated Avidin tag inserted at 3' end of Tbx1 using CRISPR/Cas9 genomic engineering and crossed them with BirA mice from the Jackson laboratory. After established double homozygous mouse colony, total twenty embryos at E9.5 were collected for each samples. After extraction of nucleus, Tbx1 binding regions were captured with Dynabeads™ MyOne™ Streptavidin T1.

2021-10-10 | GSE173521 | GEO

Proximity biotinylation and LC-MSMS identification of the molecular microenvironment of coronavirus replication complexes

Project description:To investigate virus-host interactions at the site of coronavirus replication, we developed a biotin-based proximity labelling approach by engineering a promiscuous biotin ligase, BirA-R118G, within the coronavirus replication and transcription complex (RTC). BirA-R118G was fused to non-structural protein 2 to generate MHV- BirA-R118G-nsp2. During the course of infection, viral and host factors in proximity of the viral RTC become covalently biotinylated, allowing affinity purification of biotin-tagged factors and mass spectrometry identification of RTC-proximal viral and host factors. Results provide a comprehensive library of RTC-associated factors which likely include crucial factors that promote, orchestrate and assist viral replication within the viral RTC microenvironment.

2019-01-16 | PXD009975 | Pride

Proximity biotinylation of CDK1 associated proteins in U2OS cells

Project description:BirA ligase tagged CDK1 and BirA alone were expressed in U2OS cells. Proximal proteins to CDK1 were labelled by incubating cells with Biotin for 24 hours and biotinylated proteins extracted using Streptavidin pulldown.

2021-05-12 | PXD024796 | Pride

Translational profiling through biotinylation of tagged ribosomes in zebrafish

Project description:Phenotypic heterogeneity within a population of cells of the same cell type is a common theme in metazoan development. Apprehending complex developmental and physiological processes critically relies on our ability to probe the expression profile of these genetically defined cell sub-populations. Current strategies rely on cell enrichment based on tandem or simultaneous evaluation of multiple intersecting markers starting from a heterogeneous cellular suspension. The extensive tissue manipulations required for single-cell suspension generation, as well as the complexity of the required equipment, inherently complicates these approaches. Here, we propose an alternative methodology based on a genetically encoded system in the model organism Danio rerio (zebrafish). In transgenic fish, we take advantage of the combinatorial biotin transfer system where polysome-associated mRNAs are selectively recovered from cells expressing both a tagged ribosomal subunit, Rpl10a and the bacterial biotin ligase, BirA. We have applied this technique to skeletal muscle development, identifying genes with novel regulation and have developed tools for highly specific gene expression profiling during vertebrate development.

2014-08-07 | GSE59355 | GEO

Proximal Biotinylation Based Combinatory Approach for Isolating Plasma Membrane Proteins

Project description:Comprehensive profiling of the cell surface proteome has been challenging due to the lack of tools for an effective and reproducible way to isolate plasma membrane proteins from mammalian cells. Here, we employ a proximity-dependent biotinylation approach to label and isolate plasma membrane proteins without an extra in vitro labeling step that we called plasma membrane-BioID. The lipid modified BirA* enzyme (MyrPalm BirA*) was targeted to the plasma membrane where it effectively biotinylates plasma membrane proteins. Biotinylated proteins were then affinity purified and analyzed by mass spectrometry. Our analysis demonstrates that combining conventional sucrose density gradient centrifugation and plasma membrane-BioID is ideal to overcome the inherent limitations of identification of integral membrane proteins and yields highly pure plasma components for downstream proteomic analysis.

2020-08-28 | PXD018383 | Pride

Translational profiling through biotinylation of tagged ribosomes in zebrafish

2014-08-07 | E-GEOD-59355 | biostudies-arrayexpress

Seb1 proximity dependent biotinylation (PDB) in Schizosaccharomyces pombe

Project description:Transcription by RNA polymerase I (RNAPI) represents most of the transcriptional activity in eukaryotic cells and is associated with the production of mature ribosomal RNA (rRNA). As several rRNA maturation steps are coupled to RNAPI transcription, the rate of RNAPI elongation directly influences processing of nascent pre-rRNA, and changes in RNAPI transcription rate can result in alternative rRNA processing pathways in response to growth conditions and stress. However, factors and mechanisms that control RNAPI progression by influencing transcription elongation rate remain poorly understood. Our project is to show that the conserved RNA-binding Seb1 is a pausing-promoting factor for RNA polymerases I to control cotranscriptional RNA processing. Here, we did a proximity dependent biotinylation followed by mass spectrometry (PDB-MS) of the Seb1 protein in order to assess for physical interactions with the RNAPI transcription machinery. A mutant E. coli BirA enzyme is fused to the Seb1 protein. This mutant version of BirA uses biotin to catalyze the formation of biotinoyl-5′-AMP (bioAMP), thereby generating a ‘cloud’ of activated biotin molecules that can react with free primary amines (most often lysine residues) of neighboring proteins. This experiment will support the conclusion that Seb1 is located at the rDNA locus.

2023-05-02 | PXD037768 | Pride

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