---
_id: '10117'
abstract:
- lang: eng
  text: Proximity labeling provides a powerful in vivo tool to characterize the proteome
    of subcellular structures and the interactome of specific proteins. The nematode
    Caenorhabditis elegans is one of the most intensely studied organisms in biology,
    offering many advantages for biochemistry. Using the highly active biotin ligase
    TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage
    of TurboID is that biotin's high affinity for streptavidin means biotin-labeled
    proteins can be affinity-purified under harsh denaturing conditions. By combining
    extensive sonication with aggressive denaturation using SDS and urea, we achieved
    near-complete solubilization of worm proteins. We then used this protocol to characterize
    the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among
    the smallest C. elegans cells. To probe the method's sensitivity, we expressed
    TurboID exclusively in the two AFD neurons and showed that the protocol could
    identify known and previously unknown proteins expressed selectively in AFD. The
    active zones of synapses are composed of a protein matrix that is difficult to
    solubilize and purify. To test if our protocol could solubilize active zone proteins,
    we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic
    active zone protein. We identified many known ELKS-1-interacting active zone proteins,
    as well as previously uncharacterized synaptic proteins. Versatile vectors and
    the inherent advantages of using C. elegans, including fast growth and the ability
    to rapidly make and functionally test knock-ins, make proximity labeling a valuable
    addition to the armory of this model organism.
acknowledgement: We thank de Bono lab members for helpful comments on the manuscript,
  IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions
  and comments for the optimization of mass spec analyses of worm samples. The biotin
  auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of
  Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford
  University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54
  3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg).
  Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University
  of Vienna).
article_number: '101094'
article_processing_charge: Yes
article_type: original
author:
- first_name: Murat
  full_name: Artan, Murat
  id: C407B586-6052-11E9-B3AE-7006E6697425
  last_name: Artan
  orcid: 0000-0001-8945-6992
- first_name: Stephen
  full_name: Barratt, Stephen
  id: 57740d2b-2a88-11ec-97cf-d9e6d1b39677
  last_name: Barratt
- first_name: Sean M.
  full_name: Flynn, Sean M.
  last_name: Flynn
- first_name: Farida
  full_name: Begum, Farida
  last_name: Begum
- first_name: Mark
  full_name: Skehel, Mark
  last_name: Skehel
- first_name: Armel
  full_name: Nicolas, Armel
  id: 2A103192-F248-11E8-B48F-1D18A9856A87
  last_name: Nicolas
- first_name: Mario
  full_name: De Bono, Mario
  id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
  last_name: De Bono
  orcid: 0000-0001-8347-0443
citation:
  ama: Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis
    elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological
    Chemistry</i>. 2021;297(3). doi:<a href="https://doi.org/10.1016/J.JBC.2021.101094">10.1016/J.JBC.2021.101094</a>
  apa: Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &#38;
    de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by
    TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. Elsevier.
    <a href="https://doi.org/10.1016/J.JBC.2021.101094">https://doi.org/10.1016/J.JBC.2021.101094</a>
  chicago: Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel,
    Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans
    Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>.
    Elsevier, 2021. <a href="https://doi.org/10.1016/J.JBC.2021.101094">https://doi.org/10.1016/J.JBC.2021.101094</a>.
  ieee: M. Artan <i>et al.</i>, “Interactome analysis of Caenorhabditis elegans synapses
    by TurboID-based proximity labeling,” <i>Journal of Biological Chemistry</i>,
    vol. 297, no. 3. Elsevier, 2021.
  ista: Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021.
    Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
    labeling. Journal of Biological Chemistry. 297(3), 101094.
  mla: Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses
    by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>,
    vol. 297, no. 3, 101094, Elsevier, 2021, doi:<a href="https://doi.org/10.1016/J.JBC.2021.101094">10.1016/J.JBC.2021.101094</a>.
  short: M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de
    Bono, Journal of Biological Chemistry 297 (2021).
date_created: 2021-10-10T22:01:23Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2025-04-14T07:43:46Z
day: '01'
ddc:
- '612'
department:
- _id: MaDe
- _id: LifeSc
doi: 10.1016/J.JBC.2021.101094
ec_funded: 1
external_id:
  isi:
  - '000706409200006'
file:
- access_level: open_access
  checksum: 19e39d36c5b9387c6dc0e89c9ae856ab
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-10-11T12:20:58Z
  date_updated: 2021-10-11T12:20:58Z
  file_id: '10121'
  file_name: 2021_JBC_Artan.pdf
  file_size: 1680010
  relation: main_file
  success: 1
file_date_updated: 2021-10-11T12:20:58Z
has_accepted_license: '1'
intvolume: '       297'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Journal of Biological Chemistry
publication_identifier:
  eissn:
  - 1083-351X
  issn:
  - 0021-9258
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity
  labeling
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 297
year: '2021'
...