SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling

Sami T Tuomivaara; Chin Fen Teo; Yuh Nung Jan; Arun P Wiita; Lily Y Jan

doi:10.1038/s42003-024-06729-x

SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling

Commun Biol. 2024 Aug 29;7(1):1060. doi: 10.1038/s42003-024-06729-x.

Authors

Sami T Tuomivaara^#^{1

2}, Chin Fen Teo^#^{3

4}, Yuh Nung Jan^{3

4

5}, Arun P Wiita^{6

7

8}, Lily Y Jan^{9

10

11}

Affiliations

¹ Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
² Department of Obstetrics, Gynecology & Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, CA, USA.
³ Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
⁴ Department of Physiology, University of California, San Francisco, CA, USA.
⁵ Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
⁶ Department of Laboratory Medicine, University of California, San Francisco, CA, USA. [email protected].
⁷ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. [email protected].
⁸ Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA. [email protected].
⁹ Howard Hughes Medical Institute, University of California, San Francisco, CA, USA. [email protected].
¹⁰ Department of Physiology, University of California, San Francisco, CA, USA. [email protected].
¹¹ Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA. [email protected].

^# Contributed equally.

Abstract

To facilitate our understanding of proteome dynamics during signaling events, robust workflows affording fast time resolution without confounding factors are essential. We present Surface-exposed protein Labeling using PeroxidaSe, H₂O₂, and Tyramide-derivative (SLAPSHOT) to label extracellularly exposed proteins in a rapid, specific, and sensitive manner. Simple and flexible SLAPSHOT utilizes recombinant soluble APEX2 protein applied to cells, thus circumventing the engineering of tools and cells, biological perturbations, and labeling biases. We applied SLAPSHOT and quantitative proteomics to examine the TMEM16F-dependent plasma membrane remodeling in WT and TMEM16F KO cells. Time-course data ranging from 1 to 30 min of calcium stimulation revealed co-regulation of known protein families, including the integrin and ICAM families, and identified proteins known to reside in intracellular organelles as occupants of the freshly deposited extracellularly exposed membrane. Our data provide the first accounts of the immediate consequences of calcium signaling on the extracellularly exposed proteome.

MeSH terms

Animals
Anoctamins* / genetics
Anoctamins* / metabolism
Calcium Signaling
Calcium* / metabolism
Cell Membrane* / metabolism
Humans
Hydrogen Peroxide / metabolism
Mice
Phospholipid Transfer Proteins / genetics
Phospholipid Transfer Proteins / metabolism
Phospholipids / metabolism
Proteome* / metabolism
Proteomics / methods

Substances

Proteome
Calcium
Anoctamins
Phospholipids
Phospholipid Transfer Proteins
Hydrogen Peroxide

Grants and funding

R35 NS122110/NS/NINDS NIH HHS/United States