Evidence map›Paper›PMID 36711448›Full record

ArticlebioRxiv : the preprint server for biology2023

Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome.

Tianyang Yan, Ashley R Julio, Miranda Villanueva, Anthony E Jones, Andréa B Ball, Lisa M Boatner, Alexandra C Turmon, Stephanie L Yen, Heta S Desai, Ajit S Divakaruni and 1 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 5 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 1 institution in 1 country.

Tianyang YanBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Ashley R JulioBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Miranda VillanuevaBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Anthony E JonesDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Andréa B BallDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Lisa M BoatnerBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Alexandra C TurmonBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Stephanie L YenBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Heta S DesaiBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Ajit S DivakaruniDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
Keriann M BackusBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.
University of California, Los Angeles · US

Funding

Transgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MILES Frome WILKINSON · 2003 to 2026
$40.4M
Systems in Integrative BiologyT32GM008185 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHOU, TOM · 1987 to 2022
$4.6M
Understanding How Metabolic Cofactors Control Cell Function and FateR35GM138003 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Ajit Divakaruni · 2020 to 2026
$2.8M
Chemistry Biology Interface Training ProgramT32GM136614 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Patrick G. Harran · 2020 to 2026
$2.8M
NIDDK NIH HHS P30 DK063491NIGMS NIH HHS R35 GM138003NIGMS NIH HHS T32 GM008185NIGMS NIH HHS T32 GM136614
6 · The paper itself

Abstract

Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxiCat, Biotin Switch, and SP3-Rox, they typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. To obviate requirements for laborious biochemical fractionation, here, we develop and apply an unprecedented two step cysteine capture method to establish the Local Cysteine Capture (Cys-LoC), and Local Cysteine Oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole cell proteomic analysis. Application of the Cys-LOx method to LPS stimulated murine immortalized bone marrow-derived macrophages (iBMDM), revealed previously unidentified mitochondria-specific inflammation-induced cysteine oxidative modifications including those associated with oxidative phosphorylation. These findings shed light on post-translational mechanisms regulating mitochondrial function during the cellular innate immune response.

Identifiers

PMID36711448
PMCPMC9882296
OpenAlexW4317716326

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.