Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F23%3A00569715" target="_blank" >RIV/60077344:_____/23:00569715 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11310/23:10458024

Result on the web

<a href="https://www.sciencedirect.com/science/article/pii/S0021925822011693?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/pii/S0021925822011693?via%3Dihub</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.jbc.2022.102726" target="_blank" >10.1016/j.jbc.2022.102726</a>

Result language

angličtina

Original language name

Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared

Original language description

The characterization of protein-protein interactions (PPIs) is of high value for understanding protein function. Two stra-tegies are popular for identification of PPIs direct from the cellular environment: affinity capture (pulldown) isolates the protein of interest with an immobilized matrix that specifically captures the target and potential partners, whereas in BioID, genetic fusion of biotin ligase facilitates proximity bio-tinylation, and labeled proteins are isolated with streptavidin. Whilst both methods provide valuable insights, they can reveal distinct PPIs, but the basis for these differences is less obvious. Here, we compare both methods using four different trypanosome proteins as baits: poly(A)-binding proteins PABP1 and PABP2, mRNA export receptor MEX67, and the nucleoporin NUP158. With BioID, we found that the popula-tion of candidate interacting proteins decreases with more confined bait protein localization, but the candidate population is less variable with affinity capture. BioID returned more likely false positives, in particular for proteins with less confined localization, and identified low molecular weight proteins less efficiently. Surprisingly, BioID for MEX67 identified exclu-sively proteins lining the inner channel of the nuclear pore complex (NPC), consistent with the function of MEX67, whereas the entire NPC was isolated by pulldown. Similarly, for NUP158, BioID returned surprisingly few PPIs within NPC outer rings that were by contrast detected with pulldown but instead returned a larger cohort of nuclear proteins. These rather significant differences highlight a clear issue with reli-ance on a single method to identify PPIs and suggest that BioID and affinity capture are complementary rather than alternative approaches.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10606 - Microbiology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Biological Chemistry

ISSN

0021-9258

e-ISSN

1083-351X

Volume of the periodical

299

Issue of the periodical within the volume

1

Country of publishing house

US - UNITED STATES

Number of pages

15

Pages from-to

102726

UT code for WoS article

000923287700005

EID of the result in the Scopus database

2-s2.0-85146228423