E. coli-based selection and expression systems for discovery, characterization, and purification of ubiquitylated proteins

Olga Levin-Kravets, Tal Keren-Kaplan, Ilan Attali, Itai Sharon, Neta Tanner, Dar Shapira, Ritu Rathi, Avinash Persaud, Noa Shohat, Anna Shusterman, Gali Prag*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

1 Scopus citations

Abstract

Ubiquitylation is an eukaryotic signal that regulates most cellular pathways. However, four major hurdles pose challenges to study ubiquitylation: (1) high redundancy between ubiquitin (Ub) cascades, (2) ubiquitylation is tightly regulated in the cell, (3) the transient nature of the Ub signal, and (4) difficulties to purify functional ubiquitylation apparatus for in vitro assay. Here, we present systems that express functional Ub cascades in E. coli, which lacks deubiquitylases, Ub-dependent degradations, and control mechanisms for ubiquitylation. Therefore, expression of an ubiquitylation cascade results in the accumulation of stable ubiquitylated protein that can be genetically selected or purified, thus circumventing the above challenges. Co-expression of split antibiotic resistance protein fragments tethered to Ub and ubiquitylation targets along with ubiquitylation enzymes (E1, E2, and E3) gives rise to bacterial growth on selective media. We show that ubiquitylation rate is highly correlated with growth efficiency. Hence, genetic libraries and simple manipulations in the selection system facilitate the identification and characterization of components and interfaces along Ub cascades. The bacterial expression system also facilitates the detection of ubiquitylated proteins. Furthermore, the expression system allows affinity chromatography-based purification of milligram quantities of ubiquitylated proteins for downstream biochemical, biophysical, and structural studies.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages155-166
Number of pages12
DOIs
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
Volume1844
ISSN (Print)1064-3745

Funding

FundersFunder number
Ministry of Health, State of Israel5108

    Keywords

    • Bacterial genetics
    • Expression and purification of ubiquitylated proteins
    • Identification
    • Selection

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