Targeted protein degradation in Escherichia coli using CLIPPERs.

IF 6.5 1区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

EMBO Reports Pub Date : 2025-06-25 DOI:10.1038/s44319-025-00510-9

Matylda Anna Izert-Nowakowska, Maria Magdalena Klimecka, Anna Antosiewicz, Karol Wróblewski, Jakub Józef Kowalski, Katarzyna Justyna Bandyra, Tomasz Góral, Sebastian Kmiecik, Remigiusz Adam Serwa, Maria Wiktoria Górna

{"title":"Targeted protein degradation in Escherichia coli using CLIPPERs.","authors":"Matylda Anna Izert-Nowakowska, Maria Magdalena Klimecka, Anna Antosiewicz, Karol Wróblewski, Jakub Józef Kowalski, Katarzyna Justyna Bandyra, Tomasz Góral, Sebastian Kmiecik, Remigiusz Adam Serwa, Maria Wiktoria Górna","doi":"10.1038/s44319-025-00510-9","DOIUrl":null,"url":null,"abstract":"<p><p>New, universal tools for targeted protein degradation in bacteria can help to accelerate protein function studies and antimicrobial research. We describe a new method for degrading bacterial proteins using plasmid-encoded degrader peptides which deliver target proteins for degradation by a highly conserved ClpXP protease. We demonstrate the mode of action of the degraders on a challenging essential target, GroEL. The studies in bacteria are complemented by in vitro binding and structural studies. Expression of degrader peptides results in a temperature-dependent growth inhibition and depletion of GroEL levels over time. The reduction of GroEL levels is accompanied by dramatic proteome alterations. The presented method offers a new alternative approach for regulating protein levels in bacteria without genomic modifications or tag fusions. Our studies demonstrate that ClpXP is an attractive protease for the future use in bacterial-targeted protein degradation.</p>","PeriodicalId":11541,"journal":{"name":"EMBO Reports","volume":" ","pages":""},"PeriodicalIF":6.5000,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"EMBO Reports","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1038/s44319-025-00510-9","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

New, universal tools for targeted protein degradation in bacteria can help to accelerate protein function studies and antimicrobial research. We describe a new method for degrading bacterial proteins using plasmid-encoded degrader peptides which deliver target proteins for degradation by a highly conserved ClpXP protease. We demonstrate the mode of action of the degraders on a challenging essential target, GroEL. The studies in bacteria are complemented by in vitro binding and structural studies. Expression of degrader peptides results in a temperature-dependent growth inhibition and depletion of GroEL levels over time. The reduction of GroEL levels is accompanied by dramatic proteome alterations. The presented method offers a new alternative approach for regulating protein levels in bacteria without genomic modifications or tag fusions. Our studies demonstrate that ClpXP is an attractive protease for the future use in bacterial-targeted protein degradation.

查看原文本刊更多论文

利用CLIPPERs对大肠杆菌进行靶向蛋白降解。

新的、通用的细菌靶向蛋白质降解工具可以帮助加速蛋白质功能研究和抗菌研究。我们描述了一种利用质粒编码的降解肽来降解细菌蛋白的新方法，这种降解肽可以将目标蛋白传递给高度保守的ClpXP蛋白酶。我们在一个具有挑战性的基本目标GroEL上展示了降解器的作用模式。体外结合和结构研究补充了细菌的研究。随着时间的推移，降解肽的表达导致温度依赖性生长抑制和GroEL水平的消耗。GroEL水平的降低伴随着剧烈的蛋白质组改变。提出的方法提供了一种新的替代方法来调节蛋白质水平的细菌没有基因组修饰或标签融合。我们的研究表明，ClpXP是一种有吸引力的蛋白酶，用于未来的细菌靶向蛋白质降解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

EMBO Reports 生物-生化与分子生物学

CiteScore

11.20

自引率

1.30%

发文量

267

审稿时长

1 months

期刊介绍： EMBO Reports is a scientific journal that specializes in publishing research articles in the fields of molecular biology, cell biology, and developmental biology. The journal is known for its commitment to publishing high-quality, impactful research that provides novel physiological and functional insights. These insights are expected to be supported by robust evidence, with independent lines of inquiry validating the findings. The journal's scope includes both long and short-format papers, catering to different types of research contributions. It values studies that: Communicate major findings: Articles that report significant discoveries or advancements in the understanding of biological processes at the molecular, cellular, and developmental levels. Confirm important findings: Research that validates or supports existing knowledge in the field, reinforcing the reliability of previous studies. Refute prominent claims: Studies that challenge or disprove widely accepted ideas or hypotheses in the biosciences, contributing to the correction and evolution of scientific understanding. Present null data: Papers that report negative results or findings that do not support a particular hypothesis, which are crucial for the scientific process as they help to refine or redirect research efforts. EMBO Reports is dedicated to maintaining high standards of scientific rigor and integrity, ensuring that the research it publishes contributes meaningfully to the advancement of knowledge in the life sciences. By covering a broad spectrum of topics and encouraging the publication of both positive and negative results, the journal plays a vital role in promoting a comprehensive and balanced view of scientific inquiry.