biostudies-literatureIzert-Nowakowska MAFundacja na rzecz Nauki Polskiej (FNP)Ministerstwo Edukacji i Nauki (MNiSW)Narodowe Centrum Nauki (NCN)3994-4016https://www.ebi.ac.uk/biostudies/studies/S-EPMC12373786biostudies-literatureUnknown26(16)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.EMBO reportsTargeted protein degradation in Escherichia coli using CLIPPERs.PMC12373786Initiative of Excellence - Research University,University of Warsaw I.4.1&2,BOB-IDUB-622-20/20212020/39/B/NZ2/01301POIR.04.04.00-00-5EC1/18-00Wroblewski KKowalski JJGoral TKmiecik SKlimecka MMBandyra KJGorna MWAntosiewicz ASerwa RAIzert-Nowakowska MAfalseTargeted protein degradation in Escherichia coli using CLIPPERs.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.2025-01-01T00:00:00Z2025 Aug2026-05-09T10:46:43.109Z2026-04-08T00:48:54.807ZS-EPMC123737864056279310.1038/s44319-025-00510-9