Co-translational protein aggregation and ribosome stalling as a broad-spectrum antibacterial mechanism
Laleh Khodaparast, Ladan Khodaparast, Ramon Duran‐Romaña, Guiqin Wu, Bert Houben, Wouter Duverger, Matthias De Vleeschouwer, Katerina Konstantoulea, Fleur Nysen, Thomas Schalck, Daniel J. Curwen, Lisandra L. Martin, Sébastien Carpentier, Bernard Scorneaux, J.-F. Michiels, Joost Schymkowitz, Frédéric Rousseau
Abstract
Drug-resistant bacteria pose an urgent global health threat, necessitating the development of antibacterial compounds with novel modes of action. Protein biosynthesis accounts for up to half of the energy expenditure of bacterial cells, and consequently inhibiting the efficiency or fidelity of the bacterial ribosome is a major target of existing antibiotics. Here, we describe an alternative mode of action that affects the same process: allowing translation to proceed but causing co-translational aggregation of the nascent peptidic chain. We show that treatment with an aggregation-prone peptide induces formation of polar inclusion bodies and activates the SsrA ribosome rescue pathway in bacteria. The inclusion bodies contain ribosomal proteins and ribosome hibernation factors, as well as mRNAs and cognate nascent chains of many proteins in amyloid-like structures, with a bias for membrane proteins with a fold rich in long-range beta-sheet interactions. The peptide is bactericidal against a wide range of pathogenic bacteria in planktonic growth and in biofilms, and reduces bacterial loads in mouse models of Escherichia coli and Acinetobacter baumannii infections. Our results indicate that disrupting protein homeostasis via co-translational aggregation constitutes a promising strategy for development of broad-spectrum antibacterials. Protein biosynthesis is a major target of existing antibiotics that inhibit the efficiency or fidelity of the bacterial ribosome. Here, the authors show that a synthetic peptide displays bactericidal activity through a different mechanism, inducing co-translational aggregation of nascent peptidic chains.