Activated ClpP kills persisters and eradicates a chronic biofilm infection

• Published in: Nature (London) Vol. 503; no. 7476; pp. 365 - 370
• Main Authors: Conlon, B. P., Nakayasu, E. S., Fleck, L. E., LaFleur, M. D., Isabella, V. M., Coleman, K., Leonard, S. N., Smith, R. D., Adkins, J. N., Lewis, K.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21.11.2013; Nature Publishing Group
• Subjects: 14; 14/28; 14/63; 631/326/22/1290; 64/60; 82; 82/58; 82/75; Animal models; Animals; Anti-Bacterial Agents - pharmacology; Antibiotics; Bacterial Proteins - metabolism; Bacteriology; Biofilms; Biofilms - drug effects; Biofilms - growth & development; Cell division; Chronic illnesses; Corruption; Depsipeptides - pharmacology; Dosage and administration; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Bacterial - drug effects; Drug therapy; Enzyme Activation - drug effects; Experiments; Female; Humanities and Social Sciences; Immune system; Infection; Mice; Microbial Viability - drug effects; Microbiology; multidisciplinary; Polypeptides; Properties; Protease inhibitors; Proteases; Protein synthesis; Proteins; Proteolysis - drug effects; Proteomics; Rifampin; Rifampin - pharmacology; Science; Serine Endopeptidases - metabolism; Staphylococcal Infections - drug therapy; Staphylococcal Infections - microbiology; Staphylococcus aureus - classification; Staphylococcus aureus - drug effects; Staphylococcus aureus - enzymology; Staphylococcus aureus - metabolism; Staphylococcus infections; Streptococcus infections; Transfer RNA; United States
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature12790

Chronic infections are difficult to treat with antibiotics but are caused primarily by drug-sensitive pathogens. Dormant persister cells that are tolerant to killing by antibiotics are responsible for this apparent paradox. Persisters are phenotypic variants of normal cells and pathways leading to dormancy are redundant, making it challenging to develop anti-persister compounds. Biofilms shield persisters from the immune system, suggesting that an antibiotic for treating a chronic infection should be able to eradicate the infection on its own. We reasoned that a compound capable of corrupting a target in dormant cells will kill persisters. The acyldepsipeptide antibiotic (ADEP4) has been shown to activate the ClpP protease, resulting in death of growing cells. Here we show that ADEP4-activated ClpP becomes a fairly nonspecific protease and kills persisters by degrading over 400 proteins, forcing cells to self-digest. Null mutants of clpP arise with high probability, but combining ADEP4 with rifampicin produced complete eradication of Staphylococcus aureus biofilms in vitro and in a mouse model of a chronic infection. Our findings indicate a general principle for killing dormant cells—activation and corruption of a target, rather than conventional inhibition. Eradication of a biofilm in an animal model by activating a protease suggests a realistic path towards developing therapies to treat chronic infections. Dormant bacterial persister cells evade antibiotic destruction and their survival gives rise to some chronic infections; this study reveals that persister cells can be eradicated with a compound activating the bacterial protease ClpP, providing an effective biofilm treatment in vitro and in mouse chronic infection models. An anti-persister antibiotic Concerns about the ability of today's antibiotics to cope with future infections are compounded by the dual nature of the bacterial response to the drugs. Some bacteria develop genetic resistance, but others become tolerant, able to survive in the presence of antibiotics by forming dormant cells known as persisters in which the enzymatic targets of the antibiotics are inactive. Kim Lewis and colleagues sought compounds with the potential to kill persisters by corrupting targets within these energy-limited cells. They demonstrate that the acyldepsipeptide antibiotic ADEP4 activates ClpP protease and the cell's proteolytic machinery, killing persister cells by forcing them to degrade a range of cellular proteins. This is a potentially important result, suggesting that combining compounds such as ADEP4 with conventional antibiotics could provide new and robust strategies for the control of chronic infections.