Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control

If a protein does not fold into the correct shape, it may be unable to act correctly and can harm cells. As a result, cells contain biological machines that refold or break down misfolded proteins. ATP-dependent AAA+ proteases are an example of such machines. Their activity needs to be tightly controlled because breaking down the wrong proteins can also harm cells. ATP-dependent AAA+ proteases form ring-shaped assemblies that are composed of AAA+ proteins and an associated peptidase. In bacteria, the AAA+ protein called ClpC can be crucial for resisting stress and infecting host cells. Adapter proteins help to activate ClpC by binding to extra domains that are fused to or inserted into the protein. This method of activation also requires repressing elements that ensure that the activity of ClpC remains low when the adapter proteins are not present. It was not known how this repression works. Carroni, Franke et al. have now used a technique called cryo-electron microscopy to study the structures of repressed and adapter-activated ClpC from pathogenic bacteria called Staphylococcus aureus. In the repressed state, 10 molecules of ClpC interact to form two assemblies that interact via regions called middle domains. The middle domains have a “coiled coil” structure, and they interact via their ends in a head-to-head manner. In the repressed state ClpC cannot interact with its partner peptidase and the shape of the assembly shields the sites where adapter proteins can bind. This renders ClpC inactive. Carroni, Franke et al. also studied ClpC proteins that had mutations to the middle domain that prevented the repressed state from forming. The mutant proteins remain in a constantly active state that is highly toxic to bacteria. Bacteria are increasingly evolving to resist the effects of the antibiotics commonly used to treat infections. This is a severe problem, and we need to develop new antibiotic drugs that will kill these bacteria. AAA+ proteases have been identified as possible targets for new antibacterial drugs. The results presented by Carroni, Franke et al. suggest that disrupting the repressing activity of ClpC middle domains could be an effective way for such drugs to work.