Hinge-Linker Elements in the AAA+ Protein Unfoldase ClpX Mediate Intersubunit Communication, Assembly, and Mechanical Activity

Biochemistry. 2018 Dec 11;57(49):6787-6796. doi: 10.1021/acs.biochem.8b00907. Epub 2018 Nov 20.

Abstract

The ClpXP protease plays important roles in protein homeostasis and quality control. ClpX is a ring-shaped AAA+ homohexamer that unfolds target proteins and translocates them into the ClpP peptidase for degradation. AAA+ modules in each ClpX subunit-consisting of a large AAA+ domain, a short hinge-linker element, and a small AAA+ domain-mediate the mechanical activities of the ring hexamer. Here, we investigate the roles of these hinge-linker elements in ClpX function. Deleting one hinge-linker element in a single-chain ClpX pseudohexamer dramatically decreases unfolding and degradation activity, in part by compromising the formation of closed rings, protein-substrate binding, and ClpP binding. Covalently reclosing the broken hinge-linker interface rescues activity. Deleting one hinge-linker element from a single-chain dimer or trimer prevents assembly of stable hexamers. Mutationally disrupting a hinge-linker element preserves closed-ring assembly but reduces ATP-hydrolysis cooperativity and degradation activity. These results indicate that hinge-linker length and flexibility are optimized for efficient substrate unfolding and support a model in which the hinge-linker elements of ClpX facilitate efficient degradation both by maintaining proper ring geometry and facilitating subunit-subunit communication. This model informs our understanding of ClpX as well as the larger AAA+ family of motor proteins, which play diverse roles in converting chemical into mechanical energy in all cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATPases Associated with Diverse Cellular Activities / chemistry*
  • ATPases Associated with Diverse Cellular Activities / genetics
  • ATPases Associated with Diverse Cellular Activities / metabolism*
  • Adenosine Triphosphate / metabolism
  • Biomechanical Phenomena
  • Endopeptidase Clp / chemistry*
  • Endopeptidase Clp / genetics
  • Endopeptidase Clp / metabolism*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Hydrolysis
  • Microscopy, Electron
  • Models, Molecular
  • Molecular Chaperones / chemistry*
  • Molecular Chaperones / genetics
  • Molecular Chaperones / metabolism*
  • Mutagenesis
  • Protein Interaction Domains and Motifs
  • Protein Structure, Quaternary
  • Protein Subunits
  • Proteostasis
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism
  • Unfolded Protein Response

Substances

  • Escherichia coli Proteins
  • Molecular Chaperones
  • Protein Subunits
  • RNA-Binding Proteins
  • small protein B
  • Adenosine Triphosphate
  • Endopeptidase Clp
  • ClpX protein, E coli
  • ATPases Associated with Diverse Cellular Activities