ATP-dependent proteases of bacteria: recognition logic and operating principles

Abstract

ATP-powered AAA+ proteases degrade specific proteins in intracellular environments occupied by thousands of different proteins. These proteases operate as powerful molecular machines that unfold stable native proteins before degradation. Understanding how these enzymes choose the 'right' protein substrates at the 'right' time is key to understanding their biological function. Recently, proteomic approaches have identified numerous substrates for some bacterial enzymes and the sequence motifs responsible for recognition. Advances have also been made in elucidating the mechanism and impact of adaptor proteins in regulating substrate choice. Finally, recent biochemical dissection of the ATPase cycle and its coupling to protein unfolding has revealed fundamental operating principles of this important, ubiquitous family of molecular machines. The AAA+ proteasesAAA+ proteases (the term AAA comes from 'ATPase associated with cellular activities') are multimeric machines that function with exquisite specificity in all domains of life to recognize, to unfold and to degrade proteins. Energy-dependent proteases differ widely in their complexity. For example, the 26S proteasome is built from >30 different types of protein, whereas a single type of subunit assembles to form the hexameric FtsH and Lon proteases. Nevertheless, ATP-dependent proteases share common architectural features [1][2][3].For example, the active sites that catalyze peptide bond cleavage are sequestered in a hollow interior chamber, typically constructed from rings of six or seven subunits or domains ( Figure 1a). Substrates enter these degradation compartments through axial channels or portals that are too narrow to admit folded native proteins. This restriction prevents the undesirable cleavage of most cellular proteins but requires the coordinated enzymatic recognition, unfolding and translocation of correct substrates before degradation. Hexameric rings of subunits or domains, which belong to the AAA+ ATPase family, carry out these mechanical denaturation and translocation steps. Moreover, these proteins and related AAA+ enzymes often function to disassemble macromolecular complexes and to resolubilize protein aggregates [4,5]. Substrate recognition can be mediated directly by the AAA+ domains of ATP-dependent proteases or indirectly by additional domains or adaptor proteins (Figure 1b) and ClpS). In particular, we highlight recent developments that have advanced our understanding of the mechanisms by which the AAA+ proteases and their adaptors function. Recognition through peptide 'tags'One mechanism that enables ATP-dependent proteases to recognize specific substrates involves binding to unstructured peptide sequences, which are typically located at the Nterminal or C-terminal end of a target protein. Recognition of 'degradation tags' can be the sole determinant of targeted proteolysis. For example, one quality control system in Escherichia coli adds the 'ssrA tag' sequence (AANDENYALAA) to the C terminus of proteins for which biosynthesis...

Protein targeting to ATP-dependent proteases

“…Prokaryotes also use adapter proteins for their ATP-dependent proteases [70,71]. SspB is one such adapter and it promotes degradation of several substrates, including that of ssrA-tagged proteins by ClpXP [72,73].…”

Subunit Stoichiometry, Evolution, and Functional Implications of an Asymmetric Plant Plastid ClpP/R Protease Complex in Arabidopsis

“…The Clp machinery has two oligomeric components: A barrel-shaped tetradecameric protease core with the catalytic sites sequestered inside the complex and hexameric ring-like ATP-dependent chaperones. The chaperones recognize specific substrates with or without the aid of adaptors, unfold these substrates, and translocate them into the proteolytic core for degradation (Baker and Sauer, 2006;Striebel et al, 2009). Compartmentalization of the proteolytic sites within the core complex, and coupling with chaperones and associated factors for substrate delivery, enable targeted protein degradation within the cell.…”

Structural Insights into the Conformational Diversity of ClpP from Bacillus subtilis

“…The Clp-family comprises members involved in energydependent protease systems that play important roles in protein quality control by removing misfolded or damaged proteins as well as no longer needed short-lived regulatory proteins to avoid potential aggregation (Baker and Sauer, 2006;Gottesman, 2003). Clp proteases contain two distinct functional components, Clp-ATPase which acts as an unfoldase/chaperone, and ClpP which acts as a peptidase.…”