Characterization of the Structure and Function of Escherichia coli DegQ as a Representative of the DegQ-like Proteases of Bacterial HtrA Family Proteins

Abstract

HtrA family proteins play a central role in protein quality control in the bacterial periplasmic space. DegQ-like proteases, a group of bacterial HtrA proteins, are characterized by a short LA loop as compared with DegP-like proteases, and are found in many bacterial species. As a representative of the DegQ-like proteases, we report that Escherichia coli DegQ exists in vivo primarily as a trimer (substrate-free) or dodecamer (substrate-containing). Biochemical analysis of DegQ dodecamers revealed that the major copurified protein substrate is OmpA. Importantly, wild-type DegQ exhibited a much lower proteolytic activity, and thus higher chaperone-like activity, than DegP. Furthermore, using cryo-electron microscopy we determined high-resolution structures of DegQ 12- and 24-mers in the presence of substrate, thus revealing the structural mechanism by which DegQ moderates its proteolytic activity.

Downregulation of chloroplast protease AtDeg5 leads to changes in chronological progression of ontogenetic stages, leaf morphology and chloroplast ultrastructure in Arabidopsis

“…Depending on whether the number of AtDeg5 catalytic sites is substantially or only modestly excessive in relation to functional needs a phenotypic trait may fall into group 1 or 2, respectively. 6 Diurnal changes in starch content in leaves of WT and deg5 mutant plants. Starch content was determined in juvenile (leaf 3) and mature (leaf 5) leaves of WT as well as deg5-2 and deg5-1 mutant plants that had reached secondary stage 6.0.…”

“…In fact the quality of E. coli periplasmic proteins is controlled by three Deg proteins namely DegP, DegQ and DegS whose structure and function have been solved in much detail [4][5][6]. Later Deg proteases were found to occur ubiquitously in cells of all domains of life, from Bacteria through Archea to Eukarya [7].…”

Cryo-EM structure of Nma111p, a unique HtrA protease composed of two protease domains and four PDZ domains

“…Based on the domain organization, the HtrA family proteins can be divided into distinct groups. Group 1 proteins (e.g., DegS in E. coli and Htra2 in mammal) contain one protease domain and one PDZ domain [4,5], and group 2 proteins (e.g., DegP and DegQ in E. coli) contain one protease domain and two PDZ domains [6,7]. Nma111p-like proteases in group 3 are distinctively characterized by possessing two protease domains and four PDZ domains, of which the N-terminal protease domain exhibits protease activity, whereas the C-terminal protease domain is supposed to be degenerated in protease activity.…”

“…The structures of several members of groups 1 and 2 of the HtrA family have been determined by X-ray crystallography or cryo-electron microscopy (cryo-EM) [6,7,9,10]. However, none belongs to group 3.…”

Autotransporter proteins of Uropathogenic Escherichia coli: regulation, characterisation and the role of periplasmic proteins in their expression

“…DegP exists as an inactive hexameric protein ( Figure 1.7), consisting of two face-to-face trimer complexes (Krojer et al, 2002, Jomaa et al, 2007. DegQ, however, exists primarily as substrate-free catalytically active trimer (Bai et al, 2011). Both DegP and DegQ form higher oligomeric structures, including 12-mer and 24-mer cage-like structures (Figure 1.7) (Bai et al, 2011, Malet et al, 2012, Sawa et al, 2011, Krojer et al, 2008, Jiang et al, 2008.…”