Architecture and regulation of HtrA-family proteins involved in protein quality control and stress response

Abstract

Protein quality control is vital for all living cells and sophisticated molecular mechanisms have evolved to prevent the excessive accumulation of unfolded proteins. High-temperature requirement A (HtrA) proteases have been identified as important ATP-independent quality-control factors in most species. HtrA proteins harbor a serine-protease domain and at least one peptide-binding PDZ domain to ensure efficient removal of misfolded or damaged proteins. One distinctive property of HtrAs is their ability to assemble into complex oligomers. Whereas all examined HtrAs are capable of forming pyramidal 3-mers, higher-order complexes consisting of up to 24 molecules have been reported. Tight control of chaperone and protease function is of pivotal importance in preventing deleterious HtrA-protease activity. In recent years, structural biology provided detailed insights into the molecular basis of the regulatory mechanisms, which include unique intramolecular allosteric signaling cascades and the dynamic switching of oligomeric states of HtrA proteins. Based on these results, functional models for many family members have been developed. The HtrA protein family represents a remarkable example of how structural and functional diversity is attained from the assembly of simple molecular building blocks.

Fig. 1

Domain organization and molecular assemblies of HtrA proteins. a Schematic representation of the distribution of domains in HtrA proteins discussed in this review. b Comparison of the overall dimensions of different higher-order HtrA particles. CP, cytoplasmic domain; TM, transmembrane domain; IGFBP, insulin-like growth-factor binding protein domain

Fig. 2

Three-dimensional structures of prokaryotic HtrA proteins. The proteins are shown in a surface representation with protease domain in blue, PDZ1 in orange, and PDZ2 in green. HtrA assemblies from top left to bottom right: DegS from E. coli (3-mer); DegQ from T. maritima (3-mer); HtrA2 from M. tuberculosis (3-mer); DegP from E. coli 6-mer, 12-mer, 24-mer; DegQ from L. fallonii (12-mer); DegQ from E. coli based on cryo-EM maps, 12-mer, 24-mer. The assemblies are not shown to scale relative to each other

Fig. 3

Allosteric activation cascade of HtrA proteins. a DegS_Ec monomer (gray) and protease domain of an adjacent monomer (blue) as observed in the DegS_Ec 3-mer. b DegP_Ec monomer (gray) and protease domain (brown) of an adjacent molecule taken from the DegP_Ec 24-mer. Activating peptides bound to the allosteric PDZ1 binding site are shown as sticks. Residues of the catalytic triad are shown in ball-and-stick representation (in b the catalytic Ser was replaced by Ala). Loops of the allosteric activation cascade are colored in red and the activated proteolytic sites are highlighted in green. Asterisks denote structural elements in neighboring DegS_Ec and DegP_Ec molecules in 3- and 24-mers, respectively

Fig. 4

Three-dimensional structures of eukaryotic HtrA proteins. Representation as in Fig. 2. Deg1 from A. thaliana (6-mer); human HtrA1 (3-mer); human HtrA2/Omi (3-mer). The assemblies are not shown to scale relative to each other

Fig. 5

PDZ domains in higher-order HtrA oligomers. a Position of the PDZ1 from DegQ_Lf 12-mer (blue), DegP_Ec 12-mer (orange), and DegP_Ec 24-mer (green) with respect to the superimposed protease domains (gray). b Position of PDZ2 with respect to superimposed protease and PDZ1 domains (gray). Colors as in a

Fig. 6

Interaction of PDZ domains stabilizing intertrimer interfaces of higher-order HtrA assemblies. a Interaction of PDZ1* (brown, surface representation) and PDZ2 in DegP_Ec 12-mers (orange ribbons) and PDZ2 in DegQ_Lf 12-mers (blue ribbons). b Interaction of PDZ1*/PDZ* (brown, surface representation) and PDZ1 in DegP_Ec 6-mers (purple ribbons) and PDZ in Deg1_AtQ_Lf 6-mers (green ribbons). PDZ1* (a) and PDZ1*/PDZ* (b) are shown in the same orientation. Boxes specify the interaction of structural elements responsible for stabilization of the PDZ–PDZ interaction in each case. Numbering of secondary structure elements and loops (L) as in [78]