Clustering of OB-fold domains of the partner protease complexed with trimeric stomatin from Thermococcales

Flotillin-mediated stabilization of unfolded proteins in bacterial membrane microdomains

The function of many bacterial processes depends on the formation of functional membrane microdomains (FMMs), which resemble the lipid rafts of eukaryotic cells. However, the mechanism and the biological function of these membrane microdomains remain unclear. Here, we show that FMMs in the pathogen methicillin-resistant Staphylococcus aureus (MRSA) are dedicated to confining and stabilizing proteins unfolded due to cellular stress. The FMM scaffold protein flotillin forms a clamp-shaped oligomer that holds unfolded proteins, stabilizing them and favoring their correct folding. This process does not impose a direct energy cost on the cell and is crucial to survival of ATP-depleted bacteria, and thus to pathogenesis. Consequently, FMM disassembling causes the accumulation of unfolded proteins, which compromise MRSA viability during infection and cause penicillin re-sensitization due to PBP2a unfolding. Thus, our results indicate that FMMs mediate ATP-independent stabilization of unfolded proteins, which is essential for bacterial viability during infection.

Inactive dimeric structure of the protease domain of stomatin operon partner protein

The N-terminal region of the stomatin operon partner protein (STOPP) PH1510 (1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii is a serine protease with a catalytic Ser-Lys dyad (Ser97 and Lys138) and specifically cleaves the C-terminal hydrophobic region of the p-stomatin PH1511. In a form of human hemolytic anemia known as hereditary stomatocytosis, stomatin is deficient in the erythrocyte membrane owing to mis-trafficking. Stomatin is thought to act as an oligomeric scaffolding protein to support cell membranes. The cleavage of stomatin by STOPP might be involved in a regulatory system. Several crystal structures of 1510-N have previously been determined: the wild type, the K138A mutant and its complex with a substrate peptide. Here, the crystal structure of the S97A mutant of 1510-N (1510-N S97A) was determined at 2.25 Å resolution. The structure contained two 1510-N S97A molecules in the asymmetric unit. On the superposition of one monomer of the 1510-N S97A and wild-type dimers, the S97A C^α atom of the other monomer of 1510-N S97A deviated by 23 Å from that of the wild type. This result indicates that 1510-N can greatly change the form of its dimer. Because of crystallographic symmetry in space group P6₅, a sixfold helical structure is constructed using the 1510-N dimer as a basic unit. This helical structure may be common to STOPP structures.

The lipid raft markers stomatin, prohibitin, flotillin, and HflK/C (SPFH)-domain proteins form an operon with NfeD proteins and function with apolar polyisoprenoid lipids

SPFH-domain proteins are found in almost all organisms across three domains: archaea, bacteria, and eukaryotes. In eukaryotic organelles, their subfamilies exhibit overlapping distribution and functions; thus, the rationality of annotation to discriminate these subfamilies remains unclear. In this review, the binding ability of prokaryotic SPFH-domain proteins towards nonpolar polyisoprenoides such as squalene and lycopene, rather than cholesterol, is discussed. The hydrophobic region at the C-terminus of SPFH-domain proteins constitutes the main region that binds apolar polyisoprenoid lipids as well as cholesterol and substantively contributes towards lipid raft formation as these regions are self-assembled together with specific lipids. Because the scaffolding proteins caveolins show common topological properties with SPFH-domain proteins such as stomatin and flotillin, the α-helical segments of stomatin proteins can flexibly move along with the membrane surface, with such movement potentially leading to membrane bending via lipid raft clustering through the formation of high order homo-oligomeric complexes of SPFH-domain proteins. We also discuss the functional significance and ancient origin of SPFH-domain proteins and the NfeD protein (STOPP) operon, which can be traced back to the ancient living cells that diverged and evolved to archaea and bacteria. Based on the molecular mechanism whereby the STOPP-protease degrades the C-terminal hydrophobic clusters of SPFH-domain proteins, it is conceivable that STOPP-protease might control the physicochemical properties of lipid rafts.

Exploring functional membrane microdomains in bacteria: an overview

Recent studies show that internal organization of bacterial cells is more complex than previously appreciated. A clear example of this is the assembly of the nanoscale membrane platforms termed functional membrane microdomains. The lipid composition of these regions differs from that of the surrounding membrane; these domains confine a set of proteins involved in specific cellular processes such as protease secretion and signal transduction. It is currently thought that functional membrane microdomains act as oligomerization platforms and promote efficient oligomerization of interacting protein partners in bacterial membranes. In this review, we highlight the most noteworthy achievements, challenges and controversies of this emerging research field over the past five years.

Crystal structure of the stomatin operon partner protein from Pyrococcus horikoshii indicates the formation of a multimeric assembly

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The structure of C-terminal domain of stomatin operon partner protein PH1510 was determined.

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C-terminal domain of PH1510 (1510-C) forms a five-stranded β-barrel known as an OB-fold.

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1510-C could assemble into multimers based on a dimer as a basic unit.

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1510-C functions as a scaffold protein to form a multimeric assembly with stomatin.

Stomatin, prohibitin, flotillin, and HflK/C (SPFH) domain proteins are found in the lipid raft microdomains of various cellular membranes. Stomatin/STOPP (stomatin operon partner protein) gene pairs are present in both archaeal and bacterial species, and their protein products may be involved in the quality control of membrane proteins. In the present study, the crystal structure of the C-terminal soluble domain of STOPP PH1510 (1510-C) from the hyperthermophilic archaeon Pyrococcus horikoshii was determined at 2.4 Å resolution. The structure of 1510-C had a compact five-stranded β-barrel fold known as an oligosaccharide/oligonucleotide-binding fold (OB-fold). According to crystal packing, 1510-C could assemble into multimers based on a dimer as a basic unit. 1510-C also formed a large cylinder-like structure composed of 24 subunits or a large triangular prism-like structure composed of 12 subunits. These results indicate that 1510-C functions as a scaffold protein to form the multimeric assembly of STOPP and stomatin.