The outer membrane protein A (OmpA) plays important roles in anchoring of the outer membrane to the bacterial cell wall. The C-terminal periplasmic domain of OmpA (OmpA-like domain) associates with the peptidoglycan (PGN) layer noncovalently. However, there is a paucity of information on the structural aspects of the mechanism of PGN recognition by OmpA-like domains. To elucidate this molecular recognition process, we solved the high-resolution crystal structure of an OmpA-like domain from Acinetobacter baumannii bound to diaminopimelate (DAP), a unique bacterial amino acid from the PGN. The structure clearly illustrates that two absolutely conserved Asp271 and Arg286 residues are the key to the binding to DAP of PGN. Identification of DAP as the central anchoring site of PGN to OmpA is further supported by isothermal titration calorimetry and a pulldown assay with PGN. An NMR-based computational model for complexation between the PGN and OmpA emerged, and this model is validated by determining the crystal structure in complex with a synthetic PGN fragment. These structural data provide a detailed glimpse of how the anchoring of OmpA to the cell wall of gram-negative bacteria takes place in a DAP-dependent manner.

Acinetobacter baumannii secretes outer membrane vesicles (OMVs) during both in vitro and in vivo growth, but the biogenesis mechanism by which A. baumannii produces OMVs remains undefined. Outer membrane protein A of A. baumannii (AbOmpA) is a major protein in the outer membrane and the C-terminus of AbOmpA interacts with diaminopimelate of peptidoglycan. This study investigated the role of AbOmpA in the biogenesis of A. baumannii OMVs. Quantitative and qualitative approaches were used to analyze OMV biogenesis in A. baumannii ATCC 19606T and an isogenic ΔAbOmpA mutant. OMV production was significantly increased in the ΔAbOmpA mutant compared to wild-type bacteria as demonstrated by quantitation of proteins and lipopolysaccharides (LPS) packaged in OMVs. LPS profiles prepared from OMVs from wild-type bacteria and the ΔAbOmpA mutant had identical patterns, but proteomic analysis showed different protein constituents in OMVs from wild-type bacteria compared to the ΔAbOmpA mutant. In conclusion, AbOmpA influences OMV biogenesis by controlling OMV production and protein composition.

Escherichia coli AcrAB-TolC is a multidrug efflux pump that expels a wide range of toxic substrates. The dynamic nature of the binding or low affinity between the components has impeded elucidation of how the three components assemble in the functional state. Here, we created fusion proteins composed of AcrB, a transmembrane linker, and two copies of AcrA. The fusion protein exhibited acridine pumping activity, suggesting that the protein reflects the functional structure in vivo. To discern the assembling mode with TolC, the AcrBA fusion protein was incubated with TolC or a chimeric protein containing the TolC aperture tip region. Three-dimensional structures of the complex proteins were determined through transmission electron microscopy. The overall structure exemplifies the adaptor bridging model, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel interaction with the -barrel tip region of TolC, and a direct interaction between AcrB and TolC is not allowed. These observations provide a structural blueprint for understanding multidrug resistance in pathogenic Gram-negative bacteria.

Obtaining well-diffracting crystals of macromolecules remains a significant barrier to structure determination. Here we propose and test a new approach to crystallization, in which the crystallization target is fused to a polymerizing protein module, so that polymer formation drives crystallization of the target. We test the approach using a polymerization module called 2TEL, which consists of two tandem sterile alpha motif (SAM) domains from the protein translocation Ets leukemia (TEL). The 2TEL module is engineered to polymerize as the pH is lowered, which allows the subtle modulation of polymerization needed for crystal formation. We show that the 2TEL module can drive the crystallization of 11 soluble proteins, including three that resisted prior crystallization attempts. In addition, the 2TEL module crystallizes in the presence of various detergents, suggesting that it might facilitate membrane protein crystallization. The crystal structures of two fusion proteins show that the TELSAM polymer is responsible for the majority of contacts in the crystal lattice. The results suggest that biological polymers could be designed as crystallization modules.

No abstract

Heparin lyase I (heparinase I) specifically depolymerizes heparin, cleaving the glycosidic linkage next to iduronic acid. Here, we show the crystal structures of heparinase I from Bacteroides thetaiotaomicron at various stages of the reaction with heparin oligosaccharides before and just after cleavage and product disaccharide. The heparinase I structure is comprised of a ␤-jellyroll domain harboring a long and deep substrate binding groove and an unusual thumb-resembling extension. This thumb, decorated with many basic residues, is of particular importance in activity especially on short heparin oligosaccharides. Unexpected structural similarity of the active site to that of heparinase II with an (␣/␣) 6 fold is observed. Mutational studies and kinetic analysis of this enzyme provide insights into the catalytic mechanism, the substrate recognition, and processivity.Heparin and heparan sulfate are linear, negatively charged polymers consisting of repeating units of 134-linked uronic acid (L-iduronic acid (IdoA) 4 and D-glucuronic acid (GlcA)) and glucosamine (1). Heparin consists of a high proportion of IdoA (ϳ90%) and is highly sulfated. It is widely used as an anticoagulant based on its binding to antithrombin, leading to the accelerated inhibition of the blood coagulation cascade (2). Heparin interacts with a variety of proteins, such as growth factors and chemokines, suggesting its relevance in various physiological and pathological processes (2, 3).Glycosaminoglycans in general, and heparin in particular, can be degraded by two mechanisms: hydrolysis and lytic elimination (4). Glycosaminoglycan hydrolases, present in eukaryotes and prokaryotes, break the glycosidic bond to the nonreducing end of the glucosamine, whereas glycosaminoglycan lyases, found only in prokaryotes, break the glycosidic linkage to the nonreducing end of uronic acid (5). The lyases that cleave chondroitin sulfate and hyaluronan have been extensively studied, structurally and biochemically. All of these lyases share a common fold, (␣/␣) 5 barrel, and antiparallel ␤-sheet, and have similar catalytic mechanisms (6 -8). In contrast, dermatan sulfate (chondroitin B) lyase has a completely different fold as a parallel ␤-helix, similar to pectate lyases, and employs very different catalytic machinery (9).The eliminative depolymerization of heparin/heparan sulfate affording unsaturated oligosaccharide products is carried out by three families of enzymes (10). Their primary sequences show no recognizable similarity, and they have distinct specificities (11). Thus, heparinase I is specific for heparin cleaving the glycosidic linkage to the nonreducing end of IdoA, heparin lyase III (heparinase III) cleaves the heparan sulfate next to glucuronic acid, and heparin lyase II (heparinase II) can depolymerize both of these substrates (see Fig. 1A). Structural information on the heparin degrading enzymes is limited to the Pedobacter heparinus (formerly Flavobacterium heparinum) heparinase II, which adopts an overall fold similar to chondroitin and hy...

Casey et al. integrate epigenomic, transcriptomic, and proteomic profiling of primary basal and luminal mammary cells to identify master epigenetic regulators of the mammary epithelium and uncover stem and progenitor cell vulnerabilities. They develop a pipeline to identify drugs that abrogate progenitor cell activity in normal and high-risk breast cancer patient samples in vitro and in vivo.

BackgroundOuter membrane vesicles (OMVs) of Acinetobacter baumannii are cytotoxic and elicit a potent innate immune response. OMVs were first identified in A. baumannii DU202, an extensively drug-resistant clinical strain. Herein, we investigated protein components of A. baumannii DU202 OMVs following antibiotic treatment by proteogenomic analysis.MethodsPurified OMVs from A. baumannii DU202 grown in different antibiotic culture conditions were screened for pathogenic and immunogenic effects, and subjected to quantitative proteomic analysis by one-dimensional electrophoresis and liquid chromatography combined with tandem mass spectrometry (1DE-LC-MS/MS). Protein components modulated by imipenem were identified and discussed.ResultsOMV secretion was increased > twofold following imipenem treatment, and cytotoxicity toward A549 human lung carcinoma cells was elevated. A total of 277 proteins were identified as components of OMVs by imipenem treatment, among which β-lactamase OXA-23, various proteases, outer membrane proteins, β-barrel assembly machine proteins, peptidyl-prolyl cis–trans isomerases and inherent prophage head subunit proteins were significantly upregulated.ConclusionIn vitro stress such as antibiotic treatment can modulate proteome components in A. baumannii OMVs and thereby influence pathogenicity.Electronic supplementary materialThe online version of this article (10.1186/s12014-018-9204-2) contains supplementary material, which is available to authorized users.