OprM is the outer membrane channel component of resistance-nodulation-division (RND) efflux pumps in Pseudomonas aeruginosa, a high-priority human pathogen. OprM-dependent pumps play diverse roles in bacterial physiology and mediate resistance to critical antibiotic classes, including fluoroquinolones, aminoglycosides, and broad-spectrum β-lactam/β-lactamase inhibitor combinations such as ceftazidime/avibactam. As the outer membrane component of the tripartite efflux system, OprM gates substrate export through an iris-like periplasmic pore that opens upon association with its inner membrane partners. Here we present a single-particle cryo-EM structure of OprM at 2.08 Å, the highest resolution OprM structure to date. The structure reveals a closed leucine-lined periplasmic pore, consistent with previous X-ray structures. A detailed structure-based comparison of the closed and open states reveals the conformational changes accompanying periplasmic pore opening, including iris-like twisting of the coiled-coil helices, displacement of the gating Leu429 residues, and a broader reorganization of salt bridges than previously described. Conservation of the MexA-binding interface across multiple Mex proteins suggests a shared mechanism of OprM engagement. Three lipopolysaccharide (LPS) molecules are resolved at the β-barrel interface, bridging adjacent OprM monomers through a combination of hydrophobic interactions with the fatty acyl chains and specific polar contacts with the KDO, heptose, and phosphate groups. This binding mode resembles that of other generic β-barrels and is expected to be preserved in vivo. Together, these findings provide the most detailed structural characterization of OprM to date, offering new insights into its gating mechanism and membrane interactions with implications for the development of efflux pump inhibitors.

The Ton and Tol-Pal systems are molecular machines that are essential for survival of Gram-negative bacteria.Both use the energy derived from the proton gradient at the inner membrane to generate force on protein components at the outer membrane. Ton and Tol share extensive homology, but they fulfill different functions: Ton is involved in the active transport of essential nutrients from the extracellular media into the cell, while Tol maintains the outer membrane integrity and participates in the cell division process. Despite decades of biochemical and biophysical studies, the molecular mechanism coupling the proton gradient at the inner membrane with the propagation of force and movement to the outer membrane is not understood. In this review, we discuss the recent high-resolution structures obtained for both systems, and how these structures fit with existing mechanistic models.

The Rcs phosphorelay regulates gene expression in response to cell envelope stress and is critical for the virulence of pathogenic bacteria, including Klebsiella pneumoniae, due to its regulation of genes related to extracellular capsule, cell division, and motility. The RcsC histidine kinase, RcsD phosphotransfer protein and RcsB response regulator, which form the core of the Rcs phosphorelay, are negatively regulated by the unique inner membrane protein IgaA via interaction with RcsD. An outer membrane lipoprotein, RcsF, activates signaling by interaction with IgaA, but the precise activation mechanisms remain unclear. In this study, we determined the structures of IgaA and the IgaA/RcsF complex using Cryo-electron microscopy (Cryo-EM). We also determined the structures of RcsC and RcsD, which both form homodimers stabilized by hydrophobic interactions, creating ladder-like structures. Combining the Cryo-EM structures, AlphaFold3 structure predictions of IgaA/RcsD and RcsF/IgaA/RcsD, and genetic studies, we describe a model for how RcsF modifies the IgaA/RcsD interaction, lifting negative regulation and activating the Rcs phosphorelay. Our findings provide a high-resolution depiction of the Rcs stress response system and suggest potential targets for small molecule inhibitors.

Drug-resistant bacterial infections have become a high-priority concern in the global healthcare landscape. Novel treatments for such infections are needed, but can be especially difficult to develop for Gram-negative species owing to the need to traverse the outer membrane to reach targets beneath. A promising solution is found in natural antibiotics such as albomycin, which can bind outer membrane siderophore receptors and co-opt them for import into the periplasm. Exploring this and similar mechanisms may open avenues for antibiotic development. An underappreciated class of natural antibiotics are the microcins, which are small antimicrobial proteins secreted by certain bacterial species as a means of inter-species competition. Once secreted, the microcins bind specific outer-membrane receptors of prey species and cross into the periplasm. Microcins have potent activity, bind specific targets, and have been shown to control pathobiont expansion and pathogen colonization in animal models. One such microcin, MccV, has previously been shown to utilize the E. coli colicin Ia receptor, Cir, for periplasmic import. Here, we report the first high-resolution structure of the Cir/MccV complex by Cryo-EM, revealing an interaction centered on an electropositive cavity within a usually occluded binding pocket in Cir. We also report the calculated affinity of MccV for Cir. We mutagenized putative interacting residues at this interface and identified key contacts that are critical to MccV binding and Cir-mediated import and bacteriolysis. Future efforts in this project will help us better understand the mechanisms of microcin killing, and will assess relationships between other microcins and their respective importers with the aim of understanding the potential for microcins to be used as treatment for drug-resistant pathogens.

Drug-resistant bacteria are a global concern. Novel treatments are needed, but are difficult to develop for Gram-negative species due to the need to traverse the outer membrane to reach targets beneath. A promising solution is found in natural antibiotics which bind outer membrane receptors and co-opt them for import. Exploring this mechanism may open avenues for antibiotic development. An underappreciated class of natural antibiotics are microcins - small antimicrobial proteins secreted by certain bacteria during inter-species competition. Microcins bind outer-membrane receptors of prey species for passage into the periplasm. They have potent activity, bind specific targets, and can control pathobiont expansion and colonization. One microcin, MccV, utilizes the E. coli colicin Ia receptor, Cir, for import. Here, we report the first high-resolution structure of the Cir/MccV complex by Cryo-EM, revealing an interaction centered on an electropositive cavity within the Cir extracellular loops. We also report the affinity of MccV for Cir. Lastly, we mutagenized interacting residues and identified key contacts critical to MccV binding, import, and bacteriolysis. Future efforts may help disentangle the mechanisms of microcin killing and will assess relationships between other microcins and their targets to better understand the potential for microcins to be used as antibacterial drugs.

The Ton and Tol motor proteins use the proton gradient at the inner membrane of Gram-negative bacteria as an energy source. The generated force is transmitted through the periplasmic space to protein components associated with the outer membrane, either to maintain the outer membrane integrity for the Tol system, or to allow essential nutrients to enter the cell for Ton. We have solved the high-resolution structures of the E. coli TonB-ExbB-ExbD and TolA-TolQ-TolR complexes, revealing the inner membrane embedded engine parts of the Ton and Tol systems, and showing how TonB and TolA interact with the ExbBD and TolQR subcomplexes. Structural similarities between the two motor complexes suggest a common mechanism for the opening of the proton channel and the propagation of the proton motive force into movement of the TonB and TolA subunits. Because TonB and TolA bind at preferential ExbB or TolQ subunits, we propose a new mechanism of assembly of TonB and TolA with their respective ExbBD and TolQR subcomplexes and discuss its impact on the mechanism of action for the Ton and Tol systems.

Olfactomedin 4 (OLFM4) is a member of the olfactomedin domain-containing olfactomedin glycoprotein family and plays important roles in innate immunity, inflammation, and cancer. It exhibits increased expression in gastric cancer patient tissues and has been shown to regulate proliferation and apoptosis in gastric cancer cells. However, the molecular mechanism(s) underlying OLFM4’s role in gastric cancer remain unknown. In this study, we found that OLFM4 knock-down significantly inhibited YCC3 gastric cancer cell proliferation and induced G2/M cell cycle arrest. Yeast two-hybridization screening revealed that OLFM4 directly interacts with cyclin B1 interacting protein 1 (CCNB1IP1), an E3 ubiquitin protein ligase. In YCC3 cells, OLFM4 co-immunoprecipitated and colocalized with CCNB1IP1, and underwent cell cycle phase-specific nucleo-cytoplasmic shuttling. OLFM4 knockdown decreased both cyclin B1 protein levels and CDK1 activity in YCC3 cells. Screening of a cohort of OLFM4-targeted microRNAs (miRNAs) for their impact on cell proliferation identified several that significantly downregulated OLFM4 protein levels and inhibited YCC3 cell proliferation in vitro. Rescue experiments demonstrated that these miRNAs’ inhibitory effect on cell proliferation was partially related to their downregulation of OLFM4. When three of these miRNAs were individually administered intratumorally to nude mice bearing YCC3 cell xenografts, tumor growth was significantly inhibited when compared with tumors treated with a negative control miRNA. These results suggest that OLFM4 promotes cell cycle progression and cell proliferation in gastric cancer cells and may have utility as a therapeutic target in gastric adenocarcinoma.

The folding and insertion of β-barrel proteins into the mitochondrial outer membrane is facilitated by the sorting and assembly machinery (SAM) complex. Here we report two 2.8 Å cryo-EM structures of the Thermothelomyces thermophilus SAM complex in the absence of substrate in which the Sam50 lateral gate adopts two different conformations: the first is a closed lateral gate as observed in previously published structures, while the second contains a Sam50 with the first four β-strands rotated outwards by approximately 45°, resulting in an open lateral gate. The observed monomeric open conformation contrasts our previous work where the open conformation was adopted by non-physiological up-down dimers. To understand how these lateral gate dynamics are influenced by substrate, we studied the interaction of the SAM complex with a β-signal peptide mimic, darobactin A. Darobactin A binds to the SAM complex with nanomolar affinity and inhibits the import and assembly of mitochondrial β-barrel proteins in vitro. Lastly, we solved a 3.0 Å cryo-EM structure of the Thermothelomyces thermophilus SAM complex bound to darobactin A, which reveals that darobactin A stabilizes the Sam50 lateral gate similar to the open conformation by binding to strand β1, therefore blocking β-barrel biogenesis.

β-barrels are a class of membrane proteins made up of a cylindrical, anti-parallel β-sheet with a hydrophobic exterior and a hydrophilic interior. The majority of proteins found in the outer membranes (OMs) of Gram-negative bacteria, mitochondria, and chloroplasts are β-barrel outer membrane proteins (OMPs). β-barrel OMPs have a diverse repertoire of functions, including nutrient transport, secretion, bacterial virulence, and enzymatic activity. Here, we discuss the broad functional classes of β-barrel OMPs, how they are folded into the membrane, and the future of β-barrel OMP research and its applications.

Selective incorporation of conformational constraints into thyclotides can be used to modulate their binding to complementary oligonucleotides, increase polarity, and optimize uptake into HCT116 cells without assistance from moieties known to promote cell uptake. The X-ray structure and biophysical studies of a thyclotide-DNA duplex reveal that incorporation of tetrahydrofurans into an aegPNA backbone promotes a helical conformation that enhances binding to complementary DNA and RNA. Selective incorporation of tetrahydrofurans into the aegPNA backbone allows polarity to be increased incrementally so that uptake into HCT116 cells can be optimized. The enhanced binding, polarity, and cellular uptake properties of thyclotides were used to demonstrate effective inhibition of microRNA-21 in HCT116 cells.

β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.

Small intestine adenocarcinoma is a rare intestinal malignancy with distinct clinical, pathological, and molecular characteristics. Recently, a fusion of the intestinal stem-cell marker olfactomedin 4 (OLFM4) and the proto-oncogene RET has been identified in a small intestine adenocarcinoma patient. Here we investigated the biological effects of OLFM4-RET fusion and whether it can initiate tumorigenesis in small intestine. OLFM4 expression was found to be frequently lost or reduced in human small intestine adenocarcinoma, and its downregulation correlated with high tumor grade and advanced tumor stage. Expression of OLFM4-RET fusion-induced cellular transformation in HEK293 cells and blocked RET-induced inhibition of colony growth in HuTu 80 small intestine adenocarcinoma cells. Further, expression of OLFM4-RET activated the RAS-RAF-MAPK and STAT3 cell signaling pathways in both HEK293 cells and HuTu 80 cells. OLFM4-RET expression in HEK293 cells upregulated multiple families of genes related to carcinogenesis, cancer progression, and metastasis. Targeted expression of OLFM4-RET in the small intestine led to the development of hyperplasia, adenoma, or adenocarcinoma in transgenic mice. Our study suggests that OLFM4-RET is an oncogenic driver of small intestine tumorigenesis. Therefore, the small intestine adenocarcinoma patients with OLFM4-RET fusion may benefit from treatment with RET kinase inhibitor.

Mitochondria are essential eukaryotic organelles and play a vital role in many cellular processes, including ATP production, lipid synthesis, and apoptosis. The majority of the mitochondrial proteome is translated in the cytosol and imported into the mitochondria as unfolded precursors. Outer membrane β-barrel proteins are imported by the translocase of the outer membrane (TOM complex) then folded and inserted into the membrane by the sorting and assembly machinery (SAM complex). The SAM complex is composed of three subunits: a β-barrel core (Sam50) that spans the mitochondrial outer membrane, and two accessory subunits (Sam35 and Sam37) that associate on the cytosolic side of the membrane. We recently solved cryoEM structures of the SAM complex in detergent and lipid nanodiscs to resolutions of 3.0Å and 3.4Å, respectively. These structures confirm that Sam50 is a sixteen strand β-barrel and that Sam35 and Sam37 are located on the cytosolic side of the membrane. The N-terminus of Sam35 interacts with the cytosolic loops of Sam50, blocking cytosolic access to the Sam50 β-barrel. The cytosolic domain of Sam37 forms extensive interactions with Sam35, stabilizing Sam35 association with Sam50. In the intermembrane space, Sam37 contributes a β-strand to the Sam50 N-terminal polypeptide transport-associated (POTRA) domain. Interestingly, both Sam37 and the Sam50 POTRA domain are implicated in precursor release. While our structure agrees with current biochemical knowledge of the SAM complex, it remains unclear how the β-signal is recognized by the SAM complex. Current work aims to characterize the interaction of the β-signal with the SAM complex subunits.

In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold β-barrel proteins and insert them into the mitochondrial outer membrane. We report cryoEM structures of the SAM complex from Myceliophthora thermophila , which show that Sam50 forms a 16-stranded transmembrane β-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analysis shows how the Sam50 β-barrel opens a lateral gate to accommodate its substrates.

Several tyrosine kinase inhibitors (TKIs) are currently under development for the treatment of patients with chronic myelogenous leukemia (CML) resistant or intolerant of imatinib therapy, including nilotinib, dasatinib, and bosutinib. The current paradigm of TKI therapy involves a sequential use of these compounds, with imatinib invariably used as frontline therapy followed by either dasatinib or nilotinib on an empiric basis. A more sensible approach to this sequence is the selection of the TKI best suited to overcome the resistance conferred by BCR-ABL1 mutations detected at each time-point. As more TKIs are becoming available, the management of patients with CML will require degree of "finesse" to better match each patient with the best TKI available. This match is best made based on available in vitro data regarding the activity of each agent against each specific mutation. The case herein reported supports such strategy.

Bacterial contact-dependent growth inhibition (CDI) systems use a type Vb secretion mechanism to export large CdiA toxins across the outer membrane by dedicated outer membrane transporters called CdiB. Here, we report the first crystal structures of two CdiB transporters from Acinetobacter baumannii and Escherichia coli. CdiB transporters adopt a TpsB fold, containing a 16-stranded transmembrane β-barrel connected to two periplasmic domains. The lumen of the CdiB pore is occluded by an N-terminal α-helix and the conserved extracellular loop 6; these two elements adopt different conformations in the structures. We identified a conserved DxxG motif located on strand β1 that connects loop 6 through different networks of interactions. Structural modifications of DxxG induce rearrangement of extracellular loops and alter interactions with the N-terminal α-helix, preparing the system for α-helix ejection. Using structural biology, functional assays, and molecular dynamics simulations, we show how the barrel pore is primed for CdiA toxin secretion.

LonA proteases and ClpB chaperones are key components of the protein quality control system in bacterial cells. LonA proteases form a unique family of ATPases associated with diverse cellular activities (AAA+) proteins due to the presence of an unusual N‐terminal region comprised of two domains: a β‐structured N domain and an α‐helical domain, including the coiled‐coil fragment, which is referred to as HI(CC). The arrangement of helices in the HI(CC) domain is reminiscent of the structure of the H1 domain of the first AAA+ module of ClpB chaperones. It has been hypothesized that LonA proteases with a single AAA+ module may also contain a part of another AAA+ module, the full version of which is present in ClpB. Here, we established and tested the structural basis of this hypothesis using the known crystal structures of various fragments of LonA proteases and ClpB chaperones, as well as the newly determined structure of the Escherichia coli LonA fragment (235–584). The similarities and differences in the corresponding domains of LonA proteases and ClpB chaperones were examined in structural terms. The results of our analysis, complemented by the finding of a singular match in the location of the most conserved axial pore‐1 loop between the LonA NB domain and the NB2 domain of ClpB, support our hypothesis that there is a structural and functional relationship between two coiled–coil fragments and implies a similar mechanism of engagement of the pore‐1 loops in the AAA+ modules of LonAs and ClpBs.