Mechanism Of Translocation Research Articles

Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface.

Protein-based biomaterials have played a key role in tissue engineering, and additional exciting applications as self-healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production of various fibrous proteins from microbes have been demonstrated; however, the resulting proteins typically must then be purified and processed by humans to form usable fibers and materials. Here, we show that the Gram-positive bacterium Bacillus subtilis can be programmed to secrete silk through its translocon via an orthogonal signal peptide/peptidase pair. Surprisingly, we discover that this translocation mechanism drives the silk proteins to assemble into fibers spontaneously on the cell surface, in a process we call secretion-catalyzed assembly (SCA). Secreted silk fibers form self-healing hydrogels with minimal processing. Alternatively, the fibers retained on the membrane provide a facile route to create engineered living materials from Bacillus cells. This work provides a blueprint to achieve autonomous assembly of protein biomaterials in useful morphologies directly from microbial factories.

Secretion‐Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface

AbstractProtein‐based biomaterials have played a key role in tissue engineering, and additional exciting applications as self‐healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production of various fibrous proteins from microbes have been demonstrated; however, the resulting proteins typically must then be purified and processed by humans to form usable fibers and materials. Here, we show that the Gram‐positive bacterium Bacillus subtilis can be programmed to secrete silk through its translocon via an orthogonal signal peptide/peptidase pair. Surprisingly, we discover that this translocation mechanism drives the silk proteins to assemble into fibers spontaneously on the cell surface, in a process we call secretion‐catalyzed assembly (SCA). Secreted silk fibers form self‐healing hydrogels with minimal processing. Alternatively, the fibers retained on the membrane provide a facile route to create engineered living materials from Bacillus cells. This work provides a blueprint to achieve autonomous assembly of protein biomaterials in useful morphologies directly from microbial factories.

Central role of Tim17 in mitochondrial presequence protein translocation

The presequence translocase of the mitochondrial inner membrane (TIM23) represents the major route for the import of nuclear-encoded proteins into mitochondria1,2. About 60% of more than 1,000 different mitochondrial proteins are synthesized with amino-terminal targeting signals, termed presequences, which form positively charged amphiphilic α-helices3,4. TIM23 sorts the presequence proteins into the inner membrane or matrix. Various views, including regulatory and coupling functions, have been reported on the essential TIM23 subunit Tim17 (refs. 5–7). Here we mapped the interaction of Tim17 with matrix-targeted and inner membrane-sorted preproteins during translocation in the native membrane environment. We show that Tim17 contains conserved negative charges close to the intermembrane space side of the bilayer, which are essential to initiate presequence protein translocation along a distinct transmembrane cavity of Tim17 for both classes of preproteins. The amphiphilic character of mitochondrial presequences directly matches this Tim17-dependent translocation mechanism. This mechanism permits direct lateral release of transmembrane segments of inner membrane-sorted precursors into the inner membrane.

Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit

Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum.

Genetic Incorporation of Dansylalanine in Human Ferroportin to Probe the Alternating Access Mechanism of Iron Transport.

Ferroportin (Fpn), a member of the major facilitator superfamily (MFS) of transporters, is the only known iron exporter found in mammals and plays a crucial role in regulating cellular and systemic iron levels. MFSs take on different conformational states during the transport cycle: inward open, occluded, and outward open. However, the precise molecular mechanism of iron translocation by Fpn remains unclear, with conflicting data proposing different models. In this work, amber codon suppression was employed to introduce dansylalanine (DA), an environment-sensitive fluorescent amino acid, into specific positions of human Fpn (V46, Y54, V161, Y331) predicted to undergo major conformational changes during metal translocation. The results obtained indicate that different mutants exhibit distinct fluorescence spectra depending on the position of the fluorophore within the Fpn structure, suggesting that different local environments can be probed. Cobalt titration experiments revealed fluorescence quenching and blue-shifts of λmax in Y54DA, V161DA, and Y331DA, while V46DA exhibited increased fluorescence and blue-shift of λmax. These observations suggest metal-induced conformational transitions, interpreted in terms of shifts from an outward-open to an occluded conformation. Our study highlights the potential of genetically incorporating DA into Fpn, enabling the investigation of conformational changes using fluorescence spectroscopy. This approach holds great promise for the study of the alternating access mechanism of Fpn and advancing our understanding of the molecular basis of iron transport.

Direct interaction between fd phage pilot protein pIII and the TolQ–TolR proton-dependent motor provides new insights into the import of filamentous phages

Filamentous phages are one of the simplest examples of viruses with a protein capsid that protects a circular single-stranded DNA genome. The infection is very specific, nonlytic, and can strongly affect the physiology or provide new pathogenic factors to its bacterial host. The infection process is proposed to rely on a pore-forming mechanism similar to that of certain nonenveloped eukaryotic viruses. The Ff coliphages (including M13, fd, and f1) have been intensively studied and were used to establish the sequence of events taking place for efficient crossing of the host envelope structure. However, the mechanism involved in the penetration of the cell inner membrane is not well understood. Here, we identify new host players involved in the phage translocation mechanism. Interaction studies by a combination of invivo biochemical methods demonstrate that the adhesion protein pIII located at the tip of the phage binds to TolQ and TolR, two proteins that form a conserved proton-dependent molecular motor in the inner membrane of the host cell. Moreover, invivo cysteine cross-linking studies reveal that the interactions between the pIII and TolQ or TolR occur between their transmembrane helix domains and may be responding to the proton motive force status of the cell. These results allow us to propose a model for the late stage of filamentous phage translocation mediated by multiple interactions with each individual component of the host TolQRA complex.

Cancer Drug Delivery Systems Using Bacterial Toxin Translocation Mechanisms.

Recent advances in targeted cancer therapy hold great promise for both research and clinical applications and push the boundaries in finding new treatments for various currently incurable cancers. However, these therapies require specific cell-targeting mechanisms for the efficient delivery of drug cargo across the cell membrane to reach intracellular targets and avoid diffusion to unwanted tissues. Traditional drug delivery systems suffer from a limited ability to travel across the barriers posed by cell membranes and, therefore, there is a need for high doses, which are associated with adverse reactions and safety concerns. Bacterial toxins have evolved naturally to specifically target cell subtypes via their receptor binding module, penetrating the cell membrane efficiently through the membrane translocation process and then successfully delivering the toxic cargo into the host cytosol. They have, thus, been harnessed for the delivery of various drugs. In this review, we focus on bacterial toxin translocation mechanisms and recent progress in the targeted delivery systems of cancer therapy drugs that have been inspired by the receptor binding and membrane translocation processes of the anthrax toxin protective antigen, diphtheria toxin, and Pseudomonas exotoxin A. We also discuss the challenges and limitations of these studies that should be addressed before bacterial toxin-based drug delivery systems can become a viable new generation of drug delivery approaches in clinical translation.

AMPK boosts ADAM10 shedding activity in human aortic endothelial cells by promoting Rab14-dependent ADAM10 cell surface translocation

A disintegrin and metalloprotease 10 (ADAM10) regulates the expression of cell surface receptors such as tumor necrosis factor receptor 1, toll-like receptor 4, and the receptor for advanced glycation end products (RAGE) by cleaving their extracellular regions. To function as a sheddase, ADAM10 should translocate from the intracellular compartments to the cell surface, but the translocation mechanism remains unclear. In this study, we explored the possible role of adenosine monophosphate-activated protein kinase (AMPK) in the induction of ADAM10 shedding activity. In cultured human aortic endothelial cells (HAECs), 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR), an AMPK activator, boosted ADAM10 cell surface translocation and ectodomain shedding of RAGE. ADAM10 inhibition with GI 254023X and ADAM10 siRNA silencing both prevented AICAR-induced RAGE ectodomain shedding. AICAR increased AMPK phosphorylation as well. Both Compound C-mediated AMPK inhibition and AMPKα1-siRNA-mediated AMPK depletion suppressed AICAR-induced ADAM10 cell surface translocation and RAGE ectodomain shedding. On the other hand, siRNA knockdown of Rab14, a small GTPase that facilitates the intracellular trafficking of transmembrane proteins, prevented AICAR-induced ADAM10 cell surface translocation and RAGE ectodomain shedding. In conclusion, AMPK activation is an obvious inducer of ADAM10 shedding activity. Our findings suggest that AMPK boosts ADAM10 shedding activity in HAECs by promoting Rab14-dependent ADAM10 cell surface translocation.

Molecular Dynamics Simulations Elucidate the Molecular Basis of Pre-mRNA Translocation by the Prp2 Spliceosomal Helicase.

The spliceosome machinery catalyzes precursor-messenger RNA (pre-mRNA) splicing by undergoing at each splicing cycle assembly, activation, catalysis, and disassembly processes, thanks to the concerted action of specific RNA-dependent ATPases/helicases. Prp2, a member of the DExH-box ATPase/helicase family, harnesses the energy of ATP hydrolysis to translocate a single pre-mRNA strand in the 5' to 3' direction, thus promoting spliceosome remodeling to its catalytic-competent state. Here, we established the functional coupling between ATPase and helicase activities of Prp2. Namely, extensive multi-μs molecular dynamics simulations allowed us to unlock how, after pre-mRNA selection, ATP binding, hydrolysis, and dissociation induce a functional typewriter-like rotation of the Prp2 C-terminal domain. This movement, endorsed by an iterative swing of interactions established between specific Prp2 residues with the nucleobases at 5'- and 3'-ends of pre-mRNA, promotes pre-mRNA translocation. Notably, some of these Prp2 residues are conserved in the DExH-box family, suggesting that the translocation mechanism elucidated here may be applicable to all DExH-box helicases.

In vivo and in vitro characterizations of melibiose permease (MelB) conformation-dependent nanobodies reveal sugar-binding mechanisms

Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the Na+-coupled major facilitator superfamily (MFS) transporters, which are important for the cellular uptake of molecules including sugars and small drugs. Although the symport mechanisms have been well studied, mechanisms of substrate binding and translocation remain enigmatic. We have previously determined the sugar-binding site of outward-facing MelBSt by crystallography. To obtain other key kinetic states, here we raised camelid single-domain nanobodies (Nbs) and carried out a screening against the WT MelBSt under four ligand conditions. We applied an in vivo cAMP-dependent two-hybrid assay to detect interactions of Nbs with MelBSt and melibiose transport assays to determine the effects on MelBSt functions. We found that all selected Nbs showed partial to complete inhibitions of MelBSt transport activities, confirming their intracellular interactions. A group of Nbs (714, 725, and 733) was purified, and isothermal titration calorimetry measurements showed that their binding affinities were significantly inhibited by the substrate melibiose. When titrating melibiose to the MelBSt/Nb complexes, Nb also inhibited the sugar-binding. However, the Nb733/MelBSt complex retained binding to the coupling cation Na+ and also to the regulatory enzyme EIIAGlc of the glucose-specific phosphoenolpyruvate/sugar phosphotransferase system. Further, EIIAGlc/MelBSt complex also retained binding to Nb733 and formed a stable super-complex. All data indicated that MelBSt trapped by Nbs retained its physiological functions and the trapped conformation is similar to that bound by the physiological regulator EIIAGlc. Therefore, these conformational Nbs can be useful tools for further structural, functional, and conformational analyses.

Bioavailability and translocation of platinum nanoparticles and platinum ions in rice (Oryza sativa L.): Nanoparticles biosynthesis and size-dependent transformation

Metal nanoparticles accumulation and bioavailability in plants raised much attention, specifically transformation and transportation of nanoparticles and their corresponding ions in plants are still unknown. In this work, rice seedlings were exposed to platinum nanoparticles (PtNPs) (with three sizes of 25, 50, and 70 nm) and Pt ions (with doses of 1, 2, and 5 mg/L) to investigate the influences of particle size and Pt form on bioavailability and translocation mechanism of metal nanoparticles. Results based on single particle ICP-MS (SP-ICP-MS) demonstrated the biosynthesis of PtNPs in Pt ions treated rice seedlings. The particle size ranges at 75–79.3 nm were detected in Pt ions exposed rice roots, and further migrated up to rice shoots at 21.7–44.3 nm. After exposed to PtNP-25, the particles could transfer to shoots with the original size distribution detected in roots, even with the PtNPs dose change. PtNP-50 and PtNP-70 translocated to shoots with the particle size increase. For the rice exposure with three dose levels, PtNP-70 had the highest number-based bioconcentration factors (NBCFs) in all Pt species, while Pt ions had the highest bioconcentration factors (BCFs), a range of 1.43–2.04. All PtNPs and Pt ions could be accumulated in rice plants and further transferred to shoots, and particle biosynthesis was proved through SP-ICP-MS. The finding could help us better understand the influence of particle size and form on the transformations of PtNPs in environment.

Domperidone Inhibits Clostridium botulinum C2 Toxin and Bordetella pertussis Toxin.

Bordetella pertussis toxin (PT) and Clostridium botulinum C2 toxin are ADP-ribosylating toxins causing severe diseases in humans and animals. They share a common translocation mechanism requiring the cellular chaperones Hsp90 and Hsp70, cyclophilins, and FK506-binding proteins to transport the toxins' enzyme subunits into the cytosol. Inhibitors of chaperone activities have been shown to reduce the amount of transported enzyme subunits into the cytosol of cells, thus protecting cells from intoxication by these toxins. Recently, domperidone, an approved dopamine receptor antagonist drug, was found to inhibit Hsp70 activity. Since Hsp70 is required for cellular toxin uptake, we hypothesized that domperidone also protects cells from intoxication with PT and C2. The inhibition of intoxication by domperidone was demonstrated by analyzing the ADP-ribosylation status of the toxins' specific substrates. Domperidone had no inhibitory effect on the receptor-binding or enzyme activity of the toxins, but it inhibited the pH-driven membrane translocation of the enzyme subunit of the C2 toxin and reduced the amount of PTS1 in cells. Taken together, our results indicate that domperidone is a potent inhibitor of PT and C2 toxins in cells and therefore might have therapeutic potential by repurposing domperidone to treat diseases caused by bacterial toxins that require Hsp70 for their cellular uptake.

Mechanistic Insight into the Internalization, Distribution, and Autophagy Process of Manganese Nanoparticles in Capsicum annuum L.: Evidence from Orthogonal Microscopic Analysis.

Orthogonal techniques were used to track manganese nanoparticles (MnNPs) in Capsicum annuum L. leaf tissue and cell compartments and subsequently to explain the mechanism of uptake, translocation, and cellular interaction. C. annuum L was cultivated and foliarly exposed to MnNPs (100 mg/L, 50 mL/per leaf) before analysis by using scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS) as well as dark-field hyperspectral and two-photon microscopy. We visualized the internalization of MnNP aggregates from the leaf surface and observed particle accumulation in the leaf cuticle and epidermis as well as spongy mesophyll and guard cells. These techniques enabled a description of how MnNPs cross different plant tissues as well as selectively accumulate and translocate in specific cells. We also imaged abundant fluorescent vesicles and vacuoles containing MnNPs, indicating likely induction of autophagy processes in C. annuum L., which is the bio-response upon storing or transforming the particles. These findings highlight the importance of utilizing orthogonal techniques to characterize nanoscale material fate and distribution with complex biological matrices and demonstrate that such an approach offers a significant mechanistic understanding that can inform both risk assessment and efforts aimed at applying nanotechnology to agriculture.

Strategies for Reducing Arsenic Content in Rice: A review

Arsenic (As) is one of the most toxic metalloid that can enter the food chain through ingestion of As contaminated water or food, posing a serious threat to human health. Among cereals, rice could contain the highest amount of As because of the special growing conditions. Therefore, the importance of the reduction of As concentration in rice is essential. Many studies have been conducted to understand the mechanism of arsenic uptake, accumulation and translocation. The interactions between As and plants are influenced by soil type and other factors such as pH, mineral contents and redox status of the soil, As speciation, and microbial activity. Different nutrients including phosphates, iron, silicon and sulfur effectively regulate the uptake and accumulation of As in different parts of plants. Genetic variation has also effect on As accumulation of rice grain. Water management practices can help to decrease As content of rice plants due to changing the redox status of the soil. Phosphate and silicon transporters can be used by As to enter the rice root cells, therefore detoxification mechanisms of As in rice greatly depend on the activity of these transporters. In this review, we covered the main factors that affect the uptake, accumulation, and translocation of As in different plant organs in rice. We investigated the different soil factors and plant cell transporters needed to understand the mechanisms. This study may be useful for further research to develop strategies that inhibit As entry and transport in plant cells and contribute to safe food production.

Absorption, metabolism and distribution of carbosulfan in maize plants (Zea mays L.).

The insecticide carbosulfan is usually applied as a soil treatment or seed-coating agent, and so may be absorbed by crops and pose dietary risks. Understanding the uptake, metabolism and translocation of carbosulfan in crops is conducive to its safe application. In this study, we investigated the distribution of carbosulfan and its toxic metabolites in maize plants at both the tissue and subcellular levels, and explored the uptake and translocation mechanism of carbosulfan. Carbosulfan was mainly taken up by maize roots via the apoplast pathway, was preferentially distributed in cell walls (51.2%-57.0%) and most (85.0%) accumulated in roots with only weak upward translocation. Carbofuran, the main metabolite of carbosulfan in maize plants, was primarily stored in roots. However, carbofuran could be upwardly translocated to shoots and leaves because of its greater distribution in root-soluble components (24.4%-28.5%) compared with carbosulfan (9.7%-14.5%). This resulted from its greater solubility compared with its parent compound. The metabolite 3-hydroxycarbofuran was found in shoots and leaves. Carbosulfan could be passively absorbed by maize roots, mainly via the apoplastic pathway, and transformed into carbofuran and 3-hydroxycarbofuran. Although carbosulfan mostly accumulated in roots, its toxic metabolites carbofuran and 3-hydroxycarbofuran could be detected in shoots and leaves. This implies that there is a risk in the use of carbosulfan as a soil treatment or seed coating. © 2023 Society of Chemical Industry.

Activity, substrate preferenceand structure of the HsMCM8/9 helicase.

The minichromosomal maintenance proteins, MCM8 and MCM9, are more recent evolutionary additions to the MCM family, only cooccurring in selected higher eukaryotes. Mutations in these genes are directly linked to ovarian insufficiency, infertility, and several cancers. MCM8/9 appears to have ancillary roles in fork progression and recombination of broken replication forks. However, the biochemical activity, specificitiesand structures have not been adequately illustrated, making mechanistic determination difficult. Here, we show that human MCM8/9 (HsMCM8/9) is an ATP dependent DNA helicase that unwinds fork DNA substrates with a 3'-5' polarity. High affinity ssDNA binding occurs in the presence of nucleoside triphosphates, while ATP hydrolysis weakens the interaction with DNA. The cryo-EM structure of theHsMCM8/9 heterohexamer was solved at 4.3 Å revealing a trimer of heterodimer configuration with two types of interfacial AAA+ nucleotide binding sites that become more organized upon binding ADP. Local refinements of the N or C-terminal domains (NTD or CTD) improved the resolution to 3.9 or 4.1 Å, respectively, and shows a large displacement in the CTD. Changes in AAA+ CTD upon nucleotide binding and a large swing between the NTD and CTD likely implies that MCM8/9 utilizes a sequential subunit translocation mechanism for DNA unwinding.

Determinants and mechanisms of inorganic nanoparticle translocation across mammalian biological barriers.

Biological barriers protect delicate internal tissues from exposures to and interactions with hazardous materials. Primary anatomical barriers prevent external agents from reaching systemic circulation and include the pulmonary, gastrointestinal, and dermal barriers. Secondary barriers include the blood-brain, blood-testis, and placental barriers. The tissues protected by secondary barriers are particularly sensitive to agents in systemic circulation. Neurons of the brain cannot regenerate and therefore must have limited interaction with cytotoxic agents. In the testis, the delicate process of spermatogenesis requires a specific milieu distinct from the blood. The placenta protects the developing fetus from compounds in the maternal circulation that would impair limb or organ development. Many biological barriers are semi-permeable, allowing only materials or chemicals, with a specific set of properties, that easily pass through or between cells. Nanoparticles (particles less than 100nm) have recently drawn specific concern due to the possibility of biological barrier translocation and contact with distal tissues. Current evidence suggests that nanoparticles translocate across both primary and secondary barriers. It is known that the physicochemical properties of nanoparticles can affect biological interactions, and it has been shown that nanoparticles can breach primary and some secondary barriers. However, the mechanism by which nanoparticles cross biological barriers has yet to be determined. Therefore, the purpose of this review is to summarize how different nanoparticle physicochemical properties interact with biological barriers and barrier products to govern translocation.

Insights into a viral motor: the structure of the HK97 packaging termination assembly.

Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each genome unit. Here we present the first structural data for a cos virus DNA packaging motor, assembled from the bacteriophage HK97 terminase proteins, procapsids encompassing the portal protein, and DNA containing a cos site. The cryo-EM structure is consistent with the packaging termination state adopted after DNA cleavage, with DNA density within the large terminase assembly ending abruptly at the portal protein entrance. Retention of the large terminase complex after cleavage of the short DNA substrate suggests that motor dissociation from the capsid requires headful pressure, in common with pac viruses. Interestingly, the clip domain of the 12-subunit portal protein does not adhere to C12 symmetry, indicating asymmetry induced by binding of the large terminase/DNA. The motor assembly is also highly asymmetric, showing a ring of 5 large terminase monomers, tilted against the portal. Variable degrees of extension between N- and C-terminal domains of individual subunits suggest a mechanism of DNA translocation driven by inter-domain contraction and relaxation.

Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores.

Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing. A clear molecular-level understanding of how the presence of PEGs offers such desirable outcomes in nanopore sensing is still missing. In this work, we present a new theoretical approach to probe the effect of PEG crowders on DNA capture and translocation through the αHL nanopore. We develop an exactly solvable discrete-state stochastic model based on the cooperative partitioning of individual polycationic PEGs within the cavity of the αHL nanopore. It is argued that the apparent electrostatic interactions between the DNA and PEGs control all of the dynamic processes. Our analytical predictions find excellent agreements with existing experiments, thereby strongly supporting our theory.

Emerging paradigms in exploring the interactions among diet, probiotics, and cancer immunotherapeutic response

Emerging paradigms in exploring the interactions among diet, probiotics, and cancer immunotherapeutic response