An antibiotic from an uncultured bacterium binds to an immutable target.

Antimicrobial resistance is a leading mortality factor worldwide. Here, we report the discovery of clovibactin, an antibiotic isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant Gram-positive bacterial pathogens without detectable resistance. Using biochemical assays, solid-state nuclear magnetic resonance, and atomic force microscopy, we dissect its mode of action. Clovibactin blocks cell wall synthesis by targeting pyrophosphate of multiple essential peptidoglycan precursors (C55PP, lipid II, and lipid IIIWTA). Clovibactin uses an unusual hydrophobic interface to tightly wrap around pyrophosphate but bypasses the variable structural elements of precursors, accounting for the lack of resistance. Selective and efficient target binding is achieved by the sequestration of precursors into supramolecular fibrils that only form on bacterial membranes that contain lipid-anchored pyrophosphate groups. This potent antibiotic holds the promise of enabling the design of improved therapeutics that kill bacterial pathogens without resistance development.

Teixobactin kills bacteria by a two-pronged attack on the cell envelope.

Antibiotics that use novel mechanisms are needed to combat antimicrobial resistance1-3. Teixobactin4 represents a new class of antibiotics with a unique chemical scaffold and lack of detectable resistance. Teixobactin targets lipid II, a precursor of peptidoglycan5. Here we unravel the mechanism of teixobactin at the atomic level using a combination of solid-state NMR, microscopy, in vivo assays and molecular dynamics simulations. The unique enduracididine C-terminal headgroup of teixobactin specifically binds to the pyrophosphate-sugar moiety of lipid II, whereas the N terminus coordinates the pyrophosphate of another lipid II molecule. This configuration favours the formation of a ß-sheet of teixobactins bound to the target, creating a supramolecular fibrillar structure. Specific binding to the conserved pyrophosphate-sugar moiety accounts for the lack of resistance to teixobactin4. The supramolecular structure compromises membrane integrity. Atomic force microscopy and molecular dynamics simulations show that the supramolecular structure displaces phospholipids, thinning the membrane. The long hydrophobic tails of lipid II concentrated within the supramolecular structure apparently contribute to membrane disruption. Teixobactin hijacks lipid II to help destroy the membrane. Known membrane-acting antibiotics also damage human cells, producing undesirable side effects. Teixobactin damages only membranes that contain lipid II, which is absent in eukaryotes, elegantly resolving the toxicity problem. The two-pronged action against cell wall synthesis and cytoplasmic membrane produces a highly effective compound targeting the bacterial cell envelope. Structural knowledge of the mechanism of teixobactin will enable the rational design of improved drug candidates.

High-speed atomic force microscopy reveals a three-state elevator mechanism in the citrate transporter CitS.

The secondary active transporter CitS shuttles citrate across the cytoplasmic membrane of gram-negative bacteria by coupling substrate translocation to the transport of two Na+ ions. Static crystal structures suggest an elevator type of transport mechanism with two states: up and down. However, no dynamic measurements have been performed to substantiate this assumption. Here, we use high-speed atomic force microscopy for real-time visualization of the transport cycle at the level of single transporters. Unexpectedly, instead of a bimodal height distribution for the up and down states, the experiments reveal movements between three distinguishable states, with protrusions of ∼0.5 nm, ∼1.0 nm, and ∼1.6 nm above the membrane, respectively. Furthermore, the real-time measurements show that the individual protomers of the CitS dimer move up and down independently. A three-state elevator model of independently operating protomers resembles the mechanism proposed for the aspartate transporter GltPh Since CitS and GltPh are structurally unrelated, we conclude that the three-state elevators have evolved independently.

Techno-economic feasibility and life cycle assessment analysis for a developed novel biosorbent-based arsenic bio-filter system.

Significant aquifers around the world is contaminated by arsenic (As), that is regarded as a serious inorganic pollution. In this study, a biosorbent-based bio-filter column has been developed using two different plant biomasses (Colocasia esculenta stems and Artocarpus heterophyllus seeds) to remove total As from the aqueous system. Due to its natural origin, affordability, adaptability, removal effectiveness, and possibility for integration with existing systems, the biosorbent-based bio-filter column presents an alluring and promising method. It offers a practical and eco-friendly way to lessen the damaging impacts of heavy metal contamination on ecosystems and public health. In this system, As (III) is oxidized to As (V) using chlorine as an oxidant, after this post-oxidized As-contaminated water is passed through the bio-filter column to receive As-free water (or below World Health Organization permissible limit for As in drinking water). Optimization of inlet flow rate, interference of co-existing anions and cations, and life cycle of the column were studied. The maximum removal percent of As was identified to be 500 µg L-1 of initial concentration at a flow rate of 1.5 L h-1. Furthermore, the specifications of the biosorbent material was studied using elemental analysis and Zeta potential. The particle size distribution, morphological structures, and chemical composition before and after binding with As were studied using dynamic light scattering (DLS), scanning electron microscope-energy dispersive X-Ray spectroscopy (SEM-EDX), and fourier's transform infrared spectroscopy (FTIR) analysis, respectively. SuperPro 10 software was used to analyze the techno-economic viability of the complete unit and determine its ideal demand and potential. Life cycle assessment was studied to interpret the environmental impacts associated alongside the process system. Therefore, this bio-filtration system could have a potential application in rural, urban, and industrial sectors.

Light-Triggered Disassembly of Molecular Motor-based Supramolecular Polymers Revealed by High-Speed AFM.

Photoresponsive supramolecular polymers have a major potential for applications in responsive materials that are externally triggered by light with spatio-temporal control of their polymerisation state. While changes in macroscopic properties revealed the adaptive nature of these materials, it remains challenging to capture the dynamic depolymerisation process at the molecular level, which requires fast observation techniques combined with in situ irradiation. By implementing in situ UV illumination into a High-Speed Atomic Force Microscope (HS-AFM) setup, we have been able to capture the disassembly of a light-driven molecular motor-based supramolecular polymer. The real-time visualisation of the light-triggered disassembly process not only reveals cooperative depolymerisation, it also shows that this process continues after illumination is halted. Combining the data with cryo-electron microscopy and spectroscopy approaches, we obtain a molecular-level description of the motor-based polymer dynamics reminiscent of actin chain-end depolymerisation. Our detailed understanding of supramolecular depolymerisation will drive the development of future responsive polymer systems.

Role of Curvature-Sensing Proteins in the Uptake of Nanoparticles with Different Mechanical Properties.

Nanoparticles of different properties, such as size, charge, and rigidity, are used for drug delivery. Upon interaction with the cell membrane, because of their curvature, nanoparticles can bend the lipid bilayer. Recent results show that cellular proteins capable of sensing membrane curvature are involved in nanoparticle uptake; however, no information is yet available on whether nanoparticle mechanical properties also affect their activity. Here liposomes and liposome-coated silica are used as a model system to compare uptake and cell behavior of two nanoparticles of similar size and charge, but different mechanical properties. High-sensitivity flow cytometry, cryo-TEM, and fluorescence correlation spectroscopy confirm lipid deposition on the silica. Atomic force microscopy is used to quantify the deformation of individual nanoparticles at increasing imaging forces, confirming that the two nanoparticles display distinct mechanical properties. Uptake studies in HeLa and A549 cells indicate that liposome uptake is higher than for the liposome-coated silica. RNA interference studies to silence their expression show that different curvature-sensing proteins are involved in the uptake of both nanoparticles in both cell types. These results confirm that curvature-sensing proteins have a role in nanoparticle uptake, which is not restricted to harder nanoparticles, but includes softer nanomaterials commonly used for nanomedicine applications.

Artificial Protein Cage with Unusual Geometry and Regularly Embedded Gold Nanoparticles.

Artificial protein cages have great potential in a number of areas including cargo capture and delivery and as artificial vaccines. Here, we investigate an artificial protein cage whose assembly is triggered by gold nanoparticles. Using biochemical and biophysical methods we were able to determine both the mechanical properties and the gross compositional features of the cage which, combined with mathematical models and biophysical data, allowed the structure of the cage to be predicted. The accuracy of the overall geometrical prediction was confirmed by the cryo-EM structure determined to sub-5 Å resolution. This showed the cage to be nonregular but similar to a dodecahedron, being constructed from 12 11-membered rings. Surprisingly, the structure revealed that the cage also contained a single, small gold nanoparticle at each 3-fold axis meaning that each cage acts as a synthetic framework for regular arrangement of 20 gold nanoparticles in a three-dimensional lattice.

The ESCRT-III isoforms CHMP2A and CHMP2B display different effects on membranes upon polymerization.

BACKGROUND: ESCRT-III proteins are involved in many membrane remodeling processes including multivesicular body biogenesis as first discovered in yeast. In humans, ESCRT-III CHMP2 exists as two isoforms, CHMP2A and CHMP2B, but their physical characteristics have not been compared yet. RESULTS: Here, we use a combination of techniques on biomimetic systems and purified proteins to study their affinity and effects on membranes. We establish that CHMP2B binding is enhanced in the presence of PI(4,5)P2 lipids. In contrast, CHMP2A does not display lipid specificity and requires CHMP3 for binding significantly to membranes. On the micrometer scale and at moderate bulk concentrations, CHMP2B forms a reticular structure on membranes whereas CHMP2A (+CHMP3) binds homogeneously. Thus, CHMP2A and CHMP2B unexpectedly induce different mechanical effects to membranes: CHMP2B strongly rigidifies them while CHMP2A (+CHMP3) has no significant effect. CONCLUSIONS: We therefore conclude that CHMP2B and CHMP2A exhibit different mechanical properties and might thus contribute differently to the diverse ESCRT-III-catalyzed membrane remodeling processes.

Role of tide and lunar phases on the migration pattern of juvenile Hilsa shad (Tenualosa ilisha) within a meso-macrotidal estuary.

Tide and lunar phases often influence the behaviour and life cycle of different fishes, especially migratory species. In the Hooghly River estuary, Hilsa shad is an anadromous fish species that migrates from the adjacent sea to the estuary and rivers for spawning. After spawning, the juveniles remain in the rivers and estuary for few months then start their downstream migration towards the adjacent sea. However, the pattern of their downstream migration has not been studied in detail so far. This study investigates the role of tide and lunar phases on the juvenile Hilsa shad migration pattern. In this study, we have estimated the rate of juveniles migrating through the river channel (no. m-2  h-1 ) during high tide and low tide in all of the lunar phases. The number of juvenile Hilsa shad fishes is found to be much higher during low tides in most of the observations and there is a significant difference (t = 11.904, P < 0.001) between the high tide and low tide catches in the entire study region. Among the eight lunar phases, the number of juveniles is also observed to be higher during the new moon and full moon, and there is also a significant difference in juvenile catch among the lunar phases (F = 64.372, P < 0.001) in the entire stretch of the study area. These observations enabled us to develop a plausible mechanism of the downstream migration of Hilsa shad juveniles.

Potential human health risk assessment of microplastic exposure: current scenario and future perspectives.

The vast usage of synthetic plastics has led to the global problem of plastic pollution which in turn has positively impacted the concerns regarding microplastic pollution. The major factor responsible for the increased level of pollution is the smaller size of microplastics which helps in its transportation across the globe. It has been found in most remote areas like glaciers and Antarctic regions where it is difficult for other contaminants to reach. This is ensured by the physicochemical cycle of plastic. They can either be produced for different applications or generated through the fragmentation of large plastic particles. Different studies have shown the accumulation of microplastics in different organisms, especially in aquatic animals leading to their entry into the food chain. The ultimate fate of the microplastics is accumulation inside the human body posing the risk of different health conditions like cancer, diabetes, and allergic reactions. The present review summarizes a detailed discussion on the current status of microplastic pollution, their effect on different organisms, and its impact on human health with a case study on the human health risk assessment for analyzing the global rate of microplastic ingestion.

Reversibly Photo-Modulating Mechanical Stiffness and Toughness of Bioengineered Protein Fibers.

Light-responsive materials have been extensively studied due to the attractive possibility of manipulating their properties with high spatiotemporal control in a non-invasive fashion. This stimulated the development of a series of photo-deformable smart devices. However, it remained a challenge to reversibly modulate the stiffness and toughness of bulk materials. Here, we present bioengineered protein fibers and their optomechanical manipulation by employing electrostatic interactions between supercharged polypeptides (SUPs) and an azobenzene (Azo)-based surfactant. Photo-isomerization of the Azo moiety from the E- to Z-form reversibly triggered the modulation of tensile strength, stiffness, and toughness of the bulk protein fiber. Specifically, the photo-induced rearrangement into the Z-form of Azo possibly strengthened cation-π interactions within the fiber material, resulting in an around twofold increase in the fiber's mechanical performance. The outstanding mechanical and responsive properties open a path towards the development of SUP-Azo fibers as smart stimuli-responsive mechano-biomaterials.

Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization.

Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembly remain largely obscure due to a lack of experimental tools for probing these pathways at the molecular level. Here, the self-assembly of self-replicators into fibers is visualized in real-time by high-speed atomic force microscopy (HS-AFM). Fiber growth requires the conversion of precursor molecules into six-membered macrocycles, which constitute the fibers. HS-AFM experiments, supported by molecular dynamics simulations, revealed that aggregates of precursor molecules accumulate at the sides of the fibers, which then diffuse to the fiber ends where growth takes place. This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization.

The role of VPS4 in ESCRT-III polymer remodeling.

The endosomal sorting complex required for transport-III (ESCRT-III) and VPS4 catalyze a variety of membrane-remodeling processes in eukaryotes and archaea. Common to these processes is the dynamic recruitment of ESCRT-III proteins from the cytosol to the inner face of a membrane neck structure, their activation and filament formation inside or at the membrane neck and the subsequent or concomitant recruitment of the AAA-type ATPase VPS4. The dynamic assembly of ESCRT-III filaments and VPS4 on cellular membranes induces constriction of membrane necks with large diameters such as the cytokinetic midbody and necks with small diameters such as those of intraluminal vesicles or enveloped viruses. The two processes seem to use different sets of ESCRT-III filaments. Constriction is then thought to set the stage for membrane fission. Here, we review recent progress in understanding the structural transitions of ESCRT-III proteins required for filament formation, the functional role of VPS4 in dynamic ESCRT-III assembly and its active role in filament constriction. The recent data will be discussed in the context of different mechanistic models for inside-out membrane fission.

Nematic DNA Thermotropic Liquid Crystals with Photoresponsive Mechanical Properties.

Over the last decades, water-based lyotropic liquid crystals of nucleic acids have been extensively investigated because of their important role in biology. Alongside, solvent-free thermotropic liquid crystals (TLCs) from DNA are gaining great interest, owing to their relevance to DNA-inspired optoelectronic applications. Up to now, however, only the smectic phase of DNA TLCs has been reported. The development of new mesophases including nematic, hexagonal, and cubic structures for DNA TLCs remains a significant challenge, which thus limits their technological applications considerably. In this work, a new type of DNA TLC that is formed by electrostatic complexation of anionic oligonucleotides and cationic surfactants containing an azobenzene (AZO) moiety is demonstrated. DNA-AZO complexes form a stable nematic mesophase over a temperature range from -7 to 110 °C and retain double-stranded DNA structure at ambient temperature. Photoisomerization of the AZO moieties from the E- to the Z-form alters the stiffness of the DNA-AZO hybrid materials opening a pathway toward the development of DNA TLCs as stimuli-responsive biomaterials.

Host defence peptide plectasin targets bacterial cell wall precursor lipid II by a calcium-sensitive supramolecular mechanism.

Antimicrobial resistance is a leading cause of mortality, calling for the development of new antibiotics. The fungal antibiotic plectasin is a eukaryotic host defence peptide that blocks bacterial cell wall synthesis. Here, using a combination of solid-state nuclear magnetic resonance, atomic force microscopy and activity assays, we show that plectasin uses a calcium-sensitive supramolecular killing mechanism. Efficient and selective binding of the target lipid II, a cell wall precursor with an irreplaceable pyrophosphate, is achieved by the oligomerization of plectasin into dense supra-structures that only form on bacterial membranes that comprise lipid II. Oligomerization and target binding of plectasin are interdependent and are enhanced by the coordination of calcium ions to plectasin's prominent anionic patch, causing allosteric changes that markedly improve the activity of the antibiotic. Structural knowledge of how host defence peptides impair cell wall synthesis will likely enable the development of superior drug candidates.

Electroactive properties and piezo-tribo hybrid energy harvesting performances of PVDF-AlFeO3 composites: role of crystal symmetry and agglomeration of fillers.

Inorganic filler-loaded PVDF-based composites have been very widely used for electrical and energy harvesting applications in recent times. In this regard, the effects of different parameters of fillers like size, shape, chemical states, distribution, functional properties, and many others on the output performance of PVDF have been widely studied. However, the effect of another important parameter, namely the crystal symmetry of the filler, in tuning the energy harvesting performance of PVDF has been rarely explored. Therefore, to explore this fact, here we develop PVDF-based composite films by using two types of AlFeO3 fillers, one with rhombohedral R3̄c symmetry (AFRH) and another with an orthorhombic Pc21n structure. Ferrite-based oxides have been chosen here as fillers due to their good dielectric compatibility with PVDF. On the other hand, AlFeO3 has been chosen due to the simplicity of synthesizing it with both centrosymmetric and non-centrosymmetric crystal structures and the scarcity of reports exploring the energy-harvesting performance of AlFeO3-based polymer composites. A significant difference in particle agglomeration has also been observed here between the mentioned two types of AlFeO3 fillers which was mainly due to their specific synthesis conditions. The electroactive properties of PVDF have been observed to be mostly dependent on filler agglomeration. However, the crystal symmetry has shown a strong effect on the piezoelectric energy harvesting performances. As a result of these facts, the piezo-tribo hybrid energy harvesting performance, which depends on both the dielectric permittivity and piezoelectric activity, has been observed to be better for the AFRH5-based hybrid device (AFRH5H) (with ∼72 V open circuit voltage and ∼45 µW cm-2 power density) compared to that of the AFOR5-based hybrid device (AFOR5H). The real-life applications of all the energy harvesting devices have also been demonstrated here.

Isothermal and Kinetics Modeling Approach for the Bioremediation of Potentially Toxic Trace Metal Ions Using a Novel Biosorbent Acalypha wilkesiana (Copperleaf) Leaves.

The presence of trace metals in wastewater brings serious environmental pollution that threatens human health as well as the ecosystem throughout the world due to their non-biodegradability nature. The present study focuses on the bioremediation of toxic trace metals, namely arsenic (As), cadmium (Cd), and chromium (Cr), using Acalypha wilkesiana leaf raw biomass. The optimization of various process variables was done to determine the removal percentage of trace metal using Acalypha wilkesiana leaf raw biomass, and the optimum conditions were an adsorbent dose of 0.5 g, contact time 10 h, 8 h, and 10 h, process temperature 30 °C, initial concentration of trace metal as 30 µg/L, 30 mg//L, and 40 mg/L, and pH of 7.5, 7 and 7.5 for As5+, and Cd2+ and Cr6+, respectively. Acalypha wilkesiana leaf raw biomass is characterized using a scanning electron microscope (SEM), energy dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), and Fourier transformation infrared spectroscopy (FTIR), zeta potential before and after adsorption of the trace metal ions. The study was well fitted for the equilibrium data for Langmuir isotherm for As5+, Cd2+, and Cr6+, Freundlich for As5+, Dubinin-Radushkevinch (D-R) for Cr6+, and Temkin for As5+ and Cr6+. The adsorption of all three trace metals was confirmed by the kinetics and thermodynamic studies to be following pseudo-second-order kinetics with endothermic as well as spontaneous processes, respectively. Thus, the present study indicates Acalypha wilkesiana leaf raw biomass as an effective and efficient novel biosorbent to remediate different trace metals from aqueous systems with its possible application in existing and novel methods for wastewater management.

Microbial community composition analysis to decipher the possible role of inherent bacteria for in-situ arsenic (As) bioremediation.

Biogeochemical reduction and mobilization of sediment-bound arsenic (As) is the major concern for widespread groundwater As contamination in the middle Gangetic plains. The present work examines a microcosm based bio-stimulation study and substrate amendments over 45 days to analyze the bacterial community structure and distribution to indicate the possible in-situ bioremediation strategy in the area. Initially, Bacterial phyla Proteobacteria was predominantly present in all the samples, followed by Actinobacteria, Bacteroidetes, and Firmicutes whereas Cyanobacteria was noted as the minor group. In genus level, Delftia, Acinetobacter, Lysobacter, Bacillus, and Pseudomonas were the major groups of bacteria in the As-rich aquifer system, while Planctomycetes dominated the bio-stimulated samples, followed by a minute portion of Proteobacteria. Alpha diversity and Chaol curve further determined the species richness in the samples with an As tolerant capacity of 152.28 ppb. The presence of γ-Proteobacteria as the dominating member in high As-content water indicated their predominant role in As mobilization, whereas, dominance of α-Proteobacterial members in low As-content water indicated their involvement in As detoxification. The complete change in microbial community structure within the bio-stimulated conditions indicated the extensive role of arsenite-oxidizing microbial communities within different levels of As-contaminated areas in Bihar that will enlighten the significant role of these communities in As-biogeochemical cycle. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03612-0.

Biofilm-Mediated Heavy Metal Removal from Aqueous System by Multi-Metal-Resistant Bacterial Strain Bacillus sp. GH-s29.

Worldwide ever-augmenting urbanization, modernization, and industrialization have contributed to the release of pernicious compounds and a variety of pollutants into the environment. The pollutants discharged due to industrialization are of global concern. Industrial waste and effluent are comprised of hazardous organic and inorganic chemicals including heavy metals which pose a significant threat to the environment and may bring about numerous diseases or abnormalities in human beings. This brings on greater urgency for remediation of these polluted soil and water using sustainable approaches and mechanisms. In the present research, a multi-metal-resistant, gram-positive, non-virulent bacterial strain Bacillus sp. GH-s29 was isolated from contaminated groundwater of Bhojpur district, Bihar, India. The strain had the potential to develop a biofilm that was able to remediate different heavy metals [arsenic, cadmium, and chromium] from individual and multi-heavy metal solutions. Maximum removal for As (V), Cd (II), and Cr (VI) from individual-metal and the multi-metal solution was observed to be 73.65%, 57.37%, 61.62%, and 48.92%, 28.7%, and 35.46%, respectively. SEM-EDX analysis revealed the sequestration of multi-heavy metals by bacterial biofilm. Further characterization by FTIR analysis ensured that the presence of negatively charged functional groups on the biofilm-EPS such as hydroxyl, phosphate, sulfate, and carboxyl helps in binding to the positively charged metal ions. Thus, Bacillus sp. GH-s29 proved to be an effective and economical alternative for different heavy metal remediation from contaminated sites.

Lateral membrane organization as target of an antimicrobial peptidomimetic compound.

Antimicrobial resistance is one of the leading concerns in medical care. Here we study the mechanism of action of an antimicrobial cationic tripeptide, AMC-109, by combining high speed-atomic force microscopy, molecular dynamics, fluorescence assays, and lipidomic analysis. We show that AMC-109 activity on negatively charged membranes derived from Staphylococcus aureus consists of two crucial steps. First, AMC-109 self-assembles into stable aggregates consisting of a hydrophobic core and a cationic surface, with specificity for negatively charged membranes. Second, upon incorporation into the membrane, individual peptides insert into the outer monolayer, affecting lateral membrane organization and dissolving membrane nanodomains, without forming pores. We propose that membrane domain dissolution triggered by AMC-109 may affect crucial functions such as protein sorting and cell wall synthesis. Our results indicate that the AMC-109 mode of action resembles that of the disinfectant benzalkonium chloride (BAK), but with enhanced selectivity for bacterial membranes.