Identification of trypsin-degrading commensals in the large intestine.

Increased levels of proteases, such as trypsin, in the distal intestine have been implicated in intestinal pathological conditions1-3. However, the players and mechanisms that underlie protease regulation in the intestinal lumen have remained unclear. Here we show that Paraprevotella strains isolated from the faecal microbiome of healthy human donors are potent trypsin-degrading commensals. Mechanistically, Paraprevotella recruit trypsin to the bacterial surface through type IX secretion system-dependent polysaccharide-anchoring proteins to promote trypsin autolysis. Paraprevotella colonization protects IgA from trypsin degradation and enhances the effectiveness of oral vaccines against Citrobacter rodentium. Moreover, Paraprevotella colonization inhibits lethal infection with murine hepatitis virus-2, a mouse coronavirus that is dependent on trypsin and trypsin-like proteases for entry into host cells4,5. Consistently, carriage of putative genes involved in trypsin degradation in the gut microbiome was associated with reduced severity of diarrhoea in patients with SARS-CoV-2 infection. Thus, trypsin-degrading commensal colonization may contribute to the maintenance of intestinal homeostasis and protection from pathogen infection.

TdfH selectively binds metal-loaded tetrameric calprotectin for zinc import.

To combat nutritional immunity, N. gonorrhoeae has evolved systems to hijack zinc and other metals directly from host metal-binding proteins such as calprotectin (CP). Here, we report the 6.1 Å cryoEM structure of the gonococcal surface receptor TdfH in complex with a zinc-bound CP tetramer. We further show that TdfH can also interact with CP in the presence of copper and manganese, but not with cobalt.

Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM.

In Gram-negative bacteria, the biogenesis of ß-barrel outer membrane proteins is mediated by the ß-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely understood. Here, we report the structures of BAM in nanodiscs, prepared using polar lipids and native membranes, where we observe an outward-open state. Mutations in the barrel domain of BamA reveal that plasticity in BAM is essential, particularly along the lateral seam of the barrel domain, which is further supported by molecular dynamics simulations that show conformational dynamics in BAM are modulated by the accessory proteins. We also report the structure of BAM in complex with EspP, which reveals an early folding intermediate where EspP threads from the underside of BAM and incorporates into the barrel domain of BamA, supporting a hybrid-barrel budding mechanism in which the substrate is folded into the membrane sequentially rather than as a single unit.

Molecular Insight into TdfH-Mediated Zinc Piracy from Human Calprotectin by Neisseria gonorrhoeae.

Neisseria gonorrhoeae, responsible for the sexually transmitted infection gonorrhea, is an obligate human pathogen exquisitely adapted for survival on mucosal surfaces of humans. This host-pathogen relationship has resulted in evolution by N. gonorrhoeae of pathways that enable the use of host metalloproteins as required nutrients through the deployment of outer membrane-bound TonB-dependent transporters (TdTs). Recently, a TdT called TdfH was implicated in binding to calprotectin (CP) and in removal of the bound zinc (Zn), enabling gonococcal growth. TdfH is highly conserved among the pathogenic Neisseria species, making it a potentially promising candidate for inclusion into a gonococcal vaccine. Currently, the nature and specificity of the TdfH-CP interaction have not been determined. In this study, we found that TdfH specifically interacted with human calprotectin (hCP) and that growth of the gonococcus was supported in a TdfH-dependent manner only when hCP was available as a sole zinc source and not when mouse CP was provided. The binding interactions between TdfH and hCP were assessed using isothermal titration calorimetry where we observed a multistate model having both high-affinity and low-affinity sites of interaction. hCP has two Zn binding sites, and gonococcal growth assays using hCP mutants deficient in one or both of the Zn binding sites revealed that TdfH exhibited a site preference during Zn piracy and utilization. This report provides the first insights into the molecular mechanism of Zn piracy by neisserial TdfH and further highlights the obligate human nature of N. gonorrhoeae and the high-affinity interactions occurring between TdTs and their human ligands during pathogenesis.IMPORTANCE The dramatic rise in antimicrobial resistance among Neisseria gonorrhoeae isolates over the last few decades, paired with dwindling treatment options and the lack of a protective vaccine, has prompted increased interest in identifying new bacterial targets for the treatment and, ideally, prevention of gonococcal disease. TonB-dependent transporters are a conserved set of proteins that serve crucial functions for bacterial survival within the host. In this study, binding between the gonococcal transporter, TdfH, and calprotectin was determined to be of high affinity and host restricted. The current study identified a preferential TdfH interaction at the calprotectin dimer interface. An antigonococcal therapeutic could potentially block this site on calprotectin, interrupting Zn uptake by N. gonorrhoeae and thereby prohibiting continued bacterial growth. We describe protein-protein interactions between TdfH and calprotectin, and our findings provide the building blocks for future therapeutic or prophylactic targets.

Author Correction: A new antibiotic selectively kills Gram-negative pathogens.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The big BAM theory: An open and closed case?

The ß-barrel assembly machinery (BAM) is responsible for the biogenesis of outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria. These OMPs have a membrane-embedded domain consisting of a ß-barrel fold which can vary from 8 to 36 ß-strands, with each serving a diverse role in the cell such as nutrient uptake and virulence. BAM was first identified nearly two decades ago, but only recently has the molecular structure of the full complex been reported. Together with many years of functional characterization, we have a significantly clearer depiction of BAM's structure, the intra-complex interactions, conformational changes that BAM may undergo during OMP biogenesis, and the role chaperones may play. But still, despite advances over the past two decades, the mechanism for BAM-mediated OMP biogenesis remains elusive. Over the years, several theories have been proposed that have varying degrees of support from the literature, but none has of yet been conclusive enough to be widely accepted as the sole mechanism. We will present a brief history of BAM, the recent work on the structures of BAM, and a critical analysis of the current theories for how it may function.

A new antibiotic selectively kills Gram-negative pathogens.

The current need for novel antibiotics is especially acute for drug-resistant Gram-negative pathogens1,2. These microorganisms have a highly restrictive permeability barrier, which limits the penetration of most compounds3,4. As a result, the last class of antibiotics that acted against Gram-negative bacteria was developed in the 1960s2. We reason that useful compounds can be found in bacteria that share similar requirements for antibiotics with humans, and focus on Photorhabdus symbionts of entomopathogenic nematode microbiomes. Here we report a new antibiotic that we name darobactin, which was obtained using a screen of Photorhabdus isolates. Darobactin is coded by a silent operon with little production under laboratory conditions, and is ribosomally synthesized. Darobactin has an unusual structure with two fused rings that form post-translationally. The compound is active against important Gram-negative pathogens both in vitro and in animal models of infection. Mutants that are resistant to darobactin map to BamA, an essential chaperone and translocator that folds outer membrane proteins. Our study suggests that bacterial symbionts of animals contain antibiotics that are particularly suitable for development into therapeutics.

Efficient capture, rapid killing and ultrasensitive detection of bacteria by a nano-decorated multi-functional electrode sensor.

In this work, we demonstrated a nano-decorated porous impedance electrode sensor for efficient capture, rapid killing and ultrasensitive detection of bacteria. The multi-functional sensor was prepared by a facile sonochemical method via in situ deposition of antibacterial prickly Zn-CuO nanoparticles and graphene oxide (GO) nanosheets on a Ni porous electrode. Due to the surface burr-like nanostructures, the nano-decorated impedance sensor exhibited very good bacterial-capture efficiency (70 - 80% in 20min) even at a low concentration of 50 CFU mL-1, rapid antibacterial rate (100% killing in 30min) and high detection sensitivity (as low as 10 CFU mL-1). More importantly, the nano-decorated sensor has proven to be highly effective in quantitative detection of bacteria in a biological sample, for example, a rat blood sample spiked with E. coli. Despite the complexity of blood, the sensor still exhibited excellent detection precision within 30min at bacteria concentrations ranging from 10 - 105 CFU mL-1. The simplicity, rapidity, sensitivity, practicability and multifunctionality of this impedance sensor would greatly facilitate applications in portable medical devices for on-the-spot diagnosis and even the possibility for simultaneous therapy of diseases caused by bacterial infections.

Formation of Highly Oxidized Radicals and Multifunctional Products from the Atmospheric Oxidation of Alkylbenzenes.

Aromatic hydrocarbons contribute significantly to tropospheric ozone and secondary organic aerosols (SOA). Despite large efforts in elucidating the formation mechanism of aromatic-derived SOA, current models still substantially underestimate the SOA yields when comparing to field measurements. Here we present a new, up to now undiscovered pathway for the formation of highly oxidized products from the OH-initiated oxidation of alkyl benzenes based on theoretical and experimental investigations. We propose that unimolecular H-migration followed by O2-addition, a so-called autoxidation step, can take place in bicyclic peroxy radicals (BPRs), which are important intermediates of the OH-initiated oxidation of aromatic compounds. These autoxidation steps lead to the formation of highly oxidized multifunctional compounds (HOMs), which are able to form SOA. Our theoretical calculations suggest that the intramolecular H-migration in BPRs of substituted benzenes could be fast enough to compete with bimolecular reactions with HO2 radicals or NO under atmospheric conditions. The theoretical findings are experimentally supported by flow tube studies using chemical ionization mass spectrometry to detect the highly oxidized peroxy radical intermediates and closed-shell products. This new unimolecular BPR route to form HOMs in the gas phase enhances our understanding of the aromatic oxidation mechanism, and contributes significantly to a better understanding of aromatic-derived SOA in urban areas.

Microfluidic Encapsulation of Prickly Zinc-Doped Copper Oxide Nanoparticles with VD1142 Modified Spermine Acetalated Dextran for Efficient Cancer Therapy.

Structural features of nanoparticles have recently been explored for different types of applications. To explore specific particles as nanomedicine and physically destroy cancer is interesting, which might avoid many obstacles in cancer treatment, for example, drug resistance. However, one key element and technical challenge of those systems is to selectively target them to cancer cells. As a proof-of-concept, Prickly zinc-doped copper oxide (Zn-CuO) nanoparticles (Prickly NPs) have been synthesized, and subsequently encapsulated in a pH-responsive polymer; and the surface has been modified with a novel synthesized ligand, 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl] benzenesulfonamide (VD1142). The Prickly NPs exhibit very effective cancer cell antiproliferative capability. Moreover, the polymer encapsulation shields the Prickly NPs from unspecific nanopiercing and, most importantly, VD1142 endows the engineered NPs to specifically target to the carbonic anhydrase IX, a transmembrane protein overexpressed in a wide variety of cancer tumors. Intracellularly, the Prickly NPs disintegrate into small pieces that upon endosomal escape cause severe damage to the endoplasmic reticulum and mitochondria of the cells. The engineered Prickly NP is promising in efficient and targeted cancer treatment and it opens new avenue in nanomedication.

A hierarchical rippled and crumpled PLA microstructure generated through double emulsion: the interesting roles of Pickering nanoparticles.

Herein, we propose a facile protocol for the fabrication of biomedical microstructures with fine textures of hierarchical rippled and crumpled morphologies through double emulsions by the simple addition of interior Pickering nanoparticles.

The atmospheric oxidation mechanism of 2-methylnaphthalene.

The atmospheric oxidation mechanism of 2-methylnaphthalene (2-MN) initiated by OH radicals is investigated by using quantum chemistry at BH&HLYP/6-311++G(2df,2p) and ROCBS-QB3 levels and kinetic calculations by transient state theory and unimolecular reaction theory coupled with master equation (RRKM-ME). This reaction is mainly initiated by OH additions, forming adducts Rn (2-MN-n-OH, n = 1-8). The fates of R1 and R3, representing the α- and ß-adducts, are examined. The fates of R1 and R3 are found to be drastically different. In the atmosphere, R1 reacts with O2via O2 addition to the C2 position to form R1-2OO-a/s, which will undergo a bimolecular reaction with the atmospheric NO or unimolecular isomerization via intramolecular H-shifts, of which the latter is found to be dominant and accounts for the formation of dicarbonyl compounds observed in experimental studies. The role of the tricyclic radical intermediates formed from the ring-closure of R1-2OO is rather limited because their formation is endothermic and reversible, being contrary to the important role of the analogous bicyclic radical intermediates in the oxidation of benzenes. On the other hand, the fate of R3 is similar to that of the benzene-OH adduct, and the tricyclic intermediates will play an important role. An oxidation mechanism is proposed based on the theoretical predictions, and the routes for the experimentally observed products are suggested and compared.

A hierarchical porous bowl-like PLA@MSNs-COOH composite for pH-dominated long-term controlled release of doxorubicin and integrated nanoparticle for potential second treatment.

We chemically integrated mesoporous silica nanoparticles (MSNs) and macroporous bowl-like polylactic acid (pBPLA) matrix, for noninvasive electrostatic loading and long-term controlled doxorubicin (DOX) release, to prepare a hierarchical porous bowl-like pBPLA@MSNs-COOH composite with a nonspherical and hierarchical porous structure. Strong electrostatic interaction with DOX rendered excellent encapsulation efficiency (up to 90.14%) to the composite. DOX release showed pH-dominated drug release kinetics; thus, maintaining a weak acidic pH (e.g., 5.0) triggered sustained release, suggesting the composite's great potential for long-term therapeutic approaches. In-vitro cell viability assays further confirmed that the composite was biocompatible and that the loaded drugs were pharmacologically active, exhibiting dosage-dependent cytotoxicity. Additionally, a wound-healing assay revealed the composite's intrinsic ability to inhibit cell migration. Moreover, pH- and time-dependent leaching of the integrated MSNs due to pBPLA matrix degradation allow us to infer that the leached (and drug loaded) MSNs may be engulfed by cancer cells contributing to a second wave of DOX-mediated cytotoxicity following pH-triggered DOX release.

New mechanism for the atmospheric oxidation of dimethyl sulfide. The importance of intramolecular hydrogen shift in a CH3SCH2OO radical.

Theoretical study has been carried out on the fate of methylthiomethylperoxy radical (CH3SCH2OO, MSP) in the atmosphere. The intramolecular H-shift followed by recombination with O2, MSP → CH2SCH2OOH → OOCH2SCH2OOH (MSPO2), is found to be fast enough, that is, 2.1 s(-1) at 293 K, to compete with and even surpass the possible bimolecular reactions of MSP with NOx, HO2, and RO2 in the remote marine atmosphere. MSPO2 would also undergo another intramolecular H-shift and decompose to the most important intermediate HOOCH2SCHO instead of the CH3SCH2O radical. HOOCH2SCHO would be further oxidized via the route as HOOCH2SCO (by OH radical) → HOOCH2S (by decomposition) → HOOCH2SO (by O3 or NO2) → HOOCH2SO2 (by O3 and NO2) → OH + CH2O + SO2 (by decomposition). Our calculations suggest a drastically different oxidation mechanism for dimethyl sulfide (CH3SCH3, DMS) in the remote marine atmosphere.

Atmospheric oxidation mechanism of chlorobenzene.

The atmospheric oxidation mechanism of chlorobenzene (CB) initiated by the OH radicals is investigated at M06-2X/6-311++G(2df, 2p) and ROCBS-QB3 levels. The oxidation is initiated by OH addition to the ortho (∼50%), para (∼33%) and meta (∼17%) positions, forming CB-OH adducts as R2, R3, and R4; while the ipso-addition is negligible (∼0.2%). The reactions of the CB-OH adducts with the atmospheric oxygen are further investigated in detail by coupling the unimolecular reaction rate theory calculations with master-equation (RRKM-ME). The CB-OH adducts react with O2 either by irreversible H-abstraction to form chlorophenol and HO2 or by reversible additions to form CB-OH-O2 radicals, which subsequently cyclize to bicyclic radicals. RRKM-ME calculations show that the addition reactions of CB-OH and O2 at the atmospheric pressure are close to but not yet reach their high-pressure-limits. The RRKM-ME simulations predict the yields of 93%, 38%, and 74% for ortho-, meta- and para-chlorophenols from the reactions of O2 with R2, R3 and R4, being lower than their high-pressure-limit yields of 95%, 48%, an 80%, respectively. Overall, the yield of chlorophenols is determined as 72% at the atmospheric pressure.

Atmospheric oxidation mechanism of toluene.

The atmospheric oxidation mechanism of toluene initiated by OH radical addition is investigated by quantum chemistry calculations at M06-2X, G3MP2-RAD, and ROCBS-QB3 levels and by kinetics calculation by using transition state theory and unimolecular reaction theory coupled with master equation (RRKM-ME). The predicted branching ratios are 0.15, 0.59, 0.05, and 0.14 for OH additions to ipso, ortho, meta, and para positions (forming R1-R4 adducts), respectively. The fate of R2, R4, and R1 is investigated in detail. In the atmosphere, R2 reacts with O2 either by irreversible H-abstraction to form o-cresol (36%), or by reversible recombination to R2-1OO-syn and R2-3OO-syn, which subsequently cyclize to bicyclic radical R2-13OO-syn (64%). Similarly, R4 reacts with O2 with branching ratios of 61% for p-cresol and 39% for R4-35OO-syn, while reaction of R1 and O2 leads to R1-26OO-syn. RRKM-ME calculations show that the reactions of R2/R4 with O2 have reached their high-pressure limits at 760 Torr and the formation of R2-16O-3O-s is only important at low pressure, i.e., 5.4% at 100 Torr. The bicyclic radicals (R2-13OO-syn, R4-35OO-syn, and R1-26OO-syn) will recombine with O2 to produce bicyclic alkoxy radicals after reacting with NO. The bicyclic alkoxy radicals would break the ring to form products methylglyoxal/glyoxal (MGLY/GLY) and their corresponding coproducts butenedial/methyl-substituted butenedial as proposed in earlier studies. However, a new reaction pathway is found for the bicyclic alkoxy radicals, leading to products MGLY/GLY and 2,3-epoxybutandial/2-methyl-2,3-epoxybutandial. A new mechanism is proposed for the atmospheric oxidation mechanism of toluene based on current theoretical and previous theoretical and experimental results. The new mechanism predicts much lower yield of GLY and much higher yield of butenedial than other atmospheric models and recent experimental measurements. The new mechanism calls for detection of proposed products 2,3-epoxybutandial and 2-methyl-2,3-epoxybutandial.

Atmospheric oxidation mechanism of benzene. Fates of alkoxy radical intermediates and revised mechanism.

The fate of alkoxy radicals formed in the atmospheric oxidation of benzene initiated by OH radical is investigated by using quantum chemistry and kinetics calculations. The two alkoxy radicals (R2 and R3), formed from the commonly accepted bicyclic radical intermediates, are found to undergo ring-closure preferentially, in addition to the ring-breakage, as suggested in previous studies. The ratio between the ring-closure and ring-breakage is ∼2:1. The ring-closure route will lead to equal amounts of glyoxal and 2,3-epoxybutandial, while the ring-breakage route leads to glyoxal and butenedial. Overall, the new mechanism suggests the yield of glyoxal to be three times that of butenedial, consistent with the previous experimental measurements. The new mechanism calls for the search of the newly proposed product 2,3-epoxybutandial.

Fabrication and evaluation of magnetic/hollow double-shelled imprinted sorbents formed by Pickering emulsion polymerization.

Magnetic/hollow double-shelled imprinted polymers (MH-MIPs) were synthesized by Pickering emulsion polymerization. In this method, attapulgite (ATP) particles were used as stabilizers to establish a stable oil-in-water emulsion, and a few hydrophilic Fe3O4 nanoparticles were allowed to be magnetic separation carriers. The imprinting system was fabricated by radical polymerization in the presence of the functional and polymeric monomers in the oil phase. The results of characterization indicated that MH-MIPs exhibited magnetic sensitivity (Ms = 4.76 emu g(-1)), thermal stability (especially below 200 °C), and hollow structure and were composed of exterior ATP shells and interior imprinted polymers shells. Then MH-MIPs were evaluated as sorbents for the selective binding of λ-cyhalothrin as a result of their magnetism, enhanced mechanical strength, hydrophilic surface, and recognition ability. The kinetic properties of MH-MIPs were well described by the pseudo-second-order equation, indicating that the chemical process could be the rate-limiting step in the adsorption process for λ-cyhalothrin. The equilibrium adsorption capacity of MH-MIPs was 60.06 µmol g(-1) at 25 °C, and the Langmuir isotherm model gave a better fit to the experimental data, indicating the monolayer molecular adsorption for λ-cyhalothrin. The selective recognition experiments also demonstrated the high affinity and selectivity of MH-MIIPs toward λ-cyhalothrin over fenvalerate and diethyl phthalate.