RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins.

Pseudomonas aeruginosa uses three type six secretion systems (H1-, H2- and H3-T6SS) to manipulate its environment, subvert host cells and for microbial competition. These T6SS machines are loaded with a variety of effectors/toxins, many being associated with a specific VgrG. How P. aeruginosa transcriptionally coordinates the main T6SS clusters and the multiple vgrG islands spread through the genome is unknown. Here we show an unprecedented level of control with RsmA repressing most known T6SS-related genes. Moreover, each of the H2- and H3-T6SS clusters encodes a sigma factor activator (SFA) protein called, Sfa2 and Sfa3, respectively. SFA proteins are enhancer binding proteins necessary for the sigma factor RpoN. Using a combination of RNA-seq, ChIP-seq and molecular biology approaches, we demonstrate that RpoN coordinates the T6SSs of P. aeruginosa by activating the H2-T6SS but repressing the H1- and H3-T6SS. Furthermore, RpoN and Sfa2 control the expression of the H2-T6SS-linked VgrGs and their effector arsenal to enable very effective interbacterial killing. Sfa2 is specific as Sfa3 from the H3-T6SS cannot complement loss of Sfa2. Our study further delineates the regulatory mechanisms that modulate the deployment of an arsenal of T6SS effectors likely enabling P. aeruginosa to adapt to a range of environmental conditions.

Solar Urea: Towards a Sustainable Fertilizer Industry.

Urea, an agricultural fertilizer, nourishes humanity. The century-old Bosch-Meiser process provides the world's urea. It is multi-step, consumes enormous amounts of non-renewable energy, and has a large CO2 footprint. Thus, developing an eco-friendly synthesis for urea is a priority. Herein we report a single-step Pd/LTA-3A catalyzed synthesis of urea from CO2 and NH3 under ambient conditions powered solely by solar energy. Pd nanoparticles serve the dual function of catalyzing the dissociation of NH3 and providing the photothermal driving force for urea formation, while the absorption capacity of LTA-3A removes by-product H2 O to shift the equilibrium towards urea production. The solar urea conversion rate from NH3 and CO2 is 87 µmol g-1 h-1 . This advance represents a first step towards the use of solar energy in urea production. It provides insights into green fertilizer production, and inspires the vision of sustainable, modular plants for distributed production of urea on farms.

A Pseudomonas aeruginosa TIR effector mediates immune evasion by targeting UBAP1 and TLR adaptors.

Bacterial pathogens often subvert the innate immune system to establish a successful infection. The direct inhibition of downstream components of innate immune pathways is particularly well documented but how bacteria interfere with receptor proximal events is far less well understood. Here, we describe a Toll/interleukin 1 receptor (TIR) domain-containing protein (PumA) of the multi-drug resistant Pseudomonas aeruginosa PA7 strain. We found that PumA is essential for virulence and inhibits NF-κB, a property transferable to non-PumA strain PA14, suggesting no additional factors are needed for PumA function. The TIR domain is able to interact with the Toll-like receptor (TLR) adaptors TIRAP and MyD88, as well as the ubiquitin-associated protein 1 (UBAP1), a component of the endosomal-sorting complex required for transport I (ESCRT-I). These interactions are not spatially exclusive as we show UBAP1 can associate with MyD88, enhancing its plasma membrane localization. Combined targeting of UBAP1 and TLR adaptors by PumA impedes both cytokine and TLR receptor signalling, highlighting a novel strategy for innate immune evasion.

RsmA and AmrZ orchestrate the assembly of all three type VI secretion systems in Pseudomonas aeruginosa.

The type VI secretion system (T6SS) is a weapon of bacterial warfare and host cell subversion. The Gram-negative pathogen Pseudomonas aeruginosa has three T6SSs involved in colonization, competition, and full virulence. H1-T6SS is a molecular gun firing seven toxins, Tse1-Tse7, challenging survival of other bacteria and helping P. aeruginosa to prevail in specific niches. The H1-T6SS characterization was facilitated through studying a P. aeruginosa strain lacking the RetS sensor, which has a fully active H1-T6SS, in contrast to the parent. However, study of H2-T6SS and H3-T6SS has been neglected because of a poor understanding of the associated regulatory network. Here we performed a screen to identify H2-T6SS and H3-T6SS regulatory elements and found that the posttranscriptional regulator RsmA imposes a concerted repression on all three T6SS clusters. A higher level of complexity could be observed as we identified a transcriptional regulator, AmrZ, which acts as a negative regulator of H2-T6SS. Overall, although the level of T6SS transcripts is fine-tuned by AmrZ, all T6SS mRNAs are silenced by RsmA. We expanded this concept of global control by RsmA to VgrG spike and T6SS toxin transcripts whose genes are scattered on the chromosome. These observations triggered the characterization of a suite of H2-T6SS toxins and their implication in direct bacterial competition. Our study thus unveils a central mechanism that modulates the deployment of all T6SS weapons that may be simultaneously produced within a single cell.

Cu Atoms on Nanowire Pd/HyWO3-x Bronzes Enhance the Solar Reverse Water Gas Shift Reaction.

Nanowire hydrogen bronzes of WO3 nanowires decorated with Pd (Pd/HyWO3-x) were previously demonstrated to effectively capture broadband radiation across the ultraviolet to near-infrared wavelength range and catalyze the reverse water gas shift reaction (RWGS). Herein, we report a synthetic strategy to enhance the performance of this class of photocatalysts by conformally coating Cu atoms onto the surface of Pd/HyWO3-x by anchoring Cu(I)OtBu to the Brønsted acidic protons of the bronze. The resulting materials are characterized by a suite of analytical methods, including electron microscopy and X-ray absorption spectroscopy. In addition, in situ diffuse reflectance infrared Fourier transform spectroscopy demonstrated that for the light-driven RWGS reaction, as little as 0.2 at. % Cu facilitates the formation of surface carboxylate species from CO2, resulting in a 300-500% enhancement in the rate of CO production. This metal anchoring method enables atom precise modification of the surfaces of metal oxide nanomaterials for catalytic applications, circumventing the need for complex and expensive atomic layer deposition processes.

PAAR proteins act as the 'sorting hat' of the type VI secretion system.

Bacteria exist in polymicrobial environments and compete to prevail in a niche. The type VI secretion system (T6SS) is a nanomachine employed by Gram-negative bacteria to deliver effector proteins into target cells. Consequently, T6SS-positive bacteria produce a wealth of antibacterial effector proteins to promote their survival among a prokaryotic community. These toxins are loaded onto the VgrG-PAAR spike and Hcp tube of the T6SS apparatus and recent work has started to document the specificity of effectors for certain spike components. Pseudomonas aeruginosa encodes several PAAR proteins, whose roles have been poorly investigated. Here we describe a phospholipase family antibacterial effector immunity pair from Pseudomonas aeruginosa and demonstrate that a specific PAAR protein is necessary for the delivery of the effector and its cognate VgrG. Furthermore, the PAAR protein appears to restrict the delivery of other phospholipase effectors that utilise distinct VgrG proteins. We provide further evidence for competition for PAAR protein recruitment to the T6SS apparatus, which determines the identities of the delivered effectors.

Illuminating CO2 reduction on frustrated Lewis pair surfaces: investigating the role of surface hydroxides and oxygen vacancies on nanocrystalline In2O(3-x)(OH)y.

Designing catalytic nanostructures that can thermochemically or photochemically convert gaseous carbon dioxide into carbon based fuels is a significant challenge which requires a keen understanding of the chemistry of reactants, intermediates and products on surfaces. In this context, it has recently been reported that the reverse water gas shift reaction (RWGS), whereby carbon dioxide is reduced to carbon monoxide and water, CO2 + H2 → CO + H2O, can be catalysed by hydroxylated indium oxide nanocrystals, denoted In2O(3-x)(OH)y, more readily in the light than in the dark. The surface hydroxide groups and oxygen vacancies on In2O(3-x)(OH)y were both shown to assist this reaction. While this advance provides a first step toward the rational design and optimization of a single-component gas-phase CO2 reduction catalyst for solar fuels generation, the precise role of the hydroxide groups and oxygen vacancies in facilitating the reaction on In2O(3-x)(OH)y nanocrystals has not been resolved. In the work reported herein, for the first time we present in situ spectroscopic and kinetic observations, complemented by density functional theory analysis, that together provide mechanistic information into the surface reaction chemistry responsible for the thermochemical and photochemical RWGS reaction. Specifically, we demonstrate photochemical CO2 reduction at a rate of 150 µmol gcat(-1) hour(-1), which is four times better than the reduction rate in the dark, and propose a reaction mechanism whereby a surface active site of In2O(3-x)(OH)y, composed of a Lewis base hydroxide adjacent to a Lewis acid indium, together with an oxygen vacancy, assists the adsorption and heterolytic dissociation of H2 that enables the adsorption and reaction of CO2 to form CO and H2O as products. This mechanism, which has its analogue in molecular frustrated Lewis pair (FLP) chemistry and catalysis of CO2 and H2, is supported by preliminary kinetic investigations. The results of this study emphasize the importance of engineering the surfaces of nanostructures to facilitate gas-phase thermochemical and photochemical carbon dioxide reduction reactions to energy rich fuels at technologically significant rates.

NLRP11 is a pattern recognition receptor for bacterial lipopolysaccharide in the cytosol of human macrophages.

Endotoxin-bacterial lipopolysaccharide (LPS)-is a driver of lethal infection sepsis through excessive activation of innate immune responses. When delivered to the cytosol of macrophages, cytosolic LPS (cLPS) induces the assembly of an inflammasome that contains caspases-4/5 in humans or caspase-11 in mice. Whereas activation of all other inflammasomes is triggered by sensing of pathogen products by a specific host cytosolic pattern recognition receptor protein, whether pattern recognition receptors for cLPS exist has remained unclear, because caspase-4, caspase-5, and caspase-11 bind and activate LPS directly in vitro. Here, we show that the primate-specific protein NLRP11 is a pattern recognition receptor for cLPS that is required for efficient activation of the caspase-4 inflammasome in human macrophages. In human macrophages, NLRP11 is required for efficient activation of caspase-4 during infection with intracellular Gram-negative bacteria or upon electroporation of LPS. NLRP11 could bind LPS and separately caspase-4, forming a high-molecular weight complex with caspase-4 in HEK293T cells. NLRP11 is present in humans and other primates but absent in mice, likely explaining why it has been overlooked in screens looking for innate immune signaling molecules, most of which have been carried out in mice. Our results demonstrate that NLRP11 is a component of the caspase-4 inflammasome activation pathway in human macrophages.

The Shigella Spp. Type III Effector Protein OspB Is a Cysteine Protease.

The type III secretion system is required for virulence of many pathogenic bacteria. Bacterial effector proteins delivered into target host cells by this system modulate host signaling pathways and processes in a manner that promotes infection. Here, we define the activity of the effector protein OspB of the human pathogen Shigella spp., the etiological agent of shigellosis and bacillary dysentery. Using the yeast Saccharomyces cerevisiae as a model organism, we show that OspB sensitizes cells to inhibition of TORC1, the central regulator of growth and metabolism. In silico analyses reveal that OspB bears structural homology to bacterial cysteine proteases that target mammalian cell processes, and we define a conserved cysteine-histidine catalytic dyad required for OspB function. Using yeast genetic screens, we identify a crucial role for the arginine N-degron pathway in the yeast growth inhibition phenotype and show that inositol hexakisphosphate is an OspB cofactor. We find that a yeast substrate for OspB is the TORC1 component Tco89p, proteolytic cleavage of which generates a C-terminal fragment that is targeted for degradation via the arginine N-degron pathway; processing and degradation of Tco89p is required for the OspB phenotype. In all, we demonstrate that the Shigella T3SS effector OspB is a cysteine protease and decipher its interplay with eukaryotic cell processes. IMPORTANCEShigella spp. are important human pathogens and among the leading causes of diarrheal mortality worldwide, especially in children. Virulence depends on the Shigella type III secretion system (T3SS). Definition of the roles of the bacterial effector proteins secreted by the T3SS is key to understanding Shigella pathogenesis. The effector protein OspB contributes to a range of phenotypes during infection, yet the mechanism of action is unknown. Here, we show that S. flexneri OspB possesses cysteine protease activity in both yeast and mammalian cells, and that enzymatic activity of OspB depends on a conserved cysteine-histidine catalytic dyad. We determine how its protease activity sensitizes cells to TORC1 inhibition in yeast, finding that OspB cleaves a component of yeast TORC1, and that the degradation of the C-terminal cleavage product is responsible for OspB-mediated hypersensitivity to TORC1 inhibitors. Thus, OspB is a cysteine protease that depends on a conserved cysteine-histidine catalytic dyad.

Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions.

Mechanisms underlying severe coronavirus disease 2019 (COVID-19) disease remain poorly understood. We analyze several thousand plasma proteins longitudinally in 306 COVID-19 patients and 78 symptomatic controls, uncovering immune and non-immune proteins linked to COVID-19. Deconvolution of our plasma proteome data using published scRNA-seq datasets reveals contributions from circulating immune and tissue cells. Sixteen percent of patients display reduced inflammation yet comparably poor outcomes. Comparison of patients who died to severely ill survivors identifies dynamic immune-cell-derived and tissue-associated proteins associated with survival, including exocrine pancreatic proteases. Using derived tissue-specific and cell-type-specific intracellular death signatures, cellular angiotensin-converting enzyme 2 (ACE2) expression, and our data, we infer whether organ damage resulted from direct or indirect effects of infection. We propose a model in which interactions among myeloid, epithelial, and T cells drive tissue damage. These datasets provide important insights and a rich resource for analysis of mechanisms of severe COVID-19 disease.

From Welfare to Warfare: The Arbitration of Host-Microbiota Interplay by the Type VI Secretion System.

The health of mammals depends on a complex interplay with their microbial ecosystems. Compartments exposed to external environments such as the mucosal surfaces of the gastrointestinal tract accommodate the gut microbiota, composed by a wide range of bacteria. The gut microbiome confers benefits to the host, including expansion of metabolic potential and the development of an immune system that can robustly protect from external and internal insults. The cooperation between gut microbiome and host is enabled in part by the formation of partitioned niches that harbor diverse bacterial phyla. Bacterial secretion systems are commonly employed to manipulate the composition of these local environments. Here, we explore the roles of the bacterial type VI secretion system (T6SS), present in ~25% of gram-negative bacteria, including many symbionts, in the establishment and perturbation of bacterial commensalism, and symbiosis in host mucosal sites. This versatile apparatus drives bacterial competition, although in some cases can also interfere directly with host cells and facilitate nutrient acquisition. In addition, some bacterial pathogens cause disease when their T6SS leads to dysbiosis and subverts host immune responses in defined animal models. This review explores our knowledge of the T6SS in the context of the "host-microbiota-pathogen" triumvirate and examines contexts in which the importance of this secretion system may be underappreciated.

Shigella flexneri Disruption of Cellular Tension Promotes Intercellular Spread.

During infection, some bacterial pathogens invade the eukaryotic cytosol and spread between cells of an epithelial monolayer. Intercellular spread occurs when these pathogens push against the plasma membrane, forming protrusions that are engulfed by adjacent cells. Here, we show that IpaC, a Shigella flexneri type 3 secretion system protein, binds the host cell-adhesion protein ß-catenin and facilitates efficient protrusion formation. S. flexneri producing a point mutant of IpaC that cannot interact with ß-catenin is defective in protrusion formation and spread. Spread is restored by chemical reduction of intercellular tension or genetic depletion of ß-catenin, and the magnitude of the protrusion defect correlates with membrane tension, indicating that IpaC reduces membrane tension, which facilitates protrusion formation. IpaC stabilizes adherens junctions and does not alter ß-catenin localization at the membrane. Thus, Shigella, like other bacterial pathogens, reduces intercellular tension to efficiently spread between cells.

Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients.

COVID-19 has caused over 1 million deaths globally, yet the cellular mechanisms underlying severe disease remain poorly understood. By analyzing several thousand plasma proteins in 306 COVID-19 patients and 78 symptomatic controls over serial timepoints using two complementary approaches, we uncover COVID-19 host immune and non-immune proteins not previously linked to this disease. Integration of plasma proteomics with nine published scRNAseq datasets shows that SARS-CoV-2 infection upregulates monocyte/macrophage, plasmablast, and T cell effector proteins. By comparing patients who died to severely ill patients who survived, we identify dynamic immunomodulatory and tissue-associated proteins associated with survival, providing insights into which host responses are beneficial and which are detrimental to survival. We identify intracellular death signatures from specific tissues and cell types, and by associating these with angiotensin converting enzyme 2 (ACE2) expression, we map tissue damage associated with severe disease and propose which damage results from direct viral infection rather than from indirect effects of illness. We find that disease severity in lung tissue is driven by myeloid cell phenotypes and cell-cell interactions with lung epithelial cells and T cells. Based on these results, we propose a model of immune and epithelial cell interactions that drive cell-type specific and tissue-specific damage in severe COVID-19.

Delivery of the Pseudomonas aeruginosa Phospholipase Effectors PldA and PldB in a VgrG- and H2-T6SS-Dependent Manner.

The bacterial pathogen Pseudomonas aeruginosa uses three type VI secretion systems (T6SSs) to drive a multitude of effector proteins into eukaryotic or prokaryotic target cells. The T6SS is a supramolecular nanomachine, involving a set of 13 core proteins, which resembles the contractile tail of bacteriophages and whose tip is considered as a puncturing device helping to cross membranes. Effectors can attach directly to the T6SS spike which is composed of a VgrG (valine-glycine-rich proteins) trimer, of which P. aeruginosa produces several. We have previously shown that the master regulator RsmA controls the expression of all three T6SS gene clusters (H1-, H2- and H3-T6SS) and a range of remote vgrG and effector genes. We also demonstrated that specific interactions between VgrGs and various T6SS effectors are prerequisite for effector delivery in a process we called "à la carte delivery." Here, we provide an in-depth description on how the two H2-T6SS-dependent effectors PldA and PldB are delivered via their cognate VgrGs, VgrG4b and VgrG5, respectively. We show that specific recognition of the VgrG C terminus is required and effector specificity can be swapped by exchanging these C-terminal domains. Importantly, we established that effector recognition by a cognate VgrG is not always sufficient to achieve successful secretion, but it is crucial to provide effector stability. This study highlights the complexity of effector adaptation to the T6SS nanomachine and shows how the VgrG tip can possibly be manipulated to achieve effector delivery.

Polymorph selection towards photocatalytic gaseous CO2 hydrogenation.

Titanium dioxide is the only known material that can enable gas-phase CO2 photocatalysis in its anatase and rutile polymorphic forms. Materials engineering of polymorphism provides a useful strategy for optimizing the performance metrics of a photocatalyst. In this paper, it is shown that the less well known rhombohedral polymorph of indium sesquioxide, like its well-documented cubic polymorph, is a CO2 hydrogenation photocatalyst for the production of CH3OH and CO. Significantly, the rhombohedral polymorph exhibits higher activity, superior stability and improved selectivity towards CH3OH over CO. These gains in catalyst performance originate in the enhanced acidity and basicity of surface frustrated Lewis pairs in the rhombohedral form.

The Pseudomonas aeruginosa T6SS Delivers a Periplasmic Toxin that Disrupts Bacterial Cell Morphology.

The type VI secretion system (T6SS) is crucial in interbacterial competition and is a virulence determinant of many Gram-negative bacteria. Several T6SS effectors are covalently fused to secreted T6SS structural components such as the VgrG spike for delivery into target cells. In Pseudomonas aeruginosa, the VgrG2b effector was previously proposed to mediate bacterial internalization into eukaryotic cells. In this work, we find that the VgrG2b C-terminal domain (VgrG2bC-ter) elicits toxicity in the bacterial periplasm, counteracted by a cognate immunity protein. We resolve the structure of VgrG2bC-ter and confirm it is a member of the zinc-metallopeptidase family of enzymes. We show that this effector causes membrane blebbing at midcell, which suggests a distinct type of T6SS-mediated growth inhibition through interference with cell division, mimicking the impact of ß-lactam antibiotics. Our study introduces a further effector family to the T6SS arsenal and demonstrates that VgrG2b can target both prokaryotic and eukaryotic cells.

Towards Solar Methanol: Past, Present, and Future.

This work aims to provide an overview of producing value-added products affordably and sustainably from greenhouse gases (GHGs). Methanol (MeOH) is one such product, and is one of the most widely used chemicals, employed as a feedstock for ≈30% of industrial chemicals. The starting materials are analogous to those feeding natural processes: water, CO2, and light. Innovative technologies from this effort have global significance, as they allow GHG recycling, while providing society with a renewable carbon feedstock. Light, in the form of solar energy, assists the production process in some capacity. Various solar strategies of continually increasing technology readiness levels are compared to the commercial MeOH process, which uses a syngas feed derived from natural gas. These strategies include several key technologies, including solar-thermochemical, photochemical, and photovoltaic-electrochemical. Other solar-assisted technologies that are not yet commercial-ready are also discussed. The commercial-ready technologies are compared using a technoeconomic analysis, and the scalability of solar reactors is also discussed in the context of light-incorporating catalyst architectures and designs. Finally, how MeOH compares against other prospective products is briefly discussed, as well as the viability of the most promising solar MeOH strategy in an international context.

Nickel@Siloxene catalytic nanosheets for high-performance CO2 methanation.

Two-dimensional (2D) materials are of considerable interest for catalyzing the heterogeneous conversion of CO2 to synthetic fuels. In this regard, 2D siloxene nanosheets, have escaped thorough exploration, despite being composed of earth-abundant elements. Herein we demonstrate the remarkable catalytic activity, selectivity, and stability of a nickel@siloxene nanocomposite; it is found that this promising catalytic performance is highly sensitive to the location of the nickel component, being on either the interior or the exterior of adjacent siloxene nanosheets. Control over the location of nickel is achieved by employing the terminal groups of siloxene and varying the solvent used during its nucleation and growth, which ultimately determines the distinct reaction intermediates and pathways for the catalytic CO2 methanation. Significantly, a CO2 methanation rate of 100 mmol gNi-1 h-1 is achieved with over 90% selectivity when nickel resides specifically between the sheets of siloxene.

Tailoring Surface Frustrated Lewis Pairs of In2O3-x (OH)y for Gas-Phase Heterogeneous Photocatalytic Reduction of CO2 by Isomorphous Substitution of In3+ with Bi3.

Frustrated Lewis pairs (FLPs) created by sterically hindered Lewis acids and Lewis bases have shown their capacity for capturing and reacting with a variety of small molecules, including H2 and CO2, and thereby creating a new strategy for CO2 reduction. Here, the photocatalytic CO2 reduction behavior of defect-laden indium oxide (In2O3-x (OH) y ) is greatly enhanced through isomorphous substitution of In3+ with Bi3+, providing fundamental insights into the catalytically active surface FLPs (i.e., In-OH···In) and the experimentally observed "volcano" relationship between the CO production rate and Bi3+ substitution level. According to density functional theory calculations at the optimal Bi3+ substitution level, the 6s2 electron pair of Bi3+ hybridizes with the oxygen in the neighboring In-OH Lewis base site, leading to mildly increased Lewis basicity without influencing the Lewis acidity of the nearby In Lewis acid site. Meanwhile, Bi3+ can act as an extra acid site, serving to maximize the heterolytic splitting of reactant H2, and results in a more hydridic hydride for more efficient CO2 reduction. This study demonstrates that isomorphous substitution can effectively optimize the reactivity of surface catalytic active sites in addition to influencing optoelectronic properties, affording a better understanding of the photocatalytic CO2 reduction mechanism.

Type VI secretion and anti-host effectors.

Secretion systems play a central role in infectious diseases by enabling pathogenic bacteria to deliver virulence factors into target cells. The type VI secretion system (T6SS) mediates bacterial antagonism in various environments including eukaryotic niches, such as the gut. This molecular machine injects lethal toxins directly in target bacterial cells. It provides an advantage to pathogens encountering the commensal flora of the host and indirectly contributes to colonization and persistence. Yet, the T6SS is not employed for the sole purpose of bacterial killing and several T6SS effectors are dedicated to the subversion of eukaryotic cells. As described for type III and type IV secretion systems, these effectors impede host cell functions and promote immune evasion, thereby enabling successful infection.