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Biology subjects

Wood, T. E.

Publications and source records attributed to Wood, T. E..

7 recordsLinked to original sources

Consensus substrate recognition of conserved bacterial virulence peptide-bond recombinase

Shigella OspB, a conserved type 3 effector, is a cysteine protease and peptide recombinase. Developing a protease activity-based screen, we defined and validated an OspB consensus substrate recognition motif. We found that the P1 position is aspartic acid, although cysteine is tolerated, and the P6 position an uncharged nonpolar hydrophobic residue. We demonstrate their predicted proximity to OspB active site residues within a binding groove. These findings will facilitate identification of physiological substrates of OspB and its homologs.

microbiology↗

Legacy of warming and microbial treatments shape root exudates and rhizosphere fungal communities of a tropical tree

O_LIPlant metabolites play a pivotal role in shaping rhizosphere microbial communities, yet how plant and microbial functions respond to environmental change remains poorly understood. We combined ecometabolomics and fungal community profiling to investigate how multiple abiotic and biotic treatments influence root exudate chemistry and fungal community assemblage in a tropical tree. C_LIO_LIGuarea guidonia seedlings were grown in sterilized soil primed with inoculum from long-term experimentally warmed or ambient plots in Puerto Rico. We manipulated soil microbes, soil moisture, and plant density and tested metabolite-fungi-plant trait associations. C_LIO_LIMetabolite diversity was significantly influenced by soil microbial legacy and moisture, while antimicrobial treatments altered metabolite composition without affecting diversity. Metabolite clusters exhibited distinct treatment-specific patterns. Fungal alpha diversity increased under low moisture, community composition shifted with antimicrobial treatments, and certain families showed strong treatment-specific responses. Although fungal diversity was not correlated with metabolite diversity, fungal community structure was significantly associated with metabolite composition. We also found global and pathway-specific correlations between fungal and metabolite distances, and weak but significant associations between metabolite/fungal composition and seedling traits. C_LIO_LIThese results underscore how environmental conditions shape belowground interactions, highlighting metabolite-fungal associations as potential early indicators of plant response to disturbance. C_LI

plant biology↗

Experimental Warming Alters Nitrogen Cycle in a Humid Tropical Forest

O_LIHumid tropical forests typically contain high soil nitrogen (N), supporting rapid rates of primary productivity and recovery from disturbances. Nitrogen fixation is regulated by microbial communities, which can be free-living in the soil and leaf litter (asymbiotic) or in symbioses with plants. C_LIO_LITo investigate how warming affects asymbiotic and symbiotic components of the N cycle, we analyzed soil and leaf litter samples as well as annual seedling census data from an experimental warming field site in Puerto Rico. C_LIO_LI16S and nifH sequencing revealed that warming significantly altered bacterial composition. Asymbiotic N fixation rates were 55% greater in soil (0.004 nmol N2/g/hr) and 525% greater (0.217 nmol N2/g/hr) in leaf litter from warmed compared to ambient plots. This increase in fixation was associated with changes in the N-fixing bacterial community. Under warming, N fixers experienced a 4.4-fold increase in growth rate compared to non-fixers, yet competition with neighboring N fixers eventually reduced N fixer growth. Seedling growth, especially of N fixers, initially increased following hurricane disturbances before declining. C_LIO_LITogether, our findings suggest that warming increases the flux of N from the atmosphere into this tropical forest, driving changes in both microbial and tree dynamics. C_LI

ecology↗

Tropical Forest Soil Microbiome Modulates Leaf Heat Tolerance More Strongly Under Warming than Ambient Conditions

Tropical forests are increasingly threatened by climate change. Yet, it is still unclear how tropical plants respond to increasing temperatures. Leaf heat tolerance (LHT) in tropical plants is often at its upper limit, suggesting that climate change might negatively impact tropical forests. We hypothesized that intraspecific variation in this leaf trait might be associated with changes in the soil microbiome, which might also respond to climate. Specifically, we hypothesized that warming would increase LHT through changes in the soil microbiome: this study combined an in-situ tropical warming experiment with a shade house experiment in Puerto Rico. The shade house experiment consisted of growing seedlings of Guarea guidonia, a dominant forest species, under different soil microbiome treatments (reduced arbuscular mycorrhizal fungi, reduced plant pathogens, reduced microbes, and unaltered) and soil inoculum from the field experiment. Heat tolerance was determined using chlorophyll fluorescence (FV/Fm) on individual seedlings in the field and on pooled seedlings by pot in the shade house. We sequenced soil fungal DNA to analyze the impacts of the field and shade house treatments on the soil microbiome. In the field, seedlings from ambient temperature plots showed higher FV/Fm values under high temperatures (0.648 at 46 {degrees}C and 0.067 at 52 {degrees}C) than seedlings from the warming plots (0.535 at 46 {degrees}C and 0.031 at 52 {degrees}C). In the shade house, the soil microbiome treatments, which significantly influenced the fungal community composition, significantly influenced LHT. Reduction in fungal pathogen abundance and diversity altered FV/Fm before T50 for seedlings grown with soil inoculum from the warming plots but after T50 for seedlings grown with soil inoculum from the ambient plots. Our findings emphasize that the soil microbiome might play an important role in modulating the impacts of climate change on plants. Understanding and harnessing this relationship might be vital for mitigating the effects of warming on tropical forests, emphasizing the need for further research on microbial responses to climate change.

ecology↗

Cytosolic Sensor of Bacterial Lipopolysaccharide in Human Macrophages

Endotoxin - bacterial lipopolysaccharide (LPS) - is a driver of the lethal infection sepsis through activation of innate immune responses. When delivered to the cytosol of macrophages, 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 been doubted by many investigators, as caspases-4, -5, and -11 bind and activate LPS directly in vitro. Here we show that the primate-specific protein NLRP11 is a pattern recognition receptor for cLPS required for efficient activation of the caspase-4 inflammasome in human macrophages. NLRP11 is present in humans and other primates, but absent in mice, likely explaining why it has been missed in screens looking for innate immune signaling molecules, most of which have been carried out in mice. NLRP11 is a previously missing link and a component of the human caspase-4 inflammasome activation pathway. One Sentence SummaryDiscovery that human macrophages contain a cytosolic receptor for bacterial lipopolysaccharide.

microbiology↗

A Shigella type 3 effector protein co-opts host inositol pyrophosphates for activity

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 dysenteric disease. 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, 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 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 one of the leading causes of diarrheal mortality worldwide, especially in children. Virulence depends on the Shigella type III secretion system (T3SS), and definition of the roles of the bacterial effector proteins secreted by the T3SS is key to understanding Shigella pathogenesis. The effector protein OspB has been shown to contribute to a range of phenotypes during infection, yet the mechanism of action is unknown. Here, we show that 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.

microbiology↗

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.

systems biology↗