Biology subjects

Skaar, E. P.

Publications and source records attributed to Skaar, E. P..

At least 19 recordsLinked to original sources

bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗

bioRxiv2026

''Self-gapping'' by a C-terminal domain arginine finger regulates GTP hydrolysis in bacterial zinc metallochaperones

The cellular response to transition metal scarcity is multifaceted and complex. Members of the Cluster of Orthologous Groups 0523 (COG0523) superfamily are proposed to chaperone a bound metal to activate an apoenzyme client and are thus candidate metallochaperones. COG0523 enzymes are GTPases that harbor a conserved Ras-like GTP-binding and hydrolysis domain (G-domain) and a C-terminal domain (CTD) of unknown function connected by a flexible linker. AlphaFold3 modeling posits an "open" GTPase-inactive and "closed" GTPase-active conformation where the GTP and switch 1 (G2) loop are buried at the interface of the two domains. We show here that the CTD functions as a GTP-hydrolysis activation protein (GAP) domain that stimulates GTP hydrolysis by the tethered G-domain. This "self-gapping" activity requires an invariant RxKG sequence in the {beta}2-strand of the CTD in two distantly related bacterial COG0523s from Acinetobacter baumannii, ZigA and MigC. Thermodynamic and kinetic studies reveal that the Arg is analogous to the "arginine finger" motif of a Ras-cognate GAP, while the Lys residue appears to play a catalytic role in GTP hydrolysis. Cognate CTD added in trans to full-length RxK mutant ZigA or MigC rescues Zn(II)-activated GTPase activity whereas the non-cognate CTD shows no rescue. The linker in AbZigA appears to gate Zn(II)-stimulated GTP hydrolysis. Solution NMR studies of RxK AbMigC reveal that the two domains tumble independently of one another in the absence of bound ligands, with cognate CTD added in trans forming a tight complex. The extent to which conformational switching characterizes eukaryotic COG0523s is discussed. Significance StatementThe cellular response to nutrient transition metal limitation is evolutionarily conserved in all kingdoms, providing protection from the loss of these essential inorganic cofactors that power much of metabolism. An important part of this response is the increased cell abundance of members of the enigmatic and ubiquitous Cluster of Orthologous Groups 0523 (COG0523) superfamily. In bacterial pathogens, these enzymes are often associated with the low-zinc adaptive response to host-mediated nutritional immunity, where the host deploys transition metal chelation as an innate immune response to infections. In this work, we provide new mechanistic insights into COG0523 function with the discovery of "self-gapping" by the C-terminal domain of a two-domain G-protein architecture, placed into the context of a metallochaperone model.

biochemistry↗

bioRxiv2025

DNA binding and lesion recognition by the bacterial interstrand DNA crosslink glycosylase AlkX

Interstrand DNA crosslinks (ICLs) are a highly toxic form of DNA damage. ICL repair in both eukaryotes and bacteria involves unhooking of the two strands by specialized DNA glycosylases. We recently established that the human pathogen Acinetobacter baumannii contains an ICL glycosylase (AlkX) that facilitates pathogenesis and protects the bacteria from DNA damage and acid stress. However, the physical basis for glycosylase-catalyzed ICL unhooking is unknown. Here, we describe a crystal structure of AlkX bound to DNA representing a product of the ICL unhooking reaction. Mutational analysis of ICL unhooking in vitro and A. baumannii sensitivity to the crosslinking agent mechlorethamine enabled identification of several AlkX motifs critical for ICL repair. We also found that a genetic variant from an antibiotic-resistant strain of the human pathogen Salmonella enterica significantly reduced AlkX activity in vitro and increased A. baumannii sensitivity to DNA crosslinking. This work provides a structural basis for how bacterial ICL glycosylases recognize and repair DNA adducts and contributes additional evidence that ICL repair is important for fitness of human pathogens.

biochemistry↗

bioRxiv2025

SLC11A2 affects nutritional immunity in the gastrointestinal epithelium

There is a constant tug-of-war for transition metals at the pathogen-host interface. A goal of the vertebrate host is to modulate the availability of metals to pathogens, in a process known as nutritional immunity, but pathogens have evolved numerous countermeasures to regulate intracellular trace metal levels. The bioavailability of trace metals therefore shapes the outcome of disease. In the human body, epithelial cells lining the intestine are a major site of metal absorption. Intestinal epithelial cells (IECs) are also a target for invading enteric pathogens but the contribution of epithelium-intrinsic factors towards nutritional immunity has been understudied. Using Salmonella enterica serovar Typhimurium (STm) harboring metal-responsive fluorescent reporters in a bovine ligated intestinal loop infection model, we mapped the spatiotemporal nature of metal competition during enteric salmonellosis. We show that STm experiences a temporal, cell-specific restriction of iron, manganese, and zinc in the intestinal mucosa during the early stages of infection. We have further studied the contribution of the broad specificity metal cation transporter, SLC11A2, in IECs to nutritional immunity against STm. Knockout of SLC11A2 in IECs leads to enhanced replication of STm, indicating a protective role for this transporter. Using fluorescence-based biosensors and bacterial gene deletion mutants, we pinpoint manganese and iron restriction as the mechanism by which SLC11A2 limits bacterial proliferation. We conclude that SLC11A2-mediated sequestration of metals is an intrinsic defense mechanism of the intestinal epithelium against enteric bacteria. Significance statementThere is limited source of trace metals in the gut that invading pathogens and the infected host must compete for. Using Salmonella enterica as a model enteric pathogen, along with fluorescent reporters that respond to metal ion availability, we traced the sites of metal ion limitation in the intestinal mucosa to intestinal epithelial cells (IECs) and phagocytes in the underlying lamina propria. We further show that SLC11A2 (NRAMP2), which is the sole SLC11 family member expressed in IECs and localizes to the apical membrane and endosomal network, limits the intracellular proliferation of Salmonella enterica by withholding iron and manganese. Therefore SLC11A2-mediated nutritional immunity is an IEC-intrinsic defense mechanism that protects against microbial pathogens.

microbiology↗

bioRxiv2025

Spatial Dependence and Heterogeneity in Molecular Imaging: Moran Quadrant Maps Enable Advanced Spatial-Statistical Analysis

Multiplexed molecular imaging, such as imaging mass spectrometry, provides spatially-contextualized insights that are transforming biomedical research by advancing our understanding of tissue organization and disease mechanisms. However, the spatial-statistical properties of molecular imaging data are often underutilized, and scalable computational tools to analyze them are lacking. Here, we demonstrate how local and global spatial autocorrelation (SAC) metrics can be used to quantify spatial dependence and spatial heterogeneity, properties that violate the common assumption of independent and identically distributed measurements. We develop mathematically rigorous methods for SAC-based exploratory analysis. Furthermore, we introduce a novel spatial feature extractor, the Moran quadrant map, and develop two advanced workflows based on it: Moran-Felsenszwalb segmentation for tissue domain segmentation and Moran-HOG clustering for colocalization-based image analysis. Finally, our open-source Moran Imaging toolbox (https://github.com/vandeplaslab/Moran_Imaging) provides scalable Python implementations, including a novel parallelized spatial lag algorithm, unlocking SAC-based analyses and biological insights for large-scale imaging.

bioinformatics↗

bioRxiv2025

Exploring metalloproteome remodeling in calprotectin-stressed Acinetobacter baumannii using chemoproteomics

The growth of bacterial pathogens is limited by nutritional immunity, where the infected host deploys metal scavenging proteins to starve the pathogen of essential transition metals. An important transition metal-sequestering protein is the S100A8-S100A9 heterotetramer, calprotectin (CP). Prior work reveals that CP induces a significant Zn- and Fe- starvation response in the Gram-negative opportunistic pathogen, Acinetobacter baumannii, in liquid culture. Here, we employ a quantitative chemoproteomics platform to pinpoint changes in abundance-corrected cysteine reactivity, and by extension cellular metal occupancy in metalloenzymes, that occur when A. baumannii is challenged with physiological CP in liquid culture relative to an untreated WT control. Changes in protein abundance with CP stress reveal a pronounced Zn-limitation and Fe-starvation response and reciprocal regulation of three enzymes of central carbon metabolism, including aconitase. A majority of the 2645 quantifiable Cys-containing peptides that show an increase in abundance-corrected Cys reactivity (150) are derived from known Zn-, Fe- and Fe-S-cluster proteins, revealing a significant decrease in metal occupancy (undermetalation) across the proteome. Myriad cell processes are compromised by undermetalation of the metalloproteome, including enzymes that function in the TCA cycle and respiration, GTP metabolism, ribosome remodeling, tRNA charging, and proteostasis. A direct comparison of a strain lacking the candidate metallochaperone ZigA ({Delta}zigA) with the wild-type strain reveals that the loss of ZigA is effectively silent in this assay. We conclude that CP induces a widespread, negative impact on the metalation status of the metalloproteome that results in a significant nutrient limitation response.

biochemistry↗

bioRxiv2025

The Gut Microbiome and Butyrate Differentiate Clostridioides difficile Colonization and Infection in Children

Background and AimsSymptomatic Clostridioides difficile infection (CDI) can cause significant morbidity and mortality. Conversely, patients can be colonized with toxigenic C. difficile in the absence of symptoms, termed asymptomatic colonization. We previously demonstrated that the presence and function of C. difficile toxins do not differentiate between asymptomatic colonization and CDI in children, suggesting the influence of other factors. This study aimed to interrogate the intestinal microbiome and butyrate in stool samples from children with CDI and asymptomatic colonization. MethodsDesign: Case-control study Setting: Tertiary care childrens hospital Participants and measures: Asymptomatic children had stool tested for C. difficile by nucleic-acid amplification-based testing (NAAT) and were considered colonized if positive (N=50). Residual stool was also obtained from symptomatic children who tested positive for C. difficile by NAAT (N=55). The microbiome was assessed via 16S rRNA sequencing and butyrate via liquid chromatography-mass spectrometry. ResultsCompared to clinical co-variates and comorbidities, C. difficile symptom status (i.e., asymptomatic colonization versus symptomatic CDI) demonstrated the strongest differential abundance association on gut microbes. Symptomatic CDI was associated with increased abundance of Escherichia/Shigella (Benjamini-Hochberg adjusted q=3.94x10-5), Haemophilus (q=0.022), and Gemella (q=0.085), and depleted abundance of gut commensals such as Faecalibacterium (q=0.041), Blautia (q=0.041), and Bifidobacterium (q=0.063). We also observed depletion in the abundance of microbial butyrate producers and fecal butyrate in participants with symptomatic CDI versus asymptomatic colonization. ConclusionThe gut microbiota and butyrate differ between participants with asymptomatic C. difficile colonization and symptomatic CDI, suggesting their potential role in symptom development.

microbiology↗

bioRxiv2024

Preserving Full Spectrum Information in ImagingMass Spectrometry Data Reduction

MotivationImaging mass spectrometry (IMS) has become an important tool for molecular characterization of biological tissue. However, IMS experiments tend to yield large datasets, routinely recording over 200,000 ion intensity values per mass spectrum and more than 100,000 pixels, i.e., spectra, per dataset. Traditionally, IMS data size challenges have been addressed by feature selection or extraction, such as by peak picking and peak integration. Selective data reduction techniques such as peak picking only retain certain parts of a mass spectrum, and often these describe only medium-to-high-abundance species. Since lower-intensity peaks and, for example, near-isobar species are sometimes missed, selective methods can potentially bias downstream analysis towards a subset of species in the data rather than considering all species measured. ResultsWe present an alternative to selective data reduction of IMS data that achieves similar data size reduction while better conserving the ion intensity profiles across all recorded m/z -bins, thereby preserving full spectrum information. Our method utilizes a low-rank matrix completion model combined with a randomized sparse-format-aware algorithm to approximate IMS datasets. This representation offers reduced dimensionality and a data footprint comparable to peak picking, but also retains complete spectral profiles, enabling comprehensive analysis and compression. We demonstrate improved preservation of lower signal-to-noise-ratio signals and near-isobars, mitigation of selection bias, and reduced information loss compared to current state-of-the art data reduction methods in IMS.

bioinformatics↗

bioRxiv2024

Analysis of genetic requirements and nutrient availability for Staphylococcus aureus growth in cystic fibrosis sputum

Staphylococcus aureus is one of the most common pathogens isolated from the lungs of people with cystic fibrosis (CF), but little is known about its ability to colonize this niche. We performed a Tn-seq screen to identify genes necessary for S. aureus growth in media prepared from ex vivo CF sputum. We identified 19 genes that were required for growth in all sputum media tested and dozens more that were required for growth in at least one sputum medium. Depleted mutants of interest included insertions in many genes important for surviving metal starvation as well as the primary regulator of cysteine metabolism cymR. To investigate the mechanisms by which these genes contribute to S. aureus growth in sputum, we quantified low-molecular-weight thiols, nutrient transition metals, and the host metal-sequestration protein calprotectin in sputum from 11 individuals with CF. In all samples, the abundance of calprotectin exceeded nutrient metal concentration, explaining the S. aureus requirement for metal-starvation genes. Further, all samples contain potentially toxic quantities of cysteine and sufficient glutathione to satisfy the organic sulfur requirements of S. aureus. Deletion of the cysteine importer genes tcyA and tcyP in the {Delta}cymR background restored growth to wild-type levels in CF sputum, suggesting that the mechanism by which cymR is required for growth in sputum is to prevent uncontrolled import of cysteine or cystine from this environment. Overall, this work demonstrates that calprotectin and cysteine limit S. aureus growth in CF sputum. IMPORTANCEStaphylococcus aureus is a major cause of lung infections in people with cystic fibrosis (CF). This work identifies genes required for S. aureus growth in this niche, which represent potential targets for anti-Staphylococcal treatments. We show that genes involved in surviving metal starvation are required for growth in CF sputum. We also found that the primary regulator of cysteine metabolism, CymR, plays a critical role in preventing cysteine intoxication during growth in CF sputum. To support these models, we analyzed sputum from 11 individuals with CF to determine concentrations of calprotectin, nutrient metals, and low-molecular-weight thiols, which have not previously been quantified together in the same samples.

microbiology↗

bioRxiv2024

FapR regulates HssRS-mediated heme homeostasis in Bacillus anthracis

Bacillus anthracis, a Gram-positive facultative anaerobe and the causative agent of anthrax, multiplies to extraordinarily high numbers in vertebrate blood, resulting in considerable heme exposure. Heme is an essential nutrient and the preferred iron source for bacteria during vertebrate colonization, but its high redox potential makes it toxic in excess. To regulate heme homeostasis, many Gram-positive bacteria, including B. anthracis, rely on the two-component signaling system HssRS. HssRS comprises the heme sensing histidine kinase HssS, which modulates the activity of the HssR transcription factor to enable bacteria to circumvent heme toxicity. However, the regulation of the HssRS system remains unclear. Here we identify FapR, the transcriptional regulator of fatty acid biosynthesis, as a key factor in HssRS function. FapR plays an important role in maintaining membrane integrity and the localization of the histidine kinase HssS. Specifically, disruption of fapR leads to increased membrane rigidity, which hinders the penetration of HssRS inducers, resulting in the inactivation of HssRS. Furthermore, deletion of fapR affects the loading of HssS onto the cell membrane, compromising its heme sensing function and subsequently reducing endogenous heme biosynthesis. These findings shed light on the molecular mechanisms governing bacterial adaptation to heme stress and provide potential targets for antimicrobial intervention strategies. IMPORTANCEUnderstanding the mechanisms by which B. anthracis regulates heme homeostasis is crucial for developing new strategies to combat anthrax, a serious disease affecting both humans and animals. This study uncovers the role of the transcriptional regulator FapR in maintaining membrane integrity and facilitating the proper function of the HssRS two-component signaling system, which is essential for managing heme toxicity in B. anthracis, as well as other Gram-positive pathogens. By elucidating the connection between FapR and HssRS, our findings provide new insights into the molecular adaptation of bacteria to heme stress and expand our knowledge of bacterial physiology and pathogenicity. More importantly, targeting the regulatory pathways involved in heme sensing and homeostasis presents a promising approach for developing novel therapeutics against anthrax and potentially other bacterial infections that rely on similar mechanisms.

microbiology↗

bioRxiv2024

The Staphylococcus aureus small non-coding RNA IsrR regulates TCA cycle activity and virulence

Staphylococcus aureus has evolved mechanisms to cope with low iron (Fe) availability in host tissues. S. aureus uses the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that an S. aureus {Delta}fur mutant has decreased expression of acnA, which codes for the Fe-dependent enzyme aconitase. Decreased acnA expression prevented the {Delta}fur mutant from growing with amino acids as sole carbon and energy sources. Suppressor analysis determined that a mutation in isrR, which produces a regulatory RNA, permitted growth by decreasing isrR transcription. The decreased AcnA activity of the {Delta}fur mutant was partially relieved by an {Delta}isrR mutation. Directed mutation of bases predicted to facilitate the interaction between the acnA transcript and IsrR, decreased the ability of IsrR to control acnA expression in vivo and IsrR bound to the acnA transcript in vitro. IsrR also bound to the transcripts coding the alternate TCA cycle proteins sdhC, mqo, citZ, and citM. Whole cell metal analyses suggest that IsrR promotes Fe uptake and increases intracellular Fe not ligated by macromolecules. Lastly, we determined that Fur and IsrR promote infection using murine skin and acute pneumonia models. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/601953v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1ec27b2org.highwire.dtl.DTLVardef@1224b64org.highwire.dtl.DTLVardef@83cd49org.highwire.dtl.DTLVardef@11a9cea_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Restriction of Arginine Induces Antibiotic Tolerance in Staphylococcus aureus

Staphylococcus aureus is responsible for a substantial number of invasive infections globally each year. These infections are problematic because they are frequently recalcitrant to antibiotic treatment, particularly when they are caused by Methicillin-Resistant Staphylococcus aureus (MRSA). Antibiotic tolerance, the ability for bacteria to persist despite normally lethal doses of antibiotics, is responsible for most antibiotic treatment failure in MRSA infections. To understand how antibiotic tolerance is induced, S. aureus biofilms exposed to multiple anti-MRSA antibiotics (vancomycin, ceftaroline, delafloxacin, and linezolid) were examined using both quantitative proteomics and transposon sequencing. These screens indicated that arginine metabolism is involved in antibiotic tolerance within a biofilm and led to the hypothesis that depletion of arginine within S. aureus communities can induce antibiotic tolerance. Consistent with this hypothesis, inactivation of argH, the final gene in the arginine synthesis pathway, induces antibiotic tolerance under conditions in which the parental strain is susceptible to antibiotics. Arginine restriction was found to induce antibiotic tolerance via inhibition of protein synthesis. Finally, although S. aureus fitness in a mouse skin infection model is decreased in an argH mutant, its ability to survive in vivo during antibiotic treatment with vancomycin is enhanced, highlighting the relationship between arginine metabolism and antibiotic tolerance during S. aureus infection. Uncovering this link between arginine metabolism and antibiotic tolerance has the potential to open new therapeutic avenues targeting previously recalcitrant S. aureus infections. Significance StatementMethicillin-Resistant Staphylococcus aureus (MRSA) is a leading bacterial cause of morbidity and mortality worldwide. Despite the availability of numerous antibiotics with in vitro efficacy against MRSA, there are still high rates of antibiotic treatment failure in S. aureus infections, suggesting antibiotic tolerance is common during human infections. Here, we report a direct connection between the metabolism of arginine, an essential amino acid in S. aureus, and tolerance to multiple classes of antibiotics. This represents a key pathway towards broad antibiotic tolerance in S. aureus and therefore an attractive target to help repotentiate current antibiotics and potentially reduce treatment failure.

microbiology↗

bioRxiv2023

YlaN is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in Staphylococcus aureus

Iron (Fe) is a trace nutrient required by nearly all organisms. As a result of the demand for Fe and the toxicity of non-chelated cytosolic ionic Fe, regulatory systems have evolved to tightly balance Fe acquisition and usage while limiting overload. In most bacteria, including the mammalian pathogen Staphylococcus aureus, the ferric uptake regulator (Fur) is the primary transcriptional regulator that controls the transcription of genes that code for Fe uptake and utilization proteins. YlaN was demonstrated to be essential in Bacillus subtilis unless excess Fe is added to the growth medium, suggesting a role in Fe homeostasis. Here, we demonstrate that YlaN is expendable in S. aureus; however, YlaN became essential upon Fe deprivation. A null fur allele bypassed the essentiality of YlaN. The transcriptional response of Fur derepression resulted in a reprogramming of metabolism to prioritize fermentative growth over respiratory growth. The absence of YlaN diminished the derepression of Fur-dependent transcription during Fe limitation. Bioinformatic analyses suggest that ylaN was recruited to Gram positive bacteria and once acquired was maintained in the genome as it co-evolved with Fur. Consistent with a role for YlaN in influencing Fur-dependent regulation, YlaN and Fur interacted in vivo. YlaN bound Fe(II) in vitro using oxygen or nitrogen ligands with an association constant that is consistent with a physiological role in Fe sensing and/or buffering. These findings have led to a model wherein YlaN is an Fe(II) binding protein that influences Fur-dependent regulation through direct interaction. ImportanceIron (Fe) is an essential nutrient for nearly all organisms. If Fe homeostasis is not maintained, Fe can accumulate in the cytosol where it is toxic. Questions remain about how cells efficiently balance Fe uptake and usage to prevent imbalance. Iron uptake and proper metalation of proteins are essential processes in the mammalian bacterial pathogen Staphylococcus aureus. Understanding the gene products involved in Fe ion regulation, uptake, and usage, as well as the physiological adaptations that S. aureus uses to survive in Fe-depleted conditions, will provide insight into the role that Fe has in pathogenesis. These data will also provide insight into the selective pressures imparted by the mammalian host.

microbiology↗

bioRxiv2023

Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection

During intestinal inflammation, host nutritional immunity starves microbes of essential micronutrients such as iron. Pathogens scavenge iron using siderophores, which is counteracted by the host using lipocalin-2, a protein that sequesters iron-laden siderophores, including enterobactin. Although the host and pathogens compete for iron in the presence of gut commensal bacteria, the roles of commensals in nutritional immunity involving iron remain unexplored. Here, we report that the gut commensal Bacteroides thetaiotaomicron acquires iron in the inflamed gut by utilizing siderophores produced by other bacteria including Salmonella, via a secreted siderophore-binding lipoprotein termed XusB. Notably, XusB-bound siderophores are less accessible to host sequestration by lipocalin-2 but can be "re-acquired" by Salmonella, allowing the pathogen to evade nutritional immunity. As the host and pathogen have been the focus of studies of nutritional immunity, this work adds commensal iron metabolism as a previously unrecognized mechanism modulating the interactions between pathogen and host nutritional immunity.

microbiology↗

bioRxiv2022

Differences in self-reported benefits for student-artist versus faculty experiences in a virtual artist-in-residence program.

The value of science communication in engaging the public has been well established. While many new programs bridge the arts and sciences, conducting comprehensive examination of exiting art-science programs can produce more efficient training and program development guidance for improving visual communications in the sciences. Here, we recruited a variety of scientists and artists to collaborate in creating visual science communication products over three summers. Using survey data, we performed qualitative and quantitative analyses to define sources for negative and positive experiences and outcomes from the Vanderbilt Institute for Infection, Immunology, and Inflammation (VI4) Artist-in-Residence (AiR) program. Further, we analyze responses from participants, student-artists and faculty, to specify areas for improvement and areas successful in producing a positive experience and outcome in an AiR program. We found that time and virtual delivery of the program could be modified to improve the experience. Additionally, we found that student participants had more positive responses about "learning something new" from the program than faculty members. However, the most surprising aspect of our analysis suggests that for both "way of thinking" and "science communication to the public or general audience," there may be more significant beneficial gains for faculty compared to students. We conclude this analysis with suggestions to enhance the benefits and outcomes of an AiR program and ways to minimize the difficulties, such as communication and collaboration, faced by participants and program designers.

scientific communication and education↗

bioRxiv2021

Listeria monocytogenes requires cellular respiration for NAD+ regeneration and pathogenesis

Cellular respiration is essential for multiple bacterial pathogens and a validated antibiotic target. In addition to driving oxidative phosphorylation, bacterial respiration has a variety of ancillary functions that obscure its contribution to pathogenesis. We find here that the intracellular pathogen Listeria monocytogenes encodes two respiratory pathways which are partially functionally redundant and indispensable for pathogenesis. Loss of respiration decreased NAD+ regeneration, but this could be specifically reversed by heterologous expression of a water-forming NADH oxidase (NOX). NOX expression fully rescued intracellular growth defects and increased L. monocytogenes loads >1,000-fold in a mouse infection model. Consistent with NAD+ regeneration maintaining L. monocytogenes viability and enabling immune evasion, a respiration-deficient strain exhibited elevated bacteriolysis within the host cytosol and NOX rescued this phenotype. These studies show that NAD+ regeneration, rather than oxidative phosphorylation, represents the primary role of L. monocytogenes respiration and highlight the nuanced relationship between bacterial metabolism, physiology, and pathogenesis.

microbiology↗

bioRxiv2021

Dysregulated Transferrin Receptor Disrupts T Cell Iron Homeostasis to Drive Inflammation in Systemic Lupus Erythematosus

T cells in systemic lupus erythematosus (SLE) exhibit mitochondrial abnormalities including elevated oxidative stress. Because excess iron can promote these phenotypes, we tested iron regulation of SLE T cells. A CRISPR screen identified Transferrin Receptor (CD71) as important for Th1 cells but detrimental for induced regulatory T cells (iTreg). Activated T cells induce CD71 to increase iron uptake, but this was exaggerated in T cells from SLE-prone mice which accumulated iron. Treatment of T cells from SLE-prone mice with CD71 blocking antibody reduced intracellular iron and mTORC1 signaling and restored mitochondrial physiology. While Th1 cells were inhibited, CD71 blockade enhanced iTreg. In vivo this treatment reduced pathology and increased IL-10 in SLE-prone mice. Importantly, disease severity correlated with CD71 expression on SLE patient T cells and blocking CD71 enhanced IL-10 secretion. Excess T cell iron uptake thus contributes to T cell dysfunction and can be targeted to correct SLE-associated pathology.

immunology↗

bioRxiv2021

Multimodal Imaging Mass Spectrometry of Murine Gastrointestinal Tract with Retained Luminal Content Shows Molecular Localization Patterns

Digestive diseases impact 62 million people a year in the United States. Despite the central role of the gut to human health, past imaging mass spectrometry (IMS) investigations into the gastrointestinal tract are incomplete. The gastrointestinal tract, including luminal content, harbors a complex mixture of microorganisms, host dietary content, and immune factors. Existing imaging approaches remove luminal content, and images focus on small regions of tissue. Here, we demonstrate the use of a workflow to collect multimodal imaging data for both intestinal tissue and luminal content. This workflow for matrix-assisted laser desorption/ionization imaging mass spectrometry retains luminal content and expands the amount of tissue imaged on one slide. Results comparing tissue and luminal content show unique molecular distributions using multimodal imaging modalities including protein, lipid, and elemental imaging. Leveraging this method to investigate intestinal tissue infected with Clostridioides difficile compared to control tissue shows clear differences in lipid abundance of various lipid classes in luminal content during infection. These data highlight the potential for this approach to detect unique biological and markers of infection in the gut.

biochemistry↗