mBio

Staphylococcus aureus is one of the most frequently co-isolated pathogens in polymicrobial infections, where interspecies interactions contribute to enhanced virulence, persistence, and antimicrobial tolerance. Nutrient availability plays a central role in these interactions as microorganisms compete for resources required to sustain essential cellular processes. For instance, branched-chain amino acids (BCAAs) are critical for protein synthesis, and valine synthesis pathway precursors are essential for energy production. In S. aureus, BCAAs are also the precursors for branched-chain fatty acids (BCFAs), the dominant fatty acids in the S. aureus membrane. We previously identified a second pathway that uses branched-chain carboxylic acids (BCCAs) and the high-affinity acyl-CoA synthetase MbcS to catalyze the synthesis of BCFA precursors. However, the physiological role of this pathway and the conditions triggering its activation remain unclear. Here, we show that mbcS is restricted to S. aureus and closely related human-associated staphylococci. Phylogenetic analyses suggest that MbcS arose from a refunctionalization event and represents a non-orthologous replacement for the phosphotransbutyrylase (Ptb) and butyrate kinase (Buk) enzymes. Consistent with this model, Ptb and Buk from Staphylococcus pseudintermedius catalyze the formation of branched-chain acyl-CoAs from BCCAs, but only at high substrate concentrations. We further show that mbcS expression is upregulated in a codY mutant, implicating this pathway in BCAA-limited conditions. In support, we show that mbcS is required for optimal fitness during intra-species competition. Together, our findings support a model in which the MbcS-dependent pathway enables S. aureus to scavenge BCFA precursors under nutrient-limited conditions, providing a competitive advantage in polymicrobial environments. ImportanceStaphylococcus aureus is a major contributor to polymicrobial infections, where competition for nutrients can influence bacterial physiology and survival. A deeper understanding of how S. aureus adapts to nutrient limitation is therefore essential to explain its success as a human pathogen. In S. aureus, the acyl-CoA synthetase MbcS supports BCFA synthesis from BCAA-derived carboxylic acids and aldehydes, which are released into the environment as by-products of bacterial metabolism. Herein, we provide evidence that S. aureus acquired the acyl-CoA synthetase MbcS as an adaptive trait. This metabolic innovation allows this bacterium to maintain membrane homeostasis under nutrient limitation and compete against neighboring bacteria. Our findings highlight an adaptive strategy that may contribute to the persistence of S. aureus in polymicrobial infections.

While pathogenic fungi can acquire resistance to the current arsenal of antifungals through genetic mutations, heteroresistance has emerged as an important new cause of therapeutic failures. Heteroresistance is generally thought to arise in small subpopulations that display phenotypic resistance to antifungals without genetic mutations. This study blurs that line by showing gain-of-resistance mutations in FKS2, which encodes a target of echinocandins and fungerps, cause large amounts of heteroresistance in Candida glabrata through heterogeneous expression of the gene even in clonal cell populations. Heteroresistance decreased when stress-responsive transcription factors (Crz1, Rlm1) were eliminated and was nearly abolished when the upstream regulators (calcineurin, Slt2) were mutated or inhibited. Identical gain-of-resistance mutations in FKS1, a paralog of FKS2, showed much less heteroresistance due to its constitutive expression coupled with variable levels of antagonism by wild-type FKS2. A genome-wide screen using Tn-seq revealed additional regulators of heteroresistance and resistance including IRA1, an inhibitor of the Ras1-PKA signaling pathway that senses glucose availability. IRA1 increased expression of FKS2 and decreased expression of FKS1, which increased heteroresistance and decreased resistance, respectively, when these genes carried resistance mutations. Similar principles may govern heteroresistance in other fungal pathogens such as Candida parapsilosis, which naturally carries resistance mutations in FKS1 and frequently exhibits heteroresistance to echinocandins, and Candidozyma auris, which easily acquires such mutations.

Urinary tract infections (UTIs) are a significant public health burden that impact millions of people every year and are highly prevalent among in hospital-acquired infections. Klebsiella pneumoniae is the second most common cause of UTIs after uropathogenic Escherichia coli (UPEC). Thus far, the molecular mechanisms underlying pathogenesis is better understood in UPEC than K. pneumoniae. UPEC is known to have fitness factors such as fimbrial adhesion and evasion of complement-mediated killing. In other infection types, K. pneumoniae fitness has been associated with mucoidy and diverse capsular serotypes. To establish K. pneumoniae virulence factors contributing to UTI, we examined how environmental cues regulate urovirulence-associated phenotypes in clinical K. pneumoniae UTI strains. These factors included capsular polysaccharide properties, hemagglutination, serum resistance, adherence to bladder epithelial cells, and in vivo fitness. We found that clinical K. pneumoniae UTI isolates phenotypes are highly heterogeneous and can change in response to human urine. Despite K. pneumoniae clinical isolates presenting heterogeneous fitness properties, all similarly colonize the urinary tract. These results suggest that additional fitness factors contribute to K. pneumoniae uropathogenesis. Identifying these shared fitness factors will provide mechanistic insights into Klebsiella uropathogenesis and reveal candidate therapeutic targets.

Toxoplasma gondii is a single-celled parasite belonging to the Apicomplexa phylum. Toxoplasmas single mitochondrion is highly dynamic, changing its morphology as the parasite undergoes egress and invasion. Recently, we have demonstrated that mitochondrial morphology is driven by a protein named Lasso Maintenance Factor 1 (LMF1). This protein interacts with IMC10, a protein present at the parasites inner membrane complex (IMC), mediating a unique membrane contact site between the IMC and mitochondrion. Interestingly, parasites lacking either LMF1 or IMC10 have abnormal mitochondrial morphology, cell division defects, and delayed propagation in tissue culture. Although both components of the tether were identified, the functions of this contact site remain unknown. In this work, we show that {Delta}lmf1 parasites exhibit upregulation of egress signaling and downregulation in folate metabolism and pantothenate biosynthesis. {Delta}lmf1 parasites exhibit increased intracellular calcium levels, leading to greater sensitivity to ionophore-induced egress and microneme secretion. We have confirmed that parasites have decreased levels of tetrahydrofolate and coenzyme A, showing a limitation in cofactor production. Interestingly, the {Delta}lmf1 parasites prefer glutamine instead of glucose as a catabolic substrate. Accordingly, we demonstrate for the first time that proper mitochondrial positioning is crucial for folate and Coenzyme A metabolism as well as egress signaling. IMPORTANCEToxoplasma gondii is the causative agent of Toxoplasmosis, a disease that affects a third of the worlds population. This parasite has a single, highly dynamic mitochondrion. The parasites mitochondrion changes shape depending on environmental conditions (inside or outside the host cell) or on stressors, such as drugs. Our laboratory characterized the proteins involved in regulating mitochondrial dynamics in the parasite, but the functional importance of these mitochondrial changes has not yet been described. Here, we show that the shape of Toxoplasmas mitochondrion is important for the synthesis of key cofactors, such as folates and coenzyme A. We show that mitochondrial shape in this parasite is important for signaling the parasites exit from the host cell, a critical process in its life cycle. These findings review a previously unknown function of a parasite-specific organelle contact site, providing new insights into the importance of mitochondria for these parasites.

Salmonella enterica encounters acid stress during gastrointestinal transit and within the phagosomal environment of macrophages. Acid stress resistance has been well characterized in Salmonella enterica serovar Typhimurium, but comparative studies in the human-adapted Salmonella enterica serovar Typhi are limited. We compared the growth of S. Typhimurium 14028s and S. Typhi Ty2 at pH values ranging from 3-8 and observed that Salmonella enterica serovar Typhimurium exhibits enhanced growth at pH 4.5 compared to S. Typhi. Comparative transcriptomic profiling of S. Typhimurium and S. Typhi at pH 4.5 and 7.5 identified numerous differentially expressed acid-induced genes (DEGs), including genes encoding membrane proteins (OmpC, PhoE, HydB), a transcriptional regulator (RpoS), and stress response proteins (YciG, STM14_1829, YmdF). Targeted deletion of selected genes in S. Typhimurium significantly suppressed growth at acidic pH, confirming their role in acid stress resistance. These resistance mechanisms are compromised in S. Typhi due to pseudogenization. Heterologous expression of pseudogenized genes in S. Typhi restored acid tolerance. Collectively, these findings suggest that S. Typhi has lost the ability to withstand acid stress due to genomic decay and the loss of multiple genes essential for acid survival in S. Typhimurium, reflecting divergent evolutionary paths in these two serovars. ImportanceSalmonella Typhimurium must adapt to acidic pH conditions in the intestinal tract and the intracellular environment to cause infection. In this study, we show that the enteric fever serovar Salmonella Typhi exhibits impaired growth at pH 4.5, in comparison to Salmonella Typhimurium. We further show that the loss of specific membrane proteins, a transcriptional regulator, and a family of stress response proteins in Salmonella Typhi are responsible for this difference. Collectively, these observations suggest that Salmonella Typhi has evolutionarily lost the ability to withstand acid stress due to differences in its interaction with the human host. This has important implications for the pathogenesis of typhoid fever.

The mycobacterial cell envelope consists of multiple covalently linked layers that must be synthesized in a coordinated manner to maintain cell wall integrity. Despite the importance of this coordination, its molecular mechanisms remain poorly understood. PgfA (polar growth factor A) interacts with trehalose monomycolate lipids (TMMs) (1) and the TMM transporter MmpL3 (1, 2). PgfA promotes TMM transport in the periplasm and functions as an upstream regulator of polar growth. How TMM transport is linked to the expansion of the entire multi-layered cell wall is unclear. Here, we provide evidence that PgfA regulates peptidoglycan metabolism. We show that PgfA localization correlates with peptidoglycan metabolism and that PgfA can function as both an activator and inhibitor of peptidoglycan metabolism. We further explore the role of TMMs in polar growth and find evidence that periplasmic TMMs are a signaling molecule that may regulate polar peptidoglycan metabolism. Finally, we find an epistatic connection between PgfA overexpression and altered TMM levels that suggests that PgfA and TMMs work in the same pathway to regulate peptidoglycan metabolism. Our data are consistent with a model in which TMM-free PgfA inhibits peptidoglycan metabolism, while TMM-bound PgfA promotes polar peptidoglycan metabolism. This work identifies PgfA as a key protein that coordinates synthesis of the peptidoglycan and mycolic acid envelope layers. ImportanceThe mycobacterial cell envelope consists of multiple covalently linked layers whose synthesis must be coordinated to maintain cell integrity. Despite decades of research on individual envelope components, the molecular mechanisms coordinating synthesis of different layers remain poorly understood. Here, we identify PgfA as a key regulatory protein that coordinates peptidoglycan and mycolate synthesis in mycobacteria. PgfA has both inhibitory and stimulatory effects on peptidoglycan metabolism, depending on the context. Our findings suggest PgfA may act as a regulator that senses mycolate precursor availability and prevents envelope imbalance when these precursors are limiting. This work provides new insight into how mycobacteria coordinate the synthesis of their complex cell envelope, with implications for better understanding mycobacterial physiology and developing antimycobacterial therapeutics.

Cryptosporidium is a protozoan that infects epithelial cells of the small intestine and is a cause of diarrhea and death in immunocompromised individuals and malnourished children. Immunity to this parasite is mediated by an intestinal T cell response, which is generated in gut-associated lymphoid tissues and dependent on type 1 conventional dendritic cells (cDC1s). The initial priming of T cells is accompanied by changes in integrin expression and subsequent trafficking to the site of infection. The role of specific integrins in trafficking to the ileum during cryptosporidiosis is largely unknown. The development of a transgenic Cryptosporidium strain that expresses MHCI and MHCII-restricted model antigens provides the ability to track T cell responses to this parasite. Our studies in this system revealed marked changes in the integrin profile of parasite-specific T cells as they are activated and traffic to the gut, and demonstrate that cDC1s contribute to the expression of the integrins 4, {beta}7, {beta}1, and L. Surprisingly, blockade of the canonical gut-homing integrin 4{beta}7 does not impact the ability of parasite-specific T cells to access the gut. However, blockade of integrin L decreases the parasite-specific T cell frequency at the site of infection and delays control of parasite burden. These datasets highlight an 4{beta}7-independent mechanism of T cell trafficking to the small intestine and indicate that L is an integrin required for T cell-mediated resistance to Cryptosporidium.

Aspergillus fumigatus, an opportunistic human fungal pathogen, encodes numerous secondary metabolite biosynthetic gene clusters (BGCs) that are tightly regulated and often remain silent under standard conditions. Co-cultivation with Streptomyces rapamycinicus or treatment with the secondary metabolite from this species, the arginoketide azalomycin F, induce the otherwise silent fumicycline (fcc) BGC of A. fumigatus. To elucidate the underlying regulatory circuitry, we performed transcriptome analyses of A. fumigatus exposed to azalomycin F or co-cultured with S. rapamycinicus. Both conditions triggered a coordinated antibacterial response, characterized by induction of specific secondary metabolites and antibacterial effectors, alongside repression of other BGCs, including those for fusarinine C, pyripyropene A, and fumagillin. Among the most strongly induced genes was a zinc cluster transcription factor, designated SmpR for secondary metabolite multiple pathway regulator, which is conserved within Ascomycota. SmpR expression was selectively induced by azalomycin F, specific Streptomyces species and other bacteria isolated from soil such as Kribbella spp. and Arthrobacter spp.. Functional analyses revealed that SmpR is required for activation of the fumicycline BGC: its deletion reduced, whereas its overexpression enhanced fumicycline production independently of external stimuli. We further demonstrate that SmpR acts upstream of the pathway-specific regulator FccR and additionally controls multiple antibacterial BGCs, including those for hexadehydroastechrome, helvolic acid and xanthocillin. Together, our data identify SmpR as a key regulator coordinating antibacterial secondary metabolism in response to bacterial signals in A. fumigatus.

Successful infection by the rice blast fungus Pyricularia oryzae depends on precise developmental transitions on the plant surface, yet the extracellular metabolites that regulate these events remain poorly understood. One such metabolite, 2'-deoxyuridine (dU), has been identified as a self-produced infection-promoting factor, but its mode of action has remained unclear. Exogenous dU did not significantly affect conidial germination but accelerated early appressorium initiation and promoted appressorium maturation, as indicated by increased glycogen mobilization and elevated intracellular turgor. Extracellular dU was detected during early infection-related development, indicating that dU accumulates under conditions conducive to appressorium formation. To test whether microbial turnover of dU influences pathogenicity, dU-degrading bacteria were isolated from rice field environments, and Enterobacter sp. strain C3 was identified as the most active isolate. Biochemical and structural analyses identified the responsible enzyme as the thymidine phosphorylase DeoA, which converts dU to uracil in a phosphate-dependent reaction. Recombinant DeoA reproduced this activity in vitro, and enzymatic depletion of dU attenuated invasive hyphal growth and lesion development. Appressorium-specific expression of deoA in P. oryzae likewise reduced pathogenicity. Together, these results identify extracellular dU as a factor promoting infection-related development in P. oryzae and suggest that dU degradation provides a potential approach for the biological control of rice blast disease. IMPORTANCESuccessful infection by the rice blast fungus Pyricularia oryzae depends on tightly regulated developmental changes on the plant surface. This study identifies 2'-deoxyuridine as an extracellular molecule that helps drive these early infection events. The fungus-derived nucleoside promoted appressorium formation and maturation, accumulated during early infection-related development, and could be targeted for disease suppression. A rice field bacterium, Enterobacter sp. strain C3, and its enzyme DeoA efficiently degraded 2'-deoxyuridine, and this depletion reduced fungal invasion and disease development. These findings uncover a previously unrecognized extracellular signal associated with infection-related development in the rice blast fungus and point to metabolite degradation by environmental microbes as a promising route for biological control.

The current working model of the innate immune protein calprotectin (CP) focuses on its metal-sequestering activity, which contributes to host defense against infection. Recently, CP was reported to enhance the survival of Staphylococcus aureus in coculture with Pseudomonas aeruginosa in a metal-independent manner. This prior work indicated that the CP protein scaffold, even in the absence of its metal-binding sites, possesses activities that impact interspecies dynamics between these bacterial pathogens. In this study, we employ {Delta}{Delta}, a CP variant lacking both functional metal-binding sites, to assess the responses of each pathogen to the CP protein scaffold in monoculture and coculture. Using dual-species transcriptomics, we report that {Delta}{Delta} treatment induced gene expression changes indicative of cell envelope modifications for both P. aeruginosa and S. aureus during coculture. The presence of the CP protein scaffold also attenuated the production of the quorum sensing molecule C4-homoserine lactone and the anti-staphylococcal alkylquinolone (AQ) metabolite 2-heptyl-4-hydroxyquinoline N-oxide. Cocultures with S. aureus and P. aeruginosa mutants defective in AQ biosynthesis demonstrated that AQ production was required for {Delta}{Delta} to impact expression of membrane remodeling genes in both species during coculture. Furthermore, we showed that in the absence of AQ production, the effect of CP on S. aureus in coculture resembled that of Fe depletion. Collectively, our findings demonstrate that the functional versatility of CP extends beyond multi-metal sequestration and that its intertwined metal-dependent and -independent activities have important consequences for bacterial physiology and polymicrobial interactions. IMPORTANCERecent studies of the innate immune protein calprotectin (CP), which is known for its metal-sequestering ability and contributions to nutritional immunity, have uncovered that the protein also exerts metal-independent activities on bacterial pathogens. In this work, we investigate the metal-independent effects of CP on the interspecies dynamics of Pseudomonas aeruginosa and Staphylococcus aureus, two high-priority pathogens that co-colonize various polymicrobial infection sites. We report that the ability of the CP protein scaffold to attenuate the anti-staphylococcal activity of P. aeruginosa results from perturbed quorum sensing and reduced production of alkylquinolone (AQ) metabolites. We further show that pseudomonal AQs contribute to cell envelope remodeling responses exhibited by both pathogens in the presence of the CP protein scaffold. These results afford an updated working model wherein both canonical metal-dependent and noncanonical metal-independent activities of CP elicit physiological changes in both pathogens, resulting in perturbed coculture dynamics.

Herpes simplex virus (HSV) fusion and entry is mediated by a cascade of interactions among gB, gD and gH/gL. The gB homotrimer undergoes a conformational transition from a metastable prefusion state to a more stable postfusion form, driving fusion of the viral envelope and a host cell membrane. An H516P mutation in gB domain III restricts formation of the extended core alpha helix and constrains gB in a prefusion state. Several prefusion gB structures have been determined that contain this mutation. We assessed the antigenic reactivity of gB H516P by quantitative immunodotblot using a panel of gB-reactive monoclonal antibodies All antibodies tested bound to both prefusion (H516P) gB and wild type gB. Antibodies tested to gB domains II, IV and V exhibited differential binding to H516P gB compared to wild type gB. The results suggest that gB H516P has a distinct antigenic profile. The antigenic signature of H516P may be useful as a rapid indicator of prefusion forms of gB. The low pH environment of the cellular endosome is a cell-specific factor for HSV entry and triggers antigenic changes in gB. The step at which low pH impacts gB refolding to execute fusion is not well-understood. The results suggest that gB H516P undergoes wild-type-like conformational changes in gB domains I and V triggered by low pH. We propose that pH acts on an early stage of gB fusion function, prior to extension of the domain III core helix.

Infections with multidrug resistant Acinetobacter baumannii are considered a threat to human and animal health. The widely studied A. baumannii strain AB5075 displays a high degree of antibiotic resistance. In this study, we experimentally validated that antibiotic resistance is largely mediated by resistance genes located on plasmid p1AB5075. We used a p1AB5075-deficient AB5075 strain to assess individual contributions of p1AB5075-encoded antibiotic resistance genes by ectopically (over-)expressing each gene in the {Delta}p1AB5075 background. By determining individual contributions of seven p1AB5075-encoded antibiotic resistance genes, we show individual and overlapping roles of genes for aminoglycoside resistance and uncover the importance of extended-spectrum {beta}-lactamase blaGES-11 for cephalosporin resistance in A. baumannii AB5075. We discovered that aminoglycoside N-acetyltransferase aaC(6)-Ib3 (aacA4), which was considered a potential pseudogene in A. baumannii AB5075, to be functional providing broad resistance to gentamicin, kanamycin, amikacin, streptomycin and tobramycin when overexpressed in A. baumannii AB5075. Because p1AB5075 is transferrable to a wide range of environmental and clinical A. baumannii strains and non-baumannii Acinetobacter species, the relevance of our findings extends beyond A. baumannii AB5075.

The upper respiratory tract is a primary niche for Streptococcus pyogenes colonisation and disease. Lower respiratory tract infection (pneumonia) is the most common invasive S. pyogenes syndrome. Studies have not previously examined how epithelial cells, from the airway to the alveolus, respond to S. pyogenes infection. Here, we established a scalable human in vitro model by differentiating induced pluripotent stem cells (iPSCs) into mature pseudostratified airway epithelium or alveolar type 2 epithelial cells, cultured at air-liquid interface and infected with S. pyogenes (M1UK and M75 strains). Both strains attached to iPSC-derived lung epithelial cells, with significantly greater adherence to the airway epithelium by M75 compared to M1UK. Moreover, invasion by both S. pyogenes strains of alveolar epithelial cells was greater than for the airway epithelium. Dynamic S. pyogenes gene expression changes were evident between 6 and 24 hours after infection, which was influenced by the infected cell type; however, virulence genes were not significantly altered. While infection of the airway epithelium induced rapid and dynamic inflammatory signalling, the alveolar epithelium demonstrated augmented cell death and mounted a transcriptional pro-inflammatory and proliferative response that was uncoupled from cytokine secretion. The airway epithelium model exhibited consistently higher baseline type I interferon (IFN) signalling than the alveolar epithelium. Invasion by S. pyogenes and inflammation was significantly reduced in IFN-{beta}-treated alveolar epithelial cells. In summary, we have established the first model of S. pyogenes infection in physiologically relevant airway and alveolar epithelial cells. Our findings suggest that host responses to infection are influenced by lung compartment, the S. pyogenes strain type, and infection timepoint, highlighting context-specific pathways that could be leveraged therapeutically.

Recent elucidation of the bacterial sphingolipid synthesis pathway has revealed that these lipids are produced by a range of taxonomically diverse species. In contrast to the biosynthetic pathways, the mechanism by which sphingolipids are transported from the inner membrane to the cell surface in Gram-negative bacteria remains a mystery. Here, we identify and characterize paralogs of the well-characterized lipopolysaccharide (LPS) inner membrane ABC transporter proteins encoded within the sphingolipid locus. Using Caulobacter crescentus as a model system, we analyzed three putative inner membrane proteins with homology to LptF, LptG, and LptC. Deletion of these genes was lethal, likely due to the accumulation of anionic sphingolipids in the inner membrane. We further show that the LptF and LptG homologues form a complex like their LPS counterparts and discover that they interact with the LPS ATPase LptB. Together, our data suggest that ceramide transport to the outer membrane is facilitated by an ABC transporter consisting of a sphingolipid-specific LptFG homolog coupled to the LPS LptB, supporting a model in which sphingolipid transport partially converges with the LPS transport system. Together, these findings reveal an unexpected evolutionary relationship between sphingolipid and lipopolysaccharide transport.

Francisella tularensis is a Gram-negative bacterium that causes tularemia, a fatal zoonotic disease. F. tularensis has been used in the bioweapon programs of several countries. Its potential use as a bioterrorism agent led the CDC to classify F. tularensis as a Tier 1 Select Agent. The cytosolic sensor absent in melanoma 2 (Aim2) detects double-stranded DNA in the cytosol of infected cells and subsequently assembles a multiprotein complex known as the inflammasome. Inflammasome activation drives the secretion of IL-1{beta} and IL-18, key proinflammatory cytokines required for controlling F. tularensis infection. Prior studies have shown that F. tularensis actively suppresses Aim2 inflammasome activation; however, the underlying mechanism remains unknown. We hypothesized that F. tularensis suppresses Aim2-mediated responses by modulating the intracellular redox environment. We utilized an F. tularensis mutant lacking OxyR ({Delta}oxyR), a transcriptional regulator that controls the expression of major antioxidant enzymes. Our results show that macrophages infected with the {Delta}oxyR mutant exhibit significantly higher levels of Aim2-dependent Caspase-1 and IL-1{beta} than those infected with wild-type bacteria. The expression of interferon regulatory factor 1 and the guanylate-binding proteins GBP2 and GBP5, upstream signaling components of the Aim2 inflammasome, is markedly higher in {Delta}oxyR-infected macrophages than in controls. These changes were absent in {Delta}oxyR-infected NADPH oxidase-deficient macrophages, which are unable to generate reactive oxygen species. Collectively, these findings demonstrate that macrophage redox environment plays a key role in activating signaling components required for Aim2 inflammasome activation. This work advances our understanding of how F. tularensis-encoded factors subvert host innate immune defenses.

Bacterial membranes comprise diverse lipids whose proportions vary according to environmental conditions. How cells direct lipid flux toward specific products remains unclear. We address this question in the human pathogen Staphylococcus aureus, where multiple lipid products compete for a common precursor, the major phospholipid, phosphatidylglycerol (PG). One product, lipoteichoic acid (LTA), is essential for cell division, envelope homeostasis, and virulence. Lipids and metabolites were quantified to identify factors that prioritize LTA synthesis over the other PG-derived products. We identify upstream fatty acid synthesis (FASII) pathway as a key control point for LTA production. Inhibition of FASII by antibiotics or gene inactivation causes LTA depletion. FASII inhibition similarly affects LTA in Streptococcus agalactiae, suggesting conservation of this LTA control strategy. Changes in membrane fatty acids do not account for LTA depletion. Instead, we show that FASII inhibition causes a drop in intracellular glycerophosphate (GroP), a precursor for both PG and LTA. Under these conditions of GroP limitation, PG flux favors production of a non-GroP lipid, cardiolipin. Moreover, combined inhibition of FASII and WTA blocks S. aureus growth, confirming the lethality of depleting LTA and WTA simultaneously. This study resolves how S. aureus manages phospholipid flux, by prioritizing the synthesis of GroP-rich LTA or of non-GroP-containing lipids according to FASII-controlled GroP availability.

Hydrogenosomes are mitochondria-derived organelles that produce ATP and H2 to support energy metabolism in anaerobic eukaryotes. H2 production allows reoxidation of reduced cofactors generated during fermentative metabolism; however, the metabolic mechanisms for H2 production in anaerobic eukaryotes remains incompletely understood. In particular, it remains unclear whether anaerobic fungi (AF) hydrogenosomes use a ferredoxin-dependent pathway or a distinct mechanism to regenerate NAD(P)+ and link electron transfer to H2 formation. Here, by combining genomic search, proteomic analysis, and enzymology, we reveal the molecular mechanism for H2 production in the AF strain Caecomyces churrovis. Our enzyme assays on the organelle fraction of C. churrovis revealed the activity of H2:NAD+ oxidoreductase but not pyruvate:ferredoxin oxidoreductase, which is usually linked to H2 formation. We identified genes encoding [FeFe] hydrogenase (Hyd) and NADH dehydrogenase subunits E and F (NuoE, NuoF) in C. churrovis, and confirmed their expression in the isolated hydrogenosomal fractions by proteomic analysis. Combining the individually purified enzymes, we found Hyd and NuoEF proteins formed H2 directly from NADH independently of ferredoxin, functioning as a non-bifurcating NADH-dependent enzyme rather than an electron-bifurcating enzyme. We identified homologs of hydrogenosomal NuoE, NuoF, and Hyd in many other AF, indicating this pathway is commonly shared among the AF. This work demonstrates the existence of a non-bifurcating NADH-dependent enzyme complex in eukaryotes. Moreover, this complex could potentially be exploited as a target for controlling AF H2 production and altering fungal metabolism. IMPORTANCEH2 production is a prominent feature of anaerobic energy metabolism, yet our understanding of eukaryotic mechanisms remains limited. Anaerobic fungi (AF) are key decomposers of lignocellulose and contribute to hydrogen flux in anaerobic environments. Although it has been more than 40 years since the H2 production from AF was first reported, the molecular mechanism for hydrogenosomal H2 production and redox balance remains unclear. We demonstrate that AF produce H2 from NADH utilizing a non-bifurcating NADH-dependent enzyme complex rather than an electron-bifurcating, ferredoxin-dependent variant. We show that this enzyme complex is conserved across multiple AF lineages and thus demonstrate the occurrence of a non-bifurcating NADH-dependent enzyme in eukaryotes. This discovery expands our understanding of eukaryotic hydrogenosomal metabolism, reveals a previously unknown strategy for redox balancing, and highlights potential targets for manipulating H2 production. These insights have broad implications for microbial energy metabolism, anaerobic ecosystems, and bioengineering of H2-producing systems.

Colistin is used to treat antibiotic resistant gram-negative infections, including those caused by Pseudomonas aeruginosa (Pa). Using a diverse collection of clinical isolates, we identified BWH047, a colistin-resistant isolate with an extremely high minimum inhibitory concentration (MIC, 1280 {micro}g/mL). To characterize the genes conditionally essential for colistin resistance in BWH047, we employed transposon insertion sequencing and identified 20 gene candidates. In-frame deletion validated 75% of the candidates and identified genes in several novel pathways that contribute to colistin resistance, including algU and wapH. We also identified several candidate genes from previously reported colistin resistance pathways (e.g. arn, pmrAB). We further investigated the impact of a colistin resistance-associated inner membrane DedA-family undecaprenyl phosphate flippase, which we named DpcA (DedA of Pseudomonas necessary for colistin resistance A). Deletion of dpcA in BWH047 restored sensitivity to colistin (MIC = 0.5 {micro}g/mL) and resulted in several unique changes to the structure of lipopolysaccharide (LPS), including production of decreased amounts of the colistin resistance-conferring 4-amino-4-deoxy-L-arabinose (L-Ara4N) modification on lipid A. To date, this work represents the most complete analysis of colistin resistance in Pa and identifies novel intersecting pathways that contribute to extreme phenotypic resistance. Author summaryPseudomonas aeruginosa is a bacterium that causes a wide variety of infections. It is especially problematic given its propensity to become resistant to antibiotics. One antibiotic used to treat multidrug-resistant P. aeruginosa infections is colistin. In this study, we investigated colistin resistance mechanisms in a patient-derived, extremely phenotypically resistant P. aeruginosa isolate, BWH047, using transposon insertion sequencing and mass spectrometry. We identified 13 genes conditionally essential for colistin resistance and investigated the role of one of these genes, dpcA, on the composition of the bacterial outer membrane, the target of colistin. Additionally, our study identified novel colistin resistance genes residing in several intersecting pathways that could be targeted to prevent the development of antimicrobial resistance.

Helicobacter pylori is a prevalent bacterial pathogen that chronically colonizes the human gastric epithelium, but the bacteriums physiological mechanisms that promote this are understudied. Dormancy and low growth are known to facilitate other microbial chronic infections. A critical feature of low growth states is the down regulation of ribosome translational activity via regulation factors. The H. pylori genome is predicted to encode only one ribosome regulation factor, called RsfS (Ribosomal Silencing Factor S). In other bacterial species, RsfS prevents ribosome assembly by binding to a protein called L14 on the 50S large ribosomal subunit. Although H. pylori RsfS has not been experimentally investigated prior to this work, it conserves key residues, suggesting it is a bona fide RsfS homolog. To investigate phenotypes associated with rsfS, the gene was deleted and mutant phenotypes characterized. H. pylori rsfS null mutants had no defects during exponential phase but had viability defects in stationary phase and low growth factor conditions. Additionally, rsfS null mutants could not form biofilms, and instead were only able to form monolayers of multicellular aggregates. These defects were corrected by the re-introduction of rsfS in a second site on the chromosome. To explore whether rsfS is required in vivo, a mouse model was employed. rsfS mutants initially colonized in low numbers in both the glands and total stomach but were unable to develop robust long-term colonization. This work supports that H. pylori requires RsfS for survival in low growth states and to maintain chronic infections in the host. ImportanceH. pylori chronic infections are difficult to cure in part because H. pylori is proposed to adopt low-growth states known to render bacteria tolerant to antibiotics. One key signature of a low growth state includes low translation via ribosome regulation factors. Unlike other bacterial species, H. pylori contain only one known ribosome regulation factor called Ribosomal Silencing Factor S (RsfS). This gene was previously found to be transcriptionally upregulated in at least one low growth state, biofilms. In this work, we found that H. pylori rsfS is required for this microbe to thrive in low growth states and during infection. This study is one of only two studies that investigates the phenotypes of rsfS knockout mutants in any bacterial species and the first to address knowledge gaps in ribosomal regulation by H. pylori in vivo.

We used transposon sequencing (Tn-seq) to define genetic requirements for intracellular survival of Brucella neotomae, a rodent-associated species. A near-saturating mutant library was subjected to selection during infection of J774A.1 macrophages, identifying 54 genes required for intracellular fitness. These included core components of the VirB type IV secretion system, multiple regulatory factors, an aquaporin gene with a strong fitness defect, and a set of metabolic genes involved in amino acid biosynthesis. Targeted mutagenesis revealed that methionine and histidine biosynthesis are indispensable for intracellular growth, whereas tryptophan biosynthesis was required for full intracellular fitness, with mutants exhibiting significant but incomplete attenuation. Notably, these auxotrophs grew normally in minimal medium under axenic conditions, indicating that their requirement is specific to the intracellular environment. Amino acid supplementation rescued intracellular growth in a concentration- and time-dependent manner, consistent with increased metabolic demand during intracellular replication. Disruption of the aquaporin gene similarly impaired intracellular survival, suggesting a role for water homeostasis during adaptation to the macrophage vacuolar environment. Beyond metabolic and osmotic adaptation, we identify OmpR1 as an upstream regulator of B. neotomae virulence. Biochemical, genetic, and transcriptional analyses establish a hierarchical regulatory cascade in which OmpR1 activates the BvrR/BvrS system, which in turn controls VjbR and downstream VirB expression. Under the conditions examined, OmpR1 is required for activation of this cascade. Consistent with this, OmpR1 loss is not rescued by VjbR and requires BvrR activity for restoration of intracellular growth. Phylogenetic analysis places OmpR1 in a distinct lineage relative to other well-characterized Brucella transcriptional regulators, suggesting that this regulatory pathway has been underappreciated across the genus. Together, these findings reveal that intracellular fitness in Brucella depends on metabolic capacity, osmotic homeostasis, and a hierarchical regulatory cascade centered on OmpR1. Author SummaryBrucella species are bacteria that survive and replicate inside immune cells called macrophages, where they cause persistent infection. To live within these cells, the bacteria must carefully balance their metabolism with the expression of genes required for virulence. We used a genome-wide genetic approach to determine which genes are specifically required for intracellular survival of Brucella neotomae, a rodent-associated species. We found that several amino acid biosynthesis pathways, including those required to produce methionine and histidine, are essential for replication inside macrophages but are not required during growth in laboratory media. This indicates that the intracellular environment imposes nutrient limitations not apparent in culture. We also discovered that a gene encoding an aquaporin, which regulates water movement across the bacterial membrane, is critical for intracellular survival, highlighting the importance of maintaining water balance within the host cell vacuole. In addition, we identify OmpR1 as an upstream regulator that controls a hierarchical virulence cascade required for intracellular growth. Our findings show that successful infection depends on metabolic capacity, virulence regulation and water homeostasis, and provide new insight into how Brucella adapts to its host environment.