Biology subjects

Heinrichs, D. E.

Publications and source records attributed to Heinrichs, D. E..

10 recordsLinked to original sources

bioRxiv2026

The RND family efflux pump FemT contributes to lipid homeostasis in Staphylococcus aureus

The RND efflux pump FemT encoded by SAUSA300_2213 of Staphylococcus aureus USA300 is co-transcribed with femX which has an essential role in synthesizing the Lipid II precursor of peptidoglycan. Anticipating that this arrangement reflects a critical accessory role for femT, we constructed USA300{Delta}femT to assess its function. Although growth of USA300{Delta}femT in tryptic soy broth (TSB) was not impaired, transcriptomic data revealed a mild cellular stress response, accompanied by reduced expression of ohyA and crt genes involved in fatty acid metabolism and carotenoid lipid synthesis respectively. Accordingly, USA300{Delta}femT exhibited impaired growth on exposure to saturated and unsaturated fatty acids, and exposure to subinhibitory 50 {micro}M palmitic acid promoted accumulation of reactive oxygen species, reduced respiratory activity, and altered membrane function and morphology. The transcriptome of cells grown under this condition revealed strongly attenuated expression of ohyA and crt, and several genes required for oxidative and anaerobic respiration, concomitant with strongly enhanced expression of several stress response pathways. Cellular metabolites were also profoundly altered. Finally, lipidomic analysis of USA300{Delta}femT exposed to oleic acid revealed increased incorporation of oleic acid into phosphatidylglycerol, accompanied by a significant reduction in undecaprenol C55 lipid carrier, and respiratory quinones MK-7 and MK-8. Our data are consistent with a role for FemT in maintaining cellular lipid homeostasis by promoting efflux of isoprenoid and carotenoid lipids that are prone to oxidative damage, including C55 and menaquinones that undergo cyclic reactions in peptidoglycan synthesis and electron transport.

microbiology↗

bioRxiv2025

Photochemical modification of two fluorene-based molecules yields structurally distinct DNA intercalators with potent anti-MRSA activity

Staphylococcus aureus is a leading cause of skin and soft tissue infections, endocarditis, and bloodstream infections worldwide. The emergence of methicillin-resistant S. aureus (MRSA) and growing resistance to last-resort antibiotics like vancomycin have created an urgent need for new antimicrobials with distinct mechanisms of action. In this study, we characterize DB10, a planar, fluorene-based compound identified in a high-throughput screen for MRSA inhibitors. Upon UVA exposure, DB10 undergoes photoconversion from a red-colored form (DB10-R) to a yellow-colored form (DB10-Y). In comparison with DB10-R, DB10-Y exhibits reduced hydrophobicity, lower cytotoxicity, and modestly improved minimum inhibitory concentrations (MICs) towards a number of Gram-positive bacteria. DB10-Y intercalates into DNA and induces double-stranded breaks, yet resistance emerged only at low levels after prolonged serial passaging. To optimize this scaffold, we screened a panel of fluorene analogs and identified the photoconverting analog DB33, which in its yellow form (DB33-Y) is non-toxic and retained DNA intercalation activity. DB33-Y was effective against intracellular S. aureus in macrophages and epithelial cells and significantly reduced bacterial burden and lesion size in a murine skin infection model. DB10-Y and DB33-Y both also suppressed expression of -toxin at sub-MIC concentrations, indicating an additional anti-virulence effect. Together, these findings highlight the therapeutic potential of fluorene-based DNA intercalators as a new class of antimicrobial and anti-virulence agents against MRSA.

microbiology↗

bioRxiv2025

Genetic entanglement enables ultra-stable biocontainment in the mammalian gut

Imbalances in the mammalian gut are associated with acute and chronic conditions, and using engineered probiotic strains to deliver synthetic constructs to treat them is a promising strategy. However, high rates of mutational escape and genetic instability in vivo limit the effectiveness of biocontainment circuits needed for safe and effective use. Here, we describe STALEMATE (Sequence enTAngLEd Multi lAyered geneTic buffEring), a dual-layered failsafe biocontainment strategy that entangles genetic sequences to create pseudo-essentiality and buffer against mutations. We entangled the colicin E9 immunity protein (Im9) with a thermoregulated meganu-clease (TSM) by overlapping the reading frames. Mutations that disrupted this entanglement simultaneously inactivated both biocontainment layers, leading to cell death by the ColE9 nuclease and the elimination of escape mutants. By lengthening the entangled region, refining ColE9 expression, and optimizing the TSM sequence against IS911 insertion, we achieved escape rates below 10-10 as compared to rates of 10-5 with the non-entangled TSM. The STALEMATE system contained plasmids in E. coli Nissle 1917 for over a week in the mouse gastrointestinal tract with nearly undetectable escape rates upon excretion. STALEMATE offers a modular and simple biocontainment approach to buffer against mutational inactivation in the mammalian gut without a requirement for engineered bacteria or exogenous signaling ligands.

synthetic biology↗

bioRxiv2024

Discovery of broad-spectrum bacterial polyamine detoxification inhibitors as potential antivirulence agents and antibiotic adjuvants

The alarming rise in antimicrobial resistance reinforces an urgent need for new antimicrobial strategies. Host- or bacteria-derived chemicals, such as polyamines, present at infection sites often influence microbial virulence and antibiotic response. Polyamines are cationic small molecules overproduced by the host during infection, modulating immune responses. Polyamine detoxification by several pathogens correlates with increased virulence. We sought to uncover inhibitors of polyamine detoxification through a high-throughput whole-cell screen against the community-acquired methicillin-resistant Staphylococcus aureus (MRSA) USA300, identifying the polyamine analog OES2-0017 and the catechol derivative isoproterenol (OES1-1087), which synergized with polyamines in the low-micromolar range. Chemical genomics and enzymatic assays combined with computational studies revealed that both compounds prevented polyamine detoxification by spermine/spermidine acetyltransferase SSAT (SpeG) and another previously uncharacterized S. aureus SSAT (denoted PaiASa herein). OES2-0017 directly inhibited the enzymes, whereas OES1-1087 reduced intracellular levels of acetyl-CoA required for SSAT activity. OES2-0017 perturbed the bacterial membrane at higher concentrations, likely causing the observed growth-inhibitory effects, whereas OES1-1087 increased membrane fluidity, likely increasing susceptibility to spermine-mediated membrane perturbation. The inhibitors showed broad-spectrum activity against various Gram-positive and Gram-negative bacteria, as well as Candida albicans. OES2-0017 abolished the spermine-mediated protection of MRSA USA300 from antibiotics, including vancomycin, phenocopying the {Delta}speG mutant and suggesting its potential utility as an antibiotic adjuvant. OES2-0017 eradicated SpeG-expressing Salmonella Typhimurium inside murine macrophages, whereas OES1-1087 reduced the S. Typhimurium burden in the liver and spleen in a murine gastrointestinal infection model, demonstrating their potential as antivirulence agents. Neither inhibitor exhibited cytotoxic activity against eukaryotic cells at their respective antimicrobial ranges. Small-scale structure-activity relationship experimental and computational analyses identified OES2-0017 analogs with improved specificity for the bacterial enzyme compared to the human SAT1 and no toxicity. This study provides novel antimicrobial compounds with broad-spectrum activity and a novel mode of action for multidrug-resistant priority pathogens.

microbiology↗

bioRxiv2023

Intern-based thermoregulated meganucleases for biocontainment of genetic material

Limiting the spread of synthetic genetic information outside of the intended use is essential for applications where biocontainment is critical. In particular, biocontainment of engineered probiotics and plasmids that are excreted from the mammalian gastrointestinal tract is needed to prevent escape and acquisition of genetic material that could confer a selective advantage to microbial communities. Here, we built a simple and lightweight biocontainment system that post-translationally activates a site-specific DNA endonuclease to degrade DNA at 18{degrees}C and not at higher temperatures. We constructed an orthogonal set of temperature sensitive-meganucleases, or TSMs, by inserting the yeast VMA1 L212P temperature-sensitive intein into the coding regions of LAGLIDADG homing endonucleases. We showed that the TSMs eliminated plasmids carrying the cognate TSM target site from laboratory strains of Escherichia coli at the permissive 18{degrees}C but not at higher restrictive temperatures. Plasmid elimination is dependent on both TSM endonuclease activity and intein splicing. We demonstrated that TSMs eliminated plasmids from the E. coli Nissle 1917 strain after passage through the mouse gut when fecal resuspensions were incubated at 18{degrees}C but not at 37{degrees}C. Collectively, our data demonstrates the potential of thermoregulated meganucleases as a means of restricting engineered plasmids and probiotics to the mammalian gut.

synthetic biology↗

bioRxiv2022

The Staphylococcus aureus iron-regulated surface determinant A (IsdA) increases SARS CoV-2 replication by modulating JAK-STAT signaling

The emergence and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) and the associated Coronavirus disease (COVID-19) pandemic have affected millions globally. Like other respiratory viruses, a significant complication of COVID-19 infection is secondary bacterial co-infection, which is seen in approximately 25% of severe cases. The most common organism isolated from co-infection is the Gram-positive bacterium Staphylococcus aureus. Here, we developed an in vitro co-infection model where both CoV-2 and S. aureus replication kinetics can be examined. We demonstrate CoV-2 infection does not alter how S. aureus attaches to or grows in host epithelial cells. In contrast, the presence of replicating S. aureus enhances the replication of CoV-2 by 10-15-fold. We identify this pro-viral activity is due to the S. aureus iron-regulated surface determinant A (IsdA) and this effect is mimicked across different SARS CoV-2 permissive cell lines infected with multiple viral variants. Analysis of co-infected cells demonstrated an IsdA dependent modification of host transcription. Using chemical inhibition, we determined S. aureus IsdA modifies host Janus Kinase - Signal Transducer and Activator of Transcription (JAK-STAT) signalling, ultimately leading to increased viral replication. These findings provide key insight into the molecular interactions that occur between host cells, CoV-2 and S. aureus during co-infection. ImportanceBacterial co-infection is a common and significant complication of respiratory viral infection, including in patients with COVID-19, and leads to increased morbidity and mortality. The relationship between virus, bacteria and host is largely unknown, which makes it difficult to design effective treatment strategies. In the present study we created a model of co-infection between SARS CoV-2 and Staphylococcus aureus, the most common species identified in COVID-19 patients with co-infection. We demonstrate that the S. aureus protein IsdA enhances the replication of SARS CoV-2 in vitro by modulating host cell signal transduction pathways. The significance of this finding is in identifying a bacterial component that enhances CoV-2 pathogenesis, which could be a target for the development of co-infection specific therapy in the future. In addition, this protein can be used as a tool to decipher the mechanisms by which CoV-2 manipulates the host cell, providing a better understanding of COVID-19 virulence.

microbiology↗

bioRxiv2022

In vivo growth of Staphylococcus lugdunensis is facilitated by the concerted function of heme and non-heme iron acquisition mechanisms

Acquisition of iron underpins the ability of pathogens to cause disease and Staphylococcus lugdunensis has increasingly been recognized as a pathogen that can cause serious infection. In this study, we sought to address the knowledge gap that exists regarding the iron acquisition mechanisms employed by S. lugdunensis, especially during infection of the mammalian host. Here we show that S. lugdunensis utilizes diverse genome encoded iron acquisition mechanisms to satisfy its need for this nutrient. Indeed, S. lugdunensis can usurp hydroxamate siderophores, and staphyloferrin A and B from S. aureus, using the fhuC ATPase-encoding gene. Acquisition of catechol siderophores and catecholamine stress hormones necessitates the presence of the sst-1 transporter-encoding locus, but not the sst-2 locus. Iron-dependent growth in acidic culture conditions necessitates the feoAB locus. Heme iron is acquired via expression of the iron-regulated surface determinant (isd) locus. During systemic infection of mice we demonstrate that while S. lugdunensis does not cause overt illness, it does colonize and proliferate to high numbers in the kidneys. By combining mutations in the various iron acquisition loci, we further demonstrate that only a strain mutated for all of isd, fhuC, sst-1, and feo, versus combination mutants carrying wild type copies of any one of those loci, was attenuated in its ability to proliferate to high numbers in kidneys. Taken together our data reveal that S. lugdunensis requires a repertoire of both heme and non-heme iron acquisition mechanisms to proliferate during systemic infection of mammals. ImportanceAcquisition of iron underpins the ability of pathogens to cause disease and Staphylococcus lugdunensis has increasingly been recognized as a pathogen that can cause serious infection. In this study, we sought to address the knowledge gap that exists regarding the iron acquisition mechanisms employed by S. lugdunensis, especially during infection of the mammalian host. Owing to an inability to synthesize siderophores, growth of S. lugdunensis is dramatically impaired in the presence of transferrin or serum, yet S. lugdunensis nonetheless uses several other genome-encoded iron acquisition mechanisms, in concert, to proliferate within the mammalian host. Therefore, the development of interventions that target bacterial iron acquisition systems should consider the overlapping function of distinct metal acquisition strategies deployed by bacterial pathogens.

microbiology↗

bioRxiv2021

Superantigens promote Staphylococcus aureus bloodstream infection by eliciting pathogenic interferon-gamma (IFNγ) production that subverts macrophage function

Staphylococcus aureus is a foremost bacterial pathogen responsible for a vast array of human diseases. Staphylococcal superantigens (SAgs) constitute a family of potent exotoxins secreted by S. aureus, and SAg genes are found ubiquitously in human isolates. SAgs bind directly to MHC class II molecules and T cell receptors, driving extensive T cell activation and cytokine release. Although these toxins have been implicated in serious disease including toxic shock syndrome, we aimed to further elucidate the mechanisms by which SAgs contribute to staphylococcal pathogenesis during septic bloodstream infections. As most conventional mouse strains respond poorly to staphylococcal SAgs, we utilized transgenic mice encoding humanized MHC class II molecules (HLA-DR4) as these animals are much more susceptible to SAg activity. Herein, we demonstrate that SAgs contribute to the severity of S. aureus bacteremia by increasing bacterial burden, most notably in the liver. We established that S. aureus bloodstream infection severity is mediated by CD4+ T cells and interferon-gamma (IFN{gamma}) is produced to very high levels during infection in a SAg-dependent manner. Bacterial burden and disease severity were reduced by antibody blocking of IFN{gamma}, phenocopying isogenic SAg deletion mutant strains. Additionally, cytokine analysis demonstrated that the immune system was skewed towards a proinflammatory response that was reduced by IFN{gamma} blocking. Infection kinetics and flow cytometry analyses suggested this was a macrophage driven mechanism, which was confirmed through macrophage depletion experiments. Further validation with human leukocytes indicated that excessive IFN{gamma} allowed S. aureus to replicate at a higher rate within macrophages. Together, this suggests that SAgs promote S. aureus survival by manipulating immune responses that would otherwise be effective at clearing S. aureus. This work implicates SAg toxins as critical targets for preventing persistent or severe S. aureus disease.

microbiology↗

bioRxiv2021

Heme-dependent siderophore utilization promotes iron-restricted growth of the Staphylococcus aureus hemB small colony variant

The ability to acquire iron is essential for Staphylococcus aureus to cause infection. Respiration deficient S. aureus small colony variants (SCVs) frequently cause persistent infections, which necessitates they too acquire iron. How SCVs obtain iron remains unknown and so here we addressed this outstanding question by creating a stable hemB mutant in S. aureus USA300 strain LAC. The mutant, auxotrophic for hemin, was assessed for its ability to grow under iron- restriction and with various iron sources. The hemB SCV utilizes exogenously supplied heme but was attenuated for growth under conditions of iron starvation. RNA-seq analyses showed that both WT S. aureus and the hemB mutant sense and respond to iron starvation, however, growth assays show that the hemB mutant is defective for siderophore-mediated iron acquisition. Indeed, the hemB SCV demonstrates limited utilization of endogenous staphyloferrin B or exogenously provided staphyloferrin A, Desferal, and epinephrine, which enabled the SCV to sustain only minimal growth in iron deplete media. Direct measurement of intracellular ATP in hemB and WT S. aureus revealed that both strains can generate comparable levels of ATP during exponential growth suggesting defects in ATP production cannot account for the inability to efficiently utilize siderophores. Defective siderophore utilization by hemB bacteria was also evident in vivo. Indeed, the administration of Desferal failed to promote hemB bacterial growth in vivo, in contrast to WT, in every organ analyzed except for the murine kidney where growth was enhanced. In support of the hypothesis that S. aureus accesses heme in kidney abscesses, in vitro analyses revealed that increased heme availability enables hemB bacteria to utilize siderophores for growth when iron availability is restricted. Taken together, our data support the conclusion that heme is not only used as an iron source itself, but as a nutrient that promotes utilization of siderophore-iron complexes. Author summaryS. aureus small colony variants (SCVs) represent a difficult to treat subpopulation of bacteria that are associated with chronic recurrent infection and worsened clinical outcome. Indeed, SCVs persist within the host despite appropriate administration of antibiotics. This study yields insight into the mechanisms by which S. aureus SCVs acquire iron which, during infection of a host, is a difficult-to-acquire metal nutrient. Under heme limited conditions, hemB S. aureus is severely impaired for siderophore-dependent growth and, in agreement, murine infection indicates that hemin-deficient SCVs meet their nutritional requirement for iron through utilization of heme in vivo. Importantly, we demonstrate that hemB SCVs rely upon heme as a nutrient to promote siderophore utilization. Therefore, perturbation of heme biosynthesis and/or utilization represents a viable to strategy to mitigate the ability of SCV bacteria to acquire siderophore- bound iron during infection.

microbiology↗

bioRxiv2019

Identification of key determinants of Staphylococcus aureus vaginal colonization

Staphylococcus aureus is an important pathogen responsible for nosocomial and community acquired infections in humans, and methicillin-resistant S. aureus (MRSA) infections have continued to increase despite wide-spread preventative measures. S. aureus can colonize the female vaginal tract and reports have suggested an increase in MRSA infections in pregnant and postpartum women as well as outbreaks in newborn nurseries. Currently, little is known about specific factors that promote MRSA vaginal colonization and subsequent infection. To study S. aureus colonization of the female reproductive tract in a mammalian system, we developed a mouse model of S. aureus vaginal carriage and demonstrated that both hospital-associated and community-associated MRSA isolates can colonize the murine vaginal tract. Immunohistochemical analysis revealed an increase in neutrophils in the vaginal lumen during MRSA colonization. Additionally, we observed that a mutant lacking fibrinogen binding adhesins exhibited decreased persistence within the mouse vagina. To further identify novel factors that promote vaginal colonization, we performed RNA-sequencing to determine the transcriptome of MRSA growing in vivo during vaginal carriage at 5 hours, 1-day, and 3-days post-inoculation. Over 25% of bacterial genes were differentially regulated at all time points during colonization compared to laboratory cultures. The most highly induced genes were those involved in iron acquisition, including the Isd system and siderophore transport systems. Mutants deficient in these pathways did not persist as well during in vivo colonization. These results reveal that fibrinogen binding as well as the capacity to overcome host nutritional limitation are important determinants of MRSA vaginal colonization.\n\nIMPORTANCEStaphylococcus aureus is an opportunistic pathogen able to cause a wide variety of infections in humans. Recent reports have suggested an increasing prevalence of MRSA in pregnant and postpartum women, coinciding with the increased incidence of MRSA infections in the NICU and newborn nurseries. Vertical transmission from mothers to infants at delivery is a likely route of MRSA acquisition by the newborn, however, essentially nothing is known about host and bacterial factors that influence MRSA carriage in the vagina. Here, we established a mouse model of vaginal colonization and observed that multiple MRSA strains can persist in the vaginal tract. Additionally, we determined that MRSA interactions with fibrinogen as well as iron uptake can promote vaginal persistence. This study is the first to identify molecular mechanisms which govern vaginal colonization by MRSA, the critical initial step preceding infection and neonatal transmission.

microbiology↗