Biology subjects

McLean, J. A.

Publications and source records attributed to McLean, J. A..

11 recordsLinked to original sources

bioRxiv2026

Rational engineering of facultative anaerobiosis enables commensal survival in the oxygenated gut

Life originated in the absence of oxygen. Despite its substantial energetic advantages, many modern microbes remain obligate anaerobes, confined to anoxic niches such as the mammalian gut. Why these organisms cannot tolerate oxygen has remained unresolved for more than two centuries. Here, using integrated multi-omics analyses, we identify a network of interlocking vulnerabilities in central metabolism, biosynthetic pathways, and redox homeostasis that together impose an aerobic growth barrier in the obligate anaerobic commensal Bacteroides thetaiotaomicron. Rational repair of these vulnerabilities restores metabolic integrity and progressively enhances oxygen tolerance, yielding engineered strains capable of robust growth at 10% O2 and markedly improved resilience in the oxygenated, inflamed gut. These findings define a molecular basis for obligate anaerobiosis and establish a framework for engineering commensal bacteria to function in oxidative environments, expanding their ecological range and therapeutic potential.

microbiology↗

bioRxiv2025

Dehydration promotes intracellular lipid synthesis and accumulation

Lipids can be considered a water reservoir used to offset dehydration stress as their oxidation by the mitochondria generates water. However, whether dehydration and the ensuing hypertonic stress directly regulate lipid synthesis is unknown. We found that hypertonic stress decreases cellular oxygen consumption, increases intracellular lipid synthesis, and favors glutamine oxidation as a carbon precursor for lipid synthesis via remodeling mitochondrial metabolism. These findings provide a mechanism whereby cellular dehydration leads to intracellular lipid accumulation, functionally linking water availability to lipid storage.

physiology↗

bioRxiv2025

An Anaerobic Pathogen Rewires Host Metabolism to Fuel Oxidative Growth in the Inflamed Gut

To colonize their host and cause disease, enteric pathogens must deploy their virulence factors to establish distinct nutrient niches. How obligate anaerobic pathogens construct nutrient niches in the densely populated large intestine remains poorly understood. Enterotoxigenic Bacteroides fragilis (ETBF) is considered an obligate anaerobic bacterium and has been implicated in inflammation-associated diseases, including colitis and colorectal cancer. Here we show that ETBF uses its virulence factor, Bacteroides fragilis toxin, to reprogram colonic epithelial cell metabolism to colonize the inflamed gut. Bacteroides fragilis toxin activates colonic epithelial signaling and hijacks the host bile acid recycling pathway, inducing a metabolic shift in the epithelium from oxidative phosphorylation to glycolysis. This shift increases local concentrations of lactate and oxygen, nutrients that support an oxidative metabolism in ETBF. These findings reveal an unexpected strategy by which a pathogenic organism, previously considered to be an obligate anaerobic bacterium, generates and exploits an oxidative niche in the inflamed gut.

microbiology↗

bioRxiv2025

Photoaffinity ligand of Cystic Fibrosis corrector VX-445 identifies SCCPDH as an off-target

Cystic fibrosis (CF) pharmacological correctors improve Cystic Fibrosis transmembrane conductance regulator (CFTR) protein trafficking and function. Several side-effects from these correctors and adverse drug interactions have been reported, emphasizing the need to understand off-targets. We synthesized VU439, a functionalized photoaffinity ligand (PAL) of VX-445. Chemoproteomics analysis by mass spectrometry (MS) was used to identify crosslinked proteins in CF bronchial epithelial cells expressing F508del CFTR. We identified saccharopine dehydrogenase-like oxidoreductase (SCCPDH), an uncharacterized putative oxidoreductase, as a VX-445 specific off-target. We then characterized changes in the metabolomic profiles of cells overexpressing SCCPDH to determine the consequence of VX-445 binding to SCCPDH. These data show dysregulation of amino acid metabolism and a potential inhibitory activity of VX-445 on SCCPDH. The identified off-target may explain exacerbation of psychological symptoms observed in the clinic, thus emphasizing the need for further optimization of correctors.

biochemistry↗

bioRxiv2024

Spatiochemical Investigation of Potential Biocontrol Agents Against Phytophthora capsici Infection in Tomato

Biological control agents can offer an eco-friendly and more sustainable alternative to conventional chemical pesticides, providing protection against destructive pathogens, such as Phytophthora capsici, while reducing potential environmental harm associated with synthetic pesticide use in agricultural production systems. This work demonstrates the biocontrol effectiveness of various Bacillus species, including Bacillus vallismortis, Bacillus amyloliquefaciens, Bacillus thuringiensis, and Bacillus subtilis, against the widespread plant pathogen, Phytophthora capsici. Our studies showed that Bacillus thuringiensis and Bacillus subtilis promote plant growth and provide protection against Phytophthora capsici in both in vitro and in vivo greenhouse studies, while Bacillus vallismortis and Bacillus amyloliquefaciens were effective in vitro but not in vivo. Specifically, Bacillus thuringiensis was observed to both hinder the growth of Phytophthora capsici and enhance plant resilience to this oomycete pathogen. To probe the molecular interactions between biocontrol agent and pathogen, a dual culture of Bacillus thuringiensis and Phytophthora capsici was analyzed in situ using a mass spectrometry imaging workflow that implemented desorption electrospray ionization. This imaging approach spatially investigated the complex biochemical interactions that serve as the molecular foundation for the effectiveness of these biological control agents in crop protection, including antagonistic interactions that may be fundamental to their method of action. Herein, we demonstrate the benefits of biological control agent application in tomato cultivation, including enhanced pathogen control and plant growth, and showcase the strengths of desorption electrospray ionization-mass spectrometry imaging when applied to the spatially-resolved molecular characterization of agriculturally relevant microorganisms.

plant biology↗

bioRxiv2023

ATP10A promotes endothelial cell insulin sensitivity and protects against diet-induced dyslipidemia in female mice

Genetic association studies have linked ATP10A and closely related type IV P-type ATPases (P4-ATPases) to insulin resistance and vascular complications, such as atherosclerosis. ATP10A translocates phosphatidylcholine and glucosylceramide across cell membranes, and these lipids or their metabolites play important roles in signal transduction pathways regulating metabolism. However, the influence of ATP10A on lipid metabolism in mice has not been explored. Here, we generated gene-specific Atp10A knockout mice and show that Atp10A-/- mice fed a high-fat diet did not gain excess weight relative to wild-type littermates. However, Atp10A-/-mice displayed female-specific dyslipidemia characterized by elevated plasma triglycerides, free fatty acids and cholesterol, as well as altered VLDL and HDL properties. We also observed increased circulating levels of several sphingolipid species along with reduced levels of eicosanoids and bile acids. The Atp10A-/- mice also displayed hepatic insulin resistance without perturbations to whole-body glucose homeostasis. Thus, ATP10A has a sex-specific role in regulating plasma lipid composition and maintaining hepatic liver insulin sensitivity in mice.

molecular biology↗

bioRxiv2021

Accelerating Strain Engineering using Desorption Electrospray Ionization-Imaging Mass Spectrometry and Untargeted Molecular Analysis of Intact Microbial Colonies.

Progress in the fields of genomic and biologic sciences has yielded microbial bioprocesses for the advanced production of chemicals. While biomanufacturing has the potential to address global demands for renewable fuels and chemicals, engineering microbial cell factories that can compete with synthetic chemical processes remains a challenge. Optimizing strains for enhanced chemical production is no longer limited by reading and writing DNA, rather it is impeded by the lack of high-throughput platforms for characterizing the metabolic phenotypes resulting from specific gene editing events. To address this issue, we have developed a desorption electrospray ionization- imaging mass spectrometry (DESI-IMS) screening assay that is conducive to both multiplexed sampling and untargeted analyses. This technology bridges the gap between genomic and metabolomic timescales by simultaneously characterizing the chemical output of various engineered Escherichia coli strains rapidly and directly under ambient conditions. The developed method was used to phenotype four E. coli strains on the basis of measured metabolomes, which were validated via PCR genotyping. Untargeted DESI-IMS phenotyping suggests multiple strategies for future engineering which include: (i) relative amounts of specific biosynthetic products, (ii) identification of secondary products, and (iii) the metabolome of engineered organisms. In sum, we present a workflow to accelerate strain engineering by providing rapid, untargeted, and multiplexed analyses of microbial metabolic phenotypes.

bioengineering↗

bioRxiv2020

A new microfluidic concept for successful in vitro culture of mouse embryos

Innovative techniques for gene editing have enabled accurate animal models of human diseases to be established. In order for these methods to be successfully adopted in the scientific community, the optimization of procedures used for breeding genetically altered mice is required. Among these, the in vitro fertilization (IVF) procedure is still suboptimal and the culture methods do not guarantee the development of competent embryos. Critical aspects in traditional in vitro embryo culture protocols include the use of mineral oil and the stress induced by repetitive handling of the embryos. A new microfluidic system was designed to allow for efficient in vitro culture of mouse embryos. Harmful fluidic stress and plastic toxicity were excluded by completing the industry gold standard Mouse Embryo Assay. The potential competence of the embryos developed in the device was quantified in terms of blastocyst rate, outgrowth assay, energy substrate metabolism and expression of genes related to implantation potential. Mass spectrometry analyses identified plastic-related compounds released in medium, and confirmed leaching of low molecular weight species into the culture medium that might be associated to un-crosslinked PDMS. Finally, these data show the potential for the system to study preimplantation embryo development and to improve human IVF techniques.

bioengineering↗

bioRxiv2020

MYC regulates ribosome biogenesis and mitochondrial gene expression programs through interaction with Host Cell Factor-1

The oncoprotein transcription factor MYC is a major driver of malignancy and a highly-validated but challenging target for development of anti-cancer therapies. Novel strategies to inhibit MYC may come from understanding the co-factors it uses to drive pro-tumorigenic gene expression programs, providing their role in MYC activity is understood. Here, we interrogate how one MYC co-factor, Host Cell Factor (HCF)-1, contributes to MYC activity in a Burkitt lymphoma setting. We identify genes connected to mitochondrial function and ribosome biogenesis as direct MYC/HCF-1 targets, and demonstrate how modulation of the MYC-HCF-1 interaction influences cell growth, metabolite profiles, global gene expression patterns, and tumor growth in vivo. This work defines HCF-1 as a critical MYC co-factor, places the MYC-HCF-1 interaction in biological context, and highlights HCF-1 as a focal point for development of novel anti-MYC therapies.

cancer biology↗

bioRxiv2019

Disruption of Redox Balance Enhances the Effects of BRAF-inhibition in Melanoma Cells

SummaryMelanomas harboring BRAF mutations can be treated with BRAF inhibitors (BRAFi), but responses are varied and tumor recurrence is inevitable. Here, using an integrative approach of experimentation and mathematical flux balance analyses in BRAF-mutated melanoma cells, we report that elevated antioxidant capacity is linked to BRAFi sensitivity in melanoma cells. High levels of antioxidant metabolites in cells with reduced BRAFi sensitivity confirm this conclusion. By extending our analyses to other melanoma subtypes in TCGA, we predict that elevated redox capacity is a general feature of melanomas, not previously observed. We propose that redox vulnerabilities could be exploited for therapeutic benefits and identify unsuspected combination targets to enhance the effects of BRAFi in any melanoma, regardless of mutational status.

systems biology↗

bioRxiv2019

Graphene nanoflakes for acute manipulation of membrane cholesterol and transmembrane signaling

Cholesterol is one of the most essential lipids in eukaryotic cell membranes. However, acute and selective manipulation of membrane cholesterol remains challenging. Here, we report that graphene nanoflakes (GNFs) insert into the plasma membrane and directly interact with cholesterol, resulting in acute cholesterol enrichment - and thus structural and functional changes. Using two representative cell preparations, we explore the utility of GNFs in modifying cell communication pathways sensitive to membrane cholesterol. In fibroblasts, GNFs enhance ATP-induced intracellular Ca2+-release by allosteric facilitation of P2Y receptors, a subtype of G protein-coupled receptors, in a cholesterol-dependent manner. In neurons, which possess higher membrane cholesterol levels than most cell types, GNFs further increase cholesterol. Consequently, GNFs change membrane fluidity, especially at synaptic boutons, and potentiate neurotransmitter release by accelerating synaptic vesicle turnover. Together, our results provide a molecular explanation for graphenes cellular impacts and demonstrate its potential for membrane-oriented engineering of cell signaling.

cell biology↗