Biology subjects

Brake, J.

Publications and source records attributed to Brake, J..

3 recordsLinked to original sources

bioRxiv2026

A new stress-response pathway in Mycobacterium tuberculosis

Metabolic adaptations are key in the virulence of the pathogen Mycobacterium tuberculosis (Mtb). However, our current understanding of these adaptations is limited to common pathways in central carbon metabolism. Here we apply an untargeted bottom-up approach to discover unknown stress-responsive metabolites and their biosynthetic enzyme. We show that upon exposure to hypoxia, nitric oxide and activated macrophages, Mtb rapidly produces high levels of an unknown metabolite that we identify as 6-{gamma}-amino-butyric acid-trehalose (GABA-trehalose). Formation of millimolar GABA-trehalose levels under these stresses is driven by a rapid rise in GABA, which is also excreted. We demonstrate that GABA-trehalose is produced from GABA and trehalose by the uncharacterized ATP-grasp enzyme Rv1722, involving a carboxylate-hydroxyl ligation that is non-canonical for ATP-grasp enzymes. Phylogenetic analyses demonstrate that the gene rv1722 is present in most slow-growing mycobacteria but absent in most rapid-growing mycobacteria. While the role of GABA-trehalose in Mtb metabolism remains unclear, we postulate that the increased NADH/NAD+ ratio under hypoxia and nitric oxide exposure promotes GABA formation and inhibits its breakdown, leading to GABA accumulation and excretion. Rv1722-driven coupling of GABA and trehalose constitutes an alternative to excretion that conserves carbon and nitrogen. Taken together, our bottom-up approach reveals a new stress-response pathway in Mtb that rapidly produces large quantities of GABA-trehalose. These findings extend our knowledge of the metabolic adaptations that a major human pathogen utilizes in response to immune system-imposed stresses.

biochemistry↗

bioRxiv2025

Hydrogen sulfide increases intracellular oxygen and regulates the HIF response

O2 sensing by hypoxia-inducible factor (HIF) is a principal mechanism by which aerobic organisms adjust cellular energy metabolism and adapt to O2 limitation. In this study, we show that H2S, a product of host and microbial metabolism, profoundly influences the threshold for HIF-dependent hypoxia-sensing by increasing intracellular O2. The dose-dependent destabilization of HIF by H2S is inversely correlated with sulfide quinone oxidoreductase, which oxidizes sulfide in the mitochondrion. Hypoxia sensors provide a quantitative estimate of the magnitude of H2S-induced perturbation. The O2 concentration in cells grown in a 2% O2 atmosphere is sensed as 5 or 15 % O2 in the presence of 25 or 100 ppm H2S, respectively. Sustained exposure to H2S elicits the hallmarks of hyperoxia-associated cytotoxicity, including loss of Fe-S proteins in cellular and murine models. H2S thus emerges as a powerful regulator of O2 sensing and signaling with possible implications for dysregulation in O2 toxicity diseases. Significance StatementThe mitochondrial electron transport chain (ETC) accounts for [~]90% of whole body O2 consumption. However, our understanding of how metabolites modify ETC flux and therefore, intracellular O2 availability, are poor. In this study, we demonstrate that hydrogen sulfide (H2S), which is produced by host and gut microbes alike, increases intracellular O2 by decreasing ETC flux, and destabilizes the principal hypoxia sensor, HIF-1. The upshift in intracellular O2 levels is quantitatively significant, such that 2% O2 is sensed as 5-15% O2 at varying H2S concentrations, with concomitant destabilization of Fe-S proteins, a signature of cellular hyperoxia. Our study identifies H2S as a HIF-1 regulator with important implications for the large class of mitochondrial diseases characterized by dysregulated O2 metabolism.

cell biology↗

bioRxiv2023

Multifunction Fluorescence Open-Source In Vivo/In Vitro Imaging System (openIVIS)

The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study we designed and built a multifunction fluorescent open-source in-vivo/in-vitro imaging system (openIVIS) fluorescent imaging system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the various potential applications of our system, we tested its performance against a diverse set of experiments including laboratory type assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of a couple of weeks. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.

bioengineering↗