Biology subjects

Quan, B.

Publications and source records attributed to Quan, B..

11 recordsLinked to original sources

bioRxiv2026

Unbiased and scalable reduction of diverse bacterial genomes

The genome is a complex, integrated system where the functions and regulatory interactions of its many components remain poorly understood. Genome minimization aims to reduce genomic complexity by removing non-essential elements to reveal the fundamental building blocks of cellular life. However, current minimization strategies are often slow and species-specific due to a reliance on prior information, and limited to producing single, isolated strains, which obscures the diverse ways a genome can adapt to large-scale DNA removal. Here we show the development and application of Stochastic Lineage-based Iterative Minimization (SLIM) a modular, high-throughput platform for unbiased genome reduction across phylogenetically diverse bacteria. We apply SLIM to generate a library of genome-reduced Escherichia coli lineages. We then interrogate the lineages, identifying both universal and lineage-specific transcriptional and translational reprogramming in response to deletions. We demonstrate that these expression dynamics drive environment-dependent fitness, allowing us to pinpoint a single gene deletion in one genome-reduced lineage as the driver of a measurable environmental growth defect. Beyond E. coli, we successfully deploy SLIM in phylogenetically distinct bacterial taxa to rapidly reduce the genomes of Shigella flexneri and Pseudomonas putida, distinct genus and order respectively from E. coli, without species-specific optimization. Our results establish a scalable, generalizable framework for navigating the vast landscape of minimized genomes, providing a powerful new tool for functional discovery and the rational design of synthetic genomic chassis.

synthetic biology↗

bioRxiv2026

ENAH Binding to the Huntingtin Proline-Rich Domain Modulates HTT1a Assembly

The proline-rich domain (PRD) of huntingtin (HTT), located C-terminal to the polyglutamine tract within the exon-1 region, plays a critical role in modulating the aggregation and toxicity of mutant HTT1a. To identify PRD-interacting proteins, we performed mass spectrometry analysis of PRD peptide pulldowns from human neurons. ENAH, a member of the Ena/VASP family of actin regulatory proteins, emerged as the top enriched interactor from neuronal membrane fractions. In neurons, ENAH colocalized with HTT1a species, suggesting a biologically relevant interaction. Because the EVH1 domain of ENAH binds polyproline motifs with high affinity, we examined its interaction with HTT1a using recombinant proteins. EVH1 directly bound HTT1a and unexpectedly formed condensate-like assemblies capable of recruiting HTT1a monomers. Remarkably, EVH1 robustly suppressed HTT1a oligomerization and promoted remodeling of preformed HTT1a fibrils in vitro. These findings demonstrate that ENAH-PRD interactions modulate HTT1a aggregation dynamics and identify EVH1 assembly as a potential proteostatic mechanism regulating mutant HTT1a states. More broadly, this work establishes a framework for investigating how EVH1-containing proteins may influence HTT1a proteostasis and neurotoxicity in Huntington's disease.

neuroscience↗

bioRxiv2026

Glucose selectively drives a rapid oxidative burst and immunometabolic reprogramming in human neutrophils during Mycobacterium tuberculosis infection

Neutrophil functions have been linked to tuberculosis (TB)-associated tissue damage; however, the mechanisms driving immunopathology in the human TB lung remain poorly understood, due partly to the scarcity of human tissue for study. Here, we examine the metabolic and bioenergetic reprogramming of human neutrophils in response to Mycobacterium tuberculosis (Mtb) infection. In human necrotic TB granulomas, levels of NETosis-associated proteins are increased and co-localize with GLUT3, linking nutrient uptake to tissue damage. In vitro, Mtb elicits an immediate, contact-dependent oxidative burst in human neutrophils, and the magnitude of this response is carbon source-dependent. Glucose enables the most robust responses, indicating that glucose metabolism is a key driver of neutrophil-mediated inflammatory damage during TB. Mtb-induced responses are distinct from those induced by PMA, non-tuberculous mycobacteria, or other pathogenic intracellular bacteria, and are mediated through multiple neutrophil surface receptors. Notably, our data show that while the oxidative burst is carbon source-dependent, cytokine production is not. Further, Mtb infection reprograms neutrophil metabolism from glycolysis to the pentose phosphate pathway (PPP), generating NADPH required for the oxidative burst. Inhibiting G6PD, NADPH oxidase, or PAD4 significantly reduces this response, highlighting the PPP as a promising host target for mitigating TB immunopathology.

microbiology↗

bioRxiv2025

Proteome-wide identification of metamorphic protein candidates using mass spectrometry

How protein folds remodel at low temperature remains poorly mapped at the proteome scale. We combine brief, temperature-controlled proteolysis with LC-MS/MS to chart cold-dependent conformational changes in Escherichia coli lysate. Methodological validation with the metamorphic protein Sa1V90T--whose /{beta}-plait and 3 states interchange between 30 {degrees}C and 5 {degrees}C--showed that a high-protease, short-digestion regime detects temperature-dependent exposure at four peptides, whereas the temperature-insensitive variant Sa1V90TV52D is largely unchanged. Applied to lysate, the workflow identifies >750 proteolytic sites across >250 abundant proteins (>10% of the identified proteome) whose local susceptibility shifts as temperature decreases from 35 {degrees}C to 5 {degrees}C, including five Sa1V90T peptides recapitulating purified-protein behavior. A site-level scoring model yields 338 destabilized peptides (177 proteins) and 426 stabilized peptides (138 proteins). Cold stabilization prominently marks translation machinery (>15 ribosomal proteins), while cooling also exposes regions in chaperones and cell-division factors. Sequence analysis links temperature sensitivity to charge-enriched composition, consistent with thermodynamic expectations. These data provide a proteome-wide view of cold-sensitive folding, implicate translation and cytokinetic systems in low-temperature remodeling, and illuminate a new strategy for identifying metamorphic proteins on an unprecedented scale.

biophysics↗

bioRxiv2025

Discovery of Host-Directed Small Molecules with Broad Anti-Leishmanial Efficacy

Leishmaniasis, a neglected tropical disease affecting nearly 10% of the global population, suffers from limited therapeutic options and rising drug resistance. To address this, we developed 343 analogs of AR-12, a compound that has previously illustrated host-directed anti-leishmanial effects. Primary screening using a luminescence-based assay revealed 66 analogs with greater selectivity than the parent compound, AR-12. Sixteen promising candidates, selected for high potency (IC < 1 {micro}M) or high selectivity (>15), underwent secondary screening via Giemsa staining. Four lead compounds (53, 134, 197, and 354) demonstrated therapeutic indices greater than 40. Tertiary assays confirmed their broad in vitro efficacy against both Leishmania donovani and L. mexicana. Notably, 197 exhibited potent host-directed activity and proteomic analysis identified lysozyme as a mechanistic target, implicating it in the host-mediated clearance of intracellular parasites. These findings highlight the dual host- and pathogen-directed mechanisms of these compounds and support their potential as the basis for new therapeutic strategies. Further optimization and clinical exploration of these leads are warranted to meet the urgent need for effective leishmaniasis treatments. AUTHOR SUMMARYLeishmaniasis is a parasitic infectious disease with limited therapeutic options and rising drug resistance. Drugs that act directly against Leishmania can further drive drug resistance. Host-directed therapies work to enable the host responses to enhance pathogen clearance and reduce disease progression. Host-directed therapies both limit the emergence of new drug resistance and combat drug resistant infections. In this work we screened a library of 343 AR-12 analogs for host-directed anti-leishmanial activity. This work identified 4 hit compounds. We then did proteomic analysis to understand the mechanism of action of the primary lead compound, identifying the protein lysozyme as having a role in host-directed activity against Leishmania infection.

biochemistry↗

bioRxiv2025

Determining Multivalent Interactomes of Intrinsically Disordered Proteins in Phase-Separated Condensates in Live Cells

Many intrinsically disordered protein regions (IDRs) can form liquid-liquid phase separation (LLPS) condensates via multivalent interactions, but how the interaction behaviors contribute to specific cellular functions remains unclear due to the unknown composition of the condensates. Here, we report phase-separation-induced interactome detection (PhaseID), a new method that determines the protein components within the LLPS condensates driven by any given IDR in live human cells. Using PhaseID, we demonstrated that transactivation IDRs each have unique multivalent interactomes, thereby executing transactivation through distinct pathways. In-depth analyses of PhaseID-determined IDR interactomes revealed that LLPS tunes the interaction selectivity of IDRs, enabling them to play new roles in specific cellular processes, and different LLPS condensates recruit proteins with distinct physicochemical properties encoded in their sequences.

molecular biology↗

bioRxiv2025

The Environment-Dependent Regulatory Landscape of the E. coli Genome

1All cells respond to changes in both their internal milieu and the environment around them through the regulation of their genes. Despite decades of effort, there remain huge gaps in our knowledge of both the function of many genes (the so-called y-ome) and how they adapt to changing environments via regulation. Here we describe a joint experimental and theoretical dissection of the regulation of a broad array of more than 100 biologically interesting genes in E. coli across 39 diverse environments, enabling us to identify the binding sites and transcription factors that mediate regulatory control. Using a combination of mutagenesis, massively parallel reporter assays, mass spectrometry, and tools from information theory and statistical physics, we go from complete ignorance of a promoters environment-dependent regulatory architecture to a quantitative description of its binding sites, candidate transcription factors that bind them where identifiable, and the conditions under which they act. As proof of principle of the biological insights to be gained from such a study, we chose a combination of genes from the y-ome, toxin-antitoxin pairs, and genes hypothesized to be part of regulatory modules; we discovered a host of new insights into their underlying regulatory landscape and resulting biological function. We highlight discoveries for y-ome genes, including transcription start sites and transcription factor binding sites at base-pair resolution, and their dependence on growth conditions.

molecular biology↗

bioRxiv2025

VDAC isoforms play distinct roles in modulating metabolism and maintaining mitochondrial function

The Voltage Dependent Anion Channel (VDAC) is the most ubiquitous protein in the mitochondrial outer membrane. This channel facilitates the flux of water-soluble metabolites and ions like calcium across the mitochondrial outer membrane. Beyond this canonical role, VDAC has been implicated, through interactions with protein partners, in several cellular processes such as apoptosis, calcium signaling, and lipid metabolism. There are three VDAC isoforms in mammalian cells, VDAC 1, 2, and 3, with varying tissue-specific expression profiles. From a biophysical standpoint, all three isoforms can conduct metabolites and ions with similar efficiency. However, isoform knockouts (KOs) in mice lead to distinct phenotypes, which may be due to differences in VDAC isoform interactions with partner proteins. To understand the functional role of each VDAC isoform within a single cell type, we created functional KOs of each isoform in HeLa cells and performed a comparative study of their metabolic activity and proteomics. We found that each isoform KO alters the proteome differently, with VDAC3 KO dramatically downregulating key members of the electron transport chain (ETC) while shifting the mitochondria into a glutamine-dependent state. Importantly, this unexpected dependence of mitochondrial function on the VDAC3 isoform is not compensated by the more ubiquitously expressed VDAC1 and VDAC2 isoforms. In contrast, VDAC2 KO did not affect respiration but upregulated ETC components and decreased key enzymes in the glutamine metabolic pathway. VDAC1 KO specifically reduced glycolytic activity linked to decreased hexokinase localization to mitochondria. These results reveal non-redundant roles of VDAC isoforms in cancer cell metabolic adaptability.

cell biology↗

bioRxiv2024

The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model

The pathophysiology of Parkinsons disease (PD) involves gene-environment interactions that impair various cellular processes such as autophagy, lysosomal function, or mitochondrial dysfunction. Specifically, mitochondria-associated gene mutations increase PD risk, mitochondrial respiration is altered in the PD brain, and mitochondrial-damaging toxins cause PD-like motor and gastrointestinal symptoms in animal models. The gut microbiome is altered in PD patients and represents an environmental risk, however a relationship between mitochondrial function and the microbiome in PD has not been previously established. Herein, we report that striatal mitochondria are functionally overactive in -synuclein-overexpressing (ASO) mice, a model of PD, and that microbiome depletion restores respiration and mitochondria-associated gene expression patterns to wild-type levels. ASO mice harboring a complex microbiome produce increased reactive oxygen species in the striatum whereas germ-free counterparts express elevated levels of antioxidant proteins that may buffer against oxidative damage. Indeed, antioxidant treatment improves motor performance in ASO mice and, remarkably, blocking oxidant scavenging in germ-free mice induces -synuclein-dependent motor deficits. Thus, the gut microbiome increases mitochondrial respiration and oxidative stress in the brain, which enhances motor symptoms in a mouse model of PD.

physiology↗

bioRxiv2022

Myostatin gene deletion alters gut microbiota stimulating fast-twitch glycolytic muscle growth

The host genome may influence the composition of the intestinal microbiota, and intestinal microbiota performs an important role in muscle growth and development. Here, we showed that Myostatin (MSTN), a key factor for muscle growth, deletion alters muscularis, plica, and intestinal barrier in pigs. Mice transplanted with MSTN-/- pig intestinal flora showed increase in the cross-sectional area of myofibers and fast-twitch glycolytic muscle mass. The microbes responsible for the production of short chain fatty acids (SCFAs) were enriched in both MSTN-/- pigs and recipient mice, and SCFAs levels were elevated in the colon contents. We demonstrated that valeric acid can stimulate type IIb myofiber growth by activation of the Akt/mTOR pathway via GPR43 and improve muscle atrophy induced by dexamethasone. This is the first study to identify the MSTN gene-gut microbiota-SCFA axis and its regulatory role in fast-twitch glycolytic muscle growth.

microbiology↗

bioRxiv2021

Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzdiimidazole ligand's rescue of Parkinson's-associated cell toxicity

The development of phenotypic models of Parkinsons disease (PD) has enabled screening and identification of phenotypically active small molecules that restore complex biological pathways affected by PD toxicity. While these phenotypic screening platforms are powerful, they do not inherently enable direct identification of the cellular targets of promising lead compounds. To overcome this, chemoproteomic platforms like Thermal Proteome Profiling (TPP) and Stability of Proteins from Rates of Oxidation (SPROX) can be implemented to reveal protein targets of biologically active small molecules. Here we utilize both of these chemoproteomic strategies to identify targets of an N-arylbenzdiimidazole compound, NAB2, which was previously identified for its ability to restore viability in cellular models of PD-associated -synuclein toxicity. The combined results from our TPP and SPROX analyses of NAB2 and the proteins in a neuroblastoma-derived SHSY5Y cell lysate reveal a previously unrecognized protein target of NAB2. This newly recognized target, Rab1a, is a small GTPase that acts as a molecular switch to regulate ER-to-Golgi trafficking, a process that is disrupted by -synuclein toxicity and restored by NAB2 treatment. Further validation reveals that NAB2 binds to Rab1a with selectivity for its GDP-bound form and that NAB2 treatment phenocopies Rab1a overexpression in alleviation of -synuclein toxicity. Finally, we conduct a preliminary investigation into the relationship between Rab1a and the E3 ubiquitin ligase, Nedd4, a previously identified NAB2 target. Together, these efforts expand our understanding of the mechanism of NAB2 in the alleviation of -synuclein toxicity and reinforce the utility of chemoproteomic identification of the targets of phenotypically active small molecules that regulate complex biological pathways.

biochemistry↗