Biology subjects

Chang, J. H.

Publications and source records attributed to Chang, J. H..

14 recordsLinked to original sources

bioRxiv2026

Abiotic cues modulate exopolysaccharides to influence type VI secretion system-mediated antagonism

The type VI secretion system (T6SS) enables Gram-negative bacteria to inject toxic effectors into neighboring cells, mediating contact-dependent antagonism and interbacterial competition. How the T6SS-mediated attack responds to environmental cues varies and remains unclear among different bacteria. Here, using Agrobacterium fabrum C58, a soil-borne phytopathogenic bacterium, we investigated the impact of osmolarity, moisture, surface stiffness, and glucose on T6SS-mediated antagonism. We show that these abiotic factors influenced the production of two polysaccharides, cyclic-{beta}-(1,2)-glucan (C{beta}G) and succinoglycan (SG), and modulated the T6SS-killing outcome. Mechanistically, high osmolarity inhibits C{beta}G production, thereby enhancing the expression and secretion of the T6SS. In contrast, SG biosynthesis, in response to moisture, surface stiffness, and glucose, does not impact T6SS expression and function but decreases T6SS-mediated killing efficacy. Electron microscopy revealed that SG creates a physical barrier between bacterial cells. Such physical distancing not only hinders the T6SS attack from Agrobacterium, but also confers protection against other competitors at both intra- and inter-species levels. Our results unravel the complexity of how specific environmental factors modulate the contact-dependent antagonism and highlight a balance between offensive and defensive behaviors. Significance StatementBacteria live in polymicrobial communities where they often need to fight off competitors to survive. One well-characterized weapon is the type VI secretion system (T6SS), a nanomachine mediating contact-dependent antagonism. In this study, we aim to study how the T6SS attack is influenced by environmental cues. We discovered that carbon sources, osmolarity, and surface stiffness modulate the T6SS efficacy through the secretion of sugar chains outside the cell. This sugar secretion increases the physical distance between cells, protecting against T6SS-mediated attack. However, such physical distancing also hinders the efficacy of the T6SS attack originating from Agrobacterium itself. Our results reveal a previously understudied offense-defense tradeoff between EPS production and T6SS-mediated attack. This finding underscores the intricate balance between bacterial offense and defense strategies.

microbiology↗

bioRxiv2025

Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis

The paradigms of legume-rhizobia symbiosis are derived primarily from conserved features of Inverted- Repeat Lacking Clade (IRLC) legumes and closely related species. The Dalbergioids diverged from the IRLC early in legume evolution and possess unique symbiotic features but few genetically tractable models. The small, diploid Dalbergioid Aeschynomene americana (American jointvetch) has promise as a genetic model for Dalbergioid-rhizobia symbiosis, yet only a few studies have examined its symbiotic properties. We examined the symbiont range of A. americana from central Florida and characterized a native A. americana nodule isolate, Bradyrhizobium sp. USDA3516. We find that A. americana forms effective symbioses with B. sp. USDA3516, which is closely related to Thai A. americana symbiont B. sp DOA9, and with symbionts from the Dalbergioids stylo and peanut. Interestingly, several strains that effectively nodulated A. americana exhibited branched bacteroid morphologies, but we found that branching was neither necessary nor sufficient for effective symbiosis. Our study contradicts the prevailing view that bacteroid shape is a major determinant of symbiotic efficiency and presents the A. americana-B. sp. USDA3516 interaction as an optimal model of A. americana symbiosis.

plant biology↗

bioRxiv2025

PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification

Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens and pests. Here, we present PathogenSurveillance, an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is designed with features tailored for biosurveillance and is suitable for in-field or point-of-care diagnostics. PathogenSurveillance is flexible, accommodating short- and long-read datasets and mixed samples of prokaryotes and/or eukaryotes. It automates all steps, including reference identification and retrieval from the NCBI Assembly database, and produces customizable interactive reports with summaries, phylogenetic trees, and minimum spanning networks that enable species and subspecies level identification. It also outputs quality control metrics and carefully names and organizes output files to facilitate downstream analyses. The pipeline runs on any Linux-based system and minimizes the need for advanced computational expertise. Source code is available on GitHub under the open-source MIT license. The pipeline expands the toolkit for real-time biosurveillance, enabling rapid detection and monitoring of pathogens and pests for rapid response to novel variants.

bioinformatics↗

bioRxiv2025

Everything, everywhere, all at once - Surveillance and molecular epidemiology reveal Melissococcus plutonius is endemic among Michigan, US beekeeping operations of all sizes and present in some honey bee colonies year-round

European foulbrood (EFB) is a severe bacterial disease of honey bee brood often leading to significant declines in colony health and honey production. The dearth of data on this disease in the United States (US) complicates response efforts. In this study, we combine surveillance and molecular epidemiology to investigate prevalence, diversity, and transmission dynamics of Melissococcus plutonius, the causative agent of EFB, in US honey bee colonies. Rates of infection and disease were found to be seasonal, with prevalence peaking in June when over half the colonies screened were infected. Whole genome, single nucleotide polymorphism analysis revealed wide genetic diversity even within a single hive. Operations often had multiple genotypes present which varied from year to year, consistent with high rates of transmission and reinfection. Prevalence and whole genome data provided here will be critical in tracking the efficacy of mitigation efforts and underscore the necessity of additional epidemiological investigations.

genomics↗

bioRxiv2025

Novel DNA endonuclease activity of human ERK1 protein

ERK1 is a key kinase in the mitogen-activated protein kinase pathway, which transduces extracellular signals into cellular responses. Following triggering of the pathway, cytosolic ERK1 is phosphorylated, translocates into the nucleus, and activates DNA-bound transcription factors and target genes. This study reports a novel, non-canonical role of human ERK1 as a DNA endonuclease. It catalyzes single-strand DNA breaks in sequence-unspecific yet, topology-sensitive manners. ERK1 catalysis requires magnesium ions and no ATP consumption. Comprehensive biochemical and in silico structural analyses indicate that a Mg2+ pocket, including a residue N171, which is allosterically modulated by the N-terminal domain, is important for DNA substrate binding and catalysis. Fluorescence imaging analysis suggests that ERK1 may interact with cytoplasmic DNAs in molecular condensates and destabilize them. Collectively, this study reveals an unprecedented role of ERK1 in nicking DNA molecules, which highlights the potential to regulate the fate of cytoplasmic DNAs.

molecular biology↗

bioRxiv2024

IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation

Discovering the cell-of-origin harboring the initial driver mutation provides a fundamental basis for understanding tumor evolution and development of new treatments. For isocitrate dehydrogenase (IDH)-mutant gliomas - the most common malignant primary brain tumors in adults under 50 - the cell-of-origin remains poorly understood. Here, using patient brain tissues and genome-edited mice, we identified glial progenitor cells (GPCs), including oligodendrocyte progenitor cells (OPCs), as the glioma-originating cell type harboring the IDH mutation as the initial driver mutation. We conducted comprehensive deep sequencing, including droplet digital PCR and deep panel and amplicon sequencing to 128 tissues from 62 patients (29 IDH-mutant gliomas and 33 IDH-negative controls) comprising tumors, normal cortex or normal subventricular zone (SVZ), and blood. Surprisingly, low-level IDH mutation was found in the normal cortex away from the tumor in 38.5% (10 of 26) of IDH-mutant glioma patients, whereas no IDH mutation was detected in the normal SVZ. Furthermore, by analyzing cell-type-specific mutations, the direction of clonal evolution, the single-cell transcriptome from patient brains and novel mouse model of IDH-mutant glioma arising from mutation-carrying OPCs, we determined that GPCs, including OPCs, harboring the initial driver mutation are responsible for the development and evolution of IDH-mutant gliomas. In summary, our results demonstrate that GPCs containing the IDH mutation are the cells-of-origin harboring the initial driver mutation in IDH-mutant gliomas.

cancer biology↗

bioRxiv2023

Genetically refactored Agrobacterium-mediated transformation

Members of Agrobacterium are costly plant pathogens while also essential tools for plant transformation. Though Agrobacterium-mediated transformation (AMT) has been heavily studied, its polygenic nature and its complex transcriptional regulation make identifying the genetic basis of transformational efficiency difficult through traditional genetic and bioinformatic approaches. Here we use a bottom-up synthetic approach to systematically refactor the tumor-inducing plasmid, wherein the majority of AMT machine components are encoded, into a minimal set of genes capable of plant and fungal transformation that is both controllable and orthogonal to its environment. We demonstrate that engineered vectors can be transferred to new heterologous bacteria, enabling them to transform plants. Our reductionist approach demonstrates how bottom-up engineering can be used to dissect and elucidate the genetic underpinnings of complex biological traits, and may lead to the development of strains of bacteria more capable of transforming recalcitrant plant species of societal importance.

microbiology↗

bioRxiv2022

ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes

The transcription of stress-inducible genes requires synchronized and robust activation, which is critical for organismal survival and homeostasis. The function of the mitogen-activated protein kinase (MAPK) signaling pathway is required for the activation of immediate early genes (IEGs), including EGR1 and FOS, for cell growth and proliferation1-3. In addition, recent studies have identified topoisomerase II (TOP2) as one of the important regulators of the transcriptional activation of IEGs4-6. However, the mechanism underlying transcriptional regulation involving TOP2 in IEG activation has remained unknown. Here, we demonstrate that ERK2, but not ERK1, is important for IEG transcriptional activation and report a critical ELK1 binding sequence for ERK2 function at the EGR1 gene. Our data indicate that both ERK1 and ERK2 extensively phosphorylate the C-terminal domain of TOP2B at mutual and distinctive residues. Although both ERK1 and ERK2 enhance the catalytic rate of TOP2B required to relax positive DNA supercoiling, ERK1 can relax the DNA by itself and produces a semi-relaxed DNA, which is apparently resistant to TOP2B catalysis. Inhibition of ERK2 kinase activity or ERK2 knock-down interferes with transcription and deregulates TOP2B in IEGs. Furthermore, we obtained the first cryo-EM structure of the human cell-purified TOP2B and etoposide together with the EGR1 transcriptional start site (50 nt; -30 to +20) that has the strongest affinity to TOP2B within -423 to +332. The structure elucidated in our studies showed TOP2B-mediated breakage and dramatic bending of the double-stranded DNA, comparable to previously reported structures of TOP2. Our cell-based analyses showed transcriptional activation by etoposide and transcriptional inhibition by ICRF193 at EGR1 and FOS, suggesting that TOP2B-mediated DNA break to favor transcriptional activation. Taken together, this study suggests that activated ERK2 phosphorylates TOP2B to regulate TOP2-DNA interactions and favor transcriptional activation in IEGs. We propose that TOP2B association, catalysis, and dissociation on its substrate DNA are important processes for regulating transcription and that ERK2-mediated TOP2B phosphorylation may be key for the catalysis and dissociation steps.

molecular biology↗

bioRxiv2021

Species boundaries in the Agrobacterium tumefaciens complex and multi-level modular evolution of their antibacterial type VI secretion system and tumor-inducing plasmids

BackgroundMany bacterial taxa are species complexes and uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized Agrobacterium tumefaciens, a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes. ResultsWe utilized 35 genome assemblies to achieve a comprehensive and balanced sampling of A. tumefaciens. Our confident inference of gene content and core-genome phylogeny supported a quantitative guideline for delineating 12 species and allowed for robust investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins. ConclusionsWe demonstrated that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. Our strategies for multi-level investigations at scales that range from whole-genomes to intragenic domains and phylogenetic depths of between- and within-species are applicable to other bacteria. Finally, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.

genomics↗

bioRxiv2021

Dual adhesive unipolar polysaccharides synthesized by overlapping biosynthetic pathways in Agrobacterium tumefaciens

Agrobacterium tumefaciens, is a member of the Alphaproteobacteria that pathogenizes plants, and associates with biotic and abiotic surfaces via a single cellular pole. A. tumefaciens produces the unipolar polysaccharide (UPP) at the site of surface contact. UPP production is normally surface-contact inducible, but elevated levels of the second messenger cyclic diguanylate monophosphate (cdGMP) bypass this requirement. Multiple lines of evidence suggest that the UPP has a central polysaccharide component. Using an A. tumefaciens derivative with elevated cdGMP and mutationally disabled for other dispensable polysaccharides, a series of related genetic screens have identified a large number of genes involved in UPP biosynthesis, most of which are Wzx-Wzy-type polysaccharide biosynthetic components. Extensive analyses of UPP production in these mutants have revealed that the UPP is comprised of two genetically, chemically and spatially discrete forms of polysaccharide, and that each requires a specific Wzy-type polymerase. Other important biosynthetic, processing and regulatory functions for UPP production are also revealed, some of which are common to both polysaccharides, and a subset of which are specific to each species. Many of the UPP genes identified are conserved among diverse rhizobia, whereas others are more lineage specific. Plain language summaryBacteria attach to a wide variety of surfaces including host tissues, via externalized structures described as adhesins. We define a large set of genes involved in synthesis of a complex unipolar adhesin comprised of two distinct polysaccharides, that is required for surface attachment by the plant-associated pathogen Agrobacterium tumefaciens.

microbiology↗

bioRxiv2021

Visualizing reactive astrogliosis extends survival in glioblastoma patients

Glioblastoma multiforme (GBM) is a devastating brain tumor with dismal prognosis of only 15-month survival regardless of surgical resection. Here, we report an advanced neuroimaging technique combining 11C-acetate PET and MRI (AcePET), visualizing the boundary beyond the MRI-defined tumor. Targeted biopsy of the regions with increased 11C-acetate uptake revealed the presence of reactive astrocytes with enhanced acetate-transporter MCT1, along with cancer stem cells. Reactive astrogliosis and MCT1-dependent 11C-acetate-uptake were recapitulated in U87MG-orthotopic models. Mechanistically, glycolytic tumor cells release excessive acetate causing reactive astrogliosis, leading to the release of aberrant astrocytic GABA and H2O2, which further down-regulate the neuronal glucose uptake through GLUT3. Clincally, AcePET-guided surgery allows complete tumor resection of infiltrating cancer stem cells and extends the overall survival of patients by 5.25 months compared to conventional MRI-guided surgery. We established a new concept of the metabolic interactions between GBM cells and neighboring neurons through reactive astrocytes and developed AcePET-guided surgery to fight against GBM.

cancer biology↗

bioRxiv2021

Mutational impact and signature of ionizing radiation

Whole-genome sequencing (WGS) of human tumors and normal cells exposed to various carcinogens has revealed distinct mutational patterns that provide deep insights into the DNA damage and repair processes. Although ionizing radiation (IR) is conventionally known as a strong carcinogen, its genome-wide mutational impacts have not been comprehensively investigated at the single-nucleotide level. Here, we explored the mutational landscape of normal single-cells after exposure to the various levels of IR. On average, 1 Gy of IR exposure generated [~]16 mutational events with a spectrum consisting of predominantly small nucleotide deletions and a few characteristic structural variations. In [~]30% of the post-irradiated cells, complex genomic rearrangements, such as chromoplexy, chromothripsis, and breakage-fusion-bridge cycles, were resulted, indicating the stochastic and chaotic nature of DNA repair in the presence of the massive number of concurrent DNA double-strand breaks. These mutational signatures were confirmed in the genomes of 22 IR-induced secondary malignancies. With high-resolution genomic snapshots of irradiated cells, our findings provide deep insights into how IR-induced DNA damage and subsequent repair processes operate in mammalian cells.

genomics↗

bioRxiv2020

Small molecule resensitizes Salmonella to itaconate and decreases bacterial proliferation in macrophages

Antimicrobial resistance is a global health crisis offering little reprieve. The situation urgently calls for new drug targets and therapies for infections. We have previously suggested a different approach to treat infections, termed bacterio-modulation, in which a compound modulates the bacterial response to the host immune defense. Herein we show that monocytes infected with Salmonella enterica spp. Typhimurium can be cured using non-antimicrobial compounds that resensitize the bacterium to itaconate, a macrophage-derived antimicrobial metabolite. We propose that this represents a novel strategy to treat infections.

microbiology↗

bioRxiv2019

Re-evaluation of a Tn5::gacA mutant of Pseudomonas syringae pv. tomato DC3000 uncovers roles for uvrC and anmK in promoting virulence

Pseudomonas syringae is a taxon of plant pathogenic bacteria that can colonize and proliferate within the interior space of leaf tissue. This process requires P. syringae to rapidly upregulate the production of virulence factors including a type III secretion system (T3SS) that suppress host defenses. GacS/A is a two-component system that regulates virulence of many plant and animal pathogenic bacteria including P. syringae. We recently investigated the virulence defect of strain AC811, a Tn5::gacA mutant of P. syringae pv. tomato DC3000 that is less virulent on Arabidopsis. We discovered that decreased virulence of AC811 is not caused by loss of GacA function. Here, we report the molecular basis of the virulence defect of AC811. We show that AC811 possesses a nonsense mutation in anmK, a gene predicted to encode a 1,6-anhydromuramic acid kinase involved in cell wall recycling. Expression of a wild-type allele of anmK partially increased growth of AC811 in Arabidopsis leaves. In addition to the defective anmK allele, we also show that the Tn5 insertion in gacA exerts a polar effect on uvrC, a downstream gene encoding a regulator of DNA damage repair. Expression of the wild-type anmK allele together with increased expression of uvrC fully restored the virulence of AC811 during infection of Arabidopsis. These results demonstrate that defects in anmK and uvrC are together sufficient to account for the decreased virulence of AC811, and suggest caution is warranted in assigning phenotypes to GacA function based on insertional mutagenesis of the gacA-uvrC locus.

microbiology↗