Biology subjects

Zhong, G.

Publications and source records attributed to Zhong, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Multicellularity and virulence in the budding yeast, Saccharomyces cerevisiae

In the real world, microbes must cope with environmental fluctuations, compete for scarce resources, and avoid predation. One adaptation to survive this tangled web is the formation of multicellular aggregates, such as biofilms, which are known to be associated with pathogenicity. Despite the importance of the yeast Saccharomyces cerevisiae to biomedical research, little is known about the natural variation in its multicellular, biofilm-related traits. We investigated five multicellular phenotypes in a diverse, worldwide panel of ~1000 isolates. We found that all traits varied significantly and ~2/3 of the isolates expressed at least one multicellular trait. Both recent ecology and evolutionary history explained some of this variation, with clinical isolates exhibiting increased levels of three biofilm-related traits. When tested against wax moth larvae, hyper-multicellular isolates tended to be more virulent than non-multicellular isolates. Genome-wide association analysis on each trait suggested a genetic architecture of many small effect loci, compatible with polygenic adaptation. Only four genes, SLN1, ECM5, MLP2, and ECM9, were shared among the traits; deletion of MLP2 and ECM9 verified their association with multicellularity. Our results show that this yeast expresses far more multicellularity than previously appreciated and suggest that the aggregative phenotypes are likely evolving independently.

evolutionary biology↗

bioRxiv2026

A Refined Developmental Transcriptomic Landscape Reveals Four Coordinated Programs in Chlamydia trachomatis

The developmental cycle of Chlamydia trachomatis requires coordinated transitions between infectious elementary bodies (EBs) and replicative reticulate bodies (RBs), yet the temporal organization of the underlying transcriptional programs remains incompletely resolved. We performed high-coverage RNA sequencing from 0 to 32 h post-infection (hpi), with closely spaced early sampling, and used unsupervised clustering of temporal expression profiles to identify four coordinated programs: immediate-early host adaptation and developmental program, RB formation and maintenance, RB proliferation and secondary differentiation, and EB formation and invasion. The immediate-early program peaked at 1 hpi and contained a strong representation of inclusion-membrane and intracellular-trafficking genes, together with the developmental regulator gene euo. The RB formation and maintenance program peaked at approximately 3 hpi and sustained expression throughout much of the cycle, encompassing genes that support transcription, translation, and core metabolism. The RB proliferation and secondary differentiation program combined DNA replication and cell-division genes with alternative sigma factors, partner-switching components, and type III secretion apparatus genes, consistent with developmental preparation during proliferation. The EB formation and invasion program contained genes associated with structural maturation, host-cell interaction, and infectious competence. These findings distinguish transient host-adaptation expression from sustained early biosynthetic expression, separate RB establishment from population expansion, and differentiate regulatory preparation for the RB-to-EB transition from later EB maturation. Together, the four programs define partially overlapping transcriptional priorities that provide a framework for investigating how gene expression coordinates chlamydial growth, differentiation, and preparation for the next infection cycle.

microbiology↗

bioRxiv2026

Regulation of Chlamydia trachomatis infection in the female genital tract by type I and type II interferons

Following an intravaginal inoculation with Chlamydia trachomatis, mice deficient in type I interferon receptor IFNR1 (IFNR1-/-) significantly increased the yield of live chlamydiae on days 3 & 5 but reduced it to the level of wild-type mice by day 7, while mice deficient in type II interferon receptor IFN{gamma}R1 (IFN{gamma}R1-/-) significantly increased the chlamydial yield by day 5 and the increase persisted throughout the remainder of the infection course. These observations reveal a temporal division of labor between type I & II interferons in regulating C. trachomatis infection in the female genital tract. Interestingly, mice deficient in both IFNR1 & IFN{gamma}R1 exhibited higher mortality and shed more chlamydial organisms than IFN{gamma}R1-/- mice by week 6, suggesting that IFNR1 remains critical for inhibiting C. trachomatis at late stages. An anti-IFNR1 antibody blockade significantly increased chlamydial yields in IFN{gamma}R1-/- mice, suggesting that the anti-chlamydial activities of type I & II interferon systems are both distinct and overlapping throughout the infection course. Furthermore, the anti-chlamydial activity of type I interferon signaling is localized to the lower vagina, while that of type II interferon signaling is localized to the upper vagina. Thus, we have demonstrated that type I & II interferons function complementarily and synergistically in time and space to control C. trachomatis infection, laying the foundation for further elucidating the mechanisms of IFN regulation of chlamydial infection and for developing interventional and preventive strategies against C. trachomatis in the female genital tract. ImportanceLack of information on the precise roles of type I and type II interferons during chlamydial infection has hindered the development of interferon-based strategies to prevent chlamydial infection and pathogenicity. The current study has revealed a temporal division of labor between type I & type II interferons in regulating chlamydial infection in the female genital tract, with type I acting earlier than type II during the innate phase. Nevertheless, type I remains critical for cooperating with type II to suppress chlamydia 6 weeks after infection. Finally, type I interferons seem to mainly target chlamydial infection in the lower vagina, while type II interferons target the infection in the upper vagina. These new findings on the distinct and overlapping roles of type I and type II interferons in regulating chlamydial infection may guide the development of interferon-based precision strategies to reduce chlamydial infection and pathogenicity in the female genital tract.

immunology↗

bioRxiv2026

FOXA1 preserves cell polarity and restrains lysosome biogenesis in non-small cell lung adenocarcinoma

BackgroundThis study investigates the role of the pioneer transcription factor FOXA1 as a master gene in sustaining epithelial cell polarization in early-stage lung adenocarcinoma. The partial loss of FOXA1 is explored to determine if it will affect plasticity and progression of lung adenocarcinoma. The study also addresses the transcriptional circuitry that links polarity defects to lysosome homeostasis. MethodsA multiomics approach was used to define the status of the chromatin in epithelial and mesenchymal states of A549 adenocarcinoma cells obtained with a newly synthetized TGF-{beta} receptor inhibitor or TGF-{beta} respectively. The study leveraged ATAC-seq, RNA sequencing, Cut&Tag sequencing of FOXA1 and histone marks profiling. The functional impact of FOXA1 was examined by partial silencing in vitro and by heterozygous FOXA1 deletion in a KrasG12D mouse model. Three-dimensional organoid culture, high-resolution electron microscopy, spatial transcriptomics and multiplex immunohistochemistry assessed carcinoma cell polarity, proliferation, the tumor microenvironment and organelle content. Group differences were evaluated with two-tailed t tests or one-way analysis of variance. ResultsFOXA1 binding and expression were highest in cells harboring an epithelial phenotype. In mouse KrasG12D LUAD tumors FOXA1 marked polarized, CDH1-positive cells; heterozygous loss diminished CDH1, disrupted apical-basal architecture, lowered organoid-forming efficiency and remodeled the immune microenvironment. Spatial transcriptomics and ultrastructural analyses showed that FOXA1-deficient carcinoma cells accumulated lysosomes, down-regulated vesicle fusion genes of the SNARE family and activated the lysosomal CLEAR gene network. FOXA1 occupied enhancers of lysosome-associated genes and competed with the transcription factor TFE3, thereby suppressing transcription of cathepsin B and cathepsin C and restricting lysosome biogenesis. ConclusionsFOXA1 is a central regulator that preserves epithelial cell polarity and limits lysosome formation in lung adenocarcinoma. Targeting the FOXA1-TFE3-lysosome axis may affect tumor plasticity and provide new therapeutic opportunities.

cancer biology↗

bioRxiv2026

Mining functional genes and characterizing cellular transcriptomic profiles in the single-cell atlas of adult Spodoptera litura ovary

Understanding the reproductive biology of non-model organisms remains challenging due to the limited availability of high-resolution molecular resources. Here, we present a comprehensive single-cell transcriptomic atlas of the adult ovary of Spodoptera litura (S. litura), a highly polyphagous agricultural pest with a polytrophic meroistuc ovary. By integrating single-cell RNA sequencing with cross-species comparison to Drosophila melanogaster (D. melanogaster), we define major germline and somatic cell populations and delineate conserved and species-specific features of ovarian cell composition. To enhance the interpretability and reuse of this dataset, we combine transcriptomic profiling with in situ hybridization to validate cluster-specific molecular markers across ovarian cell types. We further apply RNA interference (RNAi) to assess the contributions of germline-enriched genes (Hsc70-4, Wech, Polo, Path) to ovarian development and fecundity. Trajectory inference, together with SCENIC and CellChat analyses, provides a system-level view of transcriptional regulatory programs and predicted intercellular communication pathways during oogenesis in S. litura. Collectively, this work establishes a valuable resource for studying lepidopteran insect oogenesis, offering a comparative framework for reproductive biology in non-model insects and highlighting potential targets for RNAi-based pest control strategies.

developmental biology↗

bioRxiv2026

In vivo-directed evolution identifies AAV-WM04 as a next-generation vector for potent and durable hearing restoration in DFNB9

Efficient and cell-specific gene delivery to cochlear inner hair cells (IHCs) remains a major challenge for inner ear gene therapy. Here, we identify and characterize a novel AAV2-derived capsid, AAV-WM04, that enables highly efficient and selective IHC transduction at low doses. Using an in vivo-directed evolution strategy, we generated a randomized AAV2 capsid library with 9-amino acid insertions and performed iterative selection in the adult mouse cochlea. Next-generation sequencing revealed enrichment of several variants, among which AAV-WM04 exhibited superior packaging efficiency and pronounced IHC tropism. AAV-WM04 achieved near-complete IHC transduction throughout the cochlear axis in adult mice, outperforming clinically relevant vectors with minimal off-target expression and no detectable ototoxicity. Robust and exclusive IHC transduction was further validated in non-human primates following round window membrane delivery, underscoring translational potential. Therapeutically, AAV-WM04 enabled efficient dual-AAV trans-splicing delivery of the large OTOF gene, resulting in uniform full-length otoferlin expression in IHCs. In a humanized Otof Q829X/Q829X mouse model, AAV-WM04 restored auditory function across a broad frequency range at relatively low doses and achieved durable hearing recovery. Collectively, these findings establish AAV-WM04 as a next-generation IHC-targeted vector with high efficiency, safety, and cross-species applicability for precision gene therapy of hereditary hearing loss.

genetics↗

bioRxiv2026

Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors

Cys2-His2 -zinc-finger proteins (C2H2-ZFPs) form the largest class of human transcription factors, yet their potential role (s) in higher-order genome organization has remained largely poorly defined. To date, only a small number of family members, e.g., CTCF and YY1, have been shown to function in chromatin organization. Here, we examined the global relationship between C2H2-ZFPs and long-range chromatin interactions (LRIs). By integrating ChIP-seq datasets for 216 C2H2-ZFPs and genome-wide maps of chromatin looping, we observe that more than 40% of the human C2H2-ZFPs are significantly enriched at LRI anchors. We found that depletion of a subset of such C2H2-ZFPs is associated with altered expression of genes linked by the LRIs they occupy. To investigate whether protein-protein interactions (PPIs) contribute to this pattern, we generated a large-scale interactome using affinity purification followed by mass spectrometry experiments, encompassing 345 C2H2-ZFPs, and LUMIER binary interaction assays for 204 C2H2-ZFPs. We identified 1,732 binary interactions, suggesting extensive connectivity among the C2H2-ZFP family members. Integrative analysis of PPI, ChIP-seq, and chromatin interaction datasets revealed that interacting C2H2-ZFP pairs are significantly co-enriched at LRIs and frequently localize to either the same or opposing loop anchors. Finally, by correlating ChIP-seq with cancer mutational datasets, we observe that DNA-binding sites of [~]35% of LRI-associated C2H2-ZFPs overlap somatic mutations in cancer genomes. Together, our results reveal a widespread network of C2H2-ZFP interactions associated with chromatin loop anchors, providing an important resource for elucidating mechanisms regulating chromatin organization.

genomics↗

bioRxiv2026

ZNF121 recruits YTHDF2 to modulate mRNA stability

N6-methyladenosine (m6A) is the most abundant internal modification in mRNA and has been shown to regulate gene expression through the binding of specific reader proteins, such as YTHDF2, which promotes mRNA decay. Previous studies indicate that YTHDF2 has relatively weak intrinsic RNA-binding affinity, suggesting that additional factors may facilitate its association with target transcripts. Here, we show that the C2H2-Zinc Finger protein, ZNF121, binds mRNA in cells and physically interacts with YTHDF2 in the cytoplasm. We demonstrate that approximately 80% of ZNF121-bound mRNAs are also YTHDF2 targets, and that their binding sites highly correlate with each other. Loss of ZNF121 impairs YTHDF2 binding to shared targets and increases their stability, independent of the presence of m6A modifications. Moreover, co-regulated transcripts are enriched for cell-cycle-related pathways, and ZNF121 depletion leads to elevated expression of the oncogene MDM2, implicating ZNF121 in growth control and the DNA damage response. Our findings identify ZNF121 as a cofactor that enhances YTHDF2-mediated mRNA regulation and reveal a previously unknown layer of control in mRNA decay.

molecular biology↗

bioRxiv2026

Chlamydial Histones Control Developmental Fitness in the Next Infection Cycle

The unique chlamydial developmental cycle comprises three stages: primary differentiation of infectious elementary bodies (EBs) into reticulate bodies (RBs), RB replication, and secondary differentiation into progeny EBs. Extensive chromosome remodeling during RB-to-EB differentiation is thought to be mediated by the histones HctA and HctB. Here, we used an inducible CRISPR interference system to repress hctA, hctB, or both genes during development in Chlamydia trachomatis. Surprisingly, repression of either histone gene alone or in combination caused only modest reductions in EB yield and did not prevent nucleoid condensation during the parental developmental cycle. In contrast, when progeny EBs generated under histone-repressing conditions were used to initiate secondary infections in the absence of inducer, histone deficiency during EB maturation profoundly impaired fitness in the next infection cycle. Secondary cultures initiated with HctA-deficient EBs exhibited a delayed onset of genome replication, consistent with inefficient primary EB-to-RB differentiation, whereas combined repression of hctA and hctB caused both delayed genome replication and persistently reduced genome accumulation, indicative of defects in RB formation and subsequent growth. Repression of hctB alone did not measurably affect genome replication in secondary cultures. Together, these findings reveal a transgenerational role for chlamydial histones and establish chromosome organization during EB maturation as a key determinant of developmental fitness across infection cycles. IMPORTANCEChlamydial histones HctA and HctB are unusual among bacterial chromatin-binding proteins in that they share sequence homology with mammalian histones and are developmentally regulated during the formation of infectious particles. Here, we show that reduced expression of HctA and HctB has only modest effects on genome condensation and EB production, consistent with partial functional redundancy between the two histones and suggesting that additional chromatin factors contribute to EB chromosome compaction. In contrast, deficiency of HctA and HctB during EB maturation has profound consequences in the next infection cycle, impairing primary EB-to-RB differentiation and subsequent RB growth. These findings reveal a previously unrecognized transgenerational role for chlamydial histones and establish chromosome organization during EB maturation as a key determinant of developmental fitness across infection cycles.

microbiology↗

bioRxiv2026

Identification of collaborative cross mouse strains susceptible to chlamydial induction of hydrosalpinx

Sexually transmitted infection with Chlamydia trachomatis can cause pathology, such as hydrosalpinx, in the upper genital tract, leading to infertility. To investigate how genetic variation affects chlamydial pathogenicity, we screened five strains of Collaborative Cross (CC) mice for susceptibility to intravaginal infection and hydrosalpinx induction by C. muridarum, a mouse-adapted chlamydial species used extensively to reveal chlamydial pathogenic mechanisms. In terms of susceptibility to genital chlamydial infection, the five CC strains fell into two categories: CC011 and CC012 were resistant, while CC037, CC042 & CC080 were susceptible. The resistant strains shed significant levels of live organisms from the genital tract for only [~]2 weeks, whereas the susceptible strains shed for [~]4 weeks. However, the resistant CC012 mice developed the highest level of hydrosalpinx, while the susceptible CC042 mice were fully resistant to hydrosalpinx induction. None of the CC mice developed spontaneous hydrosalpinx in the absence of chlamydial infection. The above results, validated macroscopically and microscopically, indicate no correlation between pathology and genital infection, as observed in other inbred mice. Nevertheless, among the two infection-resistant strains, CC012 developed more severe hydrosalpinx than CC011, and hydrosalpinx was positively correlated with live organism shedding from rectal swabs but not from vaginal swabs, supporting a potential role of gastrointestinal chlamydia in chlamydial genital pathogenicity. The above results lay a foundation for using CC mice to further map the genetic determinants that regulate host susceptibility to chlamydial infection and pathogenicity in the female genital tract.

microbiology↗

bioRxiv2026

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

The basal ganglia play essential roles in motor control, emotion, learning and reward processing. Their dysfunction contributes to many neurological and psychiatric disorders. However, the gene regulatory programs defining basal ganglia cell-type identity and function remain poorly understood, limiting interpretation of disease-associated non-coding variants. Here, we present the first single-cell multiome atlas of histone modifications and transcriptomes across eight basal ganglia regions from neurotypical adult human donors. Joint profiling reveals cell-type-specific deployment of active and repressive cis-regulatory elements and gene regulatory networks, and suggests a combinatorial homeobox transcription factor code underlying cell identity. Integration with matched spatial transcriptomic MERFISH data uncovers regional heterogeneity of epigenomic landscapes. Comparative analysis between human and mouse medium spiny neurons uncovers conservation of core gene regulatory features. This atlas interprets non-coding risk variants of neuropsychiatric disorders and supports the development of a deep learning model to predict gene regulation and functional effects of disease-associated variants. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes and three histone modifications across eight human basal ganglia regions characterizes active and repressive chromatin states at cell-type resolution. C_LIO_LICell-type-specific gene regulatory programs decode combinatorial homeobox TF grammar governing the identity and diversification of basal ganglia neurons. C_LIO_LIIntergrative analyses link noncoding neuropsychiatric risk variants to specific cell types, regulatory elements, and candidate target genes. C_LIO_LIA sequence-to-function deep-learning model predicts gene regulation from DNA sequence and prioritizes functional disease-associated variants. C_LI

genomics↗

bioRxiv2026

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

Directly measuring chromatin states alongside transcription is essential for understanding how cell-type-specific regulatory programs are established and maintained in the adult human brain. We present a large-scale single-cell multimodal atlas generated by jointly profiling transcriptome with active (H3K27ac) and repressive (H3K27me3) histone modifications across 18 brain regions. We profile >750,000 nuclei spanning 160 cell types and integrate these data with chromatin accessibility, DNA methylation, 3D genome architecture, and spatial transcriptome. This framework annotates >500,000 regulatory elements and resolves cell-type-specific chromatin states. We link enhancers to target genes, infer gene regulatory networks, and classify chromatin interactions, revealing neuron-enriched long-range Polycomb repression of developmental genes. Integrating these maps with GWAS data and sequence-based model prioritizes noncoding variants, effector genes, and vulnerable cell types for neuropsychiatric disorders. Finally, cross-species comparisons show conserved activation but more divergent repression. Together, this study provides a functional reference for interpreting noncoding variants, epigenetic memory, and brain organization. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes with active or repressive histone modification in >750,000 nuclei across adult human brain. C_LIO_LIChromatin state annotation of >500,000 candidate cis-regulatory elements distinguishes active enhancers from accessible and Polycomb-repressed regions. C_LIO_LICell-type-resolved regulatory networks and sequence-based deep learning model prioritize functional neuropsychiatric risk variants. C_LIO_LISpatial epigenomic imputation reveals laminar layer-specific Polycomb repression programs. C_LIO_LIIntegration with 3D genome architecture reveals neuron-specific super long-range chromatin loops silencing early developmental genes. C_LIO_LIEvolutionary analysis uncovers conserved active regulatory grammar but divergent repressive landscape. C_LI

genomics↗

bioRxiv2025

Comparative Transcriptomics Reveals Genes Commonly Induced by Distinct Stressors in Chlamydia

Chlamydia trachomatis is a leading cause of urogenital infections that can result in serious long-term complications. This obligate intracellular bacterium undergoes a biphasic developmental cycle alternating between the infectious elementary body and the replicative reticulate body and can enter a persistent state in response to adverse environmental conditions. Although transcriptomic reprogramming is central to chlamydial stress adaptation and persistence, how responses differ across biologically distinct stressors remains incompletely defined. Here, we performed a comparative reanalysis of five published, high-quality C. trachomatis RNA-Seq datasets generated under prolonged interferon-{gamma} treatment, tryptophan starvation, iron starvation, penicillin exposure, or acute heat shock. Global transcriptomic analyses reveal extensive stress-specific reprogramming and a clear separation between the transcriptome induced by heat shock and those induced by chronic stresses. Transcriptomic overlap observed among chronic stress conditions is substantially reduced when the heat shock transcriptome is included, indicating that shared transcriptional features are stressor-dependent. Unexpectedly, tryptophan starvation and iron starvation exhibit particularly close transcriptomic similarity, consistent with regulatory cross-talk mediated by the iron-dependent transcriptional repressor YtgR. In contrast, interferon-{gamma} induces a distinct but partially overlapping transcriptome, likely reflecting activation of additional host-mediated antimicrobial mechanisms beyond tryptophan deprivation. Together, these findings demonstrate that adaptation to different biological stressors in C. trachomatis is driven by distinct transcriptomic reprogramming, while consistently involving a subset of functions that may represent points of vulnerability for disrupting chlamydial persistence.

microbiology↗

bioRxiv2025

Single-cell transcriptomic profiling of bam mutant tumor reveals germline heterogeneity and gcrf1 as a modulator in Drosophila germ cells

The bam mutant ovary of Drosophila represents a classic tumor model caused by germline stem cell (GSC) differentiation defects. To date, its molecular and genetic features have rarely been characterized in detail at the single-cell resolution. Here, we performed single-cell RNA sequencing (scRNA-seq) to comprehensively delineate the transcriptomic landscape and identify distinct germline cell types in bam mutant ovaries by using in situ hybridization. Differentially expressed gene analysis and PAGA plots reveal different transcriptional profiles and developmental relationships in ovarian cells. Based on the expression pattern of eggpl, a useful marker for undifferentiated germ cell identity, and morphological differences in bam mutant ovarioles, two potentially distinct germ cell states are distinguished. Comparative single-cell analysis reveals the potential regulatory network and cellular communication in subclusters of undifferentiated germ cells, and contributes to the identification of gcrf1 as a novel marker gene for female GSC, which involves in the regulation of early germ cell proliferation and Drosophila fertility. Collectively, our study not only provides insights into tumorigenesis caused by GSC differentiation defects but also offers a valuable transcriptomic resource that can be mined for the reproductive features of bam mutant tumors by community.

developmental biology↗

bioRxiv2025

Dendritic cell-intrinsic TLR/MyD88 signaling promotes the clearance of a live-attenuated oral vaccine

A genital tract pathogenicity-attenuated Chlamydia muridarum mutant, named intrOv, is being developed into an oral vaccine against C. trachomatis infection in the genital tract. Although wild-type C. muridarum persists in the mouse large intestine for long periods, intrOv is cleared by the group 3 innate lymphoid cells that produce IFN{gamma} (IFN{gamma}+ILC3s). The current study aims to reveal the mechanism by which intrOv induces IFN{gamma}+ILC3s for its own clearance from the large intestine. IntrOv-induced IL-23 and IL-23 signaling were required for the clearance of intrOv from the large intestine. The intrOv clearance depended on dendritic cells, as depletion of CD11c+ cells reduced both IL-23 and IFN-{gamma}, resulting in the growth of intrOv. Deletion of MyD88 from dendritic cells, but not phagocytes or epithelial cells, rescued the growth of intrOv, indicating a critical role of MyD88 signaling in dendritic cells. Furthermore, TLR2/4 signaling is also essential for inhibiting intrOv, as the deficiency in TLR2/4 fully rescues the growth of intrOv. Both the TLR and MyD88 signaling must be in the same dendritic cells to inhibit intrOv, as the growth of intrOv in the MyD88- or TLR2/4-deficient mice was blocked by only wild-type bone marrow-derived dendritic cells but not dendritic cells deficient in either MyD88 or TLR2/4. Thus, we have demonstrated a dendritic cell-intrinsic TLR/MyD88/IL-23 pathway for recruiting effectors to clear intrOv from the large intestine. The information may help further improve the efficacy and safety of intrOv and guide the design of future mucosal vaccines.

immunology↗

bioRxiv2025

A lineage-specific heat-induced feedback loop controls HrcA to promote chlamydial fitness under stress

Bacterial stress responses rely on transcriptional regulation by sigma factors and repressors. In Chlamydia, which lacks a dedicated heat shock sigma factor, repressor HrcA limits chaperone gene expression under non-stressed conditions. While HrcA function may be enhanced by the chaperone GroESL in a positive feedback loop, here we identify a heat-induced negative feedback loop mediated by HagF, a protein unique to Chlamydiota and conserved across Chlamydia species. We show that HrcA represses hagF, but heat shock induces hagF expression, leading to HagF accumulation and binding to HrcA. Structural modeling and pulldown assays indicate that HagF blocks HrcA dimerization, impairing DNA binding. This relieves repression of the hrcA-grpE-dnaK operon and promotes secondary differentiation in the developmental cycle, enabling infectious elementary bodies to form under heat stress. Our findings reveal dual feedback regulation that tunes chaperone gene expression and illustrate how transcriptional repression can be modulated in a minimal-genome pathogen.

microbiology↗

bioRxiv2024

Infectivity of a pathogenicity-attenuated Chlamydia muridarum mutant in the genital tract

A C. muridarum mutant designated as intrOv was evaluated as an intracellular Oral vaccine vector because it can induce protection in the genital tract following oral inoculation but does not elicit genital pathology following intravaginal infection. However, the mechanism of intrOvs attenuation is unclear. Here we report that few live organisms were recovered from vaginal swabs during the early stage of intrOv intravaginal infection in mice. At a low inoculating dose, an isogenic wild-type control strain established a productive infection, while intrOv failed to do so. Although a higher inoculating dose allowed intrOv and its control to productively infect mice, fewer live intrOv than the control organisms were recovered from the lower genital tract tissues on day 3 post-infection. By day 7, animals infected with intrOv or the control shed similar numbers of live organisms, suggesting the intrOvs deficiency on day 3 was transient. Consistently, intrOv reduced invasion of epithelial cells but maintained as robust intracellular replication as its control. Our results correlate intrOvs delay in infecting the lower genital tissues and reduction in invading epithelial cells with its attenuation in genital pathogenicity, laying the foundation for further revealing the mechanisms of the intrOvs attenuation in pathogenicity during genital tract infection.

microbiology↗

bioRxiv2024

The SWIB domain-containing DNA topoisomerase I of Chlamydia trachomatis mediates DNA relaxation

The obligate intracellular bacterial pathogen, Chlamydia trachomatis (Ct), has a distinct DNA topoisomerase I (TopA) with a C-terminal domain (CTD) homologous to eukaryotic SWIB domains. Despite the lack of sequence similarity at the CTDs between C. trachomatis TopA (CtTopA) and Escherichia coli TopA (EcTopA), full-length CtTopA removed negative DNA supercoils in vitro and complemented the growth defect of an E. coli topA mutant. We demonstrated that CtTopA is less processive in DNA relaxation than EcTopA in dose-response and time course studies. An antibody generated against the SWIB domain of CtTopA specifically recognized CtTopA but not EcTopA or Mycobacterium tuberculosis TopA (MtTopA), consistent with the sequence differences in their CTDs. The endogenous CtTopA protein is expressed at a relatively high level during the middle and late developmental stages of C. trachomatis. Conditional knockdown of topA expression using CRISPRi in C. trachomatis resulted in not only a developmental defect but also in the downregulation of genes linked to nucleotide acquisition from the host cells. Because SWIB-containing proteins are not found in prokaryotes beyond Chlamydia spp., these results imply a significant function for the SWIB-containing CtTopA in facilitating the energy metabolism of C. trachomatis for its unique intracellular growth. ImportanceC. trachomatis (Ct) is a medically important bacterial pathogen that is responsible for the most prevalent sexually transmitted bacterial infection. Bioinformatics, genetics, and biochemical analyses have established that the presence of a SWIB domain in CtTopA, a DNA topoisomerase I, is relevant to chlamydial physiology. Further defining the mechanisms of the C-terminal SWIB domain on the catalytic function of CtTopA in an intracellular pathogen is warranted for a more complete understanding of the interactions between C. trachomatis and its host cells.

molecular biology↗