Biology subjects

Weaver, T.

Publications and source records attributed to Weaver, T..

4 recordsLinked to original sources

bioRxiv2026

A Dynamic Search Mechanism Enables APE1 to Identify AP-Sites in DNA

Apurinic/apyrimidinic (AP) sites are among the most frequent DNA lesions, arising thousands of times per cell each day. These AP-sites threaten genomic stability and, if left unrepaired, can lead to mutagenesis and human disease. The essential base excision repair enzyme Apurinic/Apyrimidinic Endonuclease I (APE1) initiates repair by cleaving DNA at AP-sites, yet how APE1 efficiently locates and recognizes these lesions within vast excesses of undamaged DNA has remained poorly understood. Using single-molecule imaging, we show that APE1 employs a dynamic search strategy that integrates 1D and 3D diffusion to rapidly scan DNA. On non-damaged DNA, APE1 undergoes fast diffusion, enabling efficient interrogation of large genomic regions within a single binding event. Upon encountering an AP-site, APE1 transitions from a mobile search state into a stationary, lesion-bound complex that is retained at the site of damage. Additional experiments with APE1 variants demonstrate that the intrinsically disordered N-terminal domain of APE1 supports 1D diffusion, whereas residue R177 stabilizes APE1 at the AP-site once recognized, and the catalytic residues D210 and E96 facilitate enzyme release after cleavage. Together, these findings define the molecular basis by which APE1 balances rapid genome surveillance with stable lesion engagement and timely release. More broadly, this work provides a mechanistic framework for how DNA repair enzymes efficiently locate and process rare lesions embedded within an excess of undamaged DNA. Significance StatementDNA repair enzymes face the formidable challenge of locating rare lesions hidden within vast stretches of undamaged DNA. The essential enzyme APE1 is tasked with identifying and initiating repair of AP-sites, a frequent DNA lesion, to maintain genome integrity. We show that APE1 overcomes this challenge by using a dynamic search mechanism that integrates rapid scanning with precise lesion recognition. Its unstructured N-terminal domain facilitates fast movement along non-damaged DNA, while specific active site residues stabilize engagement at AP-sites and release after catalysis. This coordination of diffusion, recognition, and turnover allows APE1 to efficiently survey the genome and repair AP-sites to maintain genome stability.

biochemistry↗

bioRxiv2024

Polybacterial Intracellular Macromolecules Shape Single-Cell Epikine Profiles in Upper Airway Mucosa

The upper airway, particularly the nasal and oral mucosal epithelium, serves as a primary barrier for microbial interactions throughout life. Specialized niches like the anterior nares and the tooth are especially susceptible to dysbiosis and chronic inflammatory diseases. To investigate host-microbial interactions in mucosal epithelial cell types, we reanalyzed our single-cell RNA sequencing atlas of human oral mucosa, identifying polybacterial signatures (20% Gram-positive, 80% Gram-negative) within both epithelial- and stromal-resident cells. This analysis revealed unique responses of bacterial-associated epithelia when compared to two inflammatory disease states of mucosa. Single-cell RNA sequencing, in situ hybridization, and immunohistochemistry detected numerous persistent macromolecules from Gram-positive and Gram-negative bacteria within human oral keratinocytes (HOKs), including bacterial rRNA, mRNA and glycolipids. Epithelial cells with higher concentrations of 16S rRNA and glycolipids exhibited enhanced receptor-ligand signaling in vivo. HOKs with a spectrum of polybacterial intracellular macromolecular (PIM) concentrations were challenged with purified exogenous lipopolysaccharide, resulting in the synergistic upregulation of select innate (CXCL8, TNFSF15) and adaptive (CXCL17, CCL28) epikines. Notably, endogenous lipoteichoic acid, rather than lipopolysaccharide, directly correlated with epikine expression in vitro and in vivo. Application of the Drug2Cell algorithm to health and inflammatory disease data suggested altered drug efficacy predictions based on PIM detection. Our findings demonstrate that PIMs persist within mucosal epithelial cells at variable concentrations, linearly driving single-cell effector cytokine expression and influencing drug responses, underscoring the importance of understanding host-microbe interactions and the implications of PIMs on cell behavior in health and disease at single-cell resolution. One-sentence summaryThis study reveals how persistent intracellular bacterial macromolecules in mucosal epithelial cells drive inflammatory signaling, offering new insights into microbial-host interactions and their potential impact on inflammatory disease treatment and drug efficacy.

cell biology↗

bioRxiv2023

Polybacterial intracellular coinfection of epithelial stem cells in periodontitis

Periodontitis affects billions of people worldwide. To address interkingdom relationships of microbes and niche on periodontitis, we generated the first sin-gle-cell meta-atlas of human periodontium (34-sample, 105918-cell), harmo-nizing 32 annotations across 4 studies1-4. Highly multiplexed immunofluores-cence (32-antibody; 113910-cell) revealed spatial innate and adaptive immune foci segregation around tooth-adjacent epithelial cells. Sulcular and junctional keratinocytes (SK/JKs) within epithelia skewed toward proinflammatory phe-notypes; diseased JK stem/progenitors displayed altered differentiation states and chemotactic cytokines for innate immune cells. Single-cell metagenomics utilizing unmapped reads revealed 37 bacterial species. 16S and rRNA probes detected polybacterial intracellular pathogenesis ("co-infection") of 4 species within single cells for the first time in vivo. Challenging coinfected primary human SK/JKs with lipopolysaccharide revealed solitary and synergistic ef-fects. Coinfected single-cell analysis independently displayed proinflammatory phenotypes in situ. Here, we demonstrate the first evidence of polybacterial intracellular pathogenesis in human tissues and cells--potentially influencing chronic diseases at distant sites.

cell biology↗

bioRxiv2022

Ecosystem gross primary productivity after autumn snowfall and melt events in a mountain meadow

Vegetation productivity is increasing across much of the U.S. Northern Great Plains but is decreasing in some nearby Northern Rocky Mountain grasslands due to increases in aridity. Mountain grasslands support critical ecosystem services that are under threat from ongoing land use and climate changes, and it is important to understand their function across all changing seasons. Observing the full range of montane ecosystem productivity is challenging because site access is often difficult during the "shoulder seasons" in spring and autumn if the snowpack is not fully developed or degrading. It is unclear if decreases to montane grassland productivity from drying autumns can be offset in part by late-season green-ups after precipitation events. These include the snowfall/snowmelt periods that often characterize the summer-to-winter transition in the Northern Rockies. Here, we quantify the ecosystem carbon uptake that occurs after snowfall and melt in climatological autumn (September, October, and November) in a montane grassland in Montana, USA using a combination of eddy covariance, phenological camera, and remote sensing analyses. Carbon dioxide flux follows a diurnal pattern after autumn snowmelt events despite overall ecosystem losses of C, suggesting that post-snowmelt photosynthesis helps dampen C loss during autumn and provides fresh photosynthate to support ecosystem functioning. Light-saturated photosynthesis after two snow events was not different than before snowfall ([~]6 {micro}mol CO2 m-2 s-1 in 2016 and [~]2.5 {micro}mol CO2 m-2 s-1 in 2017); observations are consistent with the notion that canopy photosynthesis is resistant, rather than resilient, to the first snow disturbances. MODIS observations also suggest that post-snowfall increases in NDVI can occur but do not happen every year, such that late-season photosynthesis is not a reliable source of fresh photosynthate. These late-season carbon uptake events likely play a small role in the annual ecosystem carbon balance but may be disproportionately important for organisms faced with dwindling late-season forage and regrowth in spring. Future efforts should seek to understand the community and ecosystem consequences of vegetation functioning during autumn as part of an expanded effort to understand phenological changes during this under-studied and changing time of year.

ecology↗