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Biology subjects

Turan, K.

Publications and source records attributed to Turan, K..

2 recordsLinked to original sources

Nutrient availability-driven changes in extracellular matrix biochemical and mechanical properties regulate pancreatic cancer cell biology

The extracellular matrix (ECM) provides key biochemical and biomechanical cues that govern fundamental cellular processes, including growth and migration. ECM dysregulation and altered cell-matrix interactions are a driver of cancer progression, exemplified by pancreatic ductal adenocarcinoma (PDAC), where an abnormally dense, collagen-rich, and stiff ECM correlates with poor patient outcomes. The PDAC microenvironment is poorly perfused, resulting in altered nutrient availability, yet how this metabolic stress shapes the ECM and its biological activity remains poorly understood. Herein, we demonstrate that glutamine, a key amino acid depleted in poorly perfused PDAC regions, regulates the biochemical composition, mechanical properties, and biological activity of fibroblast-derived ECM. As glutamine availability increases, fibroblasts shift from producing a basement membrane-like ECM toward an interstitial, mature ECM enriched in fibrillar collagens. The ECM generated under glutamine-rich conditions is stiffer, which limits PDAC cell growth, while simultaneously, the elevated collagen I content promotes migration in a 3D spheroid model. Mechanistically, glutamine-dependent collagen I engages integrin 2 (ITGA2) to activate focal adhesion kinase signaling, driving PDAC cell migration independent of growth. In PDAC patients, glutamine stress inversely correlates with collagen expression in CAFs, with collagen I-ITGA2 as the most enriched ECM receptor interaction pair compared to the normal pancreas. These findings establish nutrient availability as a key regulator of ECM biology and offer new avenues to therapeutically intervene with dysregulated cell-matrix interactions in PDAC.

cell biology↗

DNA-utilization loci enable exogenous DNA metabolism in gut Bacteroidales

The human gut microbiome plays a central role in nutrient metabolism, yet the fate of exogenous nucleic acids within this ecosystem remains poorly understood. Here, we show that multiple Bacteroidales species efficiently metabolize exogenous DNA, with Bacteroides thetaiotaomicron converting it into the deaminated nucleobases uracil and xanthine. Using genetic and biochemical approaches, we identify ddbABCDEF, a six-gene locus encoding secreted nucleases and an outer membrane transporter, essential for exogenous DNA metabolism in B. thetaiotaomicron. Colonization of gnotobiotic mice with ddbABCDEF mutants reveals that this pathway significantly alters nucleobase pools in the gut. Comparative genomics demonstrate that ddbABCDEF is evolutionarily related to a natural transformation system present in Bacteroidota and has diversified into four distinct subtypes, each linked to unique DNA-processing activities in closely related gut Bacteroidales strains. These findings thus establish DNA as a metabolic substrate in the gut microbiome and reveal a distinctive pathway for nucleobase production with implications for host-microbe interactions. SIGNIFICANCE STATEMENTThe gut microbiome plays a crucial role in nutrient metabolism, yet the fate of extracellular DNA within this ecosystem remains poorly understood. This study identifies Bacteroidales species that actively metabolize extracellular DNA, revealing a conserved pathway that converts DNA-derived nucleotides into deaminated nucleobases. We show that Bacteroides thetaiotaomicron utilizes a specialized genetic locus, ddbABCDEF, to facilitate this process, influencing nucleobase availability in the gut. Comparative genomic analyses suggest that ddbABCDEF is evolutionarily linked to bacterial natural transformation systems but has diverged into distinct metabolic subtypes. These findings establish DNA as a metabolic substrate in the gut microbiome, with potential implications for microbial ecology, host-microbe interactions, and gut health.

microbiology↗