Biology subjects

Priya, S.

Publications and source records attributed to Priya, S..

13 recordsLinked to original sources

bioRxiv2026

Mapping Genome-wide Transcription Factor Binding Sites in two Rhodanobacter strains Isolated from Extreme Environments

Identification of target genes for bacterial transcription factors (TFs) provide a deeper understanding of bacterial response to environmental conditions. We focused on two Rhodanobacter sp. isolates from the subsurface of the U.S. Department of Energy Oak Ridge Reservation (ORR), an environment characterized by high-concentration mixed-waste contamination plumes. Bacterial strains in this subsurface ecosystem experience changing and complex environmental conditions, including variable nutrient and oxygen availability, fluctuating pH, nitrate and metals. We examined 91 DNA-binding TFs from 17 TF families in two Rhodanobacter strains, R. denitrificans FW104-10B01 and R. thiooxydans FW510-R12, using both DNA affinity purification sequencing (DAP-seq) and comparative genomics. Target genes regulated by 31 TFs were identified. Despite being isolated from different wells, the two strains shared a highly similar core regulatory network, with orthologous TFs regulating nearly identical sets of genes. These conserved networks governed essential survival functions, including nutrient uptake (e.g., phosphate), carbohydrate metabolism, motility, and stress responses to heavy metals and oxidative environment. TF-binding sequence motifs were also inferred for each of the 31 TFs. Key results include the elucidation of a global regulator Clp which regulates a large number of genes, particularly those involved in biofilm formation and motility. Functional validation through RT-qPCR confirmed that Clp activates the expression of genes critical for type IV pilin structure and flagellar regulation. Our work highlights the advantages of synergistically employing DAP-seq and comparative genomics, which enabled us to corroborate findings and obtain a larger view of the regulatory landscape of these non-model denitrifying bacteria.

microbiology↗

bioRxiv2026

Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer

Colorectal cancer (CRC) is associated with changes in the microbial communities in the tumor microenvironment. Although metabolic reprogramming is an important feature of host cells in CRC, little is known about metabolic changes in the tumor-associated microbiota and how these microbial metabolic alterations can contribute to disease. Here, we investigated metabolic host-microbiome interactions in CRC using complementary computational and experimental approaches. Using patient-specific in silico metabolic models across three independent datasets, we discovered that Fusobacterium, a cancer-promoting taxon, consistently grows faster in tumor-associated versus normal tissue-associated microbiomes. This finding prompted us to investigate whether host metabolic changes drive these microbial growth advantages. By integrating our metabolic predictions with host transcriptomics data, we identified correlations between tumor gene expression and the growth of CRC-associated taxa (including Porphyromonadaceae, Blautia, and Streptococcus), as well as associations between host genes and microbial metabolism of dietary components (including choline, amino acids, and starch). To test whether these correlations reflect causal relationships, we simulated spent medium experiments in silico, demonstrating that Blautia preferentially grows on metabolites produced by tumor versus normal host cells. We further validated the direct impact of microbes on host metabolism using an in vitro system, where colon cancer cells exposed to human microbiomes showed gene expression changes in response to specific taxa including Bilophila, Anaerotruncus, and Escherichia. Together, these findings reveal a metabolic dialogue between host and microbiome in CRC, where tumor metabolic reprogramming creates a favorable environment for pathogenic microbes, which in turn may reinforce tumorigenic processes through metabolic crosstalk.

systems biology↗

bioRxiv2026

RB-TnSeq analysis reveals alcohol and salt tolerance systems in a plant root colonizer Paraburkholderia graminis OAS925

The role of microbial strains in regulating natural stresses and their impact on plant health is well-established. However, the role of microbial tolerance mechanisms in plant response to unnatural or anthropogenic stresses is less understood. Examination of these interactions impact our deeper understanding of plant-microbe interactions and our ability to enhance beneficial functions. In this study we use the model plant Brachypodium distachyon and its prominent root colonizer Paraburkholderia graminis OAS925 to investigate mechanisms of tolerance to alcohol and salt stress. We examined the ability of OAS925 to reduce root growth inhibition during exposure to short chain alcohols and salt. We also examined the tolerance mechanism for OAS925 towards these stresses using RB-TnSeq fitness assays. The most prominent tolerance systems in OAS925 are genes specifically involved in membrane transport (such as the Mla operon), efflux systems (e.g., RND efflux systems), signaling and regulation (PrtR/PrtI, NtrY/NtrX, and EnvZ/OmpR), and oxidative stress response (GshB). Our findings provide a model where bacterial membrane integrity, active solvent efflux, and stress signaling are crucial not only for bacterial survival but also for maintaining the root colonization and biofilm formation that confer protection to the host plant.

microbiology↗

bioRxiv2026

A single BRCA2 BRC repeat supports viability while multiple repeats ensure resilience under stress

BRC repeats are integral to BRCA2 function and mediate RAD51 loading during homologous recombination (HR). Their number varies across species, but mammals, including mice and humans, harbor eight repeats. Prior studies have suggested functional redundancy among these repeats, but the biological significance of maintaining multiple repeats remains unresolved. Here, we demonstrate that the presence of a single BRC repeat, either BRC2 or BRC4, is sufficient for mouse embryonic stem cell (mESC) viability, RAD51 loading, PARP inhibitor resistance and protection of stalled replication forks. Consistent with these findings, we show that knock-in mice with a single BRC repeat 2 or 4 are viable and exhibit normal growth and fertility. In contrast, embryonic fibroblasts from these mice display genomic instability and impaired RAD51 recruitment. Notably, this defect is rescued under low oxygen culture conditions, which mimics physoxic levels, whereas exposure to oxidative stress impairs RAD51 recruitment in mESCs harboring a single BRC repeat. Together, our findings indicate that while a single BRC repeat is sufficient under physiological conditions, the evolutionary retention of multiple BRC repeats likely ensures robust genome stability under extreme oxidative stress.

genetics↗

bioRxiv2026

Targeting matrix metalloproteinase-14 disrupts DNA repair and reduces viability in adrenocortical carcinoma

BackgroundAdrenocortical carcinoma (ACC) is a rare and aggressive endocrine cancer with limited treatment options and poor prognosis. Identifying novel therapeutic targets requires understanding the molecular drivers of ACC progression and establishing translational models for preclinical validation. ResultsMatrix metalloproteinase-14 (MMP-14) is the most highly expressed MMP in ACC, and high MMP-14 expression is associated with worse overall and disease-free survival. We demonstrate that MMP-14 is essential for ACC cell survival and serves an unexpected role in maintaining genome stability. Genetic silencing or pharmacologic inhibition of MMP-14 significantly reduced viability in both NCI-H295R cells and patient-derived tumor organoids (PTOs). MMP-14 knockdown induced CHK1 activation and S-phase checkpoint arrest. Mechanistically, MMP-14 translocates to the nucleus and binds to chromatin following DNA damage induced by ionizing radiation or cisplatin. Loss of MMP-14 resulted in accumulation of DNA double-strand breaks, as evidenced by increased {gamma}H2AX foci, and impaired non-homologous end joining (NHEJ)-mediated repair. ConclusionsThese findings reveal a novel nuclear function for MMP-14 in DNA repair and identify MMP-14 as a promising therapeutic target in ACC. Targeting MMP-14 may sensitize ACC tumors to DNA-damaging chemotherapy by impairing the repair of therapy-induced lesions.

cancer biology↗

bioRxiv2025

Engineered lignin composition in Brachypodium distachyon modulates the root-associated microbiome

Lignin is a key component of the plant cell wall and a barrier to microbial interaction and biomass digestibility. While lignin biosynthesis has been engineered in grasses to reduce recalcitrance for agroindustrial applications, the consequences for root-associated microbial communities remain poorly understood. Here, we show in the model grass species Brachypodium distachyon that genetic modification of lignin biosynthetic genes, particularly caffeic acid O-methyltransferase (COMT), alters root lignin syringyl/guaiacyl (S/G) ratios, root exudate composition, and significantly reshapes the rhizosphere microbiome. Using a synthetic microbial community (SYNCOM) in controlled fabricated ecosystem (EcoFAB) environments, we observed a distinct reduction in Burkholderia colonization and enrichment of Rhodococcus in COMT mutant lines. LC-MS/MS profiling of root exudates revealed increased p-coumaric acid, caffeic acid and hydroxycinnamic acid amides in these lines, potentially linked to both metabolic remodeling and plant stress responses. These findings demonstrate that altering lignin composition can have profound, genotype-specific impacts on rhizosphere microbiome assembly, with implications for plant-microbe interactions, nutrient cycling, and biomass conversion strategies in bioenergy crops.

plant biology↗

bioRxiv2025

Epithelial eversion, a collective rearrangement from apical-in to apical-out polarity, is initiated by α6β4 integrins and sustained by increased cell proliferation and anchorage-independence

Epithelial cells primarily segregate transmembrane proteins to apical or basal surfaces, establishing apical-basal polarity. For 3D tissues, apical proteins face inwards and basal proteins are on the outer surfaces (in contact with ECM). Apical-basal polarity can become inverted such that the apical proteins are on the outer surfaces. Originally this polarity inversion was assumed to always occur due to changes in protein trafficking. However, recent work by our group showed that increased RhoA activation causes epithelial spheroids to invert apical-basal polarity via a collective rearrangement of cells, a process we and others have termed eversion. We hypothesized that specific integrin-ECM interactions could facilitate the collective cellular migration required for eversion. Using multiple integrin knockout lines, we observed that epithelial cells lacking either 6 or {beta}4 integrins do not develop apical-out polarity in response to RhoA activation. Similarly, 6 blocking antibody or culturing spheroids in collagen (lacking laminin) also inhibited the formation apical-out polarity. These data indicate that 6{beta}4-laminin interactions are required for eversion. Next, we examined the role of cell proliferation and anchorage independence in maintaining apical-out polarity of everted spheroids. Inhibition of cell proliferation (with DNA synthesis inhibitor aphidicolin) or inhibition of anchorage-independence (with FAK inhibitor 14) were sufficient to restore apical-in polarity to RhoA treated spheroids, indicating that both proliferation and anchorage-independence maintain spheroids in an apical-out state. We also observed that apical-out spheroids can revert to apical-in polarity through apoptotic cavitation of cells located in the center of the spheroids. Lastly, through RNA sequencing we demonstrate that apical-out spheroids have unique gene expression profiles. This study provides new mechanistic insights into the biochemical and biophysical mechanisms that drive eversion and maintain apical-out polarity. This work supports the concept that changing from apical-in to apical-out polarity be an important marker for phenotypic switch in epithelial cells.

cell biology↗

bioRxiv2024

Surviving in the mountains: Temperature and elevation have contrasting physiological effects on the hoverfly Eristalis tenax in the Himalayas

Insect populations are experiencing a global decline due to a variety of human-linked environmental changes. Among these changes, how insects physiology might be affected by predicted upslope migration due to climate change is unknown. Being ectotherms, insect physiology is impacted by abiotic factors like ambient temperature that change with elevation. Here, we performed in situ experiments to assess the sensory and cardiac physiology of an important generalist pollinating hoverfly Eristalis tenax (Diptera: Syrphidae), across different elevations in the eco-sensitive and biodiverse Himalayan mountains. We built a portable physiology setup and measured hoverfly antennal responses towards common floral volatiles at 3600 masl and 4200 masl. We also recorded their heart rate at 3000 masl, 3500 masl and 4000 masl. We report the first in situ physiology experiments performed in the high-altitude Himalayas. Our results show a contrasting impact of elevation and temperature on the sensory and cardiac physiology of hoverflies, with antennal sensitivity decreasing with increasing elevation, while average heart rate increased with temperature, independent of elevation. With upslope migration and climate warming, consequent sensory mismatches and cardiac stress could have deleterious effects on the health of both hoverflies and the vulnerable Himalayan ecosystem.

zoology↗

bioRxiv2024

Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs)

Horizontal gene transfer (HGT) is a major process by which genes are transferred within microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provided the first demonstration of gene transfer via triparental conjugation system in the Brachypodium distachyon rhizosphere in the EcoFABs using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor having the mobilizable and non-self-transmissible plasmid. We also observed that the frequency of conjugal plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage, and composition and amount of root exudates. The frequency of conjugation also increased with higher numbers of donor cells. We have also shown the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. showing the possibility of HGT within a rhizosphere microbial community. Environmental stresses also influence the rate of HGT in the rhizosphere between species and genera. Additionally, we observed transfer of a non-self transmissible donor plasmid without the helper strain on agar plates when supplemented with environmental stressors, indicating reduced dependency on the helper plasmid under certain conditions. This study provides a robust workflow to evaluate conjugal transfer of engineered plasmids in the rhizosphere when such plasmids are introduced in a field or plant associated environment. ImportanceWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbial interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.

microbiology↗

bioRxiv2021

Shared and disease-specific host gene-microbiome interactions across human diseases

While the gut microbiome and host gene regulation separately contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here, we developed a machine learning-based framework to jointly analyze host transcriptomic and microbiome profiles from 416 colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease, and irritable bowel syndrome. We identified potential interactions between gut microbes and host genes that are disease-specific, as well as interactions that are shared across the three diseases, involving host genes and gut microbes previously implicated in gastrointestinal inflammation, gut barrier protection, energy metabolism, and tumorigenesis. In addition, we found that mucosal gut microbes that have been associated with all three diseases, such as Streptococcus, interact with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes.

genomics↗

bioRxiv2019

Interactions between the gut microbiome and host gene regulation in cystic fibrosis

Cystic Fibrosis (CF) is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in the CFTR gene, leading to poor hydration of mucus and impairment of the respiratory, digestive, and reproductive organ functions. Advancements in medical care have lead to markedly increased longevity of patients with CF, but new complications have emerged, such as early onset of colorectal cancer (CRC). Although the pathogenesis of CRC in CF remains unclear, altered host-microbe interactions might play a critical role. Here, we characterize the changes in the gut microbiome and host gene expression in colonic mucosa of CF patients relative to healthy controls. We find that CF patients show decreased microbial diversity, decreased abundance of taxa such as Butyricimonas, Sutterella, and Ruminococcaceae, and increased abundance of other taxa, such as Actinobacteria and Firmicutes. We find that 1543 genes, including CFTR, show differential expression in the colon of CF patients compared to healthy controls. Interestingly, we find that these genes are enriched with functions related to gastrointestinal and colorectal cancer, such as metastasis of CRC, tumor suppression, cellular dysfunction, p53 and mTOR signaling pathways. Lastly, we modeled associations between relative abundances of specific bacterial taxa in the gut mucosa and host gene expression, and identified CRC-related genes, including LCN2 and DUOX2, for which gene expression is correlated with the abundance of CRC-associated bacteria, such as Ruminococcaceae and Veillonella. Our results provide new insight into the role of host-microbe interactions in the etiology of CRC in CF.

genomics↗

bioRxiv2018

Distinct Microbes, Metabolites, and Ecologies Define the Microbiome in Deficient and Proficient Mismatch Repair Colorectal Cancers

Background\n\nThe link between colorectal cancer (CRC) and the gut microbiome has been established, but the specific microbial species and their role in carcinogenesis remain controversial. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology.\n\nMethods\n\nWe collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed effects model that accounted for MMR status, sample location, intra-subject sample correlation, and read depth. Genome-scale metabolic models were then used to generate microbial interaction networks for dMMR and pMMR microbial communities. We assessed global network properties as well as the metabolic influence of each microbe within the dMMR and pMMR networks.\n\nResults\n\nWe demonstrate distinct roles for microbes in dMMR and pMMR CRC. Sulfidogenic Fusobacterium nucleatum and hydrogen sulfide production were significantly enriched in dMMR CRC, but not pMMR CRC. We also surveyed the butyrate-producing microbial species, but did not find a significant difference in predicted or actual butyrate production between dMMR and pMMR microbial communities. Finally, we observed that dMMR microbial communities were predicted to be less stable than pMMR microbial communities. Community stability may play an important role in CRC development, progression, or immune activation within the respective MMR subtypes.\n\nConclusions\n\nIntegrating tumor biology and microbial ecology highlighted distinct microbial, metabolic, and ecological properties unique to dMMR and pMMR CRC. This approach could critically improve our ability to define, predict, prevent, and treat colorectal cancers.

cancer biology↗

bioRxiv2018

Gut Microbiota Diversity across Ethnicities in the United States

Composed of hundreds of microbial species, the composition of the human gut microbiota can vary with chronic diseases underlying health disparities that disproportionally affect ethnic minorities. However, the influence of ethnicity on the gut microbiota remains largely unexplored and lacks reproducible generalizations across studies. By distilling associations between ethnicity and differences in two United States based 16S gut microbiota datasets including 1,673 individuals, we report 12 microbial genera and families that reproducibly vary by ethnicity. Interestingly, a majority of these microbial taxa, including the most heritable bacterial family, Christensenellaceae, overlap with genetically-associated taxa and form co-occurring clusters linked by similar fermentative and methanogenic metabolic processes. These results demonstrate recurrent associations between specific taxa in the gut microbiota and ethnicity, providing hypotheses for examining specific members of the gut microbiota as mediators of health disparities.

microbiology↗