Biology subjects

Paul, S.

Publications and source records attributed to Paul, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

GATA-regulated transcriptional program dictate cell fate equilibrium to establish the maternal-fetal exchange interface and fetal development

The placenta establishes a maternal-fetal exchange interface to transport nutrients and gases between the mother and the fetus. Establishment of this exchange interface relies on the development of multinucleated syncytiotrophoblasts (SynT) from trophoblast progenitors and defect in SynT development often leads to pregnancy failure and impaired embryonic development. Here, we show that mouse embryos with conditional deletion of GATA2 and GATA3 in labyrinth trophoblast progenitors have underdeveloped placenta and die [~] embryonic day 9.5 (E9.5). Single cell RNA Seq (scRNA-Seq) analysis revealed excessive accumulation of multipotent labyrinth trophoblast progenitors upon conditional deletion of GATA factors. The GATA factor-deleted multipotent progenitors were unable to differentiate to matured SynTs. We also show that the GATA factor-mediated priming of trophoblast progenitors for SynT differentiation is a conserved event during human placentation. Loss of either GATA2 or GATA3 in cytotrophoblast (CTB)-derived human trophoblast stem cells (human TSCs) drastically inhibits SynT differentiation potential. Identification of GATA2 and GATA3 target genes along with comparative bioinformatics analyses revealed that GATA factors directly regulate hundreds of common genes in human TSCs, including genes that are essential for SynT development and implicated in preeclampsia and fetal growth retardation. Thus, our study uncovers a conserved molecular mechanism, in which coordinated function of GATA2 and GATA3 promote trophoblast progenitor-to-SynT commitment ensuring establishment of the maternal-fetal exchange interface.

developmental biology↗

bioRxiv2023

Transcription factor FfmA interacts both physically and genetically with AtrR to properly regulate gene expression in the fungus Aspergillus fumigatus

Transcriptional regulation of azole resistance in the filamentous fungus Aspergillus fumigatus is a key step in development of this problematic clinical phenotype. We and others have previously described a C2H2-containing transcription factor called FfmA that is required for normal levels of voriconazole susceptibility and expression of an ATP-binding cassette transporter gene called abcG1. Null alleles of ffmA exhibit a strongly compromised growth rate even in the absence of any external stress. Here we employ an acutely repressible doxycycline-off form of ffmA to rapidly deplete FfmA protein from the cell. Using this approach, we carried out RNA-seq analyses to probe the transcriptome of A. fumigatus cells that have been deprived of normal FfmA levels. We found that 2000 genes were differentially expressed upon depletion of FfmA, consistent with the wide-ranging effect of this factor on gene regulation. Chromatin immunoprecipitation coupled with high throughput DNA sequencing analysis (ChIP-seq) identified 530 genes that were bound by FfmA using two different antibodies for immunoprecipitation. More than 300 of these genes were also bound by AtrR demonstrating the striking regulatory overlap with FfmA. However, while AtrR is clearly an upstream activation protein with clear sequence specificity, our data suggest that FfmA is a chromatin-associated factor that may bind to DNA in a manner dependent on other factors. We provide evidence that AtrR and FfmA interact in the cell and can influence one anothers expression. This interaction of AtrR and FfmA is required for normal azole resistance in A. fumigatus.

genetics↗

bioRxiv2023

Impact of Point Mutation on Shiga-like Toxin 1: A Molecular Dynamics Simulation Study

The causative agent of gastroenteritis is Shiga toxin, which belongs to a functionally and structurally associated protein family despite each individual having a unique amino acid sequence. After entering the ER lumen and relocating the toxic domain to the cytoplasm, they alter the large subunit of rRNA, preventing protein synthesis and ribosomal damage. Shiga-like toxin-1 (SLT-1) subunit B targets glycolipid receptor Gb3, which plays a significant role in cytotoxicity. Though the mutational effect on subunit B is important for cytotoxicity study, we lack better understanding. Our present study targets the mutational impact of glycine protein at their 62th amino acid sequence of subunit B. For example, how it can alter the receptor-binding capacity and virulence. We used in silico method with GROMACS software suite (version 5.2, 2020.1) on Google Colab for a 100ns (100,000ps) simulation period and UCSF Chimera software for visualizing mutant and wild-type structure similarities. Surprisingly, RMSD, RMSF, and Rg trajectories from the simulation analysis indicated a more stable and compact mutant structure than the wild type. Principle component analysis (PCA) and SASA were visualized for the entire 100ns, which pointed towards homogeneity between both structures and more solvent accessibility in the mutant structure. This mutation may elevate receptor-binding and virulence capacity. Moreover, this finding can offer a better insight for future vaccine production.

bioinformatics↗

bioRxiv2023

Uracil-DNA Glycosylase of Murine Gammaherpesvirus 68 Binds Cognate Viral Replication Factors Independently of its Catalytic Residues

Herpesviruses are large double-stranded DNA viruses that encode core replication proteins and accessory factors involved in nucleotide metabolism and DNA repair. Mammalian Uracil-DNA glycosylases (UNG) excise deleterious uracil residues from their genomic DNA. Each herpesvirus UNG studied to date has demonstrated conservation of the enzymatic function to excise uracil residues from DNA. We previously reported that a murine gammaherpesvirus (MHV68) with a stop codon in ORF46 (ORF46.stop) that encodes for vUNG was defective in lytic replication and latency in vivo. However, a mutant virus that expressed a catalytically inactive vUNG (ORF46.CM) had no replication defect, unless coupled with additional mutations in the catalytic motif of the viral dUTPase (ORF54.CM). The disparate phenotypes observed in the vUNG mutants led us to explore the non-enzymatic properties of vUNG. Immunoprecipitation of vUNG followed by mass spectrometry in MHV68-infected fibroblasts identified a complex comprised of the cognate viral DNA polymerase, vPOL encoded by ORF9, and the viral DNA polymerase processivity factor, vPPF encoded by ORF59. MHV68 vUNG colocalized with vPOL and vPPF in subnuclear structures consistent with viral replication compartments. In reciprocal co-immunoprecipitations, the vUNG formed a complex with the vPOL and vPPF upon transfection with either factor alone, or in combination. Last, we determined that key catalytic residues of vUNG are not required for interactions with vPOL and vPPF upon transfection or in the context of infection. We conclude that the vUNG of MHV68 associates with vPOL and vPPF independently of its catalytic activity. IMPORTANCEGammaherpesviruses encode a uracil-DNA glycosylase (vUNG) that is presumed to excise uracil residues from viral genomes. We previously identified the vUNG enzymatic activity, but not the protein itself, as dispensable for gammaherpesvirus replication in vivo. In this study, we report a non-enzymatic role for the viral UNG of a murine gammaherpesvirus to form a complex with two key components of the viral DNA replication machinery. Understanding the role of the vUNG in this viral DNA replication complex may inform the development of antiviral drugs that combat gammaherpesvirus associated cancers.

microbiology↗

bioRxiv2023

A Recombinant Antibody For Tracking Murine Gammaherpesvirus 68 Uracil DNA Glycosylase Expression.

Antibodies are powerful tools to detect expressed proteins. However off-target recognition can confound their use. Therefore, careful characterization is needed to validate specificity in distinct applications. Here we report the sequence and characterization of a mouse recombinant antibody that specifically detects ORF46 of murine gammaherpesvirus 68 (MHV68). This ORF encodes the viral uracil DNA glycosylase (vUNG). The antibody does not recognize murine uracil DNA glycosylase and is useful in detecting vUNG expressed in virally infected cells. It can detect expressed vUNG in cells via immunostaining and microscopy or flow cytometry analysis. The antibody can detect vUNG from lysates of expressing cells via immunoblot under native conditions but not denaturing conditions. This suggests it recognizes a confirmational based epitope. Altogether this manuscript describes the utility of the anti-vUNG antibody and suitability for use in studies of MHV68 infected cells.

molecular biology↗

bioRxiv2023

Transient expression of Helicobacter pylori cagA oncoprotein in brinjal

Helicobacter pylori is closely connected to upper gastrointestinal tract diseases including gastric cancer. Transgenic plants are found to be successful in expressing the bacterial antigens, which could elicit an immune response when consumed. The Cytotoxicity-associated immunodominant antigen protein (cagA) of H. pylori is kindred with pathogenicity and cancer risk. We expressed the cagA transgenically in the brinjal. We amplified the cagA gene from H. pylori strain 26695 chromosomal DNA and transformed it into brinjal callus derived from leaf explants using the pBI121 expression vector. The stable expression and accumulation of the recombinant cagA gene were confirmed by using quantitative real-time PCR, western blot analysis and ELISA. The RT-PCR, western blot and ELISA showed stable expression of cagA gene in the transgenic lines B3, B5, B11, B17 and B21. Among them, B11 and B17 samples showed higher expression of the cagA compared to the other samples. Besides, the immunohistochemistry assay showed the abundant expression of cagA protein in the parenchymal regions of the transgenic plants. Out of the 52 plants, a set five plants were found to be positive for cagA expression. Our experimental outcomes can be used further to design the vaccines against H. pylori from the transgenic brinjal plants.

molecular biology↗

bioRxiv2023

MACI: A machine learning-based approach to identify drug classes of antibiotic resistance genes from metagenomic data

Novel methodologies are now essential for identification of antibiotic resistant pathogens in order to resist them. Here, we are presenting a model, MACI (Machine learning-based Antibiotic resistance gene-specific drug Class Identification) that can take metagenomic fragments as input and predict the drug class of antibiotic resistant genes. We trained the model to learn underlying patterns of genes using the Comprehensive Antibiotic Resistance Database. It comprises of 116 drug classes with a total of 2960 representative sequences. Among these 116 drug classes, we found 22 categories (contributing approximately 85% of the overall sequence-data) surpassed other 94 drug classes based on the number of fragments. The model showed an average precision of 0.83 and a recall of 0.81 for these 22 drug classes. Moreover, the model predicted multidrug resistant classes with higher performance score (precision and recall: 0.9 and 0.88 respectively) compared to single drug resistant categories (0.77 and 0.75). Post to this, we analysed these 22 drug classes to find out class-specific overlapping patterns of nucleotides that led to accurate classification. This way, we found five drug classes viz. "carbapenem;cephalosporin;penam", "cephalosporin", "cephamycin", "cephalosporin;monobactam;penam;penem", and "fluoroquinolone". Additionally, the positions of these significant patterns corroborated with the functional domains of majority of antibiotic resistance genes in that drug class, indicating their biological importance. These class-specific patterns play a pivotal role in rapid identification of some drug classes comprising antibiotic resistance genes. Further analysis showed that bacterial species, containing these five-drug classes, were found to have well-known multidrug resistance property.

bioinformatics↗

bioRxiv2023

Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.

A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Further MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web-server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.

bioinformatics↗

bioRxiv2023

Functional connectivity in northern swamp deer (Rucervus duvaucelii duvaucelii) population across a fragmented, human-dominated landscape along Gangetic Plains of north India: Implications for conservation in non-protected areas

The Indian subcontinent has witnessed disproportionate declines in large mammalian herbivore communities. The northern swamp deer (Rucervus duvaucelii duvaucelii) exemplifies the conservation challenges of typical non-protected area species, where apart from distribution status other ecological information is limited for the upper Gangetic basin population. We combined elements of radio-telemetry and conservation genetics to evaluate dispersal patterns, population connectivity and assess genetic variation and inbreeding status of this population living across a highly human-dominated area. We genetically identified 266 unique swamp deer and further analyses revealed presence of two spatially-admixed genetic lineages with moderate heterozygosity (Ho=0.51, SD= 0.10) and low inbreeding (FIS=0.133) status. Multi- disciplinary evidence suggests that the small, isolated grassland patches between Jhilmil Jheel Conservation Reserve (JJCR) and Hastinapur Wildlife Sanctuary (HWLS) are highly preferred by swamp deer during migrations and are genetically connected. The southern part of the area in HWLS showed early signatures of genetic discontinuity that require immediate conservation attention. We hypothesized that the human settlement history of this landscape, river dynamics and species ability to negotiate various pressures and disperse has helped to maintain such connectivity. While these signatures are encouraging for this small, isolated cervid population, careful management interventions are required to ensure the integrity and functionality of this landscape. We recommend a scientifically robust population estimation approach across this landscape and a multi-stakeholder-driven strategies to augment population and habitat recovery, plantation and riverscape management to ensure long-term survival of this species.

ecology↗

bioRxiv2023

Characterization of uranyl ion binding to amyloid beta (Aβ) peptides: effects on Aβ structure and aggregation

AbstractUranium (U) is naturally present in ambient air, water, and soil, and depleted uranium (DU) is released into the environment via industrial and military activities. While the radiological damage from U is rather well understood, less is known about the chemical damage mechanisms, which dominate in DU. Heavy metal exposure is associated with numerous health conditions including Alzheimers disease (AD), the most prevalent age-related cause of dementia. The pathological hallmark of AD is deposition of amyloid plaques, consisting mainly of amyloid-{beta} (A{beta}) peptides aggregated into amyloid fibrils in the brain. However, the toxic species in AD are likely oligomeric A{beta} aggregates. Exposure to heavy metals such as Cd, Hg, Mn, and Pb is known to increase A{beta} production, and these metals bind to A{beta} peptides and modulate their aggregation. Possible effects of U in AD pathology have been sparsely studied. Here, we use biophysical techniques to study in vitro interactions between A{beta} peptides and uranyl ions, UO22+, of DU. We show for the first time that uranyl ions bind to A{beta} peptides with affinities in the micromolar range, induce structural changes in A{beta} monomers and oligomers, and inhibit A{beta} fibrillization. General toxic mechanisms of uranyl ions could be modulation of protein folding, misfolding, and aggregation.

biophysics↗

bioRxiv2023

Designer grass pea for transgene-free minimal neurotoxin-containing seeds with CRISPR-Cas9

Grass pea seeds are consumed as food in several South Asian and Sub-Saharan African nations. However, the presence of the neurotoxic compound N-oxalyl-L-diamino propionic acid ({beta}-ODAP) has restricted its cultivation. Although various cultivars with low {beta}-ODAP levels have been developed, their cultivation is still limited due to the risk of neurolathyrism from long-term grass pea seed ingestion. In this study, we employed the CRISPR-Cas9-mediated gene editing technique to generate grass pea seeds with zero or minimal {beta}-ODAP levels. We targeted the BAHD-AT3 gene that encodes a key enzyme in the {beta}-ODAP biosynthesis pathway. We developed bahd-at3 knock-out lines using three gRNAs targeting different regions of this gene and characterized them. Cas9-free independent lines from each event carrying the desired on-target mutation were selected and backcrossed twice with the wild-type to eliminate any off-target mutation present therein. Various agronomical parameters were analyzed from the backcrossed mutant lines and they displayed no phenotypic abnormalities. Interestingly, the seed {beta}-ODAP content ranged between 0.001 % - 0.002 % of dry weight which is 99 % lower than the wild-type. Together, our study reports the development of transgene-free, genome-edited grass peas with insignificant levels of {beta}-ODAP in seeds for safer food in the future.

plant biology↗

bioRxiv2023

Incidences of Helicobacter infection in pigs and tracing occupational hazard in pig farmers

Helicobacter species (H. sp.) is a gram-negative spiral-shaped motile bacteria that causes gastritis in pigs and also colonizes the human stomach. The current study seeks to assess the prevalence of various H. sp. in the gastric mucosa of slaughtered and dead pigs, as well as the prevalence of Helicobacter infection among pig farmers. A total of 403 stomach samples from various pig slaughter points, 74 necropsy samples from various pig farms and 97 stool samples from pig farmers were collected from Assam, India. Among 477 pig stomach samples tested, 214 samples with gastritis (20.09%) showed Gram negative, spiral-shaped organisms in brush cytology from the mucosal surface, and the rest of the 263 stomach samples without any gastric lesion showed only 3.04% Gram negative, spiral-shaped organisms. In ultrastructure investigation, Scanning Electron Microscopy (SEM) of the four urease positive stomach samples revealed a tightly coiled Helicobacter bacterium (spiral-shaped) found in the mucous lining of the stomach. In histopathological examination of pars esophagia, cardiac and fundic mucosa showed chronic gastritis associated with hemorrhagic necrosis, leucocytic infiltration with neutrophils and macrophages, and lymphoid aggregates (lymphoid follicles) etc. PCR confirmed 16S rRNA genes of Helicobacter suis (H. suis) where a total of 42 (19.63%) out of 214 pig stomach samples and 2 (2.08%) out of 96 stool samples of pig farmers were found positive for H. suis. of these 96 stool samples of pig farmers 3 (3.12%) were confirmed positive for Helicobacter pylori (H. pylori) Phosphoglucosamine mutase gene in PCR. Phylogenic analysis of the 16S rRNA gene of H. suis showed distinct clusters with other H. sp. In conclusion, this study provides evidence for the prevalence of Helicobacter both in pig gastric mucosa and human stool. The findings highlight the need for improved sanitation and hygiene practices among pig farmers to minimize the risk of Helicobacter infection in humans.

microbiology↗

bioRxiv2023

Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors

Elucidating the developmental processes of organisms requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by trajectory reconstructions. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in silico fate mapping experiments. To demonstrate the versatility of our multi-modal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of Neuro-Mesodermal Progenitors (NMPs). Our publicly accessible web-based platform, Zebrahub, is a foundational resource for studying developmental processes at both transcriptional and spatiotemporal levels, providing researchers with an integrated approach to exploring and analyzing the complexities of cellular lineages during zebrafish embryogenesis.

developmental biology↗

bioRxiv2023

High-throughput quantitative screening of glucose-stimulated insulin secretion and insulin content using automated MAL-DI-TOF mass spectrometry

Type 2 diabetes (T2D) is a metabolic disorder characterized by loss of pancreatic {beta}- cell function, decreased insulin secretion and increased insulin resistance, that affects more than 400 million people worldwide. Although several treatments are proposed to patients suffering from T2D, long-term control of glycemia remains a challenge. Therefore, identifying new potential drugs and targets that positively affect {beta}-cell function and insulin secretion remains crucial. Here, we developed an automated approach to allow the identification of new compounds or genes potentially involved in {beta}-cell function in a 384-well plate format, using the murine {beta}-cell model Min6. Using MALDI-TOF mass spectrometry, we have implemented a high-throughput screening (HTS) strategy based on the automation of a cellular assay allowing to detect insulin secretion in response to glucose, quantitative detection of insulin, in a miniaturized system. As a proof of concept, we screened siRNA targeting well-know {beta}-cell genes and 1600 chemical compounds and identified several molecules as potential regulators of insulin secretion and/or synthesis, demonstrating that our approach allows HTS of insulin secretion in vitro.

physiology↗

bioRxiv2023

An immune cell lipid atlas reveals the basis of susceptibility to ferroptosis

The cellular lipidome is comprised of thousands of unique lipid species. This complexity underpins the many roles of lipids in cellular biology. How lipidome composition varies between cell types and how such differences contribute to cell-specific functionality is poorly understood. Here, using mass spectrometry-based targeted lipidomics, we have characterised the cellular lipid landscape of the human and mouse immune systems (www.cellularlipidatlas.com). We find that myeloid and lymphoid cell lineages have unique lipid compositions, notably in the usage of ester and ether bonds within glycerophospholipids (PLs) and PL acyl chain composition. To determine if immune cell-specific lipid phenotypes promote cell-specific functional properties we focused on differences in poly-unsaturated fatty acid (PUFA)-containing PL, the levels of which are markedly higher in lymphoid cells relative to myeloid cells. We firstly show that differences in PUFA-PL content provides a mechanistic basis for previously described differences in immune cell susceptibility to ferroptosis, a form of cell death driven by iron-dependent lipid peroxidation, and secondly, that the low PUFA-PL content of neutrophils restrains NADPH oxidase-driven ferroptosis. In summary, we show that the lipid landscape is a defining feature of immune cell identity and that cell-specific lipid phenotypes underpin aspects of immune cell physiology.

cell biology↗

bioRxiv2022

Targeting Staufen 1 with antisense oligonucleotides for treating ALS and SCA2

Staufen1 (STAU1) is a multifunctional RNA binding protein that controls mRNA degradation and subcellular localization. STAU1 interacts with the ATXN2 protein, that is polyglutamine expanded in spinocerebellar ataxia type 2 (SCA2). We previously showed that STAU1 is elevated and aggregated in cells from SCA2 patients, cells from amyotrophic lateral sclerosis (ALS) patients, and in SCA2 and ALS mouse models. We also found that reduction of STAU1 abundance in vivo by genetic interaction improved motor behavior in an SCA2 mouse model, normalized the levels of several SCA2-related proteins, and reduced aggregation of polyglutamine-expanded ATXN2. Here we developed antisense oligonucleotides (ASOs) lowering STAU1 expression toward developing a therapeutic that may be effective for treating SCA2 and ALS. We performed a screen of 118 20mer phosphorothioate 2-O-methoxyethyl (MOE) ASO gapmers targeting across the STAU1 mRNA coding region for lowering STAU1 expression in HEK-293 cells. ASO hits lowering STAU1 by >45 % were rescreened in SCA2 patient fibroblasts, and 10 of these were tested for lowering STAU1 abundance in vivo in a new BAC-STAU1 mouse model. This identified efficacious ASOs targeting human STAU1 in vivo that normalized autophagy marker proteins, including ASO-45 that also targets mouse Stau1. When delivered by intracerebroventricular (ICV) injection, ASO-45 normalized autophagy markers and abnormal mRNA abundances in cerebella of ATXN2-Q127 SCA2 mice, as well as ChAT, NeuN and cleaved caspase-3 in spinal cord of Thy1- TDP-43 transgenic mice. Targeting STAU1 may be an effective strategy for treating ALS and SCA2 as well as other disorders characterized by its overabundance.

neuroscience↗

bioRxiv2022

Glutathione activates PHT1;5 gene via WRKY75 transcription factor to regulate phosphate homeostasis in Arabidopsis

Phosphorus (P) is essential for plant growth, yet inorganic phosphate (Pi) is often limiting in soil. Plants respond to Pi limitation by activating P transporters and starvation genes, which boost Pi uptake or redistribute P. While glutathione (GSH) regulates iron and zinc homeostasis in Arabidopsis, its role in P homeostasis under Pi limitation remains elusive. Here, we show that GSH-S-nitrosoglutathione (GSNO) module regulates source-to-sink P allocation in Arabidopsis by transcriptionally activating the phloem-localised transporter AtPHT1;5 via the transcription factor AtWRKY75. GSH-deficient mutants, cad2-1 and pad2-1, exhibited sensitivity to Pi-starvation with altered root system architecture, reduced anthocyanin accumulation, and disrupted root-to-shoot P transport. AtPHT1;5 transcript levels were markedly reduced in these mutants but were positively responsive to exogenous GSH or GSNO. The pht1;5 mutant failed to respond to GSH treatments, demonstrating that AtPHT1;5 is essential for GSH-mediated P mobilisation. Pharmacological and genetic manipulation of nitric oxide (NO)/GSNO levels implicated GSNO as an essential intermediary. In depth molecular analyses identified AtWRKY75 as a Pi- and GSH/GSNO-responsive activator that binds w-box motifs in the AtPHT1;5 promoter. This was further supported by the lack of AtPHT1;5 induction in the wrky75 mutants. Finally, AtWRKY75 is S-nitrosylated and stabilised by GSH/GSNO, providing a mechanistic link between redox/NO signalling and transcriptional control of P transport. We propose that elevated GSH under Pi limitation is converted to GSNO, which S-nitrosylates AtWRKY75 and promotes AtPHT1;5 expression, thus driving source-to-sink P reallocation. This pathway integrates redox and NO signalling with transcriptional regulation to maintain P homeostasis under Pi starvation. Summary statementGlutathione-S-nitrosoglutathione module regulates phosphate translocation in Arabidopsis under phosphate starvation via transcriptional activation of AtPHT1;5 gene by AtWRKY75 transcription factor.

plant biology↗

bioRxiv2022

Translesion DNA synthesis polymerase kappa functions in the nucleolar stress response

DNA polymerase kappa (Pol{kappa}) has multiple cellular roles such as translesion DNA synthesis, replication of repetitive sequences and nucleotide excision repair. However, the mechanisms regulating Pol{kappa}s cellular activities are unknown. Since all polymerases insert the canonical deoxynucleotide triphosphates, it is difficult to determine which polymerase is active at a particular genomic site. To counter this difficulty, we utilized the selective Pol{kappa} substrate, N2-(4-ethynylbenyl)-2-deoxyguanosine (EBndG), as bait to capture proteins associated with Pol{kappa} synthesized DNA. Here we show that, Pol{kappa} is active in the nucleolus and Pol{kappa} synthesized DNA are enriched with nucleolar proteins. Exposure of cells to benzo[a]pyrene diol epoxide (BPDE) induced hallmarks of nucleolar stress, increased Pol{kappa} stability and nucleolar activity. Other agents that induce nucleolar stress such as mitomycin C, cisplatin and actinomycin D also increased Pol{kappa}s nucleolar activity. The Pol{kappa} activity was cell-cycle independent and dependent on PCNA ubiquitination. In addition, we identified that the expression and activity of Pol{kappa} is regulated by the polycomb complex protein Ring Finger Protein 2 (RNF2) and by poly(ADP)-ribose polymerase 1 (PARP1) catalyzed PARylation. This study provides insight into the novel role of Pol{kappa} in ribosomal RNA synthesis, in maintaining ribosomal DNA integrity after DNA damage thus protecting the cells from nucleolar stress.

molecular biology↗