Biology subjects

Singh, D.

Publications and source records attributed to Singh, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Crosstalk Between Phosphorylation and Ubiquitination Controls the Fate and Function of Strigolactone Signal Transducers

Strigolactones (SL) are pivotal plant hormones that sculpt plant architecture by modulating shoot branching, root development, and meristem activity. While transcriptional responses downstream of SL perception have been well explored, the role of post-translational regulation fine-tuning these responses remains less understood. In this study, we identify a dual-layered regulatory module involving MPK4-mediated phosphorylation and MAX2-dependent ubiquitination that synergistically control the stability and function of BRC1, a key SL-responsive transcription factor. Phosphorylation by MPK4 stabilizes BRC1, enhancing its activity and SL sensitivity, whereas loss of phosphorylation leads to BRC1 degradation and functional inactivation. BRC1, in turn, directly activates MPK4 transcription, establishing a positive feedback loop that amplifies SL signaling. Genetic analyses of the brc1-2 x mpk4 double mutant reveals phenotypic defects and SL insensitivity additive to those observed in the brc1-2 and mpk4 single mutants, indicating that MPK4 and BRC1 act in parallel yet converging pathways downstream of SL. Additionally, MAX2 functions as a regulatory checkpoint that degrades non-phosphorylated MPK4 and BRC1, thereby resetting the signaling circuit to ensure accurate and timely response. Together, these findings illuminate a finely-tuned regulatory module integrating phosphorylation and ubiquitination to control the intensity and duration of SL responses, suggesting a model for hormone-driven developmental plasticity in plants.

molecular biology↗

bioRxiv2025

Genome-scale metabolic modelling of trimethoprim's mode of action reveals free ATP salvaged to restore purine pool

Trimethoprim is a clinically important antibiotic for treating urinary tract infections yet its mechanism of killing remains elusive due to a cascade of effected metabolic reactions. Metabolites available in growth media can selectively counteract trimethoprim which affects the interpretation of results. We sought to understand the full scope of trimethoprims impact on Escherichia coli metabolism and how metabolite availability affects trimethoprim outcomes. We applied flux balance analysis on a genome-scale metabolic model of E. coli to simulate trimethoprim activity under bacteriostatic and bactericidal conditions. Our results suggested that in the absence of environmental purines or nucleosides, trimethoprim induces salvage of ATP to repair DNA. We experimentally validated the result with ATP bioluminescence screening of 96 clinical E. coli isolates. Therefore, the choice of growth media composition significantly changes the outcome of trimethoprim challenge and should be taken into consideration when interpreting trimethoprims activity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/666800v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@cddc46org.highwire.dtl.DTLVardef@138a743org.highwire.dtl.DTLVardef@6d4857org.highwire.dtl.DTLVardef@a8502d_HPS_FORMAT_FIGEXP M_FIG C_FIG Diagrammatic representation of trimethoprim action on susceptible UPEC in bacteriostatic and bactericidal conditions. The diagram flows downwards in a time-irrespective manner with outcomes on cellular functions/properties not in order of events. The half-tone at the end represents slowing down of cellular process, however, the outcome is not clear in bactericidal conditions. Circular, green, glowing element at the end of ATP is a representation of ATP bioluminescence. Further, thinning of the line for viability and ATP denotes a reduction in the respective property. RNA and DNA components are labelled above the trimethoprim line with solid grey-to-yellow lines denoting components unaffected by trimethoprim activity. The components that are affected by trimethoprim are replenished by ATP, adenine, or uracil (U) and are denoted by the flow of lines. Abbreviations: A, adenine; C, cytosine; G, guanine; T, thymidine; U, uracil. Sources: Kwon et al. 1, Amyes and Smith 2, Makino and Munakata 6, this study.

systems biology↗

bioRxiv2025

Increased vaccine efficacy against tuberculosis with a recombinant BCG overexpressing the STING agonist cyclic di AMP

Tuberculosis (TB) remains the leading cause of death due to infection globally. Bacillus Calmette Guerin (BCG), a live attenuated bacterial strain, is the only available TB vaccine, but it has poor efficacy in preventing pulmonary TB in adults. There are advantages associated with the BCG platform however, including a remarkable safely profile, billions of administered doses and a public health ecosystem associated with its production, administration and care. A recombinant/modified BCG (rBCG/modBCG) anti-TB vaccine candidate would be able to leverage these advantages while improving on efficacy. BCG-STING is a recombinant BCG strain which overexpresses the mycobacterial diadenylate cyclase disA gene leading to the release of [~]15-fold greater levels of the endogenous small molecule STING agonist cyclic di-AMP. We evaluated vaccination with BCG-STING compared to its parental BCG-WT strain in rhesus macaques challenged with virulent Mycobacterium tuberculosis (Mtb). BCG-STING given intradermally was well-tolerated, and during life serial BAL samples showed that BCG-STING vaccinated animals had lower Mtb CFU counts than those receiving BCG-WT. At necropsy, BCG-STING vaccinated animals had significantly lower Mtb lung CFU counts, and a higher percentage of sterile lobes and granuloma lesions than the BCG-WT recipients. The enhanced protection observed in BCG-STING vaccinated animals was associated with significant elevations of antigen-specific CD4+ and CD8+ T cells. Modifying BCG to overexpress a small molecule recognized by the innate immune system significantly improves protection and cell-mediated immune responses against TB the non-human primate (NHP) model.

microbiology↗

bioRxiv2025

Microneedle-based precision payload delivery in plants

Traditional crop delivery methods, such as foliar spray and soil application, face significant limitations, including nutrient loss, environmental impacts, and low delivery efficiency. Recent advances in nanomaterials have offered novel molecular delivery platforms, but challenges such as synthesis complexity, long-term stability, and compliance with rigorous biosafety regulations persist. To provide a simpler, lower-cost, and safer alternative, we developed a polyvinyl alcohol (PVA)-based microneedle (MN) delivery system that can be precisely applied to various plant tissues (e.g., stem, lateral branch, or petiole), which demonstrates high delivery efficiency compared to the conventional methods (3.5x higher tissue accumulation) while reducing application dose (>90% less). This MN system facilitates the delivery of diverse small molecules, ranging from fluorescent dyes, growth promoters, to antiviral hormones, into plant tissues, on the other hand showing limited wounding stress to the plant. By applying fluorescent dye-loaded MNs onto tomato stems, we demonstrated effective molecular diffusion through vascular tissues. Additionally, MNs loaded with gibberellic acid (GA3) enhanced stem and branch growth in tomatoes and restored the lateral flowering phenotype in Arabidopsis ft-10 mutants, with significant upregulation of GA receptor gene expression. Lastly, salicylic acid (SA) injections with MNs induced resistance to tomato spotted wilt virus (TSWV) in Nicotiana benthamiana, comparable to conventional spray and infiltration-based approaches. This easily fabricated and cost-effective MN system offers a promising tool for precision agriculture, enhancing plant health and productivity while significantly reducing the use of agrochemicals.

plant biology↗

bioRxiv2025

Spatial control of secretory vesicle targeting by the Ync13-Rga7-Rng10 complex during cytokinesis

Cytokinesis requires precise coordination of contractile-ring constriction, vesicle trafficking and fusion to the plasma membrane, and extracellular matrix assembly/remodeling at the cleavage furrow to ensure faithful cell division and maintain cell integrity. These processes and proteins involved are broadly conserved across eukaryotes, yet molecular mechanisms controlling the spatiotemporal pathways of membrane trafficking remain poorly understood. Here, using fission yeast genetics, microscopy, and in vitro binding assays, we identify a conserved module including the Munc13 protein Ync13, F-BAR protein Rga7, and coiled-coil protein Rng10 to be critical for precise and selective vesicle targeting during cytokinesis. The module specifically recruit the TRAPP-II but not exocyst complex to tether vesicles containing the glucan synthases Bgs4 and Ags1 along the cleavage furrow. Ync13 subsequently interacts with the SM protein Sec1 for vesicle fusion. Mutations in this pathway disrupt septum integrity and lead to cell lysis. Our work provides key insights into how membrane trafficking is tightly controlled to maintain cell integrity during cytokinesis.

cell biology↗

bioRxiv2025

Evolution of Enhancers through Duplication

Duplication is appreciated as a key source of genomic novelty. In this study, we examined putative enhancers in the human genome to investigate how duplication influences the evolution of these enhancers. We strictly identified a set of 3,336 confident duplicate enhancer pairs and examined their genomic and evolutionary features. We found that, compared to non-duplicated enhancers, duplicated enhancers tend to be longer, more pleiotropic, closer to genes, and harbor greater numbers and more diverse groups of transcription factor binding motifs. These attributes were more pronounced for evolutionarily older duplicate enhancers. Therefore, the regulatory potentials of enhancers may facilitate evolutionary maintenance of duplicated enhancers. Utilizing chimpanzee and rhesus macaque as outgroups, we found that between 30-40% of the examined duplicate enhancers exhibit evidence of asymmetric sequence evolution. Notably, the majority of the "accelerating enhancers" in such pairs gained enhancer activities in novel tissues, particularly in immune-related tissues. Moreover, the accelerating enhancers tended to harbor transcription factor binding motifs previously implicated in human evolution, and enriched in associations with immune functions and stress responses. These findings indicate that duplication may contribute to the proliferation of highly pleiotropic enhancers, as well as gaining novel enhancer activities, and contribute to rapid evolution of the immune system.

evolutionary biology↗

bioRxiv2025

High and low exogenous nitrate concentrations produce distinct calcium signatures in Arabidopsis roots

Calcium (Ca2+) acts as a secondary messenger in plant responses to many stimuli, including nitrate (NO -) signaling in roots. Nitrate uptake in plants occurs through two distinct transporter systems that have different affinities for the anion, which result in divergent downstream regulatory responses. However, it is unknown if the concentration dependent NO - response is linked to differential Ca2+ response. In this study, we used an Arabidopsis transgenic line expressing CBL1-mRuby2-GCaMP6s to investigate if there are unique Ca2+ signatures in intact root tissue in response to high and low NO - concentrations. A significant Ca2+ response was observed in root hairs in response to both high (5 mM) and low (0.25 mM) NO - concentrations. A distinct Ca2+ wave was observed in the low NO - treated roots, and an asynchronous Ca2+ response was captured in individual root epidermal cells. Cell-specific analysis revealed a distinct Ca2+ profile, comprising waves and spikes in response to NO -, and prominent in root hairs but not in non-root hair bearing epidermal cells. The findings from this study demonstrate that there are distinct cell-specific and NO - condition-specific Ca2+ signatures in Arabidopsis roots.

plant biology↗

bioRxiv2025

De novo Transcriptomic Analysis to Understanding Piperine Biosynthesis in Piper chaba Hunter

Medicinal plants serve as invaluable sources of bioactive compounds, yet the molecular basis of their secondary metabolite biosynthesis remains largely unexplored. Piper chaba Hunter, an important but understudied member of the Piperaceae family, is known for its pharmacologically active alkaloids, particularly piperine. This study presents the first comprehensive transcriptomic analysis of P. chaba to uncover the genetic pathways regulating its metabolite production. The quantification of piperine, a major bioactive compound, was conducted using UPLC, which revealed its highest concentration in the spike (331.3 mg/g) followed by the stem (63.5 mg/g), root (10.3 mg/g), and leaves (2.82 mg/g). High-quality RNA sequencing of leaves, roots, and spikes using next-generation sequencing (NGS) generated 228,481 transcripts, and 184,574 unigenes were identified after redundancy removal. Coding sequences (CDS) derived from these unigenes were annotated using BLASTX and KEGG databases, which highlighted significant metabolic pathways, including those related to piperine biosynthesis. A total of thirteen genes associated with piperine biosynthesis were identified. Validation of nine selected genes, including Farnesyl pyrophosphate synthase and Piperic acid synthase, was performed through qRT-PCR using the 2-{Delta}{Delta}Ct method, confirming their involvement in piperine and other metabolite biosynthesis. Functional annotation categorized the CDS into Gene Ontology domains, with transcription factors such as bHLH and NAC families playing prominent roles in metabolic regulation. Additionally, 5,050 SSRs were identified, offering potential markers for genetic studies. This pioneering study establishes a molecular framework for understanding the biosynthetic pathways of P. chaba, providing valuable insights for its application in sustainable medicine and agriculture.

genomics↗

bioRxiv2025

Activity of Carbazole, Aminoguanidine and Diamine Anti-infectives against Toxoplasma gondii

We report the observation that carbazole anti-infectives developed as antibacterial and antifungal drug leads have activity against the tachyzoite-stage growth of the Apicomplexan parasite Toxoplasma gondii with IC50 values as low as 2 M. We show that a phenylthiazole aminoguanidine with antibacterial as well as antifungal activity inhibits growth with an IC50 value of 2.1 M. We also tested a series of 18 analogs of the diamine SQ109, a tuberculosis drug candidate which likewise has both antibacterial and antifungal activity, finding activity as low as 2.3 M. We tested all compounds for their activity in collapsing the {Delta}pH component of the promotive force, the results indicating that all compounds acted, at least in part, as protonophore uncouplers. Finally, we also investigated the correlation between the activity of all compounds against the yeast Saccharomyces cerevisiae and the bacterium Mycobacterium smegmatis, finding significant correlations between the collapse of the proton motive force and anti- fungal/antibacterial activity.

microbiology↗

bioRxiv2025

Beyond the Hype: The Complexity of Automated Cell Type Annotations with GPT-4

Recent research has shown the impressive capability of large language models like GPT-4 in various downstream tasks in single-cell data analysis. Among these tasks, cell type annotation remains particularly challenging, with researchers exploring various methods to improve accuracy and efficiency. While recent studies on GPT-like models have demonstrated annotation performance comparable to manual annotations, a significant gap remains in understanding their limitations and generalizability. In this work, we compare and evaluate the annotation performance of the GPT-4 model against traditional methods on nine randomly selected public single-cell RNA seq datasets from cellxgene, covering diverse tissue types. Our evaluation highlights the complexity of annotating cell types in single-cell data, revealing key differences between automated and manual approaches. We found specific cases where GPT-4 underperforms, demonstrating its limitations in certain contexts. We further introduce an automated approach to incorporate literature search using a RAG approach which enhances and outperforms GPT-4 cell type annotation when compared to traditional methods. We also introduce metrics based on taxonomic distance in the ontology tree to evaluate the granularity of the cell type annotations. To support future research, we also release an open-source Python package 1 that enables fully automated cell-type annotation of single-cell data using GPT-4 alongside other methods. The pipeline can take paper as an input and do cell type annotations on its own.

bioinformatics↗

bioRxiv2025

Inferring binding rates from enzymatic turnover time statistics

We present a method to extract enzyme-substrate binding rates from observations of enzymatic turnover times. Our approach involves segregating the short-time statistics of the turnover time distribution and inferring from it the binding rate in a general and robust manner. Beyond determining binding rates, the approach developed herein also allows us to infer: (i) the fertile collision probability p, i.e., the probability that a collision between an enzyme and a substrate will result in the formation of an enzyme-substrate complex; and (ii) the fertile catalysis probability{phi} cat, i.e., the probability that the enzyme-substrate complex will lead to the formation of a product. It has long been known that p{phi}cat << 1, indicating that most enzymes operate far from maximal efficiency, yet separating the contributions of fertile binding and catalysis was not possible in lieu of direct binding rate measurements. Our method overcomes this limitation by enabling precise inference of binding rates from turnover times, which in turn opens the door for a more detailed understanding of enzymatic efficiency.

biophysics↗

bioRxiv2025

Anti-Parasitics with a Triple Threat: Targeting Parasite Enzymes, the Proton Motive Force, and Host Cell-Mediated Killing

We investigated the effects of the tuberculosis drug candidate SQ109 (8a) and of its analog MeSQ109 (8b) against Leishmania mexicana in promastigote and amastigote forms, as well as against host cell macrophages finding potent activity (1.7 nM) for MeSQ109 against the intracellular forms, as well as low toxicity ([~]61 {micro}M) to host cells, resulting in a selectivity index of [~]36,000. We then investigated the mechanism of action of MeSQ109 finding that it targeted parasite mitochondria, collapsing the proton motive force, as well as targeting acidocalcisomes, rapidly increasing the intracellular Ca2+ concentration. Using an E. coli inverted membrane vesicle assay, we investigated the pH gradient collapse for SQ109 and 17 analogs finding that there was a significant correlation (on average R=0.67, p[~]0.008) between pH gradient collapse and cell growth inhibition in Trypanosoma brucei, T. cruzi, L. donovani and Plasmodium falciparum. We also investigated pH gradient collapse with other anti-leishmanial agents: azoles, antimonials, benzofurans, amphotericin B and miltefosine. The enhanced activity against intracellular trypanosomatids is seen with Leishmania spp. grown in macrophages but not with Trypanosoma cruzi in epithelial cells and is proposed to be due in part to host-based killing, based on the recent observation that SQ109 is known to convert macrophages to a pro-inflammatory (M1) phenotype.

microbiology↗

bioRxiv2025

Deep learning reveals functional archetypes in the adult human gut microbiome that underlie interindividual variability and confound disease signals

Understanding the functional diversity of the gut microbiome is essential for decoding its roles in health and disease. Using a deep-learning framework, we identified three functional archetypes defining healthy adult gut microbiomes, each characterized by specific metabolic potentials: sugar metabolism with branched-chain amino acid and cell wall synthesis (Archetype 1), fatty acid and TCA cycle metabolism (Archetype 2), and amino acid and nitrogen metabolism (Archetype 3). Archetype proximity is linked to stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility. Functional diversity emerged as a confounder in disease-associated microbial signatures. In inflammatory bowel disease, we observed archetype-specific shifts, including increased carbohydrate metabolism in Archetype 1-dominant samples and inflammatory pathways in Archetype 3-dominant samples, suggesting distinct opportunities for microbiome-targeted interventions. This framework addresses key challenges in microbiome research, including inter-individual variability and confounding, while providing robust insights into disease-associated functional shifts and microbial ecosystem dynamics. HighlightsO_LIAdult gut microbiomes are defined by three functional archetypes C_LIO_LIArchetypes reveal distinct metabolic potentials and inform on microbiome stability C_LIO_LIArchetype-specific functional profiles confound disease associations and reveal therapeutic targets C_LIO_LIA deep-learning framework enables robust characterization of microbial functional ecosystems C_LI

microbiology↗

bioRxiv2025

Regulatory Analysis of Root Architectural and Anatomical Adaptation to Nitrate and Ammonium in Brachypodium distachyon

Root system architecture plays an important role in nitrate and ammonium uptake, the two primary nitrogen (N) forms essential for plant growth. Plants deploy different strategies to optimize the N uptake by roots, based on a complicated regulatory network that controls root phenotype and physiology. Here, we studied the response of root architecture to varying N applications in the model species Brachypodium distachyon. Using a combination of phenotypic and transcriptomic analyses, we examined how different forms and concentrations of ammonium and nitrate affect root growth, biomass allocation, and N uptake. N concentrations significantly influence root traits such as root length, root hair development, and aerenchyma formation in response to nitrate and ammonium. Plants grown in ammonium conditions had thin but highly branched roots, whereas nitrate application resulted in shorter, thicker roots with denser root hair at higher nitrate concentrations. Furthermore, using advanced co-expression network analysis, we identified an Atypical Aspartic Protease (APs) gene encoding an aspartyl protease family protein and a phosphoenolpyruvate carboxylase 1 (PEPC1) gene in brachypodium, which potentially control the root architectural and anatomical adaptions to different N form. APs expression showed a positive correlation with total root length and lateral root development, along with a negative correlation with root hair density. In contrast, PEPC1 exhibited positive correlations with cortex, stele, root cross-sectional areas, and root hair density, while showing a negative correlation with total root length. These genes likely play an important role in the transcriptional regulatory networks involved in these adaptive responses, which highlight the complex interplay between root morphology, nitrogen metabolism, and environmental nutrient conditions.

plant biology↗

bioRxiv2025

An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility

Retrotransposons, multi-copy sequences that propagate via copy-and-paste mechanisms involving an RNA intermediate, occupy large portions of all eukaryotic genomes. A great majority of their manifold copies remain silenced in somatic cells, nevertheless, some are transcribed, often in a tissue specific manner, and a small fraction retains its ability to mobilize. Retrotransposon expression or mobility are increasingly recognized to contribute to normal development and tissue homeostasis, as well as to aging and disease. While it is well characterized that retrotransposon sequences may provide cis regulatory elements for neighboring genes, how their own expression and mobility are achieved in different somatic contexts is not well understood. Here, using long-read DNA sequencing, we characterize somatic retrotransposition in the Drosophila intestine. We show that retroelement mobility does not change significantly upon aging and is limited to very few active sub-families of retrotransposons. Importantly, we identify a polymorphic donor locus of an endogenous LTR retroviral element rover, active in the intestinal tissue. We reveal that gut activity of the rover donor copy depends on its genomic environment. Without affecting local gene expression, the copy co-opts its upstream enhancer sequence, rich in transcription factor binding sites, for somatic expression. Further we show that escargot, a snail-type transcription factor critical for gut progenitor cell function, can drive transcriptional activity of the active rover copy. These data provide new insights into how locus-specific features allow active retrotransposons to produce functional transcripts and mobilize in a somatic lineage.

genomics↗

bioRxiv2024

Genetic basis of immunity in Indian cattle as revealed by comparative analysis of Bos genome

Indicine cattle (Bos indicus) show notable resilience and disease resistance compared with taurine breeds, but the genomic basis of these traits remains largely unexplored. Identification of genomic elements for immunity will enable future controlled crossbreeding programs using molecular breeding methods. Therefore, we performed a genome-wide comparison among Nelore, Gir, and Hereford breeds using their whole-genome sequences, majorly focusing on immune-related structural and sequence variation. Our aims were to catalog insertions, deletions, and single nucleotide variants (SNVs) that intersect immune loci and known quantitative trait loci (QTLs), identify runs of homozygosity and selective-sweep signals, and prioritize candidate genes for follow-up functional studies. We retrieved whole-genome sequencing data for Nelore breed (n=14) and Gir breed (n=20) from NCBI using the SRA toolkit. Reads were checked with FastQC, filtered with fastp to remove low-quality bases and adaptors, and retained high-quality reads based on Q20 and Q30. The reads were mapped to the Bos taurus reference (ARS-UCD2.0) with BWA-MEM; alignments were processed with SAMtools for sorting, duplicate marking, and MAPQ [≥] 20 filtering. Variants (insertions, deletions, SNVs) were called with GATK HaplotypeCaller, hard-filtered, normalized with bcftools, and annotated with SnpEff and SnpSift. Common variants were identified via in-house Python scripts; immune loci were detected from InnateDB and keyword searches; QTL overlaps were identified using Animal QTLdb; DAVID was used for GO and KEGG enrichment (P < 0.05). ROH islands were defined in PLINK as regions shared by >50% of individuals or samples, and selective sweeps were detected with RAiSD; genes overlapping ROH islands and RAiSD peaks were prioritized as candidate selection signatures. GATK identified 1,884,058 indels and 13,997,533 SNVs in Nelore breed, and 1,457,337 indels and 11,627,881 SNVs in Gir breed, with Ti/Tv ratios of [~]2.26 and [~]2.25, respectively. Nelore breed has more number of variants than Gir. We observed frameshift insertions in TLR3 and LOC508441 (CD33) in both the breeds and frameshift deletions in JAM3 in Nelore breed and PAX5 in Gir breed. The variants are also identified in the regulatory regions of both breeds. The high-impact SNVs were in CD46 and IL26 genes in Nelore breed, and PLG gene in Gir breed. Genome-wide scans using RAiSD identified selective sweeps in 707 candidate genes in Nelore breed and 165 in Gir breed. Comparing the ROH and RAiSD results, we prioritized the genes ANKRD11, MAGI2, LOC132345096, FOXP2, TCF12, and ATP5PO in Nelore breed, and the genes MEFV and ORIF1 in Gir breed. These genes are found in QTLs linked to milk and health traits. Functional enrichment showed that the genes exhibiting all the three variants belong to immune pathways such as, NF-kappaB signaling, T-cell receptor signaling, and MAPK signaling in both breeds. These results reveal breed-specific genomic variation locating immune loci and its associated QTLs and provide a list of candidate genes and regions for experimental validation and marker development to improve disease resistance and productivity in Indicine cattle. Keywords: Hereford, Nelore, Gir, immune-related genes, QTLs, Whole genome sequence

bioinformatics↗

bioRxiv2024

A TORC1-PHR1 signaling axis regulates phosphorus starvation and immunity signaling network in Arabidopsis

The Target of Rapamycin Complex 1 (TORC1) is a crucial eukaryotic kinase that modulates growth in response to nutrient availability. Phosphorus (P) is an essential macronutrient, and its deficiency induces extensive reprogramming of growth and defense strategies in plants. This process involves Phosphate Starvation Response 1 (PHR1), a master regulator of the Phosphate Starvation Response (PSR). In this study, we identify a novel, non-canonical role for TORC1 in regulating P starvation responses in Arabidopsis. We demonstrate that P limitation activates TORC1, leading to the stabilization of PHR1. Inhibition of TORC1 increased sensitivity to P starvation, accompanied by disruption of starvation-induced transcriptional reprogramming. Additionally, our results reveal that the TORC1-PHR1 signaling axis plays a crucial role in reprogramming the expression of genes involved in the plant immune signaling network. This regulation is critical for the symbiotic association with the endophytic fungus Piriformospora indica under P starvation. These findings underscore the significant role of the TORC1-PHR1 module in orchestrating the PSR and highlight the evolutionary adaptation of TORC1 signaling pathways in plants.

plant biology↗

bioRxiv2024

G-quadruplex Structures in Dysregulated Long Non-Coding RNA of Ovarian Cancer and their Binding Interactions with Human Serum Albumin

Ovarian carcinoma (OC) is a major cause of cancer-related mortality among women worldwide, with especially poor outcomes in resource-constrained regions. Long non-coding RNAs (lncRNAs) have emerged as critical players in OC progression, influencing drug resistance, metastasis, and other cellular processes. This study examines the potential of dysregulated lncRNAs in OC to form G-quadruplex (G4) structures. Using in silico predictions and experimental validation, we identified five lncRNAs ERLNC1, DLX6-AS1, LINC01127, FMNL1-DT, and LINP1 as candidates with a high propensity towards G4 formation. A combination of circular dichroism (CD) spectroscopy, Thioflavin T (ThT) fluorescence assay, Dot Blot assay, and reverse transcriptase stop assay, confirmed the ability of the lncRNAs to fold into stable G4 structures. Competitive DNA binding assays enabled the identification of essential G-tracts within each G4 motif highlighting the subtle differences in structure and stability of the different quadruplexes. Human serum albumin (HSA), a major circulatory protein, was found to interact with these G4-forming lncRNAs, albeit with different affinities and structural implications on the G4 motifs. This study provides the first detailed characterization of G4 structures in OC-dysregulated lncRNAs and elucidates their interactions with HSA. The G4 structures identified in these lncRNAs and their interaction with HSA can be of potential value for early OC diagnosis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/624450v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@75dc3eorg.highwire.dtl.DTLVardef@1ce7b18org.highwire.dtl.DTLVardef@f371e4org.highwire.dtl.DTLVardef@ba5212_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗