Biology subjects

Singh, K.

Publications and source records attributed to Singh, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Treg-derived IκBζ promotes their conversion into Th2-like effectors and drives type 2 inflammation via BATF

Regulatory T cells (Treg cells) maintain peripheral immune tolerance but display considerable plasticity in peripheral tissues. The molecular mechanisms governing their function and plasticity, particularly under inflammatory conditions, remain poorly defined. Here, we identify the NF-{kappa}B-associated transcriptional cofactor I{kappa}B{zeta} as a critical regulator of Treg cell plasticity and function. Enforced expression of I{kappa}B{zeta} in Treg cells triggered the excessive expansion of functionally impaired Treg cells, resulting in lymphadenopathy, splenomegaly, and systemic type 2 inflammation, most prominently in the lung. Mechanistically, I{kappa}B{zeta} modified BATF expression and function, thereby driving the cell-intrinsic production of Th2-associated cytokines by Treg cells. Conversely, Treg-specific deletion of I{kappa}B{zeta} constrained IL-33-mediated expansion of tissue Treg cells and surprisingly attenuated type 2 inflammation. Thus, I{kappa}B{zeta} functions as a molecular switch that reprograms regulatory T cells into Th2-like Treg cells, thereby perturbing peripheral immune tolerance. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/707402v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1ef0b17org.highwire.dtl.DTLVardef@c12eaaorg.highwire.dtl.DTLVardef@decc86org.highwire.dtl.DTLVardef@1458767_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Transcriptomic Analysis Reveals Inflammatory and Metabolic Dysregulation in Unexplained Female Infertility

Infertility is a complex condition affecting both the male and female population. Influenced by multiple factors, it remains a constant challenge due to limited understanding of endometrial abnormalities. With this study we aim to investigate the molecular basis of infertility using transcriptomic analysis of endometrial tissue from the NCBI GEO dataset GSE92324. We performed exploratory data analysis using Principal Component Analysis (PCA) to find samples variance followed by differential gene expression (DGE) analysis using DESeq2 package where we identified 168 significant genes with adjusted p-value < 0.05 and |log2FC| > 2. Upregulated genes included GPX3, CXCL14, and PPARGC1A and downregulated genes included WNK4, GJB2, and TRPM6. Functional enrichment using KEGG and GO showed that differentially expressed genes (DEGs) are involved in immune-inflammatory pathways, lipid metabolism and steroid biosynthesis pathways. Through Ingenuity Pathway Analysis (IPA) we identified affected canonical pathways such as increased innate immune responses, altered lipid metabolism and inhibition of mitochondrial dysfunction. Upstream regulator analysis highlighted PTEN, PRKAA1, HDAC4, IL10RA, and RAD51, which were impacting metabolic pathways and anti-inflammatory signalling. Further, through Weighted Gene Co-expression Network Analysis (WGCNA) we found a Turquoise module that had very strong and highly significant negative correlation (cor = - 0.84, respectively and P < 0.0001) with traits of interest. This led to the discovery of C7orf50 as a novel insight involved in cholesterol metabolism linked to infertility. This integrative approach reveals crucial genes, co-expression modules, and underlying pathways involved in female infertility. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/701467v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@4418a6org.highwire.dtl.DTLVardef@ae7900org.highwire.dtl.DTLVardef@89f581org.highwire.dtl.DTLVardef@154f1a9_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIFrom the dataset GSE92324 total of 168 significant DEGs associated with unexplained infertility were identified using adjusted p-value < 0.05 and |log2FC| > and < 2. C_LIO_LIIn comparison with the CTD list we identified five genes C1orf106, C15orf59, LINC00461, C15orf48, and C10orf99 previously unknown as having direct evidence of involvement in infertility. C_LIO_LIWGCNA analysis highlighted the turquoise module as highly associated and gave the novel gene C7orf50 associated with cholesterol metabolism. C_LIO_LIIPA revealed PTEN, PRKAA1, IL10RA, and RAD51 as potential upstream regulators and inflammatory pathways, mitochondrial dysfunction as canonical pathways. C_LIO_LIThe study highlights a novel link between GI inflammation and endometrial receptivity. C_LI

bioinformatics↗

bioRxiv2026

A First-In-Class Broad Spectrum Inhibitor of Copper Exporting P1B-type ATPases

Copper (Cu) transporting ATPases represent a highly conserved subclass of P-type ATPases with critical roles in Cu export and metalloenzyme synthesis. Despite their important biological roles and association with a wide range of human diseases, no high-affinity small-molecule inhibitors have been described. Here, we identify MKV3 as a first-in-class inhibitor of Cu-transporting P-type ATPases that targets a conserved Cu+ entry site to the translocation pathway. In silico docking against the Xenopus ATP7B structure revealed a highly conserved pocket suitable for pharmacological inhibition. MKV3 bound human ATP7A and ATP7B with nanomolar affinity, competed with N-terminal metal-binding domains for access to the Cu+ entry site, and selectively inhibited Escherichia coli CopA ATPase activity and Cu+ transport. Mechanistically, MKV3 blocked chaperone-mediated Cu+ delivery to the intramembranous CPC site of CopA that is essential for its transport function. We further identified a single charged P-domain residue that governed MKV3 affinity and potency across species. Functionally, MKV3 phenocopied the genetic loss of Cu+-ATPases in bacteria, fungi, plants, zebrafish, and mammals, impairing copper-dependent enzymes, transporter trafficking, and copper tolerance. These findings establish a conserved, druggable vulnerability in Cu+-ATPases and introduce MKV3 as a broadly active chemical tool to modulate copper homeostasis across biological kingdoms. Significance StatementCopper-transporting P1B-type ATPases are essential for copper homeostasis in all domains of life, yet have lacked pharmacological inhibitors. This work identifies MKV3 as the first small-molecule inhibitor of Cu+-ATPases in bacteria, fungi, plants and animals, and defines a conserved, druggable Cu+ entry pocket that governs metal delivery to the transmembrane pathway. MKV3s ability to potentiate copper-mediated killing in multidrug-resistant bacterial pathogens highlights its potential as an antimicrobial adjuvant, while its attenuation of mammalian ATP7A/B function offers promise in oncology and copper-related diseases. Collectively, these findings establish a new tool for targeting of Cu+-ATPases with wide-ranging applications across biological systems.

cell biology↗

bioRxiv2026

A Systems-Level Transcriptomic Analysis of Polycystic Ovary Syndrome as a Mitochondrial-Immunometabolic Disorder

Polycystic Ovary Syndrome (PCOS) is known as an endocrine and metabolic disorder; however, emerging molecular evidence suggests a far more complex systems-level pathology. In this study, we performed an integrative transcriptomic and pathway-level analysis of endometrial tissue from women with PCOS to gain a deeper understanding of the underlying mechanism facilitating the disorder. The findings of the study highlighted mitochondrial dysfunction, chronic oxidative stress, and multi-layered immune dysregulation, adding some new insight apart from classical hyperandrogenism and insulin resistance. We identified some novel gene disease associations which involve C15orf48, ODF3B PRR15-DT, LINC01176, and LOC105379193. The upstream regulators such as (NFE2L2, TWNK, ALKBH1, BCOR, SMARCA4) involved in processes including mitochondrial genome, redox balance, and chromatin remodeling provided new insights into regulatory mechanisms. The IPA pathway analysis validated the compromised immune recovery with low grade inflammations and mitochondrial dysfunctionality. The observations emphasize on complex associations discarding its PCOS pure endocrine nature through immunometabolic-mitochondrial dysfunctionalities.

bioinformatics↗

bioRxiv2026

α-1,3-Glucan-Driven Remodeling of the Conidial Cell Wall in an Aspergillus fumigatus Vaccine Strain Alters Innate Immune Recognition

Aspergillus fumigatus is a major cause of invasive aspergillosis in immunocompromised patients, where current antifungal therapies are limited by toxicity, drug resistance, and lack of durable protection, and no vaccines are available. A mutant lacking the sterylglucosidase-encoding gene (sglA) has emerged as a candidate that induces protective immune responses, but the structural basis for this phenotype remains unclear. Here, we use cellular solid-state NMR spectroscopy to compare the organization of the conidial cell wall in {Delta}sglA and its wild-type counterpart. The {Delta}sglA conidial cell wall displays extensive remodeling, including increased -1,3-glucan content and structural polymorphism, strengthened interactions with {beta}-glucans, reduced hydration, and restricted molecular motion, together consolidating a more rigid scaffold with limited {beta}-glucan accessibility. These structural changes are associated with altered neutrophil responses and a shift in innate immune signaling. This work links cell-wall reorganization to altered immune recognition in this vaccine candidate, with implications for future immunotherapeutic strategies. TEASERMolecular-level Insights from a fungal vaccine candidate show how cell-wall remodeling could affect immune response.

biochemistry↗

bioRxiv2025

From iPSCs to NPCs to cortical neurons: bioenergetic, neuronal, and calcium signaling phenotypes in bipolar disorder with and without familial mitochondrial disease

BackgroundPsychiatric disorders frequently accompany primary mitochondrial diseases (PMDs), implicating mitochondrial dysfunction as a shared biological substrate for psychiatric vulnerability. To determine how familial mitochondrial risk influences neuronal development in bipolar disorder (BD), we generated induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs), and cortical neurons (CNs) from three healthy controls (CT), three patients with BD, and three patients with BD and a family history of mitochondrial disease (BD-FMD). MethodsAcross differentiation, we assessed mitochondrial function (ATP production, mitochondrial membrane potential, ROS generation, cytosolic cell-free mtDNA), metabolomic signatures, calcium imaging, and neuronal electrophysiological activity through multi-electrode arrays (MEA). ResultsBD neurons uniquely exhibited pronounced hyperexcitability in comparison to CT and BD-FMD groups. The BD-FMD group displayed prolonged mitochondrial calcium transients, altered membrane potential, and aberrant ROS, in comparison to CT and BD, consistent with a sustained energetic deficit. Metabolomic profiling revealed distinct pathway enrichments in BD and BD-FMD, indicating divergent bioenergetic adaptations to mitochondrial burden. ConclusionsOur findings reveal that familial mitochondrial liability actively reshapes neuronal differentiation and function, producing distinct trajectories of mitochondrial performance, calcium signaling, and network excitability. These results suggest that mitochondrial dysfunction in BD is not a secondary byproduct of illness, but a mechanistic contributor to altered neuronal energetics and communication. Together, these findings delineate how inherited mitochondrial vulnerability reshapes neuronal excitability and metabolism, revealing bioenergetic phenotypes that may inform precision stratification and therapeutic targeting in BD.

neuroscience↗

bioRxiv2025

A paradoxical impact of alcohol on sleep-memory coupling

Sleep serves a fundamental role in memory consolidation, and yet it must adapt to the organisms physiological state. The latter is impacted profoundly by acute ethanol consumption, but whether intoxication affects the role of sleep in memory consolidation remains unexplored. Here, we demonstrate that acute ethanol inverts the canonical link between sleep and memory in Drosophila. Typically, satiated flies require sleep for appetitive memory consolidation, but starved flies that must forage for food switch to sleep-independent memory. Ethanol selectively impairs memory consolidation in satiated flies by causing a switch to sleep-independent memory, which then cant be supported because of ethanol-induced sedation. Under these conditions, sleep deprivation rescues memory and requires the upregulation of neuropeptide F, which signals through NPF receptors on PPL1 dopaminergic neurons. We suggest that reward-seeking behaviors, induced by starvation or ethanol, invoke sleep-independent memory. However, ethanol has a paradoxical impact, wherein it induces a switch in memory pathways but concurrently suppresses consolidation through the preferred pathway, thereby causing sleep to become detrimental for memory consolidation.

neuroscience↗

bioRxiv2025

Dataset Documentation for Responsible AI: Analysis of Suitability and Usage for Health Datasets

Artificial Intelligence (AI) is rapidly transforming healthcare, but also raising concerns about algorithmic biases that mostly stem from the training data. It is widely supported that transparent dataset documentation is key to enabling responsible AI development. Several standardized dataset documentation approaches have been established, such as Datasheet, Dataset Nutrition Label, Accountability Documentation, Healthsheet, and Data Card. However, their suitability and usage for health datasets remain unclear. In this work, we compared all five approaches and evaluated their alignment with the STANDING Together Recommendations for Documentation of Health Datasets. We also investigated their real-world usage and gathered insights from generators and consumers of health datasets. Our findings reveal that none of these documentation approaches are used widely or fully suited for health datasets. We recommend developing a standard documentation approach for health datasets along with clear guidelines and automation tools to support adoption.

bioinformatics↗

bioRxiv2025

Insights into the mechanism of succinimide formation in an archaeal glutaminase.

Succinimide (SNN), an intermediate formed during asparaginyl deamidation or aspartyl dehydration in proteins, is generally hydrolysis-prone, leading to isomerization to L/D /{beta}-aspartyl residue, with the latter being considered deleterious to protein structure and function. An unusually stable SNN-mediated conformational rigidity through restriction of the backbone dihedral angle, {psi}, enhances the thermostability of glutamine amidotransferase (GATase) from Methanocaldococcus jannaschii (Mj). Although several structural features involved in maintaining a stable SNN and imparting SNN-mediated thermostability have been identified in MjGATase, the residues in the protein that catalyse the rapid and complete conversion of Asn109 to SNN remain unknown. Here, we investigated several site-directed mutants of MjGATase for their ability to retain Asn109 side chain in the unmodified form. Mass spectrometric analysis of 10 single mutants enabled the identification of residues that impacted the proportion of SNN and Asn population in the protein sample. This led to the generation of two double mutants that retained intact Asn109 side chain as observed in the mass spectra and crystal structures. These mutants with intact Asn residue at position 109, displayed lower thermal stability than the protein with the SNN modification. Further understanding of the deprotonation mechanism was addressed using QM/MM MD metadynamics simulations. HighlightsO_LIStable succinimide (SNN) arising from deamidation of Asn109 residue imparts hyperthermostability to MjGATase. C_LIO_LIExamination of the structure of MjGATase suggests neighbouring residues playing possible roles in deamidation and cyclization. C_LIO_LIExamination by LC-MS of single site-directed mutants of residues contacting SNN revealed varied levels of intact Asn109 enabling generation of double mutants with complete absence of deamidation. C_LIO_LIPresence of intact Asn109 confirmed by X-ray crystallography highlights the role of Y158, D110, and K151 in mediating SNN formation. C_LIO_LIQM/MM MD metadynamics simulations support experimental findings. C_LI

biochemistry↗

bioRxiv2025

A biphasic metabolism-β-lactamase production landscape governs the inoculum effect in β-lactamase-expressing Escherichia coli.

The inoculum effect (IE) reduces antibiotic efficacy in vitro and in clinical settings, yet remains difficult to predict. IE limits antibiotic efficacy but remains unpredictable, particularly in resistant bacteria, where resistance mechanisms and bacterial physiology interact in poorly understood ways. Using Escherichia coli expressing the NDM-1 {beta}-lactamase and clinical isolates, we quantified metabolism, growth rate, {beta}-lactamase expression, and IE across diverse growth environments. Across enzyme classes, antibiotics, and clinical isolates, we find that IE is governed by a conserved, biphasic dependence on metabolism normalized by growth rate. Mathematical modeling shows that this behavior reflects a tradeoff between {beta}lactamasemediated protection and metabolismpotentiated antibiotic lethality. These findings establish a predictive, physiology-based framework for IE in resistant bacteria and explain why resistance determinants alone fail to predict treatment outcomes across environments, including the clinic. Significance StatementAntibiotic efficacy depends on both bacterial resistance and physiology, yet these factors are rarely integrated when predicting treatment outcomes. One important consequence of their interaction is the inoculum effect (IE), in which antibiotic efficacy depends on the density of a resistant bacterial population. Here, we show that IE in {beta}lactamase-expressing bacteria is governed by a conserved physiological tradeoff between metabolism and growth. Across growth environments, antibiotics, inocula, and clinical isolates, IE is strongest at intermediate metabolic states, reflecting a balance between resistancemediated protection and metabolismpotentiated antibiotic lethality. This framework helps explain why resistance determinants alone are insufficient to account for IE and underscores the role of bacterial physiology in shaping antibiotic responses.

microbiology↗

bioRxiv2025

Mycoelectronics: Bioprinted Living Fungal Bioelectronics for Artificial Sensation

The intelligence of the human biological system is enabled by the highly distributed sensing receptors on soft skin that can distinguish various stimulations or environmental cues, thus establishing the fundamental logic of sensing and physiological regulation or response. To replicate biological perception, two approaches have emerged: artificial nervous systems that utilize soft electronics as biomimetic receptors to convert external stimuli into frequency-encoded signals, and biohybrid solutions that integrate living cells, plants, or even live animals with electronic components to decode environmental cues for life-like sensations. However, most current biohybrid approaches for artificial sensation are based on eukaryotic cells, which suffer from slow growth, stringent culture conditions, environmental susceptibility, and short lifespans, thus limiting their integration into practical wearables or robotic sensory skins. Here, we introduce fungi-based printable "Mycoelectronics", which are created by additive bioprinting of living fungal mycelium networks onto stretchable electronics, as a practical living thermo-responsive sensory platform. This Mycoelectronics approach leverages fungis capacity for rapid biological responsiveness, cultivability with exponential growth, stability and self-healing in ambient conditions, bioprintability for scalable manufacturing, and mechanical flexibility for seamless integration with soft electronics. Critically, we discovered that the thermal responsiveness of the fungal network arises from intrinsic cellular processes--specifically, heat-induced vacuole remodeling and fusion, which modulate ionic transport and thus the electrical conductivity of the mycelial cells and networks, enabling a rapid temperature response. By bridging the gap between cell biology and soft electronics, the Mycoelectronics device with a living mycelium network functions as a thermal sensation system with rapid response and intrinsic self-healing properties, autonomously restoring sensing capabilities after damage or autonomously establishing sensor pathways in hard-to-reach locations. Furthermore, by integrating fungal thermal sensing with electronic circuits, we established a hybrid bioelectronic reflex arc that can actuate muscles and initiate diverse actions, suggesting promising applications in future neurorobotics and neuroprosthetics.

bioengineering↗

bioRxiv2025

Chaperone AIP Couples mTORC1 Activation and Catabolic Metabolism During Neonatal Development

To grow and divide cells must tightly coordinate anabolic programs with the availability of nutrients and growth factors. This balance is especially critical during postnatal development, when biosynthetic and energetic demands are high, and nutrient supply and neonates have to adapt to periods of fasting. These conditions place acute stress on the proteostasis network, making autophagy essential for nutrient recycling. We found that the chaperone aryl hydrocarbon receptor-interacting protein (AIP) supports both arms of this metabolic balance: promoting anabolic PI3K-AKT signaling for mTORC1 activation and enabling catabolic processes such as proteasomal degradation and autophagy. Loss of AIP causes a severe neonatal metabolic disorder, where affected infants fail to thrive postnatally. Our findings establish AIP as a central regulator of neonatal metabolic adaptation and cellular homeostasis. One Sentence SummaryAIP integrates nutrient sensing and protein recycling to sustain neonatal survival.

developmental biology↗

bioRxiv2025

Targeting Lysosomal pH Restores Mitochondrial Quality Control in GBA1-Mutant Parkinsons Disease

BackgroundHeterozygous mutations in the Glucocerebrosidase gene (GBA1), which encodes the lysosomal enzyme {beta}-glucocerebrosidase (GCase), are a genetic risk factor for Parkinsons disease (PD). The pathophysiological consequences of GBA1 mutations on dopaminergic neuronal function, especially their impact on lysosomal function, mitophagy, and mitochondrial bioenergetics, remain unclear. MethodsFibroblasts and dopaminergic neurons generated from induced pluripotent stem cells (iPSCs) derived from patients with GBA1-PD were used in the study. Live-cell imaging was performed to measure lysosomal acidification, protease activity, mitochondrial membrane potential, and mitophagy. Mitochondrial morphology and autophagic vesicles were examined using transmission electron microscopy. Oxygen consumption rate was measured by Seahorse assay. V-ATPase assembly was quantified using FLIM-FRET, and pharmacological interventions included rapamycin and acidic nanoparticles. Statistical analyses involved unpaired t-tests, one-way ANOVA, and two-way ANOVA. ResultsGCase activity, lysosomal acidification, protease activity, mitophagy and mitochondrial bioenergetic function were all impaired. Mitochondria were fragmented, with reduced membrane potential and oxygen consumption. MTORC1 was constitutively phosphorylated and FLIM-FRET measurements confirmed impaired lysosomal V-ATPase assembly, which was reversed following rapamycin treatment. Rapamycin and lysosome-targeted acidic nanoparticles rescued lysosomal pH, restored mitophagy, mitochondrial membrane potential and mitochondrial OXPHOS complex levels in GBA1 mutant dopaminergic neurons. ConclusionsWe reveal a novel mechanistic link between GBA1 mutations and mitochondrial dysfunction, as disruption of V-ATPase assembly driven by MTORC1 activation impairs lysosomal acidification. Mitophagy is therefore impaired leading to mitochondrial dysfunction, undermining dopaminergic cell function and fate. Pharmacological intervention with rapamycin or acidic nanoparticles restore lysosomal pH and rescue mitochondrial function, signposting a novel therapeutic approach for GBA1-PD.

neuroscience↗

bioRxiv2025

Coin-tossing by Kinesin-1 Head and Tail Binding Collectively Drives Microtubule Patterns

Intracellular microtubule-based transport depends on an essential plus-ended molecular motor, kinesin-1. The N-terminal ATP-dependent head driving motility and a C-terminal cargo interacting tail, both bind microtubules. Previously, the interplay of both domains were hypothesized to play a role in collective microtubule sliding patterns, but the mechanisms remained unclear. Here, we show that full-length Drosophila kinesin-1 generates striking spatiotemporal patterns in gliding assays including bending, looping, and oscillations as well as stop-and-go motion of filaments. In presence of the motor domain alone these patterns are absent, but with the tail only construct, microtubules bind passively, with the tail acting as a static anchor. An equimolar mixture of these two domain constructs reproduces these spatio-temporal patterns both in terms of increased bending with length and velocity distributions. Our results support a simple coin-toss model, where either head or tail bind microtubules with equal probability, leading to antagonistic interactions that drives emergent motility patterns and velocity distributions. Thus the kinesin tail plays an active mechanical role beyond regulation or cargo binding, modulating microtubule behavior through inter-domain competition.

biophysics↗

bioRxiv2025

Whole genome sequencing-based multi-locus association mapping for kernel iron, zinc and protein content in groundnut

Malnutrition is a major global challenge, especially in the developing regions, where improving the nutritional content of staple crops is a significant step towards alleviating hidden hunger. Groundnut, a nutrient rich legume contains several mineral nutrients, high protein, essential amino-acids and vitamins that are required for human health. In this study, multi-season phenotyping data for kernel iron (Fe), zinc (Zn) content and protein content (PC) and whole genome re-sequencing (WGRS) data on mini-core collection, were used to perform genome-wide association study (GWAS) analysis. Phenotypic variability analysis revealed a large variation in the Fe (7.6 - 42.8 ppm), Zn (10.9 - 62.4 ppm) and PC (12.7 - 33.6%). GWAS analysis identified a total of 15 marker-trait associations (MTAs) and 28 candidate genes for pooled season data, as well as 44 MTAs and 62 candidate genes for individual seasons. Key candidate genes like MYB transcription factor (Arahy.QI0PHV, Arahy.1I6ZSS), Zn finger MYM type protein, RING finger MYM type protein (Arahy.7P97F6, Arahy.9R964H, Arahy.I3B88T) and NAC domain protein (Arahy.LV3APC), associated with the Fe and Zn homeostasis pathway, genes related to protein homeostasis, such as protein kinase family protein (Arahy.4D7KBI), and E3 ubiquitin-protein ligase (Arahy.PE3CF6), were also identified within significant MTA regions. These findings provide basis for the detection and characterization of the possible candidate genes related to the nutritional quality traits. Single nucleotide polymorphism (SNP)-based KASP (Kompetitive Allele Specific Polymerase Chain Reaction) markers for 9 SNPs were designed and validated. Of these, three markers (snpAH00636, snpAH00641 and snpAH00644) showed polymorphism which could be deployed in the genomics-assisted breeding for the development of nutrient-rich groundnut varieties.

plant biology↗

bioRxiv2025

Cryo-EM structures of Egl-BicD-RNA complexes reveal how diverse mRNAs are selected for subcellular localization

Localization of mRNAs is a widespread mechanism for controlling where proteins operate in cells and underpins many fundamental processes, from embryonic patterning to synaptic plasticity. This spatial control is mediated by RNA-binding proteins (RBPs) that interact with localization signals within target mRNAs. However, these signals lack overt sequence or structural patterns, even when targeted by the same protein, raising the question of how specificity is achieved. Here, we investigate this question using the Drosophila RBP Egalitarian (Egl), which couples developmentally important mRNAs to microtubule-based transport via Bicaudal D (BicD) and the dynein motor protein. We present cryo-EM structures of Egl- BicD in complex with six different RNAs. Egl uses multiple non-canonical double-stranded RNA-binding domains to cooperatively form a recognition pocket around a localization signal. Despite substantial variation in length and sequence, each signal adopts a bent stem-loop conformation that, together with base-pair identities at two defined sites, drives Egl binding. We further demonstrate that Egl dimers couple RNA binding to transport initiation through coincident detection of two RNA elements within the same transcript. Collectively, we show that diverse localizing mRNAs are recognized through a combination of shape, positional sequence features, and number of structured RNA elements. This work provides a framework for understanding how other RBPs engage highly variable mRNAs.

cell biology↗

bioRxiv2025

Differentiation of Toxoplasma into latent forms is linked to central carbon metabolism and requires a GID/CTLH-type E3 ubiquitin ligase

Toxoplasma and other Apicomplexan parasites, switch between different developmental stages to persist in and transmit between hosts. Toxoplasma can alternate between systemic tachyzoites and encysted bradyzoite forms found in the CNS and muscle tissues. How parasites sense these tissue types and trigger differentiation remains largely unknown. We show that Toxoplasma differentiation is induced under glucose-limiting conditions and using a CRISPR screen identify parasite genes required for growth under these conditions. From [~]25 identified genes important for differentiation we show that lactate and glutamine metabolism is linked to differentiation and demonstrate the importance of an E3 ubiquitin ligase complex, orthologous to glucose induced degradation deficient (GID) complex in yeast and CTLH complex in humans. We show that TgGID likely regulates translational repression of a key transcription factor required for differentiation, BFD1, through its 3 utr. Overall, this work provides important new insight into how these divergent parasites sense different host cell niches and trigger stage conversion through a ubiquitination-dependent program.

microbiology↗

bioRxiv2025

Bacterial metabolites induce cell wall remodeling, antifungal resistance, and immune recognition of commensal fungi

The fungus Candida albicans commensally colonizes mucosal surfaces in healthy individuals but can cause both superficial mucosal and life-threatening disseminated infections. The balance between commensalism and pathogenicity is complex and depends on factors including host and fungal genetic background, the host environment, and fungal interactions with local microbes. The major interaction interface of C. albicans with the host is its multilayered cell wall, which is dynamic and highly responsive to the surrounding environment. Therefore, factors that influence the fungal cell wall will directly impact C. albicans-host interactions. Our work demonstrates that multiple physiologically-relevant gastrointestinal bacteria influence fungal cell wall composition during co-culture with C. albicans, including as complex communities derived from the gut. Using Escherichia coli as a model, we show that bacterial-induced fungal cell wall remodeling occurs rapidly and is mediated by secreted bacterial metabolite(s). Fungal mutant analysis revealed that the high osmolarity glycerol (HOG) pathway, which is critical for responding to environmental stresses, has an important role in regulating this cell wall remodeling phenotype through the Sln1 histidine kinase. Importantly, bacterial-mediated fungal cell wall remodeling increases C. albicans resistance to the echinocandins, increases recognition by both dectin-1 and dectin-2, and decreases recognition by human IgA. Overall, this work comprehensively characterizes an interaction between C. albicans and common gastrointestinal bacteria that has important implications for fungal biology and host interactions.

microbiology↗