Biology subjects

Babu, K.

Publications and source records attributed to Babu, K..

11 recordsLinked to original sources

bioRxiv2026

Bivalent Inhibitor Development for a Dynamic Epigenetic Tandem Reader Protein Using a Combinatorial Histone Code

Epigenetic readers are a class of proteins that recognize specific chemical modifications on histones to differentially regulate gene expression. Aberrant expression of readers can drive the progression of many diseases and cancers, making this protein class viable therapeutic targets. Understanding the landscape of histone modifications recognized by reader domains, and the structural mechanisms that drive these molecular recognition events, is crucial for guiding the design of pharmaceutically relevant chemical probes. BPTF contains a plant homeodomain (PHD) finger and tandem bromodomain (BRD). Here, we expand upon previous studies that found the BPTF BRD can engage acetyllysine modifications on the N-terminus of histone H3. We uncover H3K4me3K14ac as the specific modifications recognized by the PHD BRD cassette, which is confirmed by crystallography. Using orthogonal methods, our work explores how these modifications can be read cooperatively, including in cis. We report the first experimental evidence proposing a ligand-induced conformational change between the two reader domains of BPTF, supporting previous computational approaches that have predicted a macromolecular rearrangement. We leverage these structural insights to rationally design a peptide-small molecule conjugate MJ-1 that inhibits both domains of BPTF and overcomes ligandability challenges associated with PHD-finger-containing proteins. The results presented here elucidate the molecular basis of the bivalent recognition of multiply modified histone H3 by BPTF and provide structural insight for developing compounds targeting the PHD finger of BPTF for therapeutic applications.

biochemistry↗

bioRxiv2026

An optopharmacological tool for on-demand perturbation of branched actin polymerization

Regulated actin cytoskeletal organization and dynamics are essential for life-sustaining processes in eukaryotic cells. The spatiotemporal regulation of filamentous actin can generate a staggering variety of higher-order architectures to meet diverse cellular needs. However, connecting a specific actin substructure to the selective cellular function remains challenging because tools to specifically inhibit F-actin in a spatiotemporally controlled manner are currently limited. To address this crucial technical gap, we have synthesized and characterized a photocrosslinkable small molecule inhibitor of a major and evolutionarily conserved actin nucleation factor, Arp2/3 complex. The new inhibitor "AZ" combines the specificity of a preexisting inhibitor CK666 with photosensitive crosslinking by an Azido group, such that a light-induced, instantaneous, on-demand, irreversible inhibition of Arp2/3 complex-dependent actin nucleation is achieved in a spatiotemporally defined manner at a subcellular, supracellular, and organismal scale. Whole cell treatment with AZ, followed by subcellular photoirradiation, revealed a divergent actin nucleation homeostasis in the cortex of different cells. Thus, AZ could be a powerful tool to infer actin polymerization homeostasis and network properties in live cells-processes which otherwise remain obscure.

cell biology↗

bioRxiv2025

The claudin-like molecule CLC-3 regulates neuromuscular function in Caenorhabditis elegans by modulating cholinergic signalling

Cell adhesion molecules (CAMs play important roles in neurons, contributing to nervous system development, synapse formation, and activity-dependent plasticity. Claudins, the cell-adhesion molecules known for their roles at tight junctions in epithelial and endothelial cells, remain underexplored in neurons, particularly in vertebrates. In contrast, emerging studies in Caenorhabditis elegans have begun to reveal neuronal functions of claudin-like proteins. However, a systematic analysis of their neuronal expression has not been performed. We conducted a transcriptional reporter screen of all claudin-like genes in C. elegans and identified several candidates with previously unreported neuronal expression, highlighting a broader role of this family in the nervous system. One candidate, clc-3, showed robust expression in head, tail, and ventral cord neurons, with no detectable expression in non-neuronal tissues. Functional analyses of clc-3 mutants revealed increased body-bend amplitude and elevated evoked postsynaptic currents at the cholinergic neuromuscular synapses. Imaging and molecular interaction studies demonstrated that CLC-3 localises to the presynaptic membranes in cholinergic neurons, where it interacts with the actin-binding protein NAB-1 and regulates cholinergic signalling. This presynaptic role of CLC-3 likely contributes to the regulation of sinusoidal movement in C. elegans. Our findings identify CLC-3 as a neuronally expressed claudin that regulates motor system output by influencing synaptic vesicle organization and illustrate how changes in synaptic organization are coupled to whole-animal behaviour.

neuroscience↗

bioRxiv2025

Neuromodulation of Swarming Behavior in C. elegans: Insights into the Conserved role of Calsyntenins

Collective animal behaviors arise from a complex interplay between internal physiological states and external environmental cues. In Caenorhabditis elegans, favorable conditions promote dispersal, while stressors like food scarcity or overcrowding trigger aggregation. Here, we describe a distinct behavior termed as swarming, where C. elegans move and feed in aggregates despite abundant food availability. While environmental factors have been implicated in this behavior, the underlying genetic and molecular mechanisms remain unclear. We identify a novel role for the conserved calsyntenin protein CASY-1 in regulating swarming. Through genetic, behavioral, and optogenetic approaches, we show that CASY-1 functions in sensory neurons to modulate the neuropeptide pigment-dispersing factor (PDF) signaling. Mutants in casy-1 show impaired PDF-1 signaling and reduced inhibition of the serotonin pathway, a known regulator of social behaviors. This dysregulation, along with its associated mechanosensory and foraging defects, likely contributes to the swarming phenotype. Our findings reveal a putative neuromodulatory pathway critical for swarming behavior in C. elegans.

neuroscience↗

bioRxiv2025

Genomic analysis reveals the interplay between ABA-GA in determining dormancy duration in groundnut

Groundnut is an important leguminous crop however; its productivity and seed quality are frequently reduced due to lack of fresh seed dormancy (FSD). To address this challenge, a mini-core collection of 184 accessions was phenotyped to identify donors in each agronomic type, in addition to analysing data on whole genome re-sequencing and multi-season phenotypic evaluations to identify stable marker-trait associations (MTAs) associated with FSD. Phenotypic analysis revealed substantial variability in dormancy durations, with days to 50% germination (DFG) ranging from 1 to 30 days. Multi-locus genome-wide association studies (ML-GWAS) identified 27 MTAs in individual seasons and 12 MTAs in pooled seasons data, respectively. Key candidate genes identified included Cytochrome P450 superfamily proteins, protein kinase superfamily proteins, and MYB transcription factors involved in the Abscisic acid (ABA) pathway, as well as F-box interaction domain proteins, ATP-binding ABC transporters, associated with the Gibberellic acid (GA) pathway. SNP-based KASP (Kompetitive Allele-Specific Polymerase chain reaction) markers for 12 SNPs were developed and validated, of these 6 markers (snpAH00577, snpAH00580, snpAH00582, snpAH00585, snpAH00586 and snpAH00588) showed polymorphism between dormant and non-dormant lines. Incorporating favourable dormant alleles into breeding strategies could enable the development of high-yielding cultivars with a dormancy period of 2-3 weeks.

genomics↗

bioRxiv2025

FLP-15 modulates the amplitude of body bends during locomotion in Caenorhabditis elegans

Locomotion is essential for executing most behaviours. In Caenorhabditis elegans. Efficient locomotion is exhibited as a result of the coordination of excitatory and inhibitory signals from the nervous system onto the body-wall muscles. Although neurotransmitters play a vital role in maintaining and executing coordinated movements, neuropeptides have emerged as important players in the regulation and sustenance of locomotory states. In our previous study we explored the role of the neuropeptide FLP-15 in regulating reversal frequency during foraging behaviour in C. elegans. We were also interested in exploring other possible locomotory defects in flp-15 mutant animals. In this work we show that flp-15 mutants show an increased length of reversals during foraging resulting in defects in maintaining the direction of reversals. Mutants in flp-15 exhibited a "floral" pattern of reversals as opposed to near linear patterns of reversal in wild-type control animals. We further show that the defect in maintaining the direction of reversals could be due to increased amplitude of the body-bends with flp-15 mutants showing a large increase in the mean amplitude of body-bends. Our data suggests that FLP-15 partially functions through the G-protein coupled receptor (GPCR), NPR-3, to regulates the amplitude of body-bends. Finally, we show that loss of flp-15 leads to an increase in the expression of another neuropeptide, NLP-12, whose over expression has been implicated in causing increased amplitude of body-bends allowing us to speculate that the regulation of NLP-12 by FLP-15 may allow for the observed locomotory defects in flp-15 mutant animals.

neuroscience↗

bioRxiv2025

FLP-15 functions through the GPCR NPR-3 to regulate local and global search behaviours in Caenorhabditis elegans

Foraging is essential for sustenance and well-being of all organisms. The transition from well-fed to food-deprived conditions in C. elegans triggers a localized exploration of the environment characterized by frequent reorientations. However, over time the cumulative frequency of these reorientations decreases, facilitating the transition to global search behaviour. To investigate the genetic regulation of foraging in C. elegans, we conducted a screen of neuropeptide mutants and identified several candidates involved in modulating this behaviour. Among these, neuropeptide FLP-15 emerged as a key regulator of both local and global search behaviours. Our observations revealed that FLP-15 regulates the frequency and duration of reversals during foraging. Further investigation indicated that FLP-15 is expressed in and functions through the I2 pharyngeal neuron via the G-protein coupled receptor NPR-3. Mutants lacking either flp-15 or npr-3 displayed a significant decrease in reversal frequency during local search behaviours. Interestingly, unlike wild-type animals, the reversal frequency in flp-15 and npr-3 mutants did not decrease over time. This study also describes the expression pattern of NPR-3, in a subset of head neurons, predominantly comprising of dopaminergic neurons. This expression pattern highlights a potential link between neuropeptide signalling and dopaminergic modulation of behaviour. Finally, exogenous dopamine supplementation assays revealed that FLP-15 may regulate foraging by modulating dopamine transmission, highlighting a novel neuropeptide-dopamine interaction involved in the control of foraging behaviours.

neuroscience↗

bioRxiv2025

Extracellular vesicles aid in the transfer of long-term associative memory between Caenorhabditis elegans

Memory formation is necessary for the survival of animals across phyla. Here, we elucidate the mechanism underlying the formation of long-term associative memory (LTAM) formed by treating Caenorhabditis elegans with a volatile chemoattractant and heat. Previous work has shown that training animals with a paradigm involving heat and isoamyl alcohol (IAA) simultaneously, causes C. elegans to lose their attraction to IAA. In this study, we elaborate on the mechanism behind this LTAM formation and suggest that during training with heat and IAA, C. elegans release extracellular vesicles (EVs) that upon being taken up by the same trained animals or their untrained counterparts causes the organism to lose attraction to IAA. Our data suggests that the vesicles are highly specific to the training paradigms used and differ with differing cues. Finally, we show that this mechanism of transfer of LTAM appears to be conserved between C. elegans and C. briggsae allowing for both intra and interspecies transfer of memory.

neuroscience↗

bioRxiv2020

The G-protein coupled receptor SRX-97 is required for concentration dependent sensing of Benzaldehyde in Caenorhabditis elegans

The G-protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors in the olfactory system function to sense the surroundings and respond to various odorants. The genes encoding for the olfactory receptors in C. elegans are larger in number in comparison to those in mammals, suggesting complexity in the receptor- odorant relationships. Recent studies have shown that the same odorant in different concentration could act on multiple receptors in different neurons to induce attractive or repulsive responses. The ASH neuron is known to be responsible for responding to high concentrations of volatile odorants. Here we characterize a new GPCR, SRX-97. We found that the srx-97 promoter shows expression specifically in the head ASH and tail PHB chemosensory neurons of C. elegans. Further, the SRX-97 protein localizes to the ciliary ends of the ASH neurons. Analysis of CRISPR/based deletion mutants of the srx-97 gene suggest that this gene is involved in the recognition of high concentrations of benzaldehyde. This was further confirmed through rescue and neuronal ablation experiments. Our work gives insight into concentration dependent receptor function in the olfactory system and provides details of an additional molecule that could help the animal navigate its surroundings.

neuroscience↗

bioRxiv2019

Loss of dop-2 causes increased dopamine release and locomotory defects in the presence of ethanol

Ethanol is a widely used drug, excessive consumption of which could lead to medical conditions with diverse symptoms. Ethanol abuse causes disinhibition of memory, attention, speech and locomotion across species. Dopamine signaling plays an essential role in ethanol dependent behaviors in animals ranging from C. elegans to humans. We devised an ethanol dependent assay in which mutants in the dopamine autoreceptor, dop-2, displayed a unique sedative locomotory behavior causing the animals to move in circles while dragging the posterior half of their body. We identify the posterior dopaminergic sensory neuron as being essential to modulate this behavior. We further demonstrate that in dop-2 mutants, ethanol exposure increases dopamine secretion and results in enhanced function of the DVA interneuron. DVA releases the neuropeptide NLP-12 and leads to the excitation of cholinergic motor neurons that affect movement. Thus, DOP-2 modulates dopamine levels at the synapse and regulates alcohol induced movement through NLP-12.

neuroscience↗

bioRxiv2019

Differential regulation of native and learned behavior by creb1/crh-1 in Caenorhabditis elegans

1.Memory formation is crucial for the survival of animals. Here, we study the effect of different crh-1 (C. elegans homolog of mammalian CREB1) mutations on the ability of C. elegans to form long-term memory (LTM). Null mutants in creb1/crh-1 are defective in LTM formation across phyla. We show that specific isoforms of CREB1/CRH-1, CRH-1c and CRH-1e, are primarily responsible for memory related functions of the transcription factor in C. elegans. Silencing of CRH-1e expressing neurons during training for LTM formation abolishes the long-term memory of the animal. Further, CRH-1e expression in RIM or AVE neurons is sufficient to rescue long-term memory defects of creb1/crh-1 null mutants. We show that apart from being LTM defective, creb1/crh-1 null mutant animals show defects in native chemotaxis behavior. We characterize the amino acids K247 and K266 as responsible for the LTM related functions of CRH-1 while being dispensable for its native chemotaxis behavior. These findings provide insight into the spatial and temporal workings of a crucial transcription factor and can be further exploited to find CREB1 targets involved in the process of memory formation.

neuroscience↗