Biology subjects

Choudhary, D.

Publications and source records attributed to Choudhary, D..

16 recordsLinked to original sources

bioRxiv2026

Calves function as social magnets in a species with high fission-fusion dynamics, the Asian elephant

Individuals living in fission-fusion societies may face unique challenges in maintaining social relationships, as the repeated fission of social units can limit opportunities for social interaction. However, the presence of young offspring may often necessitate cooperation among individuals. To understand whether offspring promote sociality in fission-fusion species, we studied wild Asian elephants (Elephas maximus) in southern India. Using nearly 5900 female group sightings collected over 9 years, we tested whether calf presence predicted female group size and associations. The numbers of adult, young adult, and subadult females in groups were 2-2.5-fold higher in calf presence than absence, which may facilitate collective defence of calves. Furthermore, the number of females without their own dependent offspring, who often provide allomaternal care, was also higher in calf presence than absence. Social network analysis revealed that adult females formed more numerous and stronger associations in calf presence than absence, which may facilitate consistent allomaternal care. Our results thus suggest that the need to protect calves and to provide allomaternal care likely promote sociality among female elephants. We propose that dependent offspring may function as social ties in fission-fusion species, contingent upon the prevailing conditions and the socioecological pressures that have shaped their social systems.

animal behavior and cognition↗

bioRxiv2026

Mapping Synthetic Circuit Design Space through Massively Parallel Measurement of Single-Cell Dynamics

Engineering predictable and robust gene-regulatory networks requires a quantitative understanding of how their dynamics depend on genetic design and environmental conditions. To investigate these relationships, we introduce BARRACUDA, a high-throughput platform that combines combinatorial assembly and programmable perturbations with lineage-resolved time-lapse imaging and optical pooled screening. Experiments using this platform follow approximately one million cell lineages, collectively sampling tens of thousands of circuit designs. We used BARRACUDA to investigate how the robustness of circuit behavior depends on molecular components and their interactions, combining quantitative dynamic measurements with precise genetic and environmental control. Antithetic integral feedback provided a model system linking a defined molecular architecture to theoretical predictions of robust adaptation. Through a hierarchy of increasingly complex libraries, we characterized individual components and used those measurements to model and interpret the dynamics of complete feedback circuits. Circuits built from wild-type inhibitory proteins rejected disturbances but also exhibited sustained overadaptation and fast disturbance-induced oscillations unexplained by a reduced control model. These discrepancies motivated a screen of de novo binders that retained inhibitory function while reducing host-stress response. Selected de novo binders supported strong feedback regulation and robust performance in the rebuilt circuits. Across more than 20,000 recovered feedback-circuit variants, binder identity and controller expression organized regimes of strong regulation and sustained oscillation. Counterintuitively, disturbances sometimes improved compensation rather than compromising it, consistent with nonlinear changes in feedback engagement. Together, these results show how structured libraries and massively parallel measurements of single-cell dynamics can test mechanistic theories across scales of circuit complexity, reveal missing biological interactions, and map the design space of gene-regulatory networks.

synthetic biology↗

bioRxiv2026

Division of labor during bacterial warfare

Division of labor is commonly associated with cooperative behavior, yet one of its most extreme forms occurs during bacterial warfare, where a subset of cells undergoes suicidal lysis to release toxins. Why bacteria divide labor among a few cells rather than producing toxin uniformly remains unknown. Here, we combine timelapse microscopy and simulations, to understand the division of labor during bacterial warfare using bacteriocin (colicin) production by the gut bacterium Escherichia coli as a model system. At the single-cell level, we find that lytic toxin production is a tightly regulated event: only cells that commit to lysis produce significant toxin and then lysis only occurs once a large amount of toxin has been made. This high threshold ensures each sacrifice delivers a large dose, which is released in a rapid burst from a lysing cell. While such burst-like release appears to provide no advantage over uniform labor in well-mixed conditions, we show it becomes extremely effective in spatially structured populations where the rapid release of toxin by one cell can generate lethal concentrations locally and eliminate competitors. Finally, we explain why the lysing fraction remains so small. While an increase in the producing cells increases toxin levels, it also increases the probability of local patch extinctions. The division of labor during bacterial warfare, therefore, enables powerful localized killing while safeguarding the population from self-destruction.

microbiology↗

bioRxiv2026

Inherited flagellar structures coordinate the onset of swimming among related E. coli cells

Bacteria commit to costly behaviors before they can benefit from them. In Escherichia coli, flagellar synthesis is expensive, yet the genes are expressed in stochastic pulses and only a small minority of pulses result in motility. Despite this noise, we find that lineage-related cells begin swimming at similar times, in groups of two to eight cells. Rare, high-amplitude pulses commit a single cell within one generation, but more commonly, pulses rise slowly and fail to trigger swimming before division. Rather than decaying, their output accumulates as cells inherit hook-basal bodies (HBBs) and continue to build new ones. This structural inheritance acts as a physical integrator, summing ongoing transcriptional activity across generations, so that an incomplete flagellar cascade is carried forward at division rather than lost. HBB accumulation sets when cells swim, and the anti-sigma factor FlgM sets how sharply. By holding late flagellar genes off until several HBBs have accumulated, FlgM makes motility depend steeply on early flagellar gene expression, so that relatives inheriting similar sets of HBBs become motile together. Without FlgM, this sharp dependence is largely lost, and activations of the full cascade do not reliably produce swimming. Together, our results show how the accumulation of a molecular machine integrates fluctuations, and how a checkpoint on its assembly sharpens them into a decision, setting both the speed and heritability of a behavioral trait.

systems biology↗

bioRxiv2026

Periplasmic detoxification of urate hydroperoxide underpins E. coli survival in the inflamed gut

Uric acid, the final product of purine metabolism in humans, accumulates in blood and tissues at relatively high concentrations1 as humans lack the enzyme uricase2,3. Under inflammatory conditions, uric acid can be oxidised to yield reactive intermediates4. In activated neutrophils, myeloperoxidase (MPO) catalyses the oxidation of uric acid by hydrogen peroxide, leading to the formation of urate hydroperoxide (UH)5,6. While recent studies have shown that UH is toxic to bacteria lacking peroxiredoxins7, its precise mechanism of toxicity and the existence of dedicated bacterial defence systems remain unknown. Here, we identify HiuH as a periplasmic enzyme, conserved across E. coli strains, that specifically degrades UH. Our findings reveal that UH selectively induces the expression of hiuH and that HiuH efficiently detoxifies UH both in vitro and in bacterial cells. HiuH cooperates with MsrP, a periplasmic methionine sulfoxide reductase that repairs UH-induced protein-bound methionine oxidation. This combined defence offering both direct detoxification and damage repair, is essential for bacterial survival under UH stress, and confers a competitive fitness advantage in a DSS-induced mouse model of colitis. Although UH is chemically transient, our work shows that it imposes durable biological consequences and a sufficient fitness cost in the in vivo niches occupied by E. coli to favour the evolution of a dedicated detoxification pathway beyond general oxidative-stress responses, defining a key adaptation to periods of gut inflammation.

microbiology↗

bioRxiv2026

UshEffect-3D: Structure-informed Classification of USH2A Missense Variants for Inherited Retinal Disease

USH2A encodes Usherin, a 5,202-residue multi-domain protein whose missense variation is a major cause of Usher syndrome type II. Interpretation remains challenging because the protein lacks a full-length experimental structure and thousands of reported missense variants remain unresolved. In an attempt to address this gap, we developed UshEffect-3D, a gene-specific machine-learning-based variant effect predictor that integrates sequence-based evolutionary measures, structure-based biochemical properties, local interaction terms, and predicted protein stability changes to prioritise USH2A missense variants of unknown significance (VUS). To ensure that the structure-derived features were extracted from reliably modelled predicted structures, the AlphaFold2 models of 47 annotated Usherin domains were compared against experimental structures of representative domain types. The predicted structures showed strong fold concordance with representative experimental structures, with 43 domains achieving TM-scores of at least 0.5. Among binary classifiers trained using a residue position-grouped cross-validation strategy, Logistic Regression was selected as the most stable performer and achieved an MCC of 0.75, AUC of 0.96, sensitivity of 0.93 and specificity of 0.81 on a group-aware held-out test set. On a benchmarking task, UshEffect-3D performed comparably to six general-purpose variant-effect predictors evaluated on the held out test set, scoring the highest on every balanced metric but no statistically resolvable advantage over any major competitors such as PolyPhen-2, VESPAl, ESM-1b and AlphaMissense. Feature ablation displayed that sequence derived evolutionary constraints were the sole detectable source of discrimination - withholding the conservation features reduced cross-validated MCC by 0.35 (paired 95% CI -0.45 to -0.25), whereas removing structural descriptors and predicted stability change negligibly affected model performance. Applying our model to the 2,639 ClinVar VUS, we reclassified 981 (37.2%) as likely pathogenic highlighting the extent of disease-relevant missense variation yet to be uncovered. Thus, UshEffect-3D serves as an interpretable protein-specific framework and a supplementary ranked resource that can be used to flag unresolved variants for further clinical and experimental review.

bioinformatics↗

bioRxiv2026

Direct observation of ATP-driven ubiquitin chain handling by Cdc48

Cdc48 (p97 or VCP in metazoans) targets polyubiquitin to selectively disassemble and degrade proteins. Cdc48 is believed to move along the ubiquitin chain towards linked proteins, but this has not been directly observed. By following single molecules in time, we find that the polypeptide branch points of ubiquitin chains are repeatedly inserted and rejected from the Cdc48 pore in ATP-driven manner, in bursts lasting up to seconds. This non-processive mode either ends by terminal substrate rejection, or advances to processive action, which drives ubiquitin unfolding in two steps, branch point translocation, and the extrusion of ubiquitin and linked protein as polypeptide loops in trans. Final retrograde movement can bring polypeptide segments back to cis. Our results establish the dynamics of ubiquitin chain handling by Cdc48, reveal key hallmarks of kinetic proofreading. We speculate that Cdc48 translocation may play a role in ubiquitin chain selection.

biophysics↗

bioRxiv2025

NAC promotes co-translational folding at the ribosomal tunnel exit

The nascent polypeptide-associated complex (NAC) coordinates enzymatic modifications and membrane targeting of nascent chains during translation. While NACs function as a dynamic hub for other factors is well-established, its direct role in co-translational folding is unclear. By proteome-wide profiling NAC co-translational interactions in human cells, we found that NAC recognizes emerging segments enriched in hydrophobicity and -helical propensity, within folded domains of cytonuclear proteins. Single-molecule and structural analyses reveal that NAC, via its {beta}-barrel domain, dynamically interacts with nascent chains at the ribosomal tunnel exit and is capable of promoting on-pathway folding. Compartment-specific nascent chain interactions of NAC further elucidate its role in targeting to the endoplasmic reticulum and mitochondrial membrane protein biogenesis. Together, these findings show that NAC acts as a bona fide co-translational chaperone that facilitates early protein folding at the ribosomal tunnel exit, expanding its functional repertoire in protein biogenesis.

biochemistry↗

bioRxiv2025

Dynamic regulation of the COPII interactome and collagen trafficking by site-specific glycosylation of Sec24D

Coat protein complex II (COPII) mediates anterograde trafficking from the endoplasmic reticulum (ER). While the core COPII machinery is well-characterized, how cells regulate COPII to accommodate large cargoes, including collagens, remains incompletely understood. Here, we show that the cargo-selecting COPII subunit Sec24D is modified by site-specific O-linked {beta}-N-acetylglucosamine (O-GlcNAc) in its N-terminal intrinsically disordered region upon induction of collagen transport. These glycosylations are required for collagen trafficking in human cells and developing zebrafish. Crosslinking proteomics demonstrated that each O-GlcNAcylation influences the Sec24D interactome in a distinct way, revealing novel mediators of COPII function. In particular, Sec24D glycosylation is required for its interaction with myoferlin, which unexpectedly facilitates fusion of ER exit sites (ERES) and the ER-Golgi intermediate compartment (ERGIC) to enable collagen transport. Our results establish Sec24D O-GlcNAcylation as a dynamic regulator of COPII protein-protein interactions and collagen trafficking and identify myoferlin as a novel mediator of this process.

cell biology↗

bioRxiv2024

A simple regulatory network coordinates a bacterial stress response in space and time

Bacteria employ diverse gene regulatory networks to protect themselves from stressful environments. While transcriptomics and proteomics show that the expression of different genes can shift strongly in response to stress, the underlying logic of large regulatory networks is difficult to understand from bulk measurements performed at discrete time points. As a result, it remains challenging to predict how these regulatory networks function at a system level. Here we use time-resolved single-cell imaging to explore the functioning of a key bacterial stress response: The Escherichia coli response to oxidative stress. Our work reveals a striking diversity in the expression dynamics of genes in the regulatory network, with differences in the timing, magnitude, and direction of expression changes. Nevertheless, we find that these patterns have a simple underlying logic. Firstly, all genes exhibit a transient increase in their protein levels simply due to the slowing down of cell growth under stress. Controlling for this effect reveals three classes of gene regulation driven by the transcription factor OxyR. Downregulated genes drop in expression level, while upregulated genes either show pulsatile expression that decays rapidly or gradual induction, dependent upon transcription factor binding dynamics. These classes appear to serve distinct functional roles in cell populations. Pulsatile genes are stress-sensitive and activate rapidly and transiently in a few cells, which provides an initial protection for cell groups. Gradually upregulated genes are less sensitive and induce more evenly generating a lasting protection that involves a larger number of cells. Our study shows how bacterial populations use simple regulatory principles to coordinate a stress response in space and time.

systems biology↗

bioRxiv2022

Environmental feedback drives oxidative stress response heterogeneity in bacterial populations

Induction of phenotypic heterogeneity is a ubiquitous consequence of bacterial stress responses. It is commonly postulated that isogenic cells exploit stochastic molecular fluctuations to generate phenotypic heterogeneity as a population survival strategy (termed bet-hedging). However, it is also possible that each cell attempts to maximise its own chances of survival. In that case, the apparent heterogeneity could either be caused by inevitable molecular noise or by underlying deterministic mechanisms which have escaped observation. Here, we investigated the sources and consequences of gene expression heterogeneity in the response of Escherichia coli cells to hydrogen peroxide (H2O2) stress. A machine-learning model accurately predicted the variable responses of individual cells growing in structured populations, indicating that the phenotypic heterogeneity has a deterministic origin. The model further showed that spatio-temporal dynamics in H2O2 concentration were dictated by the H2O2 scavenging capacity and morphology of cells in the local environment. Hence, oxidative stress response fluctuations were in fact the result of a precise and rapid feedback between each cell and its immediate environment. Although single cells optimise their individual responses, the formation of short-range H2O2 gradients by their scavenging activities increases stress tolerance at the population level and leads to spatial variation in mutation rates.

microbiology↗

bioRxiv2022

Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation

The sensory epithelium of the inner ear, found in all extant lineages of vertebrates, has been subjected to over 500 million years of evolution, resulting in the complex inner ear of modern vertebrates. Inner-ear adaptations are as diverse as the species in which they are found, and such unique anatomical variations have been well studied. However, the evolutionary details of the molecular machinery that are required for hearing are less well known. Two molecules that are essential for hearing in vertebrates are cadherin-23 and protocadherin-15, proteins whose interaction with one another acts as the focal point of force transmission when converting sound waves into electrical signals that the brain can interpret. This interaction exists in every lineage of vertebrates, but little is known about the structure or mechanical properties of these proteins in most non-mammalian lineages. Here, we use various techniques to characterize the evolution of this protein interaction. Results show how evolutionary sequence changes in this complex affect its biophysical properties both in simulations and experiments, with variations in interaction strength and dynamics among extant vertebrate lineages. Evolutionary simulations also characterize how the biophysical properties of the complex in turn constrain its evolution and provide a possible explanation for the increase in deafness-causing mutants observed in cadherin-23 relative to protocadherin-15. Together, these results suggest a general picture of tip-link evolution in which selection acted to modify the tip-link interface, while subsequent neutral evolution combined with varying degrees of purifying selection drove additional diversification in modern tetrapods.

evolutionary biology↗

bioRxiv2020

Transient delivery of A-C/EBP protein perturbs differentiation of 3T3-L1 cells and induces preadipocyte marker genes

Transformation of committed 3T3-L1 preadipocytes to lipid-laden adipocytes involves timely appearance of numerous transcription factors (TFs), foremost among them C/EBP{beta}, is expressed during early phases of differentiation. Here we describe liposome-mediated protein transfection approach to rapidly downregulate C/EBP{beta} by A-C/EBP protein inhibitor. Signals from tagged A-C/EBP were observed in 3T3-L1 cells within 2hrs of protein inhibitor transfections whereas for gene transfection signals appeared in 48hrs. Following transient transfections, expression profiles of 24 marker genes belonging to pro- and anti-adipogenic, cell cycle, and preadipocytes pathways was analyzed. mRNA and protein expression profiles of adipocyte-marker genes showed lower expression in both A-C/EBP protein and gene transfected samples. Interestingly, for preadipocytes and cell fate determinant genes, striking differences were observed between protein and gene transfected samples. Preadipocyte differentiation factors Stat5a and Creb were downregulated in A-C/EBP protein samples. Five preadipocyte markers, namely, Pdgfr, Pdgfr{beta}, Ly6A, CD34 Itgb1 showed high expression in protein samples whereas only Ly6A and CD34 were expressed in gene transfected samples. Pdgfr and Pdgfr{beta}, two known cell fate markers were expressed in protein transfected samples 5-days post-differentiation suggesting a possible reversal of differentiation. Our study provides evidences for the robust and efficient knockdown of C/EBP{beta} protein to understand time-dependent gene regulation during adipogenesis.

molecular biology↗

bioRxiv2020

Pan-genome-wide analysis of Pantoea ananatis identified genes linked to pathogenicity in onion

Pantoea ananatis is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally), for a phosphonate secondary metabolite, and the onion-virulence regions, OVR (localized on a megaplasmid), for onion pathogenicity and virulence, respectively. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-GWAS revealed a large core genome of 3,153 genes and a flexible accessory genome of [≤]5,065 genes. Phylogenomic analysis using pan-GWAS and presence and absence variants (PAVs) distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. The pan-GWAS also predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, TraR/DksA family transcriptional regulator, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. This is the first report of using pan-GWAS on P. ananatis for the prediction of novel genes contributing to pathogenicity in onion, which will be utilized for further functional analyses. Pan-genomic differences (using PAVs) differentiated onion pathogenic from non-pathogenic strains of P. ananatis, which has been difficult to achieve using single or multiple gene-based phylogenetic analyses. The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the alt cluster that aid in P. ananatis colonization in onion bulbs. We concluded that HiVir/PASVIL genes are associated with pathogenic P. ananatis strains and the alt gene cluster alone is not responsible for pathogenicity on onion. The pan-genome also provides clear evidence of constantly evolving accessory genes in P. ananatis that may contribute to host-range expansion and niche-adaptation. Author summaryPantoea ananatis is a major bacterial pathogen that causes center rot of onion and diseases of a number of other plant species. In order to understand the genome architecture and identify genes responsible for pathogenicity in onion, a pan-genome analysis was performed. We used 81 strains of P. ananatis collected over 20 years from different regions of the state of Georgia, USA. The pan-genome study identified a core genome with a conserved set of genes and an accessory genome that displayed variation among strains. We conducted pan-GWAS (pan-genome-wide association study) using presence and absence variants (PAVs) in the genomes and associated onion-pathogenic phenotypes based on a red-onion scale necrosis assay. The study resulted in identification of genes, including a cluster of chromosomal HiVir/PASVIL genes, that are significantly associated with the onion pathogenic phenotype. In addition, we identified 28 novel genes, a majority of which (n = 20) have hypothetical functions. We concluded and further substantiated earlier findings that a cluster of genes is responsible for pathogenicity on onion. The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the alt cluster that aid in bacterial colonization of onion bulbs by P. ananatis strains. We concluded that HiVir/PASVIL genes are associated with onion-pathogenic strains, and the alt gene cluster alone is not responsible for pathogenicity on onion. This study also provides potential evidence of constantly evolving accessory genes in P. ananatis which may help in host range expansion and adaptation to diverse niches.

genomics↗

bioRxiv2019

Structural determinants of protocadherin-15 elasticity and function in inner-ear mechanotransduction

Protocadherin-15 (PCDH15), an atypical member of the cadherin superfamily, is essential for vertebrate hearing and its dysfunction has been associated with deafness and progressive blindness. The PCDH15 ectodomain, made of eleven extracellular cadherin (EC1-11) repeats and a membrane adjacent domain (MAD12), assembles as a parallel homodimer that interacts with cadherin-23 (CDH23) to form the tip link, a fine filament necessary for inner-ear mechanotransduction. Here we report X-ray crystal structures of a PCDH15 + CDH23 heterotetrameric complex and ten PCDH15 fragments that were used to build complete high-resolution models of the monomeric PCDH15 ectodomain. Using molecular dynamics (MD) simulations and validated crystal contacts we propose models for complete PCDH15 parallel homodimers and the tip-link bond. Steered MD simulations of these models predict their strength and suggest conditions in which a multimodal PCDH15 ectodomain can act as a stiff or soft gating spring. These results provide a detailed view of the first molecular steps in inner-ear sensory transduction.

biophysics↗

bioRxiv2018

A Mechanically Weak Extracellular Membrane-Adjacent Domain Induces Dimerization of Protocadherin-15

The cadherin superfamily of proteins is defined by the presence of extracellular cadherin (EC) repeats that engage in protein-protein interactions to mediate cell-cell adhesion, cell signaling, and mechanotransduction. The extracellular domains of non-classical cadherins often have a large number of EC repeats along with other subdomains of various folds. Protocadherin-15 (PCDH15), a protein component of the inner-ear tip link filament essential for mechanotransduction, has eleven EC repeats and a membrane adjacent domain (MAD12) of atypical fold. Here we report the crystal structure of a pig PCDH15 fragment including EC10, EC11, and MAD12 in a parallel dimeric arrangement. MAD12 has a unique molecular architecture and folds as a ferredoxin-like domain similar to that found in the nucleoporin protein Nup54. Analytical ultracentrifugation experiments along with size exclusion chromatography coupled to multi-angle laser light scattering and small-angle X-ray scattering corroborate the crystallographic dimer and show that MAD12 induces parallel dimerization of PCDH15 near its membrane insertion point. In addition, steered molecular dynamics simulations suggest that MAD12 is mechanically weak and may unfold before tip-link rupture. Sequence analyses and structural modeling predict the existence of similar domains in cadherin-23, protocadherin-24, and the \"giant\" FAT and CELSR cadherins, indicating that some of them may also exhibit MAD-induced parallel dimerization.

biophysics↗