Biology subjects

Dutta, M.

Publications and source records attributed to Dutta, M..

14 recordsLinked to original sources

bioRxiv2026

Metabolic and transcriptional responses reveal co-option of symbiotic processes during early soybean-soybean cyst nematode interaction

The biochemical mechanisms by which virulent populations of soybean cyst nematode (Heterodera glycines, SCN) overcome host resistance are critical to understanding this economically important pathogen. Here, we deployed metabolic and transcriptome profiling of soybean roots during the SCN infection and establishment process to investigate the molecular and biochemical mechanisms of pathogen establishment. Across samples from a time series spanning nematode invasion to syncytium maturation, we demonstrate that compatible SCN infection does not bypass host immunity but systematically remodels it. In a compatible interaction between soybean carrying the high-copy Rhg1 resistance locus challenged with HG Type 2.5.7 SCN virulent on this host, we identify a 72-metabolite defense signature spanning isoflavonoids, triterpenoid saponins, and phenylpropanoids that persist across all infection stages. Despite activation of this metabolic defense signature by the pathogen on infection, defense transcription is near silence by 3 days post-infection, while defense metabolites persist, revealing a critical decoupling of transcriptional and metabolic defense programs at the precise window of syncytium initiation. Suppression of phenylpropanoid accumulation occurs downstream of PAL transcription, indicating a block at the metabolic level invisible to transcriptomics alone. By 5 days post-infection, cytokinin accumulation coincides with nodulin gene induction and phospholipid remodeling consistent with activation of the legume symbiosis program during syncytium maturation. Together, these findings establish that compatibility arises not from failed recognition but from progressive immune dismantling, including suppression of defense chemistry and co-option of the legume-rhizobium symbiosis machinery.

plant biology↗

bioRxiv2026

Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope

HIV-1 buds from infected cells as immature virion particles with a scattered envelope glycoprotein (Env) distribution on their envelope. It then undergoes maturation, during which the viral protease cleaves the Gag polyprotein at multiple sites, leading to structural reorganization of the viral particle and lateral redistribution of Env proteins, ultimately rendering the virion infectious. However, the underlying mechanism of maturation-induced Env reorganization remains elusive. In this study, we combine microsecond-long all-atom (AA), bottom-up coarse-grained (CG) molecular dynamics simulations, and diffusion model-based backmapping to investigate the structural organization and key interactions of Env in viral membranes. AA simulations of fully glycosylated Env embedded in HIV-1 mimetic asymmetric bilayers were first performed to characterize its conformational dynamics and Env-lipid interactions. We then developed a bottom-up CG model of glycosylated Env from that AA data and simulated the mature HIV-1 virion envelope containing multiple Env proteins. The CG simulations predict that Env proteins form clusters through interactions mediated by the cytoplasmic tail domain (CTD) and adopt diverse tilted conformations within these clusters. These CG simulations were then backmapped to AA resolution and further AA simulations were carried out to identify, in detail, the specific interacting residues in the Env clusters. Additionally, analysis of epitope accessibility shows that broadly neutralizing antibodies (bnAbs) targeting the V1/V2 and V3 loops may efficiently interact with Env clusters on the mature virion surface. Together, these results provide a molecular mechanism for Env oligomerization during viral maturation and offer new insights into the accessibility of bnAb epitopes on Env clusters.

biophysics↗

bioRxiv2025

An integrated workflow for structural virology with a 100 keV electron microscope

Cryo-EM has revolutionized structural biology, especially for flexible and heterogeneous samples, although access to high end microscopes that enable these studies remains a bottleneck. While 300 keV microscopes have been the go-to for high-resolution structural determination, they are expensive and restricted to institutional and national facilities needing specialized expertise, with access falling far short of the demand. Here, we present the user-managed operation of a cheaper 100 keV electron microscope within a structural biology laboratory enabling close integration with protein production, biochemical and biophysical studies. We provide details and considerations for the installation of the microscope, its day-to-day maintenance, and operations. Using virus surface glycoproteins as case studies, we illustrate the workflow from grid screening, data collection, and data processing, and provide examples of data quality. This user-administered setup provides a training platform for researchers at all levels, with beginners in cryo-EM achieving proficiency to independently operate the microscope within a month of regular use and training. We have demonstrated routine high-quality low-resolution reconstructions using a Ceta CMOS camera and high-resolution reconstructions enabling building of atomic models using a Falcon C direct detector. While there are several examples of facilities that manage cryo-EM and individual laboratories leveraging cryo-EM, we provide here the first demonstration of a modern group independently doing both successfully, something that has been talked about frequently but rarely seen.

biochemistry↗

bioRxiv2025

Mutation and ACE2-induced Allosteric Network Rewiring in Delta and Omicron SARS-CoV-2 Spike Proteins

The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates viral entry by binding its receptor-binding domain (RBD) to the host receptor ACE2. Spike mutations in different variants have been experimentally shown to influence the rate of conformational transitions and alter viral infectivity. In parallel, both experimental and computational studies have reported the presence of long-range allosteric communication within the spike protein, suggesting that such mutations may also affect allosteric signaling pathways involved in viral function. A detailed understanding of the allosteric residue network is essential for rational antiviral drug design. In this study, we performed extensive atomistic molecular dynamics (MD) simulations of the spike proteins from the Delta and Omicron variants in both ACE2-bound and unbound states. By integrating linear mutual information (LMI) calculations and graph theory-based analysis, we delineated the long-range allosteric communication networks embedded within the spike protein. Betweenness centrality metrics enabled the identification of residues that act as key mediators of information flow. Notably, ACE2 binding markedly enhances allosteric coupling throughout the spike. We identified three key linkers, Link1 (NTD-RBD), Link2 (RBD-SD1), and Link3 (SD2-FP), as primary mediators of allosteric communication. Delta exhibits stronger signaling through Link1 and Link2, whereas Omicron redirects communication via Link3. While Delta maintains localized connectivity within the S1 domain but loses long-range contact with the S2 core, Omicron forms a broader yet weaker S1 network and establishes long-range coupling. We propose that the N856K and T547K mutations reshape the conformational landscape, reconfiguring allosteric communication pathways in Omicron. Furthermore, our analysis reveals distinct domain-level allosteric couplings in Delta and Omicron, pointing to variant-specific differences in fusogenicity and immune evasion. By mapping key allosteric sites and mutation-induced conformational shifts, our study may provide a framework for developing robust antiviral strategies resilient to future emerging SARS-CoV-2 variants. SignificanceReceptor engagement at the RBD rewires long range allostery in the SARS CoV 2 spike. Using LMI and graph theory-based analyses, we map communication paths and pinpoint residues that govern spike opening and infection. ACE2 binding globally strengthens coupling, but energy and signals propagate along variant specific routes: Delta biases toward openness, channeling binding energy into RBD opening; Omicron remains less open, routing energy to the S2 core to prime fusion. Information flows through three linkers - Link1 (NTD to RBD), Link2 (RBD to SD1), and Link3 (SD2 to FP), with Delta emphasizing Link1/Link2 and Omicron shifting to Link3 and CD connections. We suggest that the N856K and T547K mutations reshape this landscape in Omicron.

biophysics↗

bioRxiv2025

METAHIT enables comprehensive and flexible genome-resolved microbiome analysis with metagenomic Hi-C

Metagenomic Hi-C (metaHi-C) adds within-cell proximity information to shotgun sequencing, but existing analyses are fragmented and short-insert intra-contig read pairs from Hi-C libraries are often underused. Here, we present METAHICT, a modular and configurable workflow spanning read processing, metagenome-assembled genome (MAG) reconstruction, and downstream analysis. METAHICT consolidates outputs from bin3C, MetaCC, and ImputeCC and uses an expectation-maximization model of mapped insert sizes to select short-insert, shotgun-like Hi-C pairs for per-bin reassembly. Across seven datasets, binning and consolidation generally recovered more near-complete and medium-quality MAGs than individual Hi-C binners. On the sheep-gut long-read assembly, METAHICT's binning and consolidation stage recovered 929 MAGs meeting at least the medium-quality threshold, including 487 near-complete MAGs. Within the reassembly module, adding EM-selected Hi-C reads to shotgun-only inputs yielded further significant reductions in contamination across multiple environments. The workflow also integrates scaffolding, taxonomic annotation, contact-map visualization, and analysis of candidate mobile genetic element (MGE)-host pairs. Together, these capabilities provide standardized outputs for comparative and hypothesis-driven genome-resolved microbiome analysis.

bioinformatics↗

bioRxiv2025

Pathogenic mutations in Clathrin Heavy Chain associated with intellectual disability impair synaptic architecture and learning in Drosophila

Clathrin-mediated endocytosis is essential for neural development and function. Recent studies have linked de novo mutations in the clathrin heavy chain (Chc) gene to a range of neurodevelopmental disorders. In this study we have modelled two pathogenic mutations: L1047P and W1108R in Drosophila melanogaster and examined their effects on vesicle dynamics, ligand uptake, neuronal development and memory formation. Our data shows that expression of these mutant forms of Chc result in reduced survival and defective learning when expressed ubiquitously or exclusively in neurons. Our analysis also reveals that these mutations have the ability to disrupt vesicle dynamics and reduce ligand uptake in cells. Although we do not see a defect in neuronal morphology and function at the larval neuro-muscular junction, we see an increase in the number of Dlg-negative boutons, and a significant reduction in Spectrin expression, indicative of disruptions in the process of synapse maturation. Overall, this study provides mechanistic insights into the cellular and molecular basis of Chc-related neurodevelopmental disorders.

cell biology↗

bioRxiv2024

Structural and antigenic characterization of novel and diverse Henipavirus glycoproteins

Henipaviruses, a genus within the Paramyxoviridae family, include the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of deadly disease. Recent discoveries of several new Paramyxoviridae species, including the zoonotic Langya virus, have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the Henipavirus and Parahenipavirus genera. Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to here as HNVs, we constructed an expanded, antigenically diverse panel of HNV fusion and attachment glycoproteins from 56 unique HNV strains that better reflects global HNV diversity. We expressed and purified the fusion protein ectodomains and the attachment protein head domains and studied their biochemical, biophysical and structural properties. We performed immunization experiments in mice leading to the elicitation of antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures of diverse fusion proteins elucidated molecular determinants of differential pre-fusion state metastability and higher order contacts. A crystal structure of the Gamak virus attachment head domain revealed an additional domain appended to the conserved 6-bladed, {beta}-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal new cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.

biochemistry↗

bioRxiv2024

Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly

M is the most abundant structural membrane protein in coronaviruses and is essential for the formation of infectious virus particles. SARS-CoV-2 M adopts two conformations, Mshort and Mlong, and regulated transition between states is hypothesized to coordinate viral assembly and budding. However, the factors that regulate M conformation and roles for each state are unknown. Here, we discover a direct M-sphingolipid interaction that controls M conformational dynamics and virus assembly. We show M binds Golgi-enriched anionic lipids including ceramide-1-phosphate (C1P). Molecular dynamics simulations show C1P interaction promotes a long to short transition and energetically stabilizes Mshort. Cryo-EM structures show C1P specifically binds Mshort at a conserved site bridging transmembrane and cytoplasmic regions. Disrupting Mshort-C1P interaction alters M subcellular localization, reduces interaction with Spike and E, and impairs subsequent virus-like particle cell entry. Together, these results show endogenous signaling lipids regulate M structure and support a model in which Mshort is stabilized in the early endomembrane system to organize other structural proteins prior to viral budding.

microbiology↗

bioRxiv2023

Divergent spike mutations impact the activation of the fusion core in Delta and Omicronvariants of SARS-CoV-2

SARS-CoV-2 infects host cells by binding the receptor-binding domain (RBD) of its spike protein to the receptor, ACE2. A subset of highly effective spike mutations plays critical roles in altering the conformational dynamics of spike protein. Here, we use molecular dynamics simulations to investigate how spike mutations affect the conformational dynamics of spike/ACE2 complex in the D614G, Delta (B.1.617.2) and Omicron (B.1.1.529) SARS-CoV-2 variants. We observe that the increased positive-charged mutations in the Omicron spike amplify its structural rigidity and reduce its structural flexibility. The mutations (P681R in Delta and P681H in Omicron) at the S1/S2 junction facilitate S1/S2 cleavage and aid the activation of the fusion core. We report that high structural flexibility in Delta lowers the barrier for the activation of the S2 core; however, high structural rigidity in Omicron enhances the barrier for the same. Our results also explain why Omicron requires the presence of a higher number of ACE2 to activate its fusion core than Delta.

biophysics↗

bioRxiv2023

The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we find the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, lipid binding is shown to occur in the N protein C-terminal domain, which is supported by extensive in silico analysis. Anionic lipid binding occurs for both the free and N oligomeric forms suggesting N can associate with membranes in the nucleocapsid form. Herein we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to M assembly sites in the lifecycle of SARS-CoV-2.

microbiology↗

bioRxiv2022

Structure of SARS-CoV-2 M protein in lipid nanodiscs

SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 [A] resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.

biophysics↗

bioRxiv2021

A holistic insight of mycobacteriophage induced changes in mycobacterial cells

Mycobacteriophages are phages that interact with mycobacteria resulting in their killing. Although lysis is the major mechanism by which mycobacteriophages cause cell death, other mechanisms may also be involved. The present study was initiated with the objective of investigating the changes that take place at the cellular level following the infection of mycobacterial cells by phage D29. To investigate this issue, we took recourse to performing immunofluorescence and electron microscopic studies. Transmission electron microscopic examination revealed the adsorption of phages on to the surface of mycobacteria, following which penetration of the tail through the thick mycoloic acid layer was seen. At later time points discrete populations of cells at different stages of lysis were observed, which comprised of completely lysed cells, in which the cells were fragmented and those at the early onset stage exhibited formation of membrane pores through which the phages and intracellular contents were released. SEM results also indicated that phages may come out through the entire surface of the cell, or alternatively through gaps in the surface. In some of the images we observed structures that apparently resembled membrane blebs which are normally encountered when cells undergo programmed cell death (PCD). In addition, we observed significant increase in DNA fragmentation as well as membrane depolarization, which are also indicative of occurrence of PCD. As several bacterial PCD pathways are mediated by the toxin-antitoxin (TA) modules, the expression profile of all the TA systems was examined before and after phage infection. Apart from specifically addressing the issue of PCD in mycobacteriophage infected cells, this investigation has led to the development of facile tools necessary for investigating mycobacteriophage-mycobacteria interactions by means of microscopic methods.

molecular biology↗

bioRxiv2021

Genome-wide identification, expression and bioinformatic analyses of GRAS transcription factor genes in rice

Our group has previously identified the activation tagging of a GRAS transcription factor (TF)gene in the gain-of-function mutant population of rice (indica rice variety BPT 5204) screened for water use efficiency (Moin et al, 2016a). This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induces drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in thirteen different developmental stages. We studied their spatio-temporal regulation and correlated them with in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements in a bioinformatics analysis. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be very highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier functional characterization (Moin et al., 2016a) followed by the genome wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.

plant biology↗

bioRxiv2020

Gain of function mutagenesis through activation tagging identifies XPB2 and SEN1 helicase genes as potential targets for drought stress tolerance in rice

We have earlier reported on the development of an activation tagged gain-of-function mutant population in an indica rice variety, BPT-5204 (Moin et al. 2016). Screening of these gain of function mutants for water-use efficiency (WUE) followed by physiological analyses revealed the activation of two helicases, ATP-dependent RNA (SEN1) and DNA (XPB2) encoding unwinding proteins in two different mutant lines. In the current study, we examined the roles of these genes in stable activation tagged mutants of rice for drought stress responses. Transcript profiling of SEN1 and XPB2 showed their significant up-regulation under various stresses (particularly ABA and PEG). The SEN1 and XPB2 tagged mutants exhibited reduced leaf wilting, improved revival efficiency, high chlorophyll and proline contents, profuse tillering, high quantum efficiency and yield-related traits in response to simulated drought (PEG) and hormone (ABA) treatments with respect to their controls. These observations were further validated under greenhouse conditions by periodic withdrawal of water. Germination of the seeds of these mutant lines indicates their ABA insensitivity under high ABA concentration. Also, the associated high up-regulation of stress-specific genes suggests that their drought tolerance might have been because of the coordinated expression of several stress responsive genes in these two mutants. Altogether, our results provided a firm basis for SEN1 and XPB2 as potential candidates for manipulation of drought tolerance and improving rice performance and yield under limited water conditions.

plant biology↗