Biology subjects

Batra, S.

Publications and source records attributed to Batra, S..

10 recordsLinked to original sources

bioRxiv2025

Engineered heat-stable variants of Trypanosoma cruzi flagellar protein Tc24 enable serological detection of Chagas disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, is one of the major neglected diseases globally, killing 12,000 people per year and silently infecting an estimated 7 million people worldwide. Current diagnostic methods are limited by cost, complexity and cold-chain requirements. The T. cruzi flagellar protein Tc24 is a promising antigen for serological tests but suffers of poor solubility and heat stability. Here, we computationally engineered and produced three variants of Tc24, which exhibit remarkable heat stability, up to 69{degrees}C, and express with higher solubility in E. coli compared to the wild-type protein, reducing production costs, eliminating the need for a cold chain and therefore facilitating cost-effective production and storage without refrigeration and even in lyophilised form. These variants remained remarkably stable for 70 days in solution at 25{degrees}C and successfully detected antibodies in human sera samples from Chagas disease patients from Northern and Southern regions of Latin America, demonstrating the preservation of their antigenicity. The best-performing engineered variant was incorporated into a prototype of lateral flow test, demonstrating potential for rapid, affordable and accessible Chagas disease diagnostics in resource-limited settings.

biochemistry↗

bioRxiv2024

Non canonical Sun1-Allan complex orchestrates nuclear envelope remodelling and Basal Body/MTOC Segregation during rapid mitosis in Plasmodium

Mitosis in eukaryotes involves reorganization of the nuclear envelope (NE) and microtubule-organizing centres (MTOCs). During male gametogenesis in Plasmodium, the causative agent of malaria, mitosis is exceptionally rapid and highly divergent. Within 8 min, the haploid male gametocyte genome undergoes three replication cycles (1N to 8N), while maintaining an intact NE. Axonemes assemble in the cytoplasm and connect to a bipartite MTOC-containing nuclear pole (NP) and cytoplasmic basal body, producing eight flagellated gametes. The mechanisms coordinating NE remodelling, MTOC dynamics, and flagellum assembly remain poorly understood. We identify the SUN1-ALLAN complex as a novel mediator of NE remodelling and bipartite MTOC coordination during Plasmodium male gametogenesis. SUN1, a conserved NE protein, localizes to dynamic loops and focal points at the nucleoplasmic face of the spindle poles. ALLAN, a divergent allantoicase, has a location like that of SUN1, and these proteins form a unique complex, detected by live-cell imaging, ultrastructural expansion microscopy, and interactomics. Deletion of either SUN1 or ALLAN genes disrupts nuclear MTOC organization, leading to basal body mis-segregation, defective spindle assembly, and impaired spindle microtubule-kinetochore attachment, but axoneme formation remains intact. Ultrastructural analysis revealed nuclear and cytoplasmic MTOC miscoordination, producing aberrant flagellated gametes lacking nuclear material. These defects block development in the mosquito and parasite transmission, highlighting the essential functions of this complex.

cell biology↗

bioRxiv2024

Cryo-EM structures of G4-stalled CMG reveal inchworm mechanism of DNA translocation

DNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we have characterized fork collisions with preformed G4s in the parental DNA using fully reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by blocking the CMG helicase. An ensemble of high-resolution cryo-EM structures of stalled yeast and human CMG complexes reveals that the G4 is fully folded and lodged inside the CMG central channel. The stalled CMG is conformationally constrained and arrests in the transition between translocation states. Unexpectedly, our analysis suggests that CMG employs an unprecedented inchworm mechanism to translocate on DNA. These findings illuminate the eukaryotic replication fork mechanism under both normal and perturbed conditions.

biochemistry↗

bioRxiv2024

Functional classification of tauopathy strains reveals the role of protofilament core residues.

Distinct tau amyloid assemblies underlie diverse tauopathies but defy rapid classification. Cell and animal experiments indicate tau functions as a prion, as different strains propagated in cells cause unique, transmissible neuropathology after inoculation. Strain amplification requires compatibility of the monomer and amyloid template. We used cryo-EM to study one cell-based YFP-tagged strain, resolving its amyloid nature. We then used sequential alanine (Ala) substitution (scan) within tau repeat domain (RD) to measure incorporation to pre-existing tau RD-YFP aggregates. This robustly discriminated strains, defining sequences critical for monomer incorporation. We then created 3R/4R or 4R WT RD (aa 246-408) biosensors. Ala scan of recombinant tau seeds with the Alzheimers Disease fold matched that of AD homogenate. We scanned 22 brain lysates comprising 4 tauopathies. This clustered cases by neuropathological syndrome, revealed the role of amino acids in protofilament folds, and allowed strain discrimination based on amino acid requirements for prion replication. TeaserDiscrimination of tau strains based on the relative contribution of each amino acid to templated propagation of the amyloid.

neuroscience↗

bioRxiv2024

Open and closed conformations of a sub-80 kDa Chagas vaccine candidate defined by a cryo-EM led integrative approach

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, remains a significant global public health concern. Despite its profound health impact in both endemic and non-endemic areas, no vaccine is available, and the existing therapies are outdated, producing severe side effects. The 80kDa prolyl oligopeptidase of Trypanosoma cruzi (TcPOP) has been recently identified as a leading candidate for Chagas vaccine development. We report the first three-dimensional structure of TcPOP in open and closed conformation, at a global resolution of 3.8 and 3.6 [A] respectively, determined using single-particle cryo-electron microscopy. Multiple conformations were observed and further characterized using plasmonic optical tweezers and hydrogen-deuterium exchange mass spectrometry. To assess the immunogenic potential of TcPOP, we immunized mice and evaluated both polyclonal and monoclonal responses against the TcPOP antigen and its homologues. The results revealed invasion blocking properties of anti-TcPOP polyclonal response via parasite lysis and its cross-reactivity versus closely-related POPs but not with human homologues. We were also able to produce and characterise three monoclonal antibodies, one of which showed neutralising properties and inhibition of parasite invasion via non-lytic mechanism. Collectively, our findings provide critical structural and functional insights necessary to understand the immunogenicity of TcPOP for future Chagas vaccine development and diagnostic applications.

biophysics↗

bioRxiv2023

VCP increases or decreases tau seeding using specific cofactors

BackgroundNeurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu can happen within hours. A cellular machinery might regulate this process, but potential players are unknown. MethodsWe used proximity labeling to identify factors that control seed amplification. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity upon seeded intracellular tau aggregation. We identified valosin containing protein (VCP/p97) 5h after seeding. Mutations in VCP underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We utilized tau biosensors, a cellular model for tau aggregation, to study the effects of VCP on tau seeding. ResultsVCP knockdown reduced tau seeding. However, distinct chemical inhibitors of VCP and the proteasome had opposing effects on aggregation, but only when given <8h of seed exposure. ML-240 increased seeding efficiency [~]40x, whereas NMS-873 decreased seeding efficiency by 50%, and MG132 increased seeding [~]10x. We screened VCP co-factors in HEK293 biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. Reduction of FAF2 and UBXN6 increased tau seeding. ConclusionsVCP uses distinct cofactors to determine seed replication efficiency, consistent with a dedicated cytoplasmic processing complex that directs seeds towards dissolution vs. amplification.

cell biology↗

bioRxiv2021

The interplay of RNA:DNA hybrid structure and G-quadruplexes determines the outcome of R-loop-replisome collisions

R-loops are a major source of genome instability associated with transcription-induced replication stress. However, how R-loops inherently impact replication fork progression is not understood. Here, we characterize R-loop-replisome collisions using a fully reconstituted eukaryotic DNA replication system. We find that RNA:DNA hybrids and G-quadruplexes at both co-directional and head-on R-loops can impact fork progression by inducing fork stalling, uncoupling of leading strand synthesis from replisome progression, and nascent strand gaps. RNase H1 and Pif1 suppress replication defects by resolving RNA:DNA hybrids and G-quadruplexes, respectively. We also identify an intrinsic capacity of replisomes to maintain fork progression at certain R-loops by unwinding RNA:DNA hybrids, repriming leading strand synthesis downstream of G-quadruplexes, or utilizing R-loop transcripts to prime leading strand restart during co-directional R-loop-replisome collisions. Collectively, the data demonstrates that the outcome of R-loop-replisome collisions is modulated by R-loop structure, providing a mechanistic basis for the distinction of deleterious from non-deleterious R-loops.

biochemistry↗

bioRxiv2020

Alternative catalytic mechanisms driven by structural plasticity is an emerging theme in HAS-GTPases, Era and FeoB

GTP hydrolysis is the underlying basis for functioning of biological switches or GTPases. Extensively studied GTPases, Ras and EF-Tu, use a conserved Gln/His that facilitates the activation of attacking water for nucleophilic attack. However, this is insufficient to explain catalysis in Hydrophobic Amino acid Substituted (HAS)-GTPases that naturally possess a hydrophobic residue in lieu of Gln/His. We had previously reported a bridging water-chain mediated catalytic mechanism for HAS-GTPase FeoB; which utilizes two distantly-located but conserved glutamates. Curiously, mutating these does not abolish GTP hydrolysis. Similarly, in this study we report our observations on another HAS-GTPase Era, wherein the mutants of catalytically important residues continue to hydrolyze GTP. We attempt to rationalize these inquisitive observations on GTP hydrolysis by FeoB and Era mutants. We propose a general theory that appears common to at least three classes of GTPases, where alternative mechanisms emerge when the primary mechanism is disrupted. Based on the analysis of crystal structures of FeoB and Era mutants, bound to the transition state analogue GDP.AlFx, this work suggests that in the absence of catalytically important residues, the active site waters in both FeoB and Era undergo re-arrangements, which in turn helps in sustaining GTP hydrolysis. Similar employment of alternative mechanisms was also suggested for the catalytic mutants of hGBP1. Importantly, such alternatives underscore the robustness of GTP hydrolysis mechanisms in these systems, and raise important questions regarding the need for persistent GTP hydrolysis and the physiological relevance of structural plasticity seen here.

biochemistry↗

bioRxiv2020

Clonal Heterogeneity Supports Mitochondrial Metabolism in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDA) is characterized by a heterogenous and densely fibrotic microenvironment. This limits functional vasculature and diffusion of nutrients through the tumor1,2. Accordingly, pancreatic cancer cells develop numerous metabolic adaptations to survive and proliferate in nutrient austere conditions3-7. Subtypes of PDA have been characterized by transcriptional and functional differences8-12, which have been reported to exist within the same tumor13-15. However, it remains unclear if this diversity extends to metabolic programming. Here, using a combination of metabolomic profiling and functional interrogation of metabolic dependencies, we identify two distinct metabolic subclasses within neoplastic populations isolated from a single pancreatic tumor. Furthermore, these populations are poised for metabolic crosstalk, and in examining this, we find an unexpected role for asparagine in maintaining cell proliferation following mitochondrial inhibition. Functionally, when challenged by mitochondrial inhibition, asparagine supplementation increases intracellular levels of asparagine and aspartate, a rate limiting biosynthetic precursor16-18. Conversely, depletion of extracellular asparagine with PEG-asparaginase sensitizes pancreatic tumors to mitochondrial targeting with phenformin. Together, these data extend the concept of metabolic diversity to neoplastic populations within individual tumors, while illustrating a new method of intratumoral communication that supports tumor fitness19,20. Finally, the combination of asparaginase with mitochondrial inhibition could provide a powerful new strategy for this difficult to treat disease.

cancer biology↗

bioRxiv2018

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

Hi-C contact maps are valuable for genome assembly (Lieberman-Aiden, van Berkum et al. 2009; Burton et al. 2013; Dudchenko et al. 2017). Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al. 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al. 2017). Here, we introduce \"Assembly Tools,\" a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly. Together, 3D-DNA and the Juicebox Assembly Tools greatly reduce the cost of accurately assembling complex eukaryotic genomes. To illustrate, we generated de novo assemblies with chromosome-length scaffolds for three mammals: the wombat, Vombatus ursinus (3.3Gb), the Virginia opossum, Didelphis virginiana (3.3Gb), and the raccoon, Procyon lotor (2.5Gb). The only inputs for each assembly were Illumina reads from a short insert DNA-Seq library (300 million Illumina reads, maximum length 2x150 bases) and an in situ Hi-C library (100 million Illumina reads, maximum read length 2x150 bases), which cost <$1000.

genomics↗