Biology subjects

Chauhan, P.

Publications and source records attributed to Chauhan, P..

15 recordsLinked to original sources

bioRxiv2026

A pan-eukaryotic analysis of mitochondrial ribosomes uncovers major evolutionary transitions

Mitochondrial ribosomes (mitoribosomes) have diverged extensively both from their bacterial ancestors and across eukaryotes, and while many general trends have been identified, fundamental features of their evolution remain unclear. We analyzed sequences from 85 eukaryotes to chart protein composition across the evolution of mitochondrial translation. We both reconstruct the LECA mitoribosomal proteome as containing nearly the full bacterial protein complement and at least 23 proteins recruited after -proteobacterial endosymbiosis and describe the subsequent extensive but lineage-specific remodeling post LECA. We further uncover previously unrecognized homologies among several mitoribosomal proteins and unify and update the mitoribosomal nomenclature. Our data also support protein retargeting between organellar ribosomes, documenting remarkable intercompartmental structural compatibility. Together, these findings highlight the exceptional evolutionary plasticity of mitoribosomes and provide a comprehensive reference framework for future analysis.

evolutionary biology↗

bioRxiv2026

Pichinde virus models intrauterine infection by hemorrhagic fever-causing arenaviruses

Arenavirus infection during pregnancy can cause severe maternal disease, congenital infection, and fetal demise. Many arenaviruses are endemic in economically disadvantaged areas and must be studied in high containment laboratories, which has limited our understanding of arenavirus pathogenesis in the placenta. Pichinde virus (PICV) is a nonpathogenic arenavirus that recapitulates many aspects of viral hemorrhagic fever in guinea pigs. Using a combination of experiments in human placental cells and guinea pigs, we characterized the tropism and impact of PICV infection during pregnancy. PICV replicated in human trophoblast stem cells (TSCs), TSC-derived trophoblasts, and explanted term placenta. When guinea pigs were infected at mid-gestation, PICV caused fetal demise. High infectious titers were recovered from placenta and decidua, but PICV was infrequently detected in fetal tissues or amniotic fluid. In situ hybridization confirmed that the placenta, decidua, and fetal membranes were all infected by the virus. Transcriptional profiling of PICV-infected human trophoblasts and guinea pig tissues revealed that infection upregulated canonical antiviral responses, which could contribute to placental dysfunction and pregnancy loss. Thus, PICV is safe and tractable model of zoonotic arenavirus infection during pregnancy with utility for preclinical therapeutic and vaccine development.

microbiology↗

bioRxiv2026

A p32 family RNA editing factor acts in mitochondrial ribosome biogenesis

Biogenesis of mitochondrial ribosomes (mitoribosomes) in the unicellular parasite Trypanosoma brucei requires an exceptionally large toolkit of assembly factors, identified in stable precursors of large and small mitoribosomal subunits (mtLSU and mtSSU) by cryoEM. Here, using genetic modifications and proteomic characterization of the immunoprecipitated assemblosome, the earliest characterized mtSSU precursor, we determined that a cap of its distinctive protrusion of hitherto unknown composition consists of a p22 homotrimer. This protein was previously implicated in the uridine-insertion editing of the cytochrome c oxidase subunit II transcript. Our functional analysis confirmed this role but revealed that its ablation also causes a loss of mtSSU and a systemic reduction in mitochondrial translation, phenocopying the depletion of established mitoribosomal assembly factors. Consequently, the oxidative phosphorylation system and mitochondrial function are compromised. The p22 protein belongs to the p32 family. We showed that five of its six trypanosomal members are involved in mtSSU biogenesis. Notably, p32 proteins are associated with mitoribosomes in two other distant eukaryotic lineages. A eukaryote-wide mapping of p32 proteins documented that their presence correlates with the retention of mitochondrial genomes. Together, our findings redefine trypanosomal p22 as a dual-function coordinator of mitochondrial gene expression and reveal that the ancestral role of the p32 family is associated with mitochondrial translation.

molecular biology↗

bioRxiv2026

Distinct roles of three trypanosomal Oxa1 insertases in biogenesis of mitochondrial membrane complexes

The insertase Oxa1 is required for protein insertion into the inner mitochondrial membrane and for the biogenesis of oxidative phosphorylation complexes. While most eukaryotes encode one or two Oxa1 proteins, we identified three paralogs in Trypanosoma brucei: TbOxa1-1, TbOxa1-2, and TbOxa1-3. Knock-out of individual paralogs followed by phenotypic analyses and proteomic characterization of submitochondrial fractions revealed distinct functions. Respiratory chain complexes I and IV are primarily affected by loss of TbOxa1-1, whereas complex III and ATP synthase depend on TbOxa1-2; the ablation of TbOxa1-3 results in minor phenotypes in culture. In TbOxa1-2-depleted cells, ATP synthase biogenesis is compromised by the defective import or processing of the nuclear-encoded subunit-c, which also requires a rhomboid peptidase-like protein. Further, the ablation of TbOxa1-2 triggers accumulation of membrane proteins in the matrix, supporting its role in conservative sorting. Together, our results demonstrate that the trypanosomal Oxa1 machinery evolved a paralog-specific division of labor to manage a highly divergent mitochondrial membrane proteome.

biochemistry↗

bioRxiv2026

Oscillating Hypercapnia Induces Neural Abundant Protein Efflux and Potential Depletion in Health and Chronic Traumatic Brain Injury

Emerging preclinical and clinical evidence suggests that low frequency hemodynamic oscillations drive CSF flow, which in turn mediates glymphatic clearance. The current study investigated whether CO2-induced low frequency hemodynamic oscillations during magnetic resonance imaging would increase clearance of proteins (glial fibrillary acidic protein, neurofilament light chain, ptau217 and brain-derived tau) from brain to blood, and temporarily improve cognitive performance in individuals with chronic traumatic brain injury (TBI) and age/sex-matched healthy controls. Results indicated that cerebrovascular reactivity, normalized CSF volume, and predicted brain age significantly differed between chronic TBI and controls, while bulk CSF flow differed only at trend levels. Multiple protein concentrations were significantly increased at [~]45 minutes post-hypercapnia, decreased at [~]90 minutes, and returned to pre-hypercapnia levels by [~]150 minutes. Protein efflux was more strongly associated with total CSF volume and total white matter volume rather than cerebrovascular reactivity or bulk CSF flow. Both groups exhibited reduced cognitive interference post-hypercapnia, and hypercapnia associated symptoms quickly returned to baseline levels. In conclusion, hypercapnia temporarily increases clearance of multiple neural abundant proteins into blood, and this effect is moderated by atrophy. Current results suggest that hypercapnia may therapeutically combat pathological protein aggregation post-trauma, and prophylactically during normal aging.

neuroscience↗

bioRxiv2026

Visible Light Optical Coherence Tomography Reveals Aging at the RetinalPigment Epithelium-Bruch's Membrane Interface

Landmark histological studies have shown that as the retina ages, lipids and other debris accumulate within Bruchs membrane (BM) and in spaces introduced between BM and the retinal pigment epithelium (RPE). These deposits grow with age, increasing the risk of age-related macular degeneration (AMD), the leading cause of irreversible vision loss for older adults globally. Current in vivo imaging lacks specificity to study BM and the important spaces at the RPE/BM interface in living human eyes, while histological techniques suffer from processing artifacts that distort photoreceptors. Here we employ visible light Optical Coherence Tomography (OCT), with 1 micrometer depth resolution, to quantitatively analyze these tissues in living eyes. We identify age-related changes in a human cohort without retinal pathology: thickening and loss of contrast of the hyper-reflective BM band, and thickening of the RPE together with the sub-RPE basal laminar space (RPE+sBL). Both forms of thickening were locally coupled depending on eccentricity, suggesting related biosynthetic mechanisms. A thicker BM and RPE+sBL were locally associated with anomalies in the overlying photoreceptors. Thus, sub-clinical changes in aging eyes detected by visible light OCT resemble early versions of deposits found in AMD. Visible light OCT depicts the relationship between RPE+sBL, BM, and photoreceptors in aging, holding promise to precisely and non-invasively grade ocular phenotypes ranging from normal aging to early AMD. Significance StatementAs humans age, lipids and other debris deposit in Bruchs membrane (BM) of the human eye (1) and spaces introduced between the retinal pigment epithelium (RPE) and BM. These deposition processes are linked to the eventual development of age-related macular degeneration (AMD), the leading blinding disease amongst older adults. Here we investigate these deposits with visible light OCT imaging in living human subjects without overt retinal pathology. Whereas early RPE/BM deposits were previously assessed only in donor eyes postmortem via preparations that distort photoreceptors, our results shed light on these AMD precursors and overlying photoreceptor changes in living human eyes.

biophysics↗

bioRxiv2026

MYH9, a cytosolic myosin protein, binds to dengue virus 3'UTR and facilitates replication and cellular entry

Dengue infections are considered an increasing threat to mankind due to their rapid global spread rate. The development of a widely accepted drug/vaccine is hindered due to an incomplete understanding of the virus lifecycle. Present data suggest that a cytoskeleton protein, called MYH9 binds to the 3UTR, at A4 region, a highly conserved part of the UTR across the serotypes. The levels of this protein were found to be elevated in the cells infected with the virus and the above increase is commensurate with the virus load. This protein is found to accumulate at the endoplasmic reticulum (site of virus replication) and interacts with dsRNA (a replicative intermediate), suggesting its involvement in replication. Inhibition of this proteins expression by its siRNA reduced viral load, supporting its role in viral replication. Immunofluorescence studies indicate that this protein accumulates at the cell periphery and pulldown studies suggest that this protein interacts with the viral envelope protein, suggesting a role in the dengue viruss cellular entry, possibly by acting as a receptor. Use of an anti-MYH9 drug, ML-7 indicated the reduction of the virus load, prevented the accumulation at the periphery and aided in regaining the cell morphology of virus infected cells, confirming its role in replication and entry. Collectively, these studies demonstrate a dual function of MHY9 in the virus life cycle, which may serve as a general paradigm for the other viruses and hence to develop specific drugs.

microbiology↗

bioRxiv2025

Hybridization outcomes reflect context-dependent reproductive isolation in two damselfly hybrid zones

Pair of species with multiple hybrid zones provide powerful systems to examine how reproductive isolation and reinforcement may depend on ecological and demographic contexts. We conducted a comparative analysis of two hybrid zones between Ischnura elegans and Ischnura graellsii in North-central (NC) and North-western (NW) Spain to evaluate how differences in reproductive barriers shape patterns of hybridization and admixture. First, we quantified five prezygotic barriers in the NC hybrid zone--where no barrier estimates previously existed--and compared them with published data from the NW hybrid zone. Second, we conducted genomic analyses using 5,702 SNPs to assess genetic structure, differentiation, and diversity between species; and 381 SNPs with species-specific alleles to characterize hybrid classes and introgression across both regions. Reproductive isolation was strongly context dependent. Mechanical reinforcement acted in the same cross direction in both hybrid zones, but the NC hybrid zone also showed stronger gametic (fertility) isolation. Consequently, total prezygotic isolation was higher in the NC hybrid zone. These differences were also observed genomically: the NC hybrid zone exhibited limited and largely unidirectional introgression, whereas the NW hybrid zone showed more extensive admixture, bidirectional gene flow, and reduced interspecific differentiation, consistent with a longer or more sustained history of hybridization. Our results demonstrate that hybridization outcomes can differ markedly between hybrid zones involving the same pair of species, underscoring the importance of evaluating spatial variation in reproductive barriers and introgression to assess the presence, asymmetry, and repeatability of reinforcement, as well as the microevolutionary processes shaping hybrid zone structure.

evolutionary biology↗

bioRxiv2025

Time-dependent processing of dengue virus polyprotein yields multiple capsid forms that disrupt cellular homeostasis

Dengue virus infections spread to new geographical regions every year, cause significant morbidity and mortality, yet the progress in drug/vaccine development is limited due to an incomplete understanding of its life cycle. While a few of the proteins coded by this virus exist in multiple forms, the sequential events of polyprotein processing to yield them and the consequential effects on host cells are unclear. In this study, the virus infected cell culture data suggest that the polyprotein undergoes a time-dependent processing to yield multiple capsid forms, ie, capsid, capsid-anchor, capsid-anchor-pr, capsid-anchor-prM. Among them, the c-anc and c-anc-pr were found to localize to the mitochondria upon transfection into the HEK cells. The transmission electron microscopy studies suggest that c-anc induces mitochondrial fragmentation. Further studies showed that c-anc affects the mitochondrial fusion-related proteins and the genes involved in their functions. The pulldown experiments indicate that c-anc also interacts with 1-syntrophin (SNTA1), a cytoplasmic protein that plays a role in redox potential, oxidative stress and mitochondrial biogenesis. Importantly, the mitostress analyses suggest that c-anc triggers impaired mitochondrial dysfunctions like potential, respiration and ATP generation. In this study, we also identify ursonic acid (UNA) as a c-anc binding compound that restores mitochondrial functions and suppresses virus multiplication in vitro, ex vivo and in mice. The revealed disrupted mitochondrial homeostasis appears to be common to DENV, ZIKV, JEV, YFV, HCV, ASFV and SARS-CoV-2; hence, UNA or its related compounds could be considered as inhibitors for the above virus infections.

microbiology↗

bioRxiv2025

Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome

The assembly of the mitoribosomal small subunit involves folding and modification of rRNA, and its association with mitoribosomal proteins. This process is assisted by a dynamic network of assembly factors. Conserved methyltransferases Mettl15 and Mettl17 act on the solvent-exposed surface of rRNA. Binding of Mettl17 is associated with the early assembly stage, whereas Mettl15 is involved in the late stage, but the mechanism of transition between the two was unclear. Here, we integrate structural data from Trypanosoma brucei with mammalian homologs and molecular dynamics simulations. We reveal how the interplay of Mettl15 and Mettl17 in intermediate steps links the distinct stages of small subunit assembly. The analysis suggests a model wherein Mettl17 acts as a platform for Mettl15 recruitment. Subsequent release of Mettl17 allows a conformational change of Mettl15 for substrate recognition. Upon methylation, Mettl15 adopts a loosely bound state which ultimately leads to its replacement by initiation factors, concluding the assembly. Together, our results indicate that assembly factors Mettl15 and Mettl17 cooperate to regulate the biogenesis process, and present a structural data resource for understanding molecular adaptations of assembly factors in mitoribosome.

molecular biology↗

bioRxiv2024

CD4+ but not CD8+ T cells are required for protection against severe guinea pig cytomegalovirus infections

Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus and the leading cause of infectious disease related birth defects worldwide. How the immune response modulates the risk of intrauterine transmission of HCMV after maternal infection remains poorly understood. Maternal T cells likely play a critical role in preventing infection at the maternal-fetal interface and limiting spread across the placenta, but concerns exist that immune responses to infection may also cause placental dysfunction and adverse pregnancy outcomes. This study investigated the role of CD4+ and CD8+ T cells in a guinea pig model of primary cytomegalovirus infection. Monoclonal antibodies specific to guinea pig CD4 and CD8 were used to deplete T cells in non- pregnant and in pregnant guinea pigs after mid-gestation. CD4+ T cell depletion increased the severity of illness, caused significantly elevated viral loads, and increased the rate of congenital guinea pig cytomegalovirus (GPCMV) infection relative to animals treated with control antibody. CD8+ T cell depletion was comparably well tolerated and did not significantly affect the weight of infected guinea pigs or viral loads in their blood or tissue. However, significantly more viral genomes and transcripts were detected in the placenta and decidua of CD8+ T cell depleted dams post-infection. This study corroborates earlier findings made in nonhuman primates that maternal CD4+ T cells play a critical role in limiting the severity of primary CMV infection during pregnancy while also revealing that other innate and adaptive immune responses can compensate for an absent CD8+ T cell response in -CD8-treated guinea pigs. Author SummaryCongenital cytomegalovirus infection is a leading cause of adverse pregnancy outcomes and preventable disability in children. Using guinea pigs, a well-established small animal model of congenital infection and intrauterine development, this study tested how depleting T cells affects the course of primary cytomegalovirus infections. Severe illness and high rates of congenital infection were observed when helper CD4+ T cells were depleted. The depletion of killer CD8+ T cells did not affect the severity of disease or the rate of congenital infection but did increase the amount of virus that was detected in the placenta. A greater understanding how an immune response can prevent the infection of the placenta and developing offspring is needed to inform vaccine and therapeutic development. This study not only describes a new reagent that can be used to study the guinea pig immune system but also sheds new light in how adaptive immunity regulates congenital viral infection.

immunology↗

bioRxiv2024

The BMP2 prodomain promotes dimerization and cleavage of BMP6 homodimers and BMP2/6 heterodimers in vivo

Bone morphogenetic protein 2 (BMP2) and BMP6 are key regulators of systemic iron homeostasis. All BMPs are generated as inactive precursor proteins that dimerize and are cleaved to generate the bioactive ligand and inactive prodomain fragments, but nothing is known about how BMP2 or BMP6 homodimeric or heterodimeric precursor proteins are proteolytically activated. Here, we conducted in vitro cleavage assays, which revealed that BMP2 is sequentially cleaved by furin at two sites, initially at a site upstream of the mature ligand, and then at a site adjacent to the ligand domain, while BMP6 is cleaved at a single furin motif. Cleavage of both sites of BMP2 is required to generate fully active BMP2 homodimers when expressed in Xenopus embryos or liver endothelial cells, and fully active BMP2/6 heterodimers in Xenopus. We analyzed BMP activity in Xenopus embryos expressing chimeric proteins consisting of the BMP2 prodomain and BMP6 ligand domain, or vice versa. We show that the prodomain of BMP2 is necessary and sufficient to generate active BMP6 homodimers and BMP2/6 heterodimers, whereas the BMP6 prodomain cannot generate active BMP2 homodimers or BMP2/6 heterodimers. We examined BMP2 and BMP6 homodimeric and heterodimeric ligands generated from native and chimeric precursor proteins expressed in Xenopus embryos. Whereas native BMP6 is not cleaved when expressed alone, it is cleaved to generate BMP2/6 heterodimers when co-expressed with BMP2. Furthermore, BMP2-6 chimeras are cleaved to generate BMP6 homodimers. Our findings reveal an important role for the BMP2 prodomain in dimerization and proteolytic activation of BMP6.

cell biology↗

bioRxiv2022

Spatially controlled microtubule nucleation and organization from crosslinker MAP65 condensates

Microtubule organization in cells is essential for the internal structure and coordination of events of intracellular transport, mitosis, and cell motility. For many cell types, microtubule organization is dominated by centrosomal nucleation that use gamma-tubulin to template filaments. Yet, some cell types lack centrosomes or centrioles, such as plant cells. Instead, microtubules nucleate from regions with high concentrations of microtubule binding and nucleating proteins. A mechanism that can drive high local concentrations of nucleators is liquid-liquid phase separation of proteins with intrinsically disordered regions. Here, we report that the plant microtubule nucleator and crosslinking protein, MAP65-1, can form phase separated condensates at physiological salt and temperature without extra crowding agents. These condensates are liquid at first and can mature to gel-like phases over time and with different environmental conditions. We show that these condensates can nucleate and grow microtubule bundles that form asters, regardless of the viscoelasticity of the condensate. When gel-like droplets nucleate and grow asters from a shell of tubulin at the surface, the microtubules are able to re-fluidize the MAP65 condensate. Condensate-induced cytoskeletal formation could be a universal mechanism for organization of the microtubule and actin cytoskeletons in all cell types, especially cells without centrosomes.

biophysics↗

bioRxiv2021

Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies

Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and allow to shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridisation. Moreover, they are thought to contribute to Haldanes rule which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of Ischnura elegans, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species Ischnura graellsii. We analysed genome-wide SNPs in the Spanish I. elegans and I. graellsii hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes and (ii) that males are underrepresented among admixed individuals as predicted by Haldanes rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data adds to the few studies on species with X0 sex determination system and contradicts the hypothesis that the absence of a Y chromosome causes exceptions to Haldanes rule.

evolutionary biology↗

bioRxiv2019

Genomics of expanded avian sex chromosomes shows that certain chromosomes are predisposed towards sex-linkage in vertebrates

Sex chromosomes have evolved from the same autosomes multiple times across vertebrates, suggesting that certain genomic regions are predisposed towards sex-linkage. However, to test this hypothesis detailed studies of independently originated sex-linked regions and their gene content are needed. Here we address this problem through comparative genomics of birds where multiple chromosomes appear to have formed neo-sex chromosomes: larks (Alaudidae; Sylvioidea). We detected the largest known avian sex chromosome (195.3 Mbp) and show that it originates from fusions between (parts of) four avian chromosomes (Z, 3, 4A and 5). We found evidence of five evolutionary strata where recombination has been suppressed at different time points, and that these time points correlate with the level of Z-W gametolog differentiation. We show that there is extensive homology to sex chromosomes in other vertebrate lineages: three of the fused chromosomes (Z, 4A, 5) have independently evolved into sex chromosomes in fish (Z), turtles (Z, 5), lizards (Z, 4A) and mammals (Z, 4A). Moreover, we found that the fourth chromosome, chromosome 3, was significantly enriched for genes with predicted sex-specific functions. These results support a key role of chromosome content in the evolution of sex chromosomes in vertebrates.

evolutionary biology↗