Biology subjects

Chakraborty, S.

Publications and source records attributed to Chakraborty, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Biliverdin Reductase A is a major determinant of neuroprotective Nrf2 signaling

Biliverdin reductase A (BVRA), the terminal enzyme in heme catabolism, generates the neuroprotective and lipophilic antioxidant bilirubin. Here, we identify a novel non-enzymatic role for BVRA in redox regulation. We show that BVRA directly interacts with nuclear factor erythroid-derived factor-like 2 (Nrf2), the master regulator of redox homeostasis, to modulate target signaling pathways. ChIP-seq and RNA-seq analyses reveal that this interaction coordinates the expression of neuroprotective genes that are typically dysregulated in Alzheimers disease and other neurodegenerative conditions. Thus, this previously unknown BVRA-Nrf2 axis controls an essential pathway of redox signaling in neuroprotection. Our findings establish BVRA as a dual-function integrator of antioxidant defenses in both the lipophilic and hydrophilic subcellular compartments, bridging these two distinct and critical cellular protection mechanisms in the brain. This advancement in understanding the endogenous antioxidant system of the brain positions the BVRA-Nrf2 axis as a promising therapeutic target for neurodegenerative disease. Significance StatementWe show a non-canonical role for biliverdin reductase A (BVRA), classically known as the biosynthetic enzyme for bilirubin, in nonenzymatic modulation of antioxidant neuroprotective nuclear factor erythroid-derived factor-like 2 (Nrf2) signaling in the brain. Both BVRA and Nrf2 signaling are compromised in neurodegenerative diseases such as Alzheimers disease, and the BVRA-Nrf2 axis offers a new direction for developing neuroprotective therapies.

neuroscience↗

bioRxiv2025

The distribution of fitness effects varies phylogenetically across animals

1The distribution of fitness effects (DFE) describes the selection coefficients (s) of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (Pagels{lambda} = 0.84, P = 0.01). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (PGLS{lambda}, P = 0.03), and the proportion of new beneficial mutations ([Formula], P < 0.001). These findings align with Fishers Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGMs predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals. 2 Significance StatementUnderstanding how mutations affect fitness is fundamental in evolution, but little is known about how and why the distribution of fitness effects (DFE) varies across species. In this study, we examine the DFE in diverse animal populations and show that closely related species exhibit similar patterns of mutation effects, with new mutations being more deleterious in mammals compared with birds and insects. Our findings corroborate Fishers Geometric Model, which explains the variation in the DFE across species as a function of organismal complexity and long-term population size. By connecting organismal complexity and population size with the DFE, we offer a phylogenetic view into the selective forces shaping species adaptation and evolution.

evolutionary biology↗

bioRxiv2025

Glucocorticoid receptor and RUNX transcription factors cooperatively drive CD8 T cells dysfunction in human cancer

Glucocorticoids (GCs) are potent modulators of immune responses; however, the mechanisms by which GCs regulate gene expression in human CD8 T cells remain incompletely defined. Here, we delineate how physiological cortisol signalling shapes the transcriptional and chromatin landscapes of primary human CD8 T cells. We identify a substantial cohort of GC-responsive genes that are co-regulated through the cooperative activity of the glucocorticoid receptor (GR) and RUNX transcription factors. Integrative RNA sequencing and ChIP sequencing analyses identified genome-wide cortisol-responsive immunoregulatory genes. Genetic deletion of the GR (encoded by NR3C1) abolished cortisol-induced gene expression changes, confirming GR-dependency. Notably, GR chromatin occupancy in cortisol-treated CD8 T cells was strongly enriched at RUNX transcription factor (TF) motif rather than canonical GC response elements (GREs). Co-immunoprecipitation assays validated a ligand-dependent physical interaction between GR and RUNX and revealed the interacting domains. Single-cell transcriptomic analyses of tumour infiltrating CD8 T cells revealed significant enrichment of cortisol-responsive genes, indicating an active GC signalling (response) within the tumour microenvironment. GR-RUNX dual controlled genes were enriched in tumour-infiltrating CD8 T cells across multiple cancer types, including lung adenocarcinoma, head and neck squamous carcinoma, pancreatic cancer, and breast cancer. We found GR-RUNX co-regulated genes are predominantly expressed in the predysfunctional state of CD8 T cell population of different solid tumours. These results suggest that local cortisol signalling within tumour microenvironments drives CD8 T cell dysfunction through GR-RUNX TF cooperation. Collectively, our findings identify RUNX3 TF as a critical mediator of GR signalling in human CD8 T cells and reveal a novel mechanism by which endogenous GCs influence antitumour immunity, which could be therapeutically targetable.

immunology↗

bioRxiv2025

GPCR-targeted imaging and manipulation of homeostatic microglia in living systems

Microglia, the resident innate immune cells of the brain, are known to perform key roles such as synaptic pruning, apoptotic debris removal, and pathogen defense in the central nervous system. Microglial mutations are directly linked to many neurodevelopmental (e.g., schizophrenia) and neurodegenerative (e.g., Alzheimers disease) disorders, indicating the diagnostic and therapeutic potential of microglia for treating these conditions. Currently, we lack robust molecular tools to specifically image and manipulate microglia in vivo, which presents a major hurdle in our understanding of the brain-wide functions of these cells during the early onset of brain diseases. Here, we describe a molecular technology for imaging and manipulation of homeostatic microglia in live organisms (e.g., in zebrafish and mice) by covalently targeting the purinergic receptor, P2RY12. Using this technology, we imaged microglia-pathogen interactions in the larval zebrafish brain and revealed various morphological states of microglia in the adult mouse brain. We further expanded the microglia labelling approach to single-microglia tracking and microglial surfaceome mapping using photoactivatable fluorophores and photoproximity labelling, respectively. We anticipate the use of this universal tool for studying microglial biology across species to reveal the dynamics and polarization of resting microglia into a reactive state found in many neurodegenerative diseases.

immunology↗

bioRxiv2025

Tubulin hyperacetylation drives HMGB1 nuclear exit via the ROS-PARP1 axis leading to rotenone-induced G2/M Arrest

Rotenone, a lipophilic pesticide, is strongly linked to dopaminergic neuronal loss in Parkinsons disease (PD), primarily through mitochondrial complex I inhibition. While rotenone induces G2/M arrest in dividing cells, the underlying molecular events remain unclear. We identify HMGB1 as a key player in this process. HMGB1, known for its roles in genomic integrity and inflammation, exits the nucleus during rotenone-induced G2/M arrest, whereas its nuclear retention protects against mitotic DNA damage. We further reveal that tubulin hyperacetylation precedes HMGB1 nuclear release. Notably, reducing tubulin acetyltransferase lowers mitochondrial ROS (mtROS), preventing HMGB1 nuclear exit and mitotic DNA damage. Additionally, inhibiting PARP1 hyperactivation with PJ34 blocks HMGB1 exit and prevents G2/M arrest. These findings suggest that ROS-induced DNA damage elevates PARP1 activity, promoting HMGB1 nuclear exit and interfering with DNA repair. This tubulin acetylation/mtROS/HMGB1 axis may underlie rotenone-induced neurotoxicity, contributing to dopaminergic neuron vulnerability in PD and offering potential neuroprotective targets.

cell biology↗

bioRxiv2025

Deciphering the Proteome of Escherichia coli K-12: Integrating Transcriptomics and Machine Learning to Annotate Hypothetical Proteins

Omics technologies have led to the discovery of a vast number of proteins that are expressed but have no functional annotation - so called hypothetical proteins (HPs). Even in the best-studied model organism Escherichia coli K-12, over 2% of the proteome remains uncharacterized. This knowledge gap becomes even worse when looking at microbial dark matter. However, knowing the functions of proteins is crucial for elucidating cellular and metabolic processes and harnessing biotechnological potentials. Here, we employed machine learning to decipher the transcriptional regulatory network of E. coli K-12, as well as other in silico tools to assign functions to uncharacterized HPs. We further provide experimental validation of in silico predicted functions for three HP-encoding genes (yhdN, yeaC and ydgH) as proof of concept, by analyzing growth patterns of deletion mutants compared to the wild type, as well as their transcriptional responses to specific conditions. This study demonstrates that the use of Big Omics Data in combination with Artificial Intelligence and experimental controls is a powerful approach to illuminate functional dark matter. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/643886v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@9f5035org.highwire.dtl.DTLVardef@14ad641org.highwire.dtl.DTLVardef@385573org.highwire.dtl.DTLVardef@722780_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Unveiling Interaction Signatures Across Viral Pathogens through VASCO: Viral Antigen-Antibody Structural COmplex dataset

Viral antigen-antibody (Ag-Ab) interactions shape immune responses, drive pathogen neutralization, and inform vaccine strategies. Understanding their structural basis is crucial for predicting immune recognition, optimizing immunogen design to induce broadly neutralizing antibodies (bnAbs), and developing antiviral therapeutics. However, curated structural benchmarks for viral Ag-Ab interactions remain scarce. To address this, we present VASCO (Viral Antibody-antigen Structural COmplex dataset), a high-resolution, non-redundant collection of [~]1225 viral Ag-Ab complexes sourced from the Protein Data Bank (PDB) and refined via energy minimization. Spanning Coronaviruses, Influenza, Ebola, HIV, and others, VASCO provides a comprehensive structural reference for viral immune recognition. By comparing VASCO against general protein-protein interactions (GPPI), we identify distinct sequence and structural features that define viral Ag-Ab binding. While conventional descriptors show broad similarities across datasets, deeper analyses reveal key sequence-space interactions, secondary structure preferences, and manifold-derived latent features that distinguish viral complexes. These insights highlight the limitations of GPPI-trained predictive models and the need for specialized computational frameworks. VASCO serves as a critical resource for advancing viral immunology, improving predictive modeling, and guiding immunogen design to elicit protective antibody responses. By bridging sequence and structural immunological datasets, VASCO should enable better docking, affinity prediction, and antiviral therapeutic development--key to pandemic preparedness and emerging pathogen response.

biophysics↗

bioRxiv2025

Cleaved vs. Uncleaved: How Furin Cleavage Reshapes the Conformational Landscape of SARS-CoV-2 Spike

The SARS-CoV-2 Spike protein is the primary target for vaccine design, with immunogens typically engineered to enhance stability by introducing proline mutations (2P) and mutating or deleting the Furin Cleavage Site (FCS). While these modifications improve structural integrity, studies suggest that furin cleavage can play a functional role in Spike protein dynamics, potentially enhancing ACE2 receptor binding. However, the impact of this cleavage on the unbound form of the Spike protein remains unclear. In this study, we use extensive all-atom molecular dynamics (MD) simulations to compare the structural and dynamic properties of cleaved and uncleaved Spike proteins in their pre-fusion, unbound state. Our results show that Furin cleavage significantly alters allosteric communication within the protein, increasing correlated motions between the Receptor Binding Domain (RBD) and N-terminal Domain (NTD), which may facilitate receptor engagement. Principal Component Analysis (PCA) reveals that the cleaved and uncleaved Spike proteins sample distinct conformational landscapes, with the cleaved form displaying enhanced flexibility and a broader range of RBD tilt angles. Additionally, Furin cleavage primes the S2 subunit by expanding the central helix, potentially influencing the transition to the post-fusion state. Glycan clustering patterns further suggest an adaptive structural response to cleavage, particularly in the NTD and RBD regions. These findings highlight the potential functional consequences of FCS deletion in immunogen design and underscore the importance of considering the native cleavage state in vaccine and therapeutic development.

biophysics↗

bioRxiv2025

Allosteric Control and Glycan Shielding Adaptations in the SARS-CoV-2 Spike from Early to Peak Virulence

The SARS-CoV-2 Spike glycoprotein is central to viral infectivity and immune evasion, making it a key target for vaccine and therapeutic design. This trimeric peplomer undergoes dynamic conformational changes, particularly in its Receptor Binding Domain (RBD), which transitions between closed (down) and ACE2-accessible (up) states relative to the rest of the protein, to facilitate host cell entry. Structural understanding of such critical inter-domain motions, as well as epitope exposure quantification, is essential for obtaining an effective molecular handle over this protein and, in turn, exploiting it towards improved immunogen development. Focusing on the early circulating D614G form and the later emerging Delta (B.1.617.2) variant with higher virulence, we performed large-scale molecular dynamics simulations of the soluble form of the Spike in both down and up conformations of the RBD. Guided by differences in overall fluctuations, we described reaction coordinates based on domain rotations and tilting to extract features that distinguish D614G versus Delta structural behavior of the N-terminal Domain (NTD) and RBD. Using reaction coordinate analysis and Principal Component Analysis (PCA), we identify allosteric coupling between the N-terminal Domain (NTD) and RBD, where NTD tilting influences RBD gating. While some of these motions are conserved across variants, Delta exhibits an optimized RBD-gating mechanism that enhances ACE2 accessibility. Additionally, glycan remodeling in Delta enhances shielding at the NTD supersite, contributing to reduced sensitivity to neutralizing antibodies. Finally, we uncover the impact of the D950N mutation in the HR1 region, which modulates downstream Spike dynamics and immune evasion. Together, our findings reveal variant-specific and conserved structural determinants of SARS-CoV-2 Spike function, providing a mechanistic basis for allosteric modulation, glycan-mediated immune evasion, and viral adaptation. These insights offer valuable guidance for rational vaccine and therapeutic design against SARS-CoV-2 and emerging variants.

biophysics↗

bioRxiv2025

Identification and evaluation of besifloxacin as repurposed antifungal drug in combination with fluconazole against Candida albicans

Emergence of life-threatening fungal infections like systemic candidiasis concurrently with bacterial infections and limitations of current antifungal therapies warrants the discovery of novel inhibitors. We identified besifloxacin (BS), an FDA-approved antibacterial, as a potent antifungal inhibitor. A combination of besifloxacin with fluconazole showed a positive synergy ({delta} = 29.58) resulting in 80% inhibition of microbial growth. BS was able to reduce the MIC of FLC from 2mg/L to 0.5 mg/L when used in combination. Additionally in murine systemic Candida infection, BS reduced fungal load by 83% in mice kidneys at a dose of 100 mg/kg/day. The findings demonstrated the antifungal potential of BS, proposing its use in combination therapy with fluconazole to combat resistance through alternative mechanisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=165 HEIGHT=200 SRC="FIGDIR/small/642842v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1ed17org.highwire.dtl.DTLVardef@74b345org.highwire.dtl.DTLVardef@1a5aea3org.highwire.dtl.DTLVardef@6c816a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Noncoding and Coding Mechanisms of Aging Heart Failure with Preserved Ejection Fraction with Thyroid Dysfunction

Heart Failure with preserved Ejection Fraction (HFpEF) is a heterogeneous geriatric syndrome with complex pathophysiology and comorbidities. Long noncoding RNAs (lncRNAs) account for a large majority of the functional mammalian transcriptome and act as key regulators in complex physiological and pathological processes. However, the role of lncRNAs and the development of thyroid dysfunction in aging HFpEF is not clear. We investigated the ZSF1 model in both early and more severe stages of HFpEF (5-, 13- and 20-months old [mo]). We assessed molecular, biochemical, and pathophysiological roles involving lncRNAs, mRNAs, and inflammatory markers. Thyroid hormone (TH) immuno-sorbent assays showed significant decreases in serum T3 levels in 5-mo and serum T4 levels in 5-mo and 13-mo obese HFpEF groups compared to lean controls. Morphometric analyses showed significant increases in heart and LV weights in obese HFpEF rats indicating cardiac hypertrophy. LncRNA microarray and RT-qPCR revealed that three key lncRNAs were significantly increased in 13-mo obese HFpEF but not in 5-mo obese HFpEF left ventricles compared to the ZSF1 lean controls. Microarray analyses showed that Sik1 mRNA was significantly upregulated and Anxa13 was downregulated in early obese HFpEF hearts compared to the lean controls. Additionally, we also uncovered previously unreported tissue and serum inflammatory cytokine profiles in early and late HFpEF. This study has identified key novel lncRNA and inflammatory markers in early and late hypothyroid HFpEF. Further studies may help in better understanding and development of diagnostic and therapeutic targets for HFpEF that presents with severe morbidity and mortality.

genomics↗

bioRxiv2025

Primitive steroidogenesis in mast cells: A novel regulatory mechanism for mast cell function

Mast cells, ancient immune sentinels, are crucial in immune responses, tissue homeostasis and inflammatory pathologies. This study unveils a previously unknown regulatory mechanism in mast cell biology: de novo steroidogenesis. Through comprehensive multi-omics analysis and functional assays, we demonstrate that mast cells express Cyp11a1 and produce pregnenolone, representing a primitive form of steroidogenesis. This cell-intrinsic steroidogenic pathway is essential for mast cell development, survival, and functional regulation. Genetic abrogation of mast cell steroidogenesis leads to exaggerated inflammatory and anaphylactic responses in vivo. Our integrative approach reveals extensive transcriptional and proteomic remodelling during mast cell regranulation, with steroidogenesis playing a pivotal role in coordinating recovery and tissue repair processes. We uncover significant sexual dimorphism in mast cell proteomes and a global uncoupling of transcriptional and translational programmes. These findings advance our understanding of mast cell physiology and provide a foundation for developing targeted therapies for mast cell-associated pathologies.

immunology↗

bioRxiv2025

Multi-modal analysis of satellite cells reveals early impairments at pre-contractile stages of myogenesis in Duchenne muscular dystrophy

Recent studies on the role of myogenic satellite cells (SC) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SC in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. Addressing this, we isolated SC from muscle biopsies of a porcine DMD model for characterization. Traction force microscopy (TFM) revealed that DMD SC produce a significantly higher strain energy than wild-type cells (WT; 0.136 {+/-} 0.016 {micro}J vs. 0.057 {+/-} 0.008 {micro}J). By RNA-seq, we identified 1,390 differentially expressed genes and proteomics measurements detected 1,261 proteins with altered abundance in DMD vs. WT. Dysregulated pathways uncovered by Gene Ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. We integrated the data using multi-omics factor analysis (MOFA) and identified five factors accounting for the variance with an overall higher contribution of the transcriptomic (61.95 %) than the proteomic data (54.02 %). Our findings suggest SC impairments result from their inherent genetic abnormality rather than environmental influences. The observed biological changes are independent and not reactive to the pathological surrounding of DMD muscle.

pathology↗

bioRxiv2025

PAX3-FOXO1 drives targetable cell state-dependent metabolic vulnerabilities in rhabdomyosarcoma

PAX3-FOXO1, an oncogenic transcription factor, drives a particularly aggressive subtype of rhabdomyosarcoma (RMS) by enforcing gene expression programs that support malignant cell states. Here we show that PAX3-FOXO1+ RMS cells exhibit altered pyrimidine metabolism and increased dependence on enzymes involved in de novo pyrimidine synthesis, including dihydrofolate reductase (DHFR). Consequently, PAX3-FOXO1+ cells display increased sensitivity to inhibition of DHFR by the chemotherapeutic drug methotrexate, and this dependence is rescued by provision of pyrimidine nucleotides. Methotrexate treatment mimics the metabolic and transcriptional impact of PAX3-FOXO1 silencing, reducing expression of genes related to PAX3-FOXO1-driven malignant cell states. Accordingly, methotrexate treatment slows growth of multiple PAX3-FOXO1+ tumor xenograft models, but not fusion-negative counterparts. Taken together, these data demonstrate that PAX3-FOXO1 induces cell states characterized by altered pyrimidine dependence and nominate methotrexate as an addition to the current therapeutic arsenal for treatment of these malignant pediatric tumors.

cancer biology↗

bioRxiv2025

An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in Candida albicans during host infection

Candida albicans (CAL), one of the leading causes of fungal infections affecting nearly 70% of the population, poses a significant global health threat. With the emergence of drug-resistant strains, mortality rates have reached a staggering 63.6% in severe cases, complicating treatment options and demanding the discovery of novel therapeutic targets. To address this pressing need, we employed a unique multidisciplinary approach to elucidate the metabolic pathways that enable CAL to switch from a commensal to a virulent state. Condition-specific genome-scale metabolic models (GSMMs), along with a novel integrated host-CAL model developed in this study, highlighted the central role of arginine (Arg) metabolism and uncovered ALT1, an arginine biosynthesis enzyme, as a critical metabolic vulnerability in CAL virulence. Heightened expression of arginine biosynthesis genes indicated that increased arginine synthesis mainly occurs through proline intermediates during host interaction. Significantly impaired virulence and in vivo pathogenicity of ALT1-deleted CAL highlighted the potential of targeting arginine metabolism as a novel strategy to combat antifungal resistance and underscored the power of integrating systems biology with experimental approaches in identifying new therapeutic targets. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/632533v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@ac1b89org.highwire.dtl.DTLVardef@143c3d1org.highwire.dtl.DTLVardef@1ecfd26org.highwire.dtl.DTLVardef@1dfe98d_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Antimicrobial resistance, pathogenicity and virulence patterns of Escherichia coli isolated from cockroaches (Blattella germanica) across diverse environments: a public health concern

This investigation explores the prevalence and antimicrobial resistance (AMR) of Escherichia coli isolated from Blattella germanica (cockroaches) from diverse locations, including homes, kitchens, and laboratories, over the course of six months, from August 2022 to January 2023. A total of 125 cockroaches were analyzed, yielding 67 (53%) of positive E. coli isolates, with kitchen environments having the highest incidence (57.77%). The existence of virulence genes (stx1, stx2, and rfbO157) was confirmed by pathogenicity assessments carried out on mouse model, which led to a considerable increase in morbidity and mortality. 82.08% of isolates showed evidence of resistance to at least one antibiotic, according to the antimicrobial susceptibility test with {beta}-lactams displaying the highest rates of resistance. Remarkably, complex resistance patterns were observed in 77.61% of the isolates, which were categorized as multidrug-resistant. Multiple antibiotic resistance genes (ARGs) were found by molecular analysis, particularly blaTEM and tetA as well as virulence-associated genes (VAGs) linked to extraintestinal pathogenic E. coli. Phylogenetic grouping indicated that 90.38% of the MDR isolates belonged to virulent groups B2 and D. These findings highlight the role of cockroaches as potential reservoirs for pathogenic E. coli, raising significant public health concerns regarding AMR. The study underscores the imperative need for thorough investigation and feasible control strategies to ease the dissemination of AMR in diverse contexts.

microbiology↗

bioRxiv2024

Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii

In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate structures of biomolecules in their native context. However, challenges remain in the efficient production of large-scale cryo-ET datasets, as well as the community sharing of this information-rich data. Here, we applied a cryogenic plasma-based focused ion beam (cryo-PFIB) instrument for high-throughput milling of the green alga Chlamydomonas reinhardtii, a useful model organism for in situ visualization of numerous fundamental cellular processes. Combining cryo-PFIB sample preparation with recent advances in cryo-ET data acquisition and processing, we generated a dataset of 1829 reconstructed and annotated tomograms, which we provide as a community resource to drive method development and inspire biological discovery. To assay the quality of this dataset, we performed subtomogram averaging (STA) of both soluble and membrane-bound complexes ranging in size from >3 MDa to [~]200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset, as well as the promise of modern cryo-ET workflows and open data sharing towards visual proteomics.

cell biology↗

bioRxiv2024

The ketone body β-Hydroxybutyrate mediated epigenetic chromatin β-hydroxybutyrylation protects kidneys

Starvation, intermittent fasting and exercise, all of which are recommended lifestyle modifiers share a common metabolic signature, ketogenesis to generate the ketone bodies, predominantly {beta}-hydroxybutyrate. {beta}-hydroxybutyrate exerts beneficial effects across various contexts, preventing or mitigating disease. We hypothesized that these dynamic health benefits of {beta}-hydroxybutyrate might stem from its ability to regulate genome architecture through chromatin remodeling via histone {beta}-hydroxybutyrylation, thereby influencing the transcriptome. Focusing on the kidney, which is an end organ protected by {beta}-hydroxybutyrate, we examined histone {beta}-hydroxybutyrylation-mediated chromatin remodeling. Notably, regions of the genome associated with lipid catabolism were predominantly in an open chromatin configuration, leading to active transcription and translation. Significant {beta}-hydroxybutyrylation was observed in the kidneys and the most highly upregulated gene actively transcribed and translated was 3-hydroxy-3-methyglutaryl CoA Synthase 2 (Hmgcs2), a gene responsible for the biosynthesis of {beta}-hydroxybutyrate in mitochondria. In contrast, regions with more compact chromatin structures were enriched with genes related to immune function such as protein tyrosine phosphatase receptor type C (Ptprc) and lymphocyte cytosolic protein 1 (Lcp1), which exhibited reduced transcription and translation. These results reveal that renal epigenetic histone {beta}-hydroxybutyrylation is a novel mechanism by which transcriptional regulation of both energy metabolism and immune function occur concomitantly to protect kidneys and lower hypertension. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/628574v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@f16cdorg.highwire.dtl.DTLVardef@a22427org.highwire.dtl.DTLVardef@f3a6d3org.highwire.dtl.DTLVardef@4d705d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

physiology↗