Biology subjects

Chakraborty, M.

Publications and source records attributed to Chakraborty, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Hepatocyte UBE4A protects against MASLD/MASH by maintaining ER homeostasis via UBXN4 interaction

Molecular understanding of the regulation of endoplasmic reticulum (ER) functions in healthy and MASLD livers is limited. Here, we elucidate that Ube4A, a cytosolic E3 ubiquitin ligase, protects against MASLD development by maintaining ER homeostasis during nutritional stress. Hepatocyte-Ube4A deletion (HUKO) augments Gubra-Amylin-diet (GAN-D)-induced steatosis, inflammation, insulin resistance, ER stress and markers of steatohepatitis of the liver in both sexes of mice. Proteomic studies reveal that in addition to altered metabolic and fibrogenic pathways, levels of many ER proteins are also changed in HUKO livers. Impaired ER functions sensitize HUKO livers to nutrition- or chemical (tunicamycin)-induced ER stress. Moreover, HUKO primary hepatocytes exhibit increased ER stress. Furthermore, Ube4A maintains ER homeostasis by facilitating ER-associated protein degradation (ERAD). The lipogenic protein SCD1 is identified as one of the ERAD targets of Ube4A. SCD1 stability and triglyceride accumulation are amplified in HUKO primary hepatocytes. The liver Ube4A-interactome studies identified the ERAD mediator UBXN4 as a major Ube4A interacting protein. Alphafold3-based molecular modelling and interaction site mapping analyses pinpointed the Ube4A binding residues for UBXN4. ER-localized Ube4A-UBXN4 complex facilitates ERAD (e.g., SCD1) and UBXN4-binding deficient Ube4A mutants fail to enhance this process. Finally, Ube4A and UBXN4 are downregulated in the livers of human MASLD and MASH patients and this complex is diminished in GAN-D-fed mouse livers. In conclusion, Ube4A preserves ER homeostasis by maintaining ERAD via its interaction with UBXN4, which maintains liver health. Enhancing levels and/or preserving interaction of these proteins may offer new therapeutic strategies for MASLD treatment.

physiology↗

bioRxiv2026

A microproteome screen identifies immunomodulatory bacterial microproteins encoded in expanded gene arrays in Leptotrichia

The human microbiome exerts broad influence in health and disease with associative studies implicating the microbiome in influencing immunity, cancer outcomes, and neurodegeneration. However, the molecular mediators of microbe-host communication remain poorly defined. Bacterial microproteins from the microbiome represent a largely uncharacterized class of potential regulators of host immunity. Here, we utilize functional genomics to interrogate 3,552 microproteins in order to identify novel microbial-immune interactions. We constructed a microproteome library from microbial metagenomic datasets, expressed it in macrophages and assayed for immunomodulatory activity. We identify several bacterial microproteins that drive macrophage M1 polarization. Among the strongest hits are a cluster of structurally related microproteins from Leptotrichia species, which are oral Gram-negative commensals associated with differential cancer outcomes. Genomic analysis reveals that Leptotrichia species encode these putative immunomodulatory microproteins in tandem arrays of up to 44 copies. These genes encode microproteins with varying sequences but conserved predicted structures. In an orthogonal approach, we demonstrate that bacterial expression of Leptotrichia microproteins influences macrophage cell state and function. As a whole, our findings identify novel microbial microproteins with immunomodulatory activity and provide a framework for future discovery of host-microbe interactions that influence human health.

microbiology↗

bioRxiv2026

Size-dependent membrane remodelling at Myomerger clusters during myoblast fusion

Myomerger drives fusion pore formation after hemifusion of membranes during myogenic cell-cell fusion in myogenesis, but its mechanical impact has been characterised largely in liposomes. In differentiating C2C12 cells, hemifusion began at 8 hr and peaked at 24 hr, whereas the earliest content-mixing events appeared only at 24 hr - Myomerger is therefore present much before it is competent to complete fusion. Using Interference Reflection Microscopy (IRM), we found that basal membrane tension in hemifusing cells was indistinguishable from that of non-fusing cells at 8-24 hr, and became significantly higher by 48 hr. Knockdown showed that Myomerger switched across this window from tension-reducing to enhancing cell-scale tension, unlike Myomaker, which enhanced tension in both the early and late phases. Addressing the local impact, Stimulated Emission Depletion microscopy (STED) imaging resolved Myomerger clusters built from a [~]40 nm basic unit that aggregate further. Small clusters induced nanometric outward bulges, a topology rare outside Myomerger-enriched regions; these bulges damped membrane fluctuations and showed higher lipid compaction at the centre, as deciphered by Flipper-TR FLIM, at the lateral as well as the basal membrane, and may be central to the hemifusion-to-pore transition. Larger clusters indented the membrane, showed enhanced fluctuations and associated with the clathrin-coated pits, consistent with surface clearance by endocytosis. Myomerger colocalized poorly with actin fibres and cholesterol-enriched nanodmains despite lying close to both. Together, these findings establish size-based clustering of Myomerger as a determinant of membrane topology and lipid compaction when hemifusion peaks and content mixing begins.

biophysics↗

bioRxiv2026

Higher-order Architecture Shapes Concerted Evolution in a Y-linked repeat array

The maintenance of functional repeat arrays on nonrecombining sex chromosomes presents an evolutionary paradox: tandem repeats are intrinsically unstable yet must preserve sequence identity and copy number to remain functional. The Y-linked Suppressor of Stellate (Su(Ste)) locus in Drosophila melanogaster is a large tandem array that produces piRNAs to silence the X-linked meiotic driver Stellate, but how such arrays are maintained remains unclear. Here, we reconstruct and compare repeat-resolved assemblies of the Su(Ste)/PCKR tandem array across three strains and show that the array is partitioned into discrete domains of elevated sequence identity. These domains exhibit an alternating pattern of similarity, in which nonadjacent regions are more similar to each other than to neighboring regions, and this organization is conserved across strains. Copy-number variation occurs primarily within specific domains, while overall array architecture remains stable. These results indicate that concerted evolution in the Su(Ste) array operates within structurally defined domains rather than uniformly across the array. The association of domain boundaries with inverted repeat elements suggests that higher-order structure constrains gene conversion, shaping both sequence homogenization and copy-number dynamics. In contrast, Y-linked rDNA arrays show uniform sequence similarity across long genomic distances, indicating a distinct mode of homogenization. Together, our findings demonstrate that gene conversion on nonrecombining chromosomes is structured by higher-order array architecture, providing a general framework for the maintenance of functional repeat arrays.

genomics↗

bioRxiv2026

A conserved architectural domain shapes centromere evolution in Drosophila

Centromeres ensure faithful chromosome segregation despite being embedded within rapidly evolving repetitive DNA, a contradiction known as the centromere paradox. While centromere identity is defined by the histone variant CENP-A, how conserved function is maintained amid rapid DNA turnover remains unclear. Here, we generate highly contiguous genome assemblies from single Drosophila melanogaster individuals that, for the first time, resolve a chromosome through its centromere, linking the chromosome 3 arms within a continuous sequence. Comparative assemblies from wild-derived strains reveal extensive structural variation in pericentromeric satellites, including large-scale expansions, contractions, and sequence divergence. Despite this variation, the CENP-A-associated centromeric core exhibits conserved organization across strains. Integration of Hi-C interaction maps with sequence analyses shows that flanking dodeca satellite arrays form a spatially interacting domain that bridges both sides of the centromere, whereas adjacent Prodsat arrays are more variable and show weaker interactions. These results support a model in which rapidly evolving centromeric DNA is constrained by conserved higher-order architecture, providing a framework for reconciling the rapid evolution of centromere sequence with its conserved function.

genomics↗

bioRxiv2026

Loss of E3 ligase Ube4A disrupts colon homeostasis and accelerates experimental colitis via altered lipid handling

BackgroundUbiquitin-dependent signaling is essential for maintaining intestinal homeostasis and its dysregulation contributes to chronic intestinal disorders, such as Inflammatory Bowel Disease (IBD). Ube4A is a U-box E3/E4 ubiquitin ligase involved in lipid metabolism and insulin signaling in metabolic tissues. Autoantibodies against Ube4A have been identified in patients with IBD and are associated with disease long-term complications. Despite these clinical associations, the physiological role of Ube4A in the gastrointestinal tract remains unknown. This study aimed to define the function of Ube4A in the colon and determine how its loss influences susceptibility to experimental colitis. MethodsUBE4A expression in human colonic tissue from healthy individuals and patients with IBD was analyzed using publicly available single-cell RNA sequencing datasets. The role of Ube4A in colonic homeostasis and colitis pathogenesis was examined using global Ube4A knockout (UKO) mice subjected to dextran sulfate sodium (DSS)-induced colitis. UKO colon phenotypes were characterized using transcriptomic analyses, immunofluorescence, and flow cytometry. ResultsUBE4A is highly expressed in human colonic epithelial cells, and its expression is reduced from healthy to IBD inflamed tissues. In mice, Ube4A deficiency significantly exacerbated DSS-induced colitis, as evidenced by increased weight loss, disease activity scores, shortened colon length, and more severe histological injury. Transcriptomic profiling revealed enhanced inflammatory signaling, alongside dysregulation of lipid transport and storage, as well as antimicrobial defense pathways. DSS-treated UKO mice also exhibited increased mast cell activation and elevated expression of matrix metalloproteinases. Importantly, colons from UKO mice displayed baseline transcriptional alterations indicative of epithelial stress and disrupted lipid metabolic programs, even in the absence of injury. ConclusionsUbe4A is a previously unrecognized regulator of colon homeostasis. Its loss induces existing epithelial stress and metabolic reprogramming that sensitize the colon to exaggerated inflammatory responses during injury such as experimental colitis.

pathology↗

bioRxiv2025

VEGF/ERK activation and PI3K inhibition together drive a vein-to-artery transition in an in vitro model of human angiogenesis

Artery endothelial cells (ECs) arise through different pathways, including differentiation from mesodermal cells (vasculogenesis) or from already established vein or capillary plexus ECs (angiogenesis), the latter being most common during embryonic development and regeneration. Understanding the vein-to-artery (v2a) transition could improve revascularization therapies, but progress is limited by a lack of human models. Here, we develop a human pluripotent stem cell (hPSC) differentiation protocol that models the v2a EC conversion. Comparing v2a and mesoderm-to-artery (m2a) transcriptomes with publicly available single cell RNA sequencing (scRNA-seq) data from human embryos showed they reflected angiogenesis- and vasculogenesis-derived artery ECs, respectively. This reductionist system revealed that VEGF activation alongside PI3K inhibition was sufficient for vein ECs to acquire arterial identity within 48 hours. We model a critical step in vascular development and define the minimal signals required for artery differentiation from veins, providing a framework to promote this conversion in revascularization or therapeutic contexts.

developmental biology↗

bioRxiv2025

Cisplatin and Copper Induce Distinct Endocytic Pathways of Copper Transporter-1 and Elicits Unique Response on Copper Homeostasis Proteins

Cisplatin (CDDP), a widely used chemotherapy drug is imported in mammalian cells by copper transporter CTR1. We observed that CDDP cytotoxicity is significantly reduced in CTR1 deficient yeast and in copper loaded mammalian cells indicating its shared uptake pathway with copper. CTR1 resides on the plasma membrane undergoes endocytosis during CDDP import as in copper, involving its amino-terminal His-Met-motifs and the conserved 150MXXM154 pore motif. Unlike Copper, CDDP directs endocytosed CTR1 toward lysosomes rather than being sorted through VPS35-positive endosome. CDDP enhances lysosomal acidity and cathepsin activity. Furthermore, CDDP selectively downregulate cuproproteins, CCS and SOD1, disrupting copper homeostasis. This study highlights the unique aspects of copper versus CDDP uptake by CTR1 and its differential downstream ramification on lysosomes and cuproproteins.

cell biology↗

bioRxiv2025

A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions

Viruses are key modulators of human gut microbiome composition and function. While metagenomic sequencing has enabled culture-independent discovery of gut bacteriophage diversity, existing genomic catalogues suffer from limited geographic representation, sparse taxonomic classification, and insufficient functional annotation, hindering detailed investigation into phage biology. Here, we present the Unified Human Gastrointestinal Virome (UHGV), a collection of 873,994 viral genomes from globally diverse populations that addresses these limitations. UHGV provides high-quality virome references with extensive host predictions, comprehensive functional annotations, protein structures, a classification framework for comparative analysis, and a web portal to facilitate data access. Using UHGV to profile worldwide metagenomes, we found that host range breadth is strongly associated with phage prevalence. Additionally, we identified diversity-generating retroelements and DNA methyltransferases as key factors enabling phage populations to access diverse hosts, revealing how specific genomic features contribute to global phage distribution patterns. UHGV is available at http://uhgv.jgi.doe.gov.

genomics↗

bioRxiv2025

Age-related microbiome metabolites modulate splicing and chromatin accessibility in the brain

The gut microbiome generates diverse metabolites that can enter the bloodstream and alter host biology, including brain function. Hundreds of physiologically relevant, gut-brain signaling molecules likely exist; however, there has been no systematic, high-throughput effort to identify and validate them. Here, we integrate computational, in vitro, and in vivo approaches to pinpoint microbiome-derived metabolites whose blood levels change during aging, and that induce molecular changes in the mouse brain. First, we mine large-scale metabolomics datasets from human cohorts (each n [≥] 1200) to identify 30 microbiome-associated metabolites whose blood levels change with age. We then screen this panel in an in vitro transcriptomic assay to identify metabolites that perturb genes linked to age-related neurodegeneration. To assess in vivo relevance, we then test four metabolites in male mice by acute exposure, using multi-omic approaches to evaluate the metabolites impact on cellular functions in the brain. With RNA-seq, we confirm known effects of trimethylamine N-oxide (TMAO), including changes in mitochondrial pathways, and further discover its effects on the pathways of glycolysis, GABAergic signaling, and RNA splicing. Additionally, using both RNA- and ATAC-seq, we identify glycodeoxycholate (GDCA), a microbiome-derived secondary bile acid, as a potent regulator of chromatin accessibility and of genes involved in protecting the brain from age-related stressors. GDCA also acutely reduces locomotion in male but not female mice. In summary, we present a generalizable framework for identifying microbiome metabolites that impact host biology, and apply it to identify age-related microbial metabolites that affect processes related to brain aging and neurodegeneration.

neuroscience↗

bioRxiv2025

Structural variants are enriched in deleterious visible phenotypes in Drosophila

Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore long reads. These assemblies enabled the creation of a pangenome graph containing comprehensive, nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncovered new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, we mapped the tarsal joint defect AblpeyD to an 8 kb Roo retrotransposon insertion into an intergenic enhancer, a finding validated via CRISPR-Cas9. The wing vein phenotype plexus (px1) was linked to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c1) wing phenotype was linked to a 7.5 kb DM412 retrotransposon inserted into the coding sequence of the muscle protein gene Strn-Mlck. We also unveiled 8 SV alleles of previously identified causal genes, including previously uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of the genes causing phenotypic changes harbored candidate SVs over 100 bp, whereas only 28% is expected based on euchromatic SVs. Our data, based on the 50 Drosophila phenotypes, 44 of which are strongly deleterious, suggests a disproportionately larger contribution of SVs to deleterious changes in visible phenotypes in Drosophila.

genomics↗

bioRxiv2025

Enhanced muscle uptake of chemically optimized miR-23b antisense oligonucleotides as lead compounds for Myotonic Dystrophy type 1

Myotonic dystrophy type 1 (DM1) is a multisystemic disorder caused by CTG repeat expansions in DMPK. Mutant transcripts containing expanded CUG repeats form ribonuclear foci that sequester muscleblind-like splicing regulator (MBNL) proteins, key regulators of RNA splicing and metabolism. This functional depletion leads to widespread mis-splicing and persistence of fetal transcript profiles, which underlie muscle weakness, myotonia, and muscle atrophy. In addition, miR-23b is upregulated in DM1 muscle and further represses MBNL1 translation, amplifying molecular defects. We developed chemically optimized miRNA-targeting antisense oligonucleotides (antimiRs) to inhibit miR-23b and restore functional MBNL1 levels. Using a multi-step screening process, we evaluated antimiRs with varying sequences, lengths, chemical modifications, and lipid conjugations. A key optimization was a 3-oleic acid conjugation combined with specific chemical modifications, which enhanced muscle uptake and efficacy. Lead candidates showed strong activity in preclinical models (HSALR and DMSXL mice, and human myoblasts), increasing MBNL1 levels, correcting mis-splicing, improving muscle strength, and reducing myotonia. They also exhibited efficient biodistribution to skeletal muscle, a critical DM1-affected tissue. In vitro toxicology indicated a favorable safety profile with minimal immune or renal toxicity. The antimiR mechanism was conserved in rat and pig fibroblasts. Overall, two lead antimiRs emerged as promising therapeutic candidates for DM1, with improved pharmacokinetics, tissue targeting, and safety, supporting the potential of microRNA-based approaches to correct key molecular defects in this disorder.

genetics↗

bioRxiv2025

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline

Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pan-genome construction and facilitates the interpretation of previously unexplored genomic regions.

bioinformatics↗

bioRxiv2024

BRDKRM: An Explainable Framework for Disease Modifying Drug Identification

Drug classification into disease-modifying (DM) and symptomatic (SYM) categories is crucial for clinical decision-making and therapeutic strategy development. To address the limitations of current methods, which often lack transparency and interpretability, we propose the Boundary Restricted Dynamic Key Route Mapping (BRDKRM) framework. This novel approach leverages the contextual overlap between disease and drug nodes in a heterogeneous graph, aggregating genes from the top K shortest paths to delineate disease neighborhood boundaries. Inspired by the classic Hansel and Gretel folklore, BRDKRM metaphorically marks boundary nodes along metapaths from disease to drug, akin to Hansel s breadcrumbs, which are then used to classify the therapeutic effect of candidate drugs. Our method achieved 86.78% accuracy in categorizing drug-disease treatments and identified 530 genes involved in both disease modification and symptomatic relief. The efficacy of BRDKRM is demonstrated through case studies on multiple sclerosis, offering an explainable approach to drug classification that bypasses extensive clinical trials. By providing biologically sound interpretations of drug classifications, our framework enhances understanding of therapeutic interventions, paving the way for more precise and efficient healthcare solutions while offering a novel approach to mapping disease-drug interactions.

bioinformatics↗

bioRxiv2024

Genome structural variants shape adaptive success of an invasive urban malaria vector Anopheles stephensi

Global changes are associated with the emergence of several invasive species. However, the genomic determinants of the adaptive success of an invasive species in a new environment remain poorly understood. Genomic structural variants (SVs), consisting of copy number variants, play an important role in adaptation. SVs often cause large adaptive shifts in ecologically important traits, which makes SVs compelling candidates for driving rapid adaptations to environmental changes, which is critical to invasive success. To address this problem, we investigated the role SVs play in the adaptive success of Anopheles stephensi, a primary vector of urban malaria in South Asia and an invasive malaria vector in several South Asian islands and Africa. We collected whole genome sequencing data from 115 mosquitoes from invasive island populations and four locations from mainland India, an ancestral range for the species. We identified 2,988 duplication copy number variants and 16,038 deletions in these strains, with [~]50% overlapping genes. SVs are enriched in genomic regions with signatures of selective sweeps in the mainland and invasive island populations, implying a putative adaptive role of SVs. Nearly all high-frequency SVs, including the candidate adaptive variants, in the invasive island populations are present on the mainland, suggesting a major contribution of existing variation to the success of the island populations. Among the candidate adaptive SVs, three duplications involving toxin-resistance genes evolved, likely due to the widespread application of insecticides in India since the 1950s. We also identify two SVs associated with the adaptation of An. stephensi larvae to brackish water in the island and two coastal mainland populations, where the mutations likely originated. Our results suggest that existing SVs play a vital role in the evolutionary success of An. stephensi in new environmental conditions.

evolutionary biology↗

bioRxiv2024

Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome

Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.

genomics↗

bioRxiv2024

Adipogenic differentiation and inflammatory response is orchestrated by regulating euchromatic histone methyltransferases.

Euchromatic histone methyltransferases (EHMT1/2) play a key role in adipogenesis by regulating gene expression. While the downstream gene functions of EHMTs in adipogenic differentiation have been studied, their regulation and precise individual contributions remain elusive. We discovered the existence of a regulatory mechanism, wherein EHMT1 governs the interdependent expression of itself and the master regulator PPAR during the early phase of adipogenesis. In later stages, EHMT2 levels decline along with reduction in H3K9 dimethylation. Alteration of above sequence of events alone or in the presence of saturated-fatty acids lead to precocious induction of high levels of PPAR, accelerated adipogenesis and hypertrophic adipocytes with a pro-inflammatory phenotype. Countering the decrease in EHMTs effectively abrogated the inflammatory response of the adipocytes. Accordingly, induction of obesity by a high fat diet was sufficient to downregulate H3K9me2 levels and expression of EHMTs along with enhanced IL-6 generation. Taken together, our studies reveal a critical regulatory role played by EHMTs, which coordinates adipogenesis and obesity-induced inflammation.

cell biology↗

bioRxiv2024

Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool

Deep-sea brine pools represent rare, extreme environments that focus biodiversity at bathyal to abyssal depths. Despite their small size and distribution, brine pools represent important ecosystems to study because they provide unique insight into the limits of life on Earth, and by analogy, the plausibility of life beyond it. A distinguishing feature of many brine pools is the presence of thick benthic microbial mats which develop at the brine-seawater interface. While these bacterial and archaeal communities have received moderate attention, little is known about the viral communities and their interactions with host populations in these environments. To bridge this knowledge gap, we leveraged metagenomic and metatranscriptomic data from three distinct zones within the NEOM brine pool system (Gulf of Aqaba) to gain insights into the active viral ecology around the pools. Here, we report a remarkable diversity and activity of viruses of all nucleic acid types and genome sizes that infect prokaryotic and eukaryotic hosts in this environment. These include giant viruses (phylum: Nucleocytoviricota), RNA viruses, jumbo phages, and polinton-like viruses (PLVs). Many of these appeared to form distinct clades showing the possibility of untapped viral diversity in the brine pool ecosystem. Zone-specific differences in viral community composition and infection strategy were also observed with lysogenic phages seeming to dominate the bacterial mat further away from the pools center. Through host matching, viruses infecting metabolically important bacteria and archaea were observed - including a linkage between a jumbo phage and a key manganese-oxidizing and arsenic-metabolizing bacterium. Our findings shed light on the role of viruses in modulating the brine pool microbial community dynamics and biogeochemistry through revealing novel viral diversity, host-virus associations, and spatial-scale heterogeneity in viral dynamics in these extreme environments. These results will provide crucial foundation for further investigation into the adaptations of viruses and their microbial hosts in extreme habitats in the marine ecosystem.

microbiology↗