Biology subjects

Nandi, S.

Publications and source records attributed to Nandi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A CAR T cell-amplified suppressive B cell circuit in AML

Immunotherapy in acute myeloid leukemia (AML) is constrained by a hostile bone marrow niche. Here we identify atypical memory B cells (Batyp) as a suppressive population within this microenvironment. Across single cell and flow cytometry cohorts, Batyp were expanded in AML, and their molecular and phenotypic profiles resembled those of atypical B cells associated with chronic inflammatory conditions. Batyp were polarized within the AML microenvironment, and this was amplified by CAR T cell-AML interactions. Mechanistically, polarization was dependent on Toll-like receptor, interferon and CD70-CD27 signaling. Batyp suppressed T cell and CAR T cell responses via PD-1- and TGF-beta signaling, and were enriched in non-responding patients with AML and myeloma. CD180-directed CAR T cells, targeting an antigen shared by Batyp and AML blasts, resisted suppression in vitro and cleared disease in B cell-humanized xenografts while sparing hematopoietic stem cells, with B cell engagement further enhancing their expansion. CAR T cells thus reinforce their own suppressive niche through Batyp polarization, a constraint that can be relieved by dual blast- and B cell-targeting strategies.

immunology↗

bioRxiv2026

Multimodal MRI Clustering Reveals an Elevated Free-Water Biotype in Autism with Increased Social Symptoms

Background: Autism spectrum disorder (ASD) is neurobiologically heterogeneous, and group comparisons may mask effects confined to subgroups. We tested whether distinct biotypes exist within ASD using unsupervised clustering of multimodal MRI. Methods: We analyzed 149 participants with ASD and 129 typically developing (TD) controls from the Autism Brain Imaging Data Exchange II (6 sites; age 5 to 64 years). Site-harmonized features comprised free water (FW), tissue anisotropy and diffusivity, diffusion tensor image analysis along the perivascular space (DTI-ALPS), cerebrospinal fluid (CSF) volumes and exploratory resting-state regional homogeneity. ASD participants were clustered with k-means using global (7 features) and regional (17 features) sets, with robustness tested by permutation and two further algorithms. TD participants were projected post hoc to test specificity. A composite imaging score was related to Social Responsiveness Scale (SRS) subscales, symptom severity and IQ using partial correlations with false discovery rate correction. Results: Clustering identified an elevated free-water (EFW) biotype comprising approximately 10% of ASD participants, defined by markedly increased FW (d = +4.91 versus remaining ASD participants), reduced tissue anisotropy, reduced DTI-ALPS and enlarged ventricles. It was recovered across feature sets and algorithms (permutation p < .0001) and departed from TD norms, unlike the remaining ASD participants. The composite score correlated with social-perceptual and communicative SRS subscales, most strongly social awareness (r = +0.253, q = .026), but not with symptom severity or IQ. FW related to social motivation in children and adolescents (r = +0.287, q = .037) but not adults. Limitations: Each person was scanned once, so we cannot tell whether these brain differences cause social difficulties or how they change with age. The subgroup was small, clinical data were incomplete, the sample was mostly male with a wide age range, and the findings await confirmation in an independent group. Free water can reflect inflammation, swelling or tissue loss, so its biological meaning remains uncertain. Conclusions: We identify an ASD subgroup defined by extracellular fluid excess and altered white matter that is associated with greater social difficulties. If replicated, this signature may help stratify autistic individuals in mechanistic studies and clinical trials.

neuroscience↗

bioRxiv2026

White matter cognition mapping in pediatric cancer survivors: a two-cohort NODDI-Bingham study

Childhood cancer survivors (CS) treated with chemotherapy frequently experience long-term cognitive impairments, commonly referred to as CRCI. Whether these deficits reflect disrupted white matter microstructure, altered relationships between microstructure and cognition, or both remains unclear. Here, we applied the NODDI-Bingham model, which quantifies neurite density (NDI), isotropic free water (ISO), and orientation dispersion along primary (ODIp), secondary (ODIs), and total (ODIt) fiber axes, to characterize biophysically specific white matter microstructure in CS and examine its relationship to cognition. Twenty-one pediatric cancer survivors and 21 age-matched healthy controls (HC) underwent multi-shell diffusion MRI. Voxel-wise NODDI-Bingham analyses were performed within JHU atlas regions. Group differences were tested by ANCOVA, and associations between microstructure and cognition were examined with the NIH Toolbox Crystallized, Fluid, and Early Childhood composites using group-specific regressions. Confirmatory analyses were performed in an age-matched subsample of the HCP (n = 679). Notably, CS showed reduced NDI in the corona radiata, cerebral peduncles, and corpus callosum, with elevated ODIt and ODIp in the middle cerebellar peduncle, pathways that subserve processing speed and interhemispheric integration, cognitive domains among the most vulnerable in CRCI. Group-specific regressions revealed qualitatively different relationships between microstructure and cognition: HC exhibited mixed positive and negative relationships across four of five metrics (138 clusters spanning approximately 305,000 voxels; peak Cohen's d up to 3.00), whereas CS showed a predominantly uniformly negative pattern (67 clusters across 57,000 voxels), with no positive clusters for ISO, ODIt, ODIp, or ODIs, thus highlighting that reduced dispersion and extracellular free water are linked to better cognitive performance in CS. HCP analyses reproduced the HC pattern across all five metrics at proportionally smaller effect sizes, ruling out sample-size effects. NODDI-Bingham identifies two aspects of chemotherapy-related white matter pathology that standard diffusion metrics cannot resolve. First, pediatric cancer survivors show selective elevation of ODIp and ODIt in the cerebellar peduncles and reduced NDI in the corona radiata and corpus callosum, localizing group-level injury to specific fanning and neurite density signatures. Second, whereas in healthy controls white matter shows mixed positive and negative relationships between microstructure and cognition, survivors retain only negative relationships for ODIp and ODIt and a diminished mixed pattern for NDI, such that in the chemotherapy-exposed brain, only reduced neurite density and increased primary-axis fanning relate to cognitive impairment. These findings implicate a biophysically specific restructuring of the relationships between white matter and cognition as a candidate mechanism for CRCI and support NODDI-Bingham as a targeted biomarker panel for monitoring and intervention trials.

neuroscience↗

bioRxiv2026

Proteomic analysis of Stony Coral Tissue Loss Disease demonstrates coral-algal dysbiosis during disease progression

Stony Coral Tissue Loss Disease (SCTLD) has devastated Caribbean reefs, yet the host molecular response to infection is poorly understood. Previous gene expression studies of diseased corals identified shifts in the immune response, apoptosis, and coral-algal dysbiosis. Here, we characterized the proteomic response of Diploria labyrinthiformis to SCTLD by comparing protein abundance in healthy tissue from uninfected colonies and apparently healthy and neighboring diseased tissue from infected colonies. These results were compared with existing metagenomic data from the same samples that previously demonstrated significant shifts in the coral microbiome due to SCTLD. We identified 480 differentially abundant proteins when comparing diseased lesion and healthy tissues, but only 12 between apparently healthy and healthy tissues. Pathway-level analysis provides evidence of immune suppression in apparently healthy tissue, suggesting that host molecular responses precede visible disease progression. Diseased lesion tissues showed wound-healing responses combined with a decreased abundance of proteins involved in symbiosome maintenance and increased oxidative stress responses, consistent with host-algal dysbiosis. This result correlates with the previous metagenomic analysis of these samples which found that infected colonies exhibit distinct algal symbiont communities dominated by Symbiodinium necroappetens, whereas healthy colonies are dominated by Durusdinium trenchii and Breviolum spp. Comparison with existing transcriptomic studies revealed both shared and distinct molecular responses, underscoring the importance of integrating multi-omics approaches to understand coral diseases. Our results suggest that SCTLD in D. labyrinthiformis is associated with early immune suppression, coral-algal dysbiosis, oxidative stress, and subsequent wound-healing responses.

ecology↗

bioRxiv2026

Cognitive Control in Pediatric Cancer Survivors: A task-fMRI study

BackgroundChemotherapy-related cognitive impairment is a well-documented concern among cancer survivors, yet the neural mechanisms underlying deficits in cognitive control remain poorly understood. This study examined group differences in brain activation during a flanker task using functional MRI (fMRI) between chemotherapy-exposed participants and healthy controls. MethodsParticipants (21 survivors (24.9 years old; 71.4 % female; 15 years from diagnosis) and 21 healthy controls (26.7 years old; 61.9 % female) completed a flanker task during fMRI, with congruent and incongruent conditions. Reaction time, accuracy, and Flanker scores were collected. Whole-brain group comparisons were performed for congruent, incongruent, and incongruent > congruent contrasts. Associations between the incongruent > congruent contrast and cognitive performance were examined. ResultsCompared to controls, the Chemo group had longer reaction times in both congruent and incongruent conditions (p < .001) and lower NIH Flanker scores (p = .01), with no differences in accuracy. They showed reduced activation in the bilateral inferior frontal gyri, supplementary motor area, and bilateral caudate, but greater activation in the right inferior temporal and cerebellar regions. The incongruent > congruent contrast correlated with increased activation in the orbitofrontal cortex, inferior temporal gyri, and fusiform gyrus with cognitive performance. ConclusionsChemotherapy-exposed participants showed cognitive control deficits and altered neural activation during a flanker task, indicating disrupted recruitment of frontoparietal and subcortical regions key for conflict processing. These findings improve understanding of neural causes of chemotherapy-related cognitive impairment and may help identify at-risk survivors and guide personalized rehabilitation.

neuroscience↗

bioRxiv2025

Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10

The evolutionarily conserved methyltransferase Trm10 catalyzes N1 methylation of guanosine 9 (G9) in select tRNAs, but the basis of specific substrate recognition and modification has remained unclear. Using an S-adenosyl-L-methionine analog, we trapped a post-catalytic state of the Trm10-tRNAGly complex for structure determination by cryogenic electron microscopy. Three distinct complexes were captured: two monomeric Trm10-tRNA complexes with distinct tRNA acceptor stem orientations ("closed" and "open"), and a minor dimeric complex with two Trm10s bound to the same tRNA. The monomeric structures identify conserved residues involved in tRNA interactions across a positively charged surface that guide G9 into the catalytic site and stabilize the flipped nucleotide. In the tRNAopen conformation, acceptor stem rotation weakens tRNA-protein contacts, consistent with a product-release state. The dimeric complex, supported by tRNA-dependent protein crosslinking and molecular dynamics (MD) simulations, positions one Trm10 on G9 similarly to the monomeric complexes, while the other contacts distal tRNA regions, suggesting a functional role in promoting functionally critical conformational transition(s). MD simulations also show how Trm10 achieves selective stabilization of G9 over A9 in the binding pocket. Overall, our findings reveal the mechanism of G9-specific tRNA methylation by Trm10 and suggest a unique mechanism of action among RNA-modifying SPOUT methyltransferases.

biochemistry↗

bioRxiv2025

Synergy unleashed: Leishmania donovani GP63 paralogues cooperatively function to drive parasite infectivity at various pathogenic stages and regulate host survival mechanisms

Highly plastic genome of Leishmania is thought to underlie its remarkable ability to adapt to diverse host microenvironments, yet how this plasticity translates into dermal versus visceral persistence remains unclear. GP63, a zinc metalloprotease, is a well-established determinant of promastigote infectivity, particularly in cutaneous leishmaniasis. Despite this, its role in amastigote stage and in visceral disease caused by Leishmania donovani remains undefined. Here, using an integrated approach combining phylogenetics, CRISPR-mediated genome editing, and biochemical analyses, we demonstrate that GP63 paralogues in L. donovani have undergone independent evolutionary diversification to support visceral infection. While GP63-paralogues encoded on chromosome 10, previously implicated in cutaneous manifestation caused by L. major, were found severely truncated and dispensable in L. donovani, two distinct GP63-paralogues encoded on chromosome 28 and 31 were found essential to establish visceral infection. LdGP63_31 facilitates promastigote attachment to macrophages by promoting lipid raft engagement and complement inactivation, thereby enabling host entry and subsequent amastigote differentiation. LdGP63_28 is essential for intracellular amastigote survival by suppressing host inflammatory pyroptosis. Structural and enzymatic analyses revealed preferential host localization and substrate specificities, possibly resulting from distinct amino acid substitution within conserved motifs of these proteases, indicating independent evolutionary adaptations. Importantly, loss of the LdGP63_28 more severely impaired amastigote reinfection than loss of its counterpart LdGP63_31. Together, these findings reveal coordinated functional specialization of GP63-paralogues ensuring visceral adaptation.

microbiology↗

bioRxiv2025

KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models

New and improved methods for visualizing complex macromolecules in atomic detail continue to expand structural information in the Protein Data Bank but accurately refining atomic models from experimental maps remains a challenge due to efficiency limitations of current refinement approaches. Standard PHENIX refinement can partially address these limitations with its speed and accessibility but often fails to yield the best model compared to more computationally demanding approaches. We therefore developed "KNexPHENIX", a customized PHENIX-based workflow, to support optimal macromolecular model building. KNexPHENIX can be used to refine macromolecular structures obtained via cryo-electron microscopy (cryo-EM) or X-ray crystallography, regardless of molecular size or composition. KNexPHENIX was evaluated on deposited structures and de novo models and consistently produced models with lower MolProbity scores, indicating improved model stereochemistry, compared to default PHENIX, REFMAC Servalcat, REFMAC, or CERES refinement. Importantly, this was accomplished while maintaining model-to-map correlation for cryo-EM datasets and maintaining or reducing the Rfree-Rwork difference below accepted thresholds for X-ray crystallographic structures, thus limiting overfitting while preserving refinement accuracy. These results establish the KNexPHENIX workflow as a practical, accessible approach for refining both cryo-EM and crystallographic structures, enabling the generation of high-quality models for deposition and guiding further experimental studies.

bioinformatics↗

bioRxiv2025

Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression

Chronic exposure to the common aeroallergen house dust mite (HDM) induces lung inflammation and DNA damage, but its impact on lung cancer development remains largely unexplored. Using whole-genome sequencing, RNA-seq, and DNA methylation profiling, we assessed HDM effects in lung epithelial cell lines and a mouse orthotopic lung cancer model. HDM accelerated tumor growth without altering mutational burden. Transcriptomic and epigenetic analyses revealed tissue-specific effects: in normal lung, HDM enhanced pro-inflammatory and immune activation programs, whereas in tumors it suppressed T cell responses, antigen presentation, and chemokine signaling. Immune deconvolution showed a shift toward myeloid enrichment and lymphoid suppression, with reduced cytotoxic T and NK signatures. Notably, HDM-driven tumor promotion was abolished in Il17a-/- but not Il1b-/-mice, identifying IL-17A as a critical mediator. These findings demonstrate that chronic aeroallergen exposure reshapes the lung microenvironment to promote immune suppression and accelerate lung cancer progression. HighlightsChronic house dust mite (HDM) exposure accelerates lung tumor growth through non-mutagenic, immune-mediated mechanisms. HDM activates pro-inflammatory and immune programs in normal lung tissue but suppresses antitumor T cell responses in tumors. Multi-omics profiling reveals epigenetic silencing of immune genes and a myeloid-enriched, lymphoid-deficient tumor microenvironment. HDM-driven tumor promotion depends on IL-17A but not IL-1{beta}, establishing IL-17A as a central driver of lung tumor promotion.

cancer biology↗

bioRxiv2025

A Universal Duplex Sequencing Approach for Accurate Detection of Somatic Mutations

Ultra-accurate detection of rare somatic mutations is critical for understanding mutational processes in human disease, aging, and environmental exposures, yet current methods are limited by error rates, restricted genome coverage, and high DNA input. We present UDSeq, a duplex sequencing protocol combining random fragmentation, efficient UMI ligation, and quantitative input control to achieve near-complete genome/exome representation from as little as 100 pg DNA. Benchmarking in human sperm estimates a UDSeq error rate of [~]2.5x10-9 per base pair. UDSeq captures mutational signatures from heterogeneous populations without clonal expansion, reproduces exposure-specific patterns in cell lines and rodent models, and enables cross-species profiling. Compared with prior duplex methods, UDSeq yields up to fourfold more usable duplex molecules, improves library conversion, and remains cost-effective. We include a step-by-step protocol with quality-control checkpoints for fragment size, ligation yield, library conversion, and duplication rate. UDSeq provides a scalable, low-input platform for accurate profiling of somatic mutagenesis.

genomics↗

bioRxiv2025

Mechanism of 30S subunit recognition and modification by the conserved bacterial ribosomal RNA methyltransferase RsmI

Ribosomal RNA (rRNA) modifications are important for ribosome function and can influence bacterial susceptibility to ribosome-targeting antibiotics. The universally conserved 16S rRNA nucleotide C1402, for example, is the only 2-O-methylated nucleotide in the bacterial small (30S) ribosomal subunit and this modification fine tunes the shape and structure of the peptidyl tRNA binding site. The Cm1402 modification is incorporated by the conserved bacterial 16S rRNA methyltransferase RsmI, but it is unclear how RsmI is able to recognize its 30S substrate and specifically modify its buried target nucleotide. We determined a 2.42 [A] resolution cryo-EM structure of the RsmI-30S complex and, with accompanying functional analyses, show that RsmI anchors itself to the 30S subunit through multiple contacts with a conserved 16S rRNA surface previously only seen in the assembled subunit. This positions RsmI to induce an extensive h44 distortion to access C1402 that is unprecedented among 16S rRNA methyltransferases characterized to date. These analyses also reveal an essential contribution to 30S subunit interaction made by the previously structurally uncharacterized RsmI C-terminal domain, RsmI-induced RNA-RNA interactions with C1402, and an unappreciated dependence on a divalent metal ion for activity that suggests RsmI may be first of a distinct class of metal- and SAM-dependent RNA O-methyltransferases. This study significantly expands our mechanistic understanding of how intrinsic bacterial methyltransferases like RsmI modify their rRNA targets. Further, recognition of distant ribosome features and extensive unfolding of a critical rRNA functional center point to a potential role in accurate 30S subunit biogenesis.

biochemistry↗

bioRxiv2025

Decoding Amyloid Plaque Penetrability: Exploring Extracellular Space and Rheology2in Plaque-rich Cortex

A hallmark of Alzheimers disease (AD) is the accumulation of amyloid plaques, primarily composed of misfolded amyloid {beta} (A{beta}) peptides. We employed complementary high-resolution imaging techniques to investigate the plaque penetrability and the extracellular space (ECS) rheology in a mouse model of AD. Two-photon shadow imaging in vivo confirmed that a dense ring of cells surrounds cortical amyloid plaques but highlighted the diffusional penetrability of the amyloid core. Quantum dot tracking unveiled that ECS diffusional parameters are heterogeneous in and around plaques, with an elevated diffusivity within and around plaques compared to WT-tissue. The amyloid core showed low nanoparticle density, varying by plaque phenotype. Carbon nanotube tracking confirmed these altered local rheological properties at the level of the whole cortex of AD mice. Finally, we found the extracellular matrix to be dysregulated within the amyloid plaque, which may account for the observed alterations in diffusivity. Our study provides fresh insights for understanding A{beta} plaque penetration, a prerequisite for therapeutic development.

neuroscience↗

bioRxiv2025

Improved Mutation Detection in Duplex Sequencing Data with Sample-Specific Error Profiles

Duplex sequencing enables highly accurate detection of rare somatic mutations, but existing variant callers often rely on protocol-specific heuristics that limit sensitivity, reproducibility, and cross-study comparability. We present DupCaller, a probabilistic variant caller that builds sample-specific error profiles and applies a strand-aware statistical model for mutation detection. Across 50 synthetic datasets, DupCaller identified 1.25-fold more single-base substitutions (SBSs) and 1.41-fold more indels than a state-of-the-art method, while exhibiting equal or better precision. In three duplex-sequenced cell lines treated with aristolochic acid, it recovered expected mutational signatures while detecting 3.5-fold more SBSs and 2.8-fold more indels. In 93 tissue samples-- including neurons, cord blood, sperm, saliva, and blood--DupCaller showed consistent gains, detecting 1.21- to 2.7-fold more mutations. Sensitivity scaled with sample duplication rate, yielding approximately 1.5-fold more mutations under optimal conditions and over 3-fold more in low-duplication samples where other tools falter. These results establish DupCaller as a robust and scalable solution for somatic mutation profiling in duplex sequencing across diverse biological and technical contexts.

bioinformatics↗

bioRxiv2025

Stony coral tissue loss disease (SCTLD) destabilizes the coral microbiome

Stony coral tissue loss disease (SCTLD) is a rapidly spreading lethal coral disease, the etiology of which remains poorly understood. In this study, using deep metagenomic sequencing, we investigate microbial and viral community dynamics associated with SCTLD progression in the Caribbean stony coral Diploria labyrinthiformis. We assembled 264 metagenome-assembled genomes (MAGs) and correlated their abundance with disease phenotypes, revealing significant shifts in both the prokaryotic microbiome and virome. Our results provide clear evidence of microbial destabilization in diseased corals, suggesting that microbial dysbiosis is an outcome of SCTLD progression. We identified DNA viruses that increase in abundance in infected corals and are present in SCTLD-affected corals at other sites. In addition, we identify the first putative instance of asymptomatic/resistant SCTLD-affected colonies, suggesting potential microbial induced resilience (i.e., beneficial microbiome). Finally, we propose a mechanistic model of SCTLD progression, in which viral dynamics may contribute to a microbiome collapse. These findings provide novel insights into SCTLD pathogenesis and offer consistent molecular signals of disease across diverse geographic sites, presenting new opportunities for disease monitoring and mitigation.

microbiology↗

bioRxiv2025

PLIERv2: bigger, better and faster

Gene expression analysis has long been fundamental for elucidating molecular pathways and gene-disease relationships, but traditional single-gene approaches cannot capture the coordinated regulatory networks underlying complex phenotypes; although unsupervised matrix factorization methods (e.g., PCA, NMF) reveal coexpression patterns, they lack the ability to incorporate prior biological knowledge and often struggle with interpretability and technical noise correction. Semi-supervised strategies such as PLIER have improved interpretability by integrating pathway annotations during latent variable extraction, yet the original PLIER implementation is prohibitively slow and memory-intensive, making it impractical for modern large-scale resources like ARCHS4 or recount3. Here, we introduce CLAMP, which overcomes these constraints through a two-phase algorithmic design (an unsupervised "CLAMPbase" initialization followed by a "CLAMPfull" regression that incorporates priors via glmnet), rigorous internal cross-validation to tune regularization parameters for each latent variable, and efficient on-disk data handling using memory-mapped matrices from the bigstatsr package. Benchmarking on GTEx, recount2, and ARCHS4 demonstrates that CLAMP achieves 7x-41x speedups over PLIER, succeeds in modeling hundreds of thousands of samples that PLIER cannot handle, and maintains or improves biological specificity of latent variables as shown by tissue-alignment and pathway enrichment analyses. By filling the gap in scalable, biologically informed latent variable extraction, CLAMP enables comprehensive analysis of modern transcriptomic compendia and paves the way for deeper insights into gene regulatory networks and downstream applications in translational genomics.

bioinformatics↗

bioRxiv2025

Expression and Characterization of SARS-CoV-2 Spike Protein in Thermothelomyces heterothallica C1

The COVID-19 pandemic demonstrated a pressing need for rapid, adaptive, and scalable manufacturing of vaccines and reagents. With the transition into an endemic disease and rising threats of other emerging pandemics, production of these biologicals requires a stable and sustainable supply chain and accessible distribution methods. In this study, we demonstrate the strength of an engineered filamentous fungal platform, Thermothelomyces heterothallica C1, for high volumetric productivity of the full-length spike glycoprotein. Spike protein produced in this system is highly thermostable and immunization of mice with spike made in C1 or mammalian platforms resulted in a similar humoral response. Additionally, it was shown that the native N-glycan profile can be redecorated with complex sialylated structures, if necessary, resulting in a more human-like glycan profile, without impacting binding characteristics as shown experimentally and in simulations. Through extensive physicochemical analysis, the C1 produced spike performs similarly to spike proteins produced in other commercially available systems. The data presented is evidence that C1 can be a strong platform for production of complex glycosylated recombinant proteins such as subunit antigen vaccines.

bioengineering↗

bioRxiv2025

Metaproteome analysis of the coral holobiont demonstrates algal symbiont dampening under thermal stress

The accelerating loss of coral reefs worldwide due to anthropogenic climate change has led to a myriad of studies aimed at understanding the basis of coral resilience to support reef conservation. Here, we integrate physiological measurements with proteomic and metabolomic profiles to examine species-specific responses to increased temperature in three sympatric reef-building corals from the Great Barrier Reef: Acropora hyacinthus, Porites lobata, and Stylophora pistillata. We find species-specific stress response strategies with A. hyacinthus, a thermally sensitive species, exhibiting rapid decline in endosymbiont physiology, coupled with a one-third reduction in protein abundance. In contrast, P. lobata displayed a delayed physiological response to stress and a muted proteome response, suggesting greater resilience. S. pistillata initially showed minor shifts in the proteome followed by colony "bail-out". Overall, we observed markedly different responses in most biochemical pathways in the three coral species. Nonetheless, some known biomarkers of stress, including heat-shock proteins, showed conserved responses to thermal stress with differences in temporal abundance reflecting bleaching resistance. Our results underscore the species-specific nature of coral responses to thermal stress and highlight proteomic signatures associated with symbiosis breakdown, offering mechanistic insights into coral bleaching susceptibility and resilience.

microbiology↗

bioRxiv2024

Distant Ribose 2'-O-Methylation of 23S rRNA Helix 69 Pre-Orders the Capreomycin Drug Binding Pocket at the Ribosome Subunit Interface

Loss of ribosomal RNA (rRNA) modifications incorporated by the intrinsic methyltransferase TlyA results in reduced sensitivity to tuberactinomycin antibiotics such as capreomycin. However, the mechanism by which rRNA methylation alters drug binding, particularly at the distant but functionally more important site in 23S rRNA Helix 69 (H69), is currently unknown. We determined high-resolution cryo-electron microscopy structures of the Mycolicibacterium smegmatis 70S ribosome with or without the two ribose 2-O-methyl modifications incorporated by TlyA. In the unmodified ribosome, the tip of H69 adopts a more compact conformation, positioning two key nucleotides (A2137 and C2138) such that interactions with capreomycin would be lost and the binding pocket partially occluded. In contrast, methylation of 23S rRNA nucleotide C2144 results in conformational changes that propagate from the site of modification to the H69 tip, resulting in its movement away from h44, a more favorable positioning of C2138 and adoption of a more open conformation to enable capreomycin binding. Methylation of h44 also results in structural rearrangements at the H69-h44 interface that further support antibiotic binding. These structures thus reveal the effect and regulation of distant rRNA methylation on ribosome-targeting antibiotic binding.

microbiology↗