Biology subjects

Xiao, J.

Publications and source records attributed to Xiao, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies

Elucidating the mechanisms by which broadly neutralizing antibodies (bnAbs) develop to confer durable immunity in humans is pivotal for the rational design of next-generation vaccines and therapeutics. VH3-53/3-66-encoded public antibodies are widely elicited in the population after the COVID-19 pandemic. Here, we isolated 15 VH3-53/3-66-encoded bnAbs from elite neutralizers who experienced sequential SARS-CoV-2 Omicron breakthrough infections. These bnAbs exhibit exceptional potency and breadth against circulating variants and, as members of a long-lived public antibody lineage, likely contribute to durable humoral protection. Genetic analysis of VH3-53/3-66-encoded bnAbs reveals a convergent somatic hypermutation pattern at seven positions in and around the CDR loops that emerges with repeated viral exposures and distinguishes them from non-bnAbs. Grafting these combined mutations onto clinically escaped antibodies broadens their breadth and restores neutralization activity. Structural analysis shows that these convergent mutations cooperatively remodel CDRs to bind and tolerate virus receptor-binding domain mutations. Using an AI-based antibody language model trained on data linking somatic hypermutations to binding affinity and neutralization, the model is able to identify mutational patterns predictive of breadth, enabling the discovery of a rare bnAb with protective activity against the latest variants from early-pandemic antibody repertoires. This demonstrates the feasibility of establishing an AI-empowered pipeline to identify mutation-tolerant bnAbs from early-pandemic antibody repertoires to fight fast-evolving newly introduced viruses.

immunology↗

bioRxiv2025

Arsenic Trioxide Underpins Delayed Neuroinflammation and Impaired Synaptic Integrity involving Integrative Stress Response Signaling

Arsenic trioxide (ATO), an industrial and environmental chemical with potential for accidental or intentional exposure, exerts profound neurotoxic effects. Its single acute exposure has been linked to delayed neurological and neurodegenerative outcomes. However, the molecular and cellular pathways driving these long-term manifestations remain poorly defined. In this study, combining human iPSC-derived neuronal and in vivo mouse model, we uncovered that the acute ATO exposure activates cellular stress pathway, which drives long-term neurotoxic and associated functional outcomes. We found that ATO induces integrated stress response (ISR) signaling in human iPSC-derived neurons. To model the impact of accidental ATO exposure in vivo, we administered a single high dose of ATO to C57BL/6J wild type mice. Four weeks post-treatment, ATO-exposed mice displayed neuropsychological symptoms and cognitive deficits. Brain analyses of ATO-challenged mice revealed elevated ISR activity marked by the increased phosphorylation of PERK and eIF2 and upregulation of the transcription factors, CHOP and ATF4. Transcriptomic profiling using bulk RNAseq revealed activation of pathways associated with stress and neuroinflammatory responses. Consistently, increased DNA damage and dysregulation of the STING-mediated innate immune response were also found in the brain of ATO-challenged mice. Pharmacological inhibition of the ISR with a small-molecule inhibitor, ISRIB mitigated ISR activation and preserved synaptic integrity in mouse hippocampal cells. In conclusion, our data identify ISR activation and DNA damage-driven immune dysregulation as key pathogenic drivers of ATO-induced delayed neurotoxicity and cognitive deficits and highlight ISR inhibitors as promising therapeutics to mitigate these effects.

neuroscience↗

bioRxiv2025

Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli

Chromosomal topology and transcription are tightly coupled, yet the quantitative impact of topological constraints on transcription, supercoiling, and the potential coupling between neighboring genes in vivo remains unclear. In this work, we constructed synthetic chromosomal domains in Escherichia coli that contained two genes inside a topology-controllable domain and a third gene outside. Using three-color single-molecule fluorescence in situ hybridization (smFISH), we measured transcription output from the three genes in individual cells under conditions in which gene orientation, domain formation state, and global chromosomal supercoiling density were varied. We found that topological domain formation repressed transcription, diminished gene orientation-dependent differences in transcription, and modulated the supercoiling sensitivity of genes located both within and near the domain. Relaxing global negative supercoiling through gyrase inhibition broadly repressed transcription; increasing global negative supercoiling level through topoisomerase I inhibition repressed highly expressed genes, while activating lowly expressed ones. Besides single-gene effects, we also observed an intrinsic coupling between neighboring genes with a non-monotonic dependence on the underlying supercoiling state, which shifted with domain topology and gene syntax. Our results establish chromosome topology as a major regulator of both transcription levels and the coupling between adjacent genes.

biophysics↗

bioRxiv2025

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

The increasing scale and complexity of proteomics data demand robust, scalable, and interpretable quality control (QC) frameworks to ensure data reliability and reproducibility. Here, we present pmultiqc, an open-source Python package that standardizes and generates web-based QC reports across multiple proteomics data analysis platforms. Built on top of the widely adopted MultiQC framework, pmultiqc offers specialized modules tailored to mass spectrometry workflows, with full initial support for quantms, DIA-NN, MaxQuant/MaxDIA, and mzIdentML/mzML-based pipelines. The package computes a wide range of QC metrics, including raw intensity distributions, identification rates, retention time consistency, and missing value patterns, and presents them in interactive, publication-ready reports. By leveraging sample metadata in the SDRF format, pmultiqc enables metadata-aware QC and introduces, for the first time in proteomics, QC reports and metrics guided by standardized sample metadata. Its modular architecture allows easy extension to new workflows and formats. Alongside comprehensive documentation and examples for running pmultiqc locally or integrated into existing workflows, we offer a cloud-based service that enables users to generate QC reports from their own data or public PRIDE datasets.

bioinformatics↗

bioRxiv2025

Stimulus-specific recruitment of human amygdala neurons predicts episodic memory encoding success

Controlling whether a given experience is encoded into long-term memory and thus later remembered is a crucial component of our memory system whose failure is often at the root of memory disorders. One brain area that takes part in controlling which experiences are remembered is the amygdala, but the mechanisms by which it does so remain poorly understood. Here we examined single-neuron activity and local field potentials as human participants performed recognition memory tasks with visual stimuli. Category-selective amygdala neurons exhibited elevated firing rates during encoding of later remembered items versus forgotten items. This subsequent memory effect was restricted to images of the preferred category of a given cell, was stronger and appeared earlier in the amygdala compared to the hippocampus, and did not depend on the valence and arousal of the stimuli. In contrast, category selective cells immediately upstream in the ventral temporal cortex did not exhibit a subsequent memory effect, highlighting specificity to the amygdala. Successful memory formation was accompanied by enhanced spike-field coherence between the activity of category cells in the amygdala and hippocampal field potentials. These findings, replicated in two large independent datasets with two different tasks, demonstrate that recruitment of stimulus-specific amygdala representations predicts episodic memory formation, particularly in the right amygdala. This data suggests category cells in the right amygdala as a cellular target for interventions to treat memory disorders in humans.

neuroscience↗

bioRxiv2025

Cell cycle-driven epigenetic resetting maintains stem cell fate for shoot branching

Adult mammalian stem cells typically maintain stem cell identity through proliferative quiescence. In contrast, we demonstrate that stem cell maintenance in Arabidopsis bud precursor cells requires active cell-cycle progression. Inhibiting division silences the shoot meristem marker gene SHOOT MERISTEMLESS (STM) and promotes differentiation. Whereas proliferation dilutes H3K27me3 levels to counteract silencing. Meanwhile, we identified two classes of transcription factors recruiting polycomb repressive complex 2 (PRC2) to epigenetically silence STM. The balance between these forces establishes a cell cycle-coupled epigenetic "Sisyphus" mechanism that maintains pluripotency. This cell fate switch is bistable; modeling and experimental data confirm that prolonged quiescence triggers irreversible differentiation. We propose that sequence-dependent PRC2 recruitment in plants enables precise silencing of fate-determining genes, while cell proliferation sustains pluripotency by resetting epigenetic marks.

plant biology↗

bioRxiv2025

Magnesium isoglycyrrhizinate alleviates alcohol-associated liver disease through targeting HSD11B1

While magnesium isoglycyrrhizinate (MgIG) is a clinically approved therapy for alcohol-associated liver disease (ALD), its precise molecular targets and mechanisms remain uncharacterized. This study aimed to define MgIGs hepatoprotective actions in chronic-binge ALD mouse models and ethanol/palmitic acid-exposed AML-12 hepatocytes. Through an integrated strategy encompassing RNA sequencing, molecular docking, and microscale thermophoresis, we discovered that MgIG directly binds to hydroxysteroid 11-beta dehydrogenase 1 (HSD11B1) at residue 187, a finding corroborated by molecular dynamics simulations. In vivo, MgIG markedly attenuated alcohol-induced liver injury, evidenced by ameliorated histological damage, reduced hepatic steatosis, and normalized liver-to-body weight ratios. In vitro, it effectively reduced lipid accumulation, inflammation, and apoptosis. Mechanistically, RNA sequencing identified isopentenyl diphosphate delta isomerase 1 (IDI1) as a key downstream effector. Hepatocyte-specific genetic manipulations confirmed that MgIG modulates the SREBP2-IDI1 axis, thereby suppressing lipogenesis, inflammatory responses, and apoptotic pathways. We reveal HSD11B1 as a novel direct molecular target of MgIG and elucidate its therapeutic mechanism through the HSD11B1-SREBP2-IDI1 signaling axis, which profoundly impacts ALD pathogenesis. These findings not only validate MgIGs clinical utility but also highlight a promising new therapeutic target for ALD.

pharmacology and toxicology↗

bioRxiv2025

Harnessing cGAS-STING signaling to counteract the genotoxic-immune nexus in tauopathy

Tauopathies are progressive neurodegenerative disorders characterized by aberrant tau aggregation, cognitive decline, and persistent neuroinflammation, yet the mechanisms driving neuroinflammation and disease progression remain incompletely understood. Here, utilizing human postmortem AD brains and a mouse model of tauopathy, we report that genotoxic stress-induced cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) immune pathway form a self-amplifying loop that fuels neuropathology and cognitive deficits. Targeted disruption of this cycle through either genetic deletion of cGAS or pharmacological inhibition of STING restores immune homeostasis and attenuates tau pathology and cognitive deficits. Our results showed a significant accumulation of DNA double-strand breaks (DDSBs) and impaired DNA repair function, alongside elevated cGAS-STING signaling and type I interferon (IFN-I) responses in human AD brains compared to non-AD. In the PS19 transgenic (PS19Tg) mouse model of tauopathy, we found significantly elevated levels of DDSBs and altered expression of DNA repair proteins during early stages of disease, which preceded the dysregulation of cGAS-STING signaling and emergence of significant neuropathology in the later stage. Interestingly, genetic deletion of cGAS shifted microglial polarization from a pro-inflammatory M1 phenotype toward an anti-inflammatory M2 state, accompanied by a reduction in IFN-I signaling and improved cognitive performance in PS19Tg mice. Pharmacological STING inhibition reshaped the transcriptomic landscape, revealing selective regulation of pathways governing synaptic plasticity, and immune responses. This transcriptional reprogramming was accompanied by suppression of inflammatory responses, reduction in synaptic pathology, and attenuation of tau pathology in PS19Tg mice, underscoring STING as a therapeutic target for tauopathy. In conclusion, our findings reveal that genotoxic-immune crosstalk drives neuroinflammation and tau pathology and identify a conserved, druggable cGAS-STING axis that can be targeted to impede or slow disease progression in tauopathies. O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/678980v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1339c89org.highwire.dtl.DTLVardef@16a1d5borg.highwire.dtl.DTLVardef@1ad4631org.highwire.dtl.DTLVardef@db4615_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

NicheScope: Identifying Multicellular Niches and Niche-Regulated Cell States in Spatial Transcriptomics

The functional state of a cell is intrinsically linked to its local microenvironment, or cell niche, a complex milieu formed by multiple interacting cell types. Deciphering how these multicellular niches regulate cell states is fundamental to understanding tissue biology and disease mechanisms, yet remains challenging with current computational approaches. Here, we present NicheScope, a computational framework for transcriptome-wide identification and characterization of Multicellular Niches (MCNs) and their corresponding Niche-Regulated Cell States (NRCSs) from spatial transcriptomics data. NicheScope operates on the principle that a cells transcriptional state is associated with its local multicellular composition. It employs a robust statistical approach to jointly model neighborhood composition and transcriptome-wide gene expression, enabling the simultaneous discovery of MCNs, defined by specific combinations of neighboring cell types, and their associated NRCSs, characterized by distinct gene programs. We demonstrate NicheScopes power and versatility across diverse tissues and platforms, including lymph node, lung adenocarcinoma, and head and neck cancer. NicheScope reproducibly dissected established tissue structures in lymph nodes across tissue regions and platforms, uncovered clinically relevant tumor cell-associated MCNs in lung adenocarcinoma, and revealed shared and condition-specific MCNs in primary and metastatic tumors. Our results establish NicheScope as a powerful, robust, scalable, and interpretable framework for dissecting the spatial and functional organization of complex tissues, providing new insights into multicellular coordination in health and disease.

bioinformatics↗

bioRxiv2025

Complement C3 recognition by C3 convertases

The complement system plays a fundamental role in human immunity, and its dysregulation is implicated in numerous diseases. Activation of the complement occurs through three main pathways: classical, lectin, and alternative; which converge at the central component, C3. The classical and lectin pathways utilize the C4b2a convertase to cleave C3 and initiate complement activation, while the alternative pathway employs the C3bBb convertase, which is further stabilized by properdin. The molecular mechanisms governing C3 recognition by these convertase complexes remain incompletely understood. Here, we first present a 3.1 [A] cryo-electron microscopy (cryo-EM) structure of the C4b2a-C3 complex, alongside the 2.9 [A] and 3.1 [A] structures of the C4b2 zymogen in the loading and activation states. These structural snapshots elucidate the structural basis for C3 engagement by C4b2a, and illustrate sequential conformational changes during the classical/lectin pathway convertase maturation. Furthermore, we determine a 2.6 [A] cryo-EM structure of the C3bBb-properdin-C3 complex, which uncovers unique substrate-binding features of C3bBb and sheds light on how properdin stabilizes the alternative pathway convertase. These results offer comprehensive mechanistic insights into complement activation.

molecular biology↗

bioRxiv2025

Xenopus IgX informs engineering strategies of IgM and IgG hexamers

Polymeric immunoglobulins are essential components of the immune system in jawed vertebrates. While mammalian immunoglobulin M (IgM) typically forms a pentamer linked by the joining chain (J-chain), Xenopus laevis IgX assembles into a J-chain-independent polymer. Here, we present the cryo-electron microscopy (cryo-EM) structure of IgX, revealing its hexameric configuration. By incorporating the IgX tailpiece into human IgM, we achieved efficient IgM hexamer formation. Truncating IgMs natural tailpiece to a range of 11-16 residues also substantially enhanced hexamerization efficiency. Furthermore, introducing a shortened IgM tailpiece to IgG resulted in effective IgG hexamer formation. We further show that the engineered IgM and IgG hexamers targeting CD20 demonstrated robust complement-dependent cytotoxicity (CDC) against several B lymphoma cells. Additionally, the IgG-Fc hexamer functioned as a decoy, attenuating CDC in cell cultures. These findings deepen our understanding of polymeric immunoglobulin evolution and introduce innovative strategies for the development of IgM- and IgG-based biologics. One Sentence SummaryThe cryo-EM structure of the African clawed frog immunoglobulin IgX reveals a uniform hexameric assembly, inspiring innovative strategies for the development of therapeutic human IgM and IgG hexamers.

immunology↗

bioRxiv2025

NTM-DB: A Comprehensive Non-Tuberculosis Mycobacteria Genomic Database

Non-tuberculous mycobacteria (NTM) are a major group of environmental bacteria, with approximately one-third of them causing serious human infections, particularly respiratory diseases. The global rise in the prevalence and severity of NTM infections has posed a major public health challenge. While high-throughput sequencing has generated vast genomic data on NTM, there remains a lack of comprehensive resources for cross-species genomic analysis. To address these limitations, we have developed a specialized database called NTM-DB (https://ngdc.cncb.ac.cn/ntmdb) tailored for NTM researchers and clinicians. NTM-DB offers the most comprehensive collection of NTM genomic and bioinformatic resources, including 16,469 genome assemblies (13,134 newly assembled genomes), 189 type/standard strain genomes representing 177 species and 12 subspecies, 705 MLST types, 33,240 resistance genes, and 74,315 virulence genes. A user-friendly interactive website has been constructed to enable efficient browsing, MLST profiling, searching, online analysis, and downloading of the aforementioned data. Notably, with online analysis tools, users can perform customized genotyping, cross-species phylogeny, pan-genome, and virulence and drug resistance gene annotation analyses using our data and/or their uploaded data. Overall, with its comprehensive data, intuitive interface, and powerful analysis tools, NTM-DB serves as an important resource and reference for NTM researchers and clinicians, improving diagnosis and treatment for various NTM-related diseases, and supporting both scientific discovery and clinical practice.

microbiology↗

bioRxiv2025

Protein Malnutrition Facilitates Intestinal Colonization with Highly Resistant Klebsiella pneumoniae

Pediatric infections with Highly Resistant Enterobacterales (HRE), including Klebsiella pneumoniae resistant to 3rd-generation cephalosporins and/or carbapenems, disproportionately affect low- and middle-income countries where malnutrition is prevalent. The underlying mechanisms linking malnutrition to HRE colonization in children have not been established. In this study we developed a mouse model of pediatric malnutrition and intestinal colonization with clinical isolates of carbapenem-resistant K. pneumoniae (CR-Kp). Juvenile mice fed a protein-deficient diet (PD) were more susceptible to intestinal colonization after inoculation with human-derived strains of CR-Kp, demonstrating a 3-4 log higher colonization burden in comparison to mice fed a control diet (CD). Colonization in PD-fed mice persisted for up to 6 weeks and CR-Kp were transmitted between PD-fed but not CD-fed cage mates. Antibiotic treatment resulted in similar CR-Kp colonization burdens regardless of diet, suggesting that nutrition-dependent colonization resistance is reliant on an intact microbiota. Secondary bile acids, a product of resident intestinal microbiota, were reduced in PD-fed and antibiotic treated mice and demonstrated an inverse correlation with CR-Kp burden. Secondary bile acids directly inhibited CR-Kp growth in vitro, suggesting that a loss of these inhibitory metabolites may mediate malnutrition-induced susceptibility to HRE colonization.

microbiology↗

bioRxiv2025

Inorganic phosphate in Arp2/3 complex acts as a rapid switch for the stability of actin filament branches

The rate at which actin filaments turn over modulates actin network architecture and mechanosensitivity. Actin filaments often appear as branches, nucleated by the Arp2/3 complex. Within the Arp2/3 complex, Arp2 and Arp3 are ATPases, which, similar to actin, may adopt slightly different conformations depending on their bound nucleotide. We investigate the impact of the nucleotide state of Arp2/3 complexes on branch stability, by mechanically pulling on them. Remarkably, we find that branches with mammalian ADP-Pi and ADP-Arp2/3 complexes detach with the same exponential increase as a function of force, but ADP-Pi-Arp2/3 complex branch junctions are 20 times more stable at all forces. We observe that inorganic phosphate (Pi) is in rapid equilibrium with ADP-Arp2/3 at the branch junction, and is released at a rate greater than 1 s-1. Upon branch dissociation, the surviving Arp2/3 complex, remaining attached to the mother filament, is a thousand times more stable in the ADP-Pi than in the ADP state. Surprisingly, branch regrowth from surviving ADP-Pi-Arp2/3 complex does not require reloading ATP, indicating that the Arp2/3 complex remained in an active state upon debranching. We reveal that GMF destabilizes ADP-Arp2/3 complex branch junctions by accelerating first the dissociation of the daughter filament, and then the dissociation of the surviving Arp2/3 complex from the mother filament. We also report that cortactin stabilizes branches in a force dependent manner, and enhances branch renucleation. GMF and cortactin do not bind to Arp2/3 in the ADP-Pi state. Overall, Our results give a new importance to cytoplasmic Pi, as a possible regulator of branched actin network stability.

biophysics↗

bioRxiv2025

Self-Reactive B Cells in Artery Tertiary Lymphoid Organs Encode Pathogenic High Affinity Autoantibody in Atherosclerosis

Artery tertiary lymphoid organs (ATLOs) emerge in atherosclerosis which is a chronic inflammatory artery disease with an autoimmune component. However, whether disease-relevant autoimmune B cells emerge in ATLOs and their impacts remains unknown. To map atherosclerosis-specific humoral autoimmunity and define its roles, we isolated germinal-center (GC) B cells from ATLOs and lymph-nodes, expression-cloned 60 autoantibodies and screened them for arterial wall reactivity. ATLO-derived autoantibodies markedly skewed to atherosclerosis-relevant autoantigens versus those of lymph-nodes. One ATLO GC-derived autoantibody bound to histone 2B (H2B) with high-affinity ([~]25 nM). Moreover, vaccination with H2B or adoptive transfer of its cognate autoantibody markedly accelerated atherosclerosis suggesting that ATLOs fail to delete pathogenic high-affinity self-reactive B cells. In a human cohort, total circulating anti H2B antibody titers positively correlated with aortic and coronary artery calcification. We conclude that ATLOs harbor a dysregulated immune tolerance environment permissive for autoreactive B cells that express pathogenic autoantibodies driving atherosclerosis.

immunology↗

bioRxiv2025

Facilitating Analysis and Dissemination of Proteomics data through Metadata Integration in MaxQuant

Metadata plays an essential role in the analysis and dissemination of proteomics data. It annotates sample information for output tables from library searches and displays sample information from data files in public repositories. However, integrating metadata into data analysis can be time-consuming and is not well standardized. Then inconsistent metadata formats in public repositories would make it even more difficult for other researchers to reproduce and reuse these public datasets. Here we present the metadata integration in MaxQuant, which provides a user-friendly way to export metadata as SDRF, the standard format that maps sample properties to proteomics data files. We have also implemented the annotation of output tables with the SDRF file, enabling users to perform seamless downstream data analysis with annotated output tables. These new features provide a simple and standardized approach to creating and leveraging standardized metadata. They will greatly facilitate data analysis and improve the reusability and reproducibility of public proteomics datasets.

bioinformatics↗

bioRxiv2025

Neurodevelopmental Impact of Bipolar Disorder Genetic Risk on Cortical Thickness and Network Topology in Adolescents

Bipolar disorder (BD) is a highly heritable psychiatric condition characterized by recurrent mood episodes that commonly manifest during adolescence. Although polygenic risk scores (PRS) effectively quantify genetic susceptibility to BD, the neurobiological correlates of this genetic risk during adolescent brain development remain unclear. Using normative modeling and longitudinal neuroimaging data from the Adolescent Brain Cognitive Development (ABCD) cohort (N = 4519), we examined cortical thickness (CT) deviations and structural covariance network (SCN) alterations in adolescents stratified into high and low BD genetic risk groups based on PRS. Adolescents with high PRS for bipolar disorder exhibited greater cortical thickening in the inferior frontal gyrus and primary visual cortex, whereas those with low PRS demonstrated greater thickening in the posterior cingulate cortex and middle precentral gyrus. These patterns suggest PRS-related variations in cortical maturation, potentially reflecting distinct neurodevelopmental trajectories associated with genetic susceptibility to bipolar disorder. Furthermore, high PRS individuals displayed altered SCN topology, characterized by decreased local clustering and enhanced global network efficiency. Longitudinal data show that these abnormal regions exhibit atypical developmental trajectories, accompanied by a global reorganization of network topology. Additionally, high genetic risk was associated with lifestyle factors, especially correlated with increased positive expectancies toward substance use. Eventually, we found three potential BD risk genes during adolescence, including PLEKHA2, ZSCAN31 and ANK3, encoding the function of the postsynaptic membrane and synaptic membrane. These findings elucidate early neurodevelopmental deviations linked to genetic risk for BD, highlighting potential biomarkers for early identification and targeted interventions.

neuroscience↗

bioRxiv2025

Mycobacterium tuberculosis MutT4 is an RNA pyrophosphohydrolase that forms biomolecular condensates and sensitizes mRNAs to degradation

Bacterial adaptation to stress involves changes in transcription and mRNA degradation rates. In Escherichia coli, the Nudix hydrolase RppH initiates mRNA degradation by removing pyrophosphate from mRNA 5-ends, converting 5-triphosphates to 5-monophosphates. We aimed to identify the RppH homolog in the globally important pathogen Mycobacterium tuberculosis (Mtb). We deleted each non-essential Nudix gene from Mtb to determine their impacts on mRNA phosphorylation states. Deletion of mutT4 (Rv3908) increased the relative abundance of 5-triphosphates on myriad mRNAs across the transcriptome. Purified MutT4 converted mRNA 5-triphosphates into monophosphates, and stimulated degradation by RNase E and RNase J. MutT4 has intrinsically disordered regions (IDRs), a common domain for biomolecular condensate formation. Microscopy showed that MutT4 forms condensates that dissociate upon addition of rifampicin, and that the N-terminal IDR is sufficient for condensate formation. These MutT4 condensates localize with RNase E and RNase J. Deletion of mutT4 in Mtb leads to a higher outer membrane permeability and resistance to oxidative stress. We conclude that MutT4 is the RppH homolog of Mtb, assembling in condensates that may act as degradation hubs. Our data indicate that MutT4 is unlikely to participate in DNA repair or nucleotide pool cleansing, and as such would more accurately be named RppH.

microbiology↗