Biology subjects

Zhu, L.

Publications and source records attributed to Zhu, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Ribosome-tethered in situ sequencing for single-cell translatome analysis

Translational regulation plays a critical role in shaping cellular states and functions, yet approaches for spatially resolved translatome profiling at single-cell resolution remain limited. Here, we develop Ribosome-tethered In Situ Sequencing (Ribo-ISS), an imaging-based spatial translatomics technology that enables high-throughput mapping of ribosome-associated mRNAs in intact tissues. Ribo-ISS integrates ribosome-dependent molecular anchoring with multiplexed in situ sequencing, allowing specific detection of translation-associated transcripts without genetic manipulation or exogenous ribosome labeling. We demonstrate that Ribo-ISS achieves high specificity and enables single-cell spatial translatome profiling in mouse brain, accurately recapitulating major cell types and their anatomical organization. Applied to a sleep deprivation model, Ribo-ISS simultaneously resolved transcriptional and translational changes, revealing extensive transcription-translation uncoupling and distinct cell-type-specific translational responses. Ribo-ISS provides a scalable framework for investigating spatially organized translational programs and expands the capability of spatial omics toward understanding gene regulation beyond transcription. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/740970v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@40da8dorg.highwire.dtl.DTLVardef@1cc76b4org.highwire.dtl.DTLVardef@8535c8org.highwire.dtl.DTLVardef@18e009d_HPS_FORMAT_FIGEXP M_FIG C_FIG Ribo-ISS integrates ribosome-dependent molecular anchoring with multiplexed in situ sequencing, enabling specific detection of ribosome-bound transcripts in intact tissues without genetic manipulation or exogenous labeling. As an imaging-based spatial translatomics technology, it resolves translatome profiling at single-cell resolution. This scalable approach reveals spatial translational programs, extending spatial omics beyond transcription.

molecular biology↗

bioRxiv2026

A superfolding sfPepper enables superresolution and single-molecule RNA imaging in live cells

Fluorescent RNAs (FRs) have emerged as powerful tools for the visualization of RNA in live cells. However, the poor folding of FRs is a major limiting factor in many advanced RNA imaging applications. Here, we describe a novel strategy to significantly increase the folding efficiency of FRs. By introducing a stabilizing stem and performing targeted mutagenesis at key junction regions, we develop a superfolder variant of the Pepper aptamer, termed sfPepper, that exhibits a striking twofold increase in folding efficiency compared with Pepper under physiological conditions. sfPepper exhibits much improved thermostability and reduced ion dependence and, most importantly, is substantially brighter than Pepper in live cells. sfPepper enables robust imaging of diverse noncoding RNAs and messenger RNAs with increased signal-to-background ratios and stimulated emission depletion (STED) superresolution imaging of CUG trinucleotide repeat-containing toxic RNAs. Remarkably, only four sfPepper repeats facilitate sensitive single-molecule mRNA tracking, revealing dynamic heterogeneity among ER-associated mRNA molecules. Together, this study establishes an efficient strategy for improving FR folding and offers a powerful tool for fluorescently labelling RNAs in live cells.

molecular biology↗

bioRxiv2026

Designing Fidelity of CRISPR-Cas Endonucleases by Kinetic Insights

Finding high-fidelity CRISPR-Cas variants is critical for both the precision of in vitro DNA detection and the safety of in vivo gene-editing therapeutics. However, the large size of the Cas enzyme and the distinct selection criteria between its natural evolution and clinical practice lead to extensive experimental trials and limited success rate for de novo design, directed evolution, protein language model (PLM)-based filtering. Here, we present a PLM-assisted physics-driven approach that utilizes atomistic molecular dynamics simulations and automated path searching to efficiently obtain the complete kinetic insights, including the transition state structures, for the conformational changes of Cas before DNA cleavage. We show that these kinetic insights can pinpoint a few fidelity-diminishing protein residues during the early stage of target recognition, and have led to SpyCas9 and FnCas12a variants with ultra-high fidelity surpassing previously reported counterparts at minimal cost of a few wet-lab trials.

biophysics↗

bioRxiv2026

Hepatic Cholesteryl Ester Transfer Protein Regulates Sex-specific Liver Metabolic Adaptation and Metabolic-Associated Steatotic Liver Disease Risk in Diet-induced Obesity

Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) and associated dyslipidemia is a growing health issue that gives rise to cardiovascular risk. Men are more prone to development of MASLD than women. Understanding mechanisms underlying sex differences in MASLD may lead to improved prevention and treatment approaches. Cholesteryl ester transfer protein (CETP) is a lipid transfer protein that shuttles triglycerides and cholesteryl esters between blood lipoproteins and tissues. In this study investigate the impact of hepatic CETP expression on MASLD. Hepatic CETP expression (L-HuCETP) was achieved by injecting liver-targeted CETP-expressing adeno-associated virus into C57BL/6J mice. In females, L-HuCETP improved glucose tolerance, consistent with our prior clamp results in global human CETP transgenic mice. Whereas in males, L-HuCETP worsened glucose metabolism and impaired insulin signaling. Correspondingly, L-HuCETP expression reduced the expression of gluconeogenic pathway genes in females but upregulated these genes in males. In males, L-HuCETP mice exhibited increased hepatic lipid droplet accumulation, lipogenesis proteins and these changes were not observed in females. L-HuCETP expression resulted in sex-specific hepatic responses, with increased expression of inflammation and fibrosis related genes in male, but decreased expression of these genes in females. Mechanistic studies indicate that L-HuCETP had sex specific effects on transcription factors ChREBP and HNF4, which are important for glucose and lipid metabolism. Our studies suggest that sex-specific roles of L-HuCETP with regard to liver metabolic adaptation and MASLD risk in obesity, highlighting CETP-mediated pathways as potential targets for sex-specific precision medicine approaches to improve MASLD.

physiology↗

bioRxiv2026

Cardiovascular Benefits of Menopause Hormone Treatment is Age-Dependent

BackgroundHormone therapy (HT) has not consistently reduced atherosclerotic cardiovascular disease (ASCVD) events in post-menopausal women, yet the underlying mechanisms remain poorly understood. MethodsFemale Ldlr-/- mice with established atherosclerosis were subjected to surgical menopause and treated with 17{beta}-estradiol (E2) following lipid normalization. Studies were performed in aging and young mice. To determine whether inflammation mediates the age-dependent response to HT, a cohort of aging mice underwent transplantation with Ifn{gamma}-/- bone marrow (BM) before hormone treatments. Metabolic parameters, HDL function, systemic inflammation, atherosclerotic burden, liver metabolic and oxidative stress signaling, and hepatic estrogen receptor signaling were evaluated. ResultsIn aging mice, menopause E2 treatment failed to reduce established atherosclerosis as shown in sham operated mice during lipid normalization. Instead, E2 treatment increased circulating IFN{gamma} and IL-6, impaired HDL antioxidant and cholesterol efflux functions, and promoted inflammatory and vulnerable plaque phenotypes. Suppression of inflammation through Ifn{gamma}-/-BM transplantation restored HDL function and significantly reduced atherosclerosis in E2-treated aging mice. In contrast to aging mice, young mice exhibited reduced systemic and plaque inflammation, improved HDL functions and atherosclerosis following E2 treatment. Liver RNA sequencing and qPCR validation identified activation of inflammatory, oxidative stress, and lipid metabolic pathways in aging E2-treated mice, which were largely attenuated following Ifn{gamma}-/-bone marrow transplantation as well as in young mice. Compared to young mice, aging mice presented hepatic estrogen receptor remodeling characterized by reduced estrogen receptor (ER) expression and increased G-protein coupled estrogen receptor (GPER) expression. Constitutive GPER activation was accompanied by induction of NOX1-dependent oxidative stress, which was further exacerbated by E2 treatment, leading to persistent inflammation. ConclusionsThe cardiovascular effects of estrogen therapy are fundamentally age dependent. Aging shifts estrogen signaling toward hepatic oxidative stress and inflammation through increased GPER. While E2 treatment preserves both metabolic and cardiovascular protection in young mice, aging exacerbates GPER-NOX1-mediated oxidative stress, resulting in impaired HDL function and persistent residual ASCVD risk. These findings identify inflammation-driven, non-lipid mechanisms as potential therapeutic targets to improve cardiovascular outcomes during hormone therapy in postmenopausal women.

physiology↗

bioRxiv2026

Function-guided design of active enzymes

Designing enzymes from functional descriptions remains challenging because catalytic activity is governed by sequence-structure-function relationships. Here we present EnzymeArt, a function-conditioned enzyme-design framework centred on a generative sequence model. EnzymeArt couples function-conditioned sequence generation with structure-guided refinement, annotation checks and substrate-aware computational prioritization to select candidates for synthesis and biochemical testing. Across alcohol dehydrogenase (ADH), malate dehydrogenase (MDH) and triacylglycerol lipase design campaigns, 57 of 60 synthesized designs showed crude-lysate activity above matched background controls. Purified representatives further showed quantitative steady-state catalytic activity. The best designed ADH reached kcat = 223.7 s-1 and exceeded a wild-type reference under matched conditions, an MDH reached kcat = 267.57 s-1 despite having only 33% sequence identity to its closest BLASTP hit, and a designed lipase hydrolysed both short- and long-chain triglycerides with apparent activity modestly above that of a commercial lipase reference. Together, these results establish a route for converting functional descriptions into experimentally validated enzyme designs with quantitative steady-state kinetic activity.

bioinformatics↗

bioRxiv2026

Multisensory integration of a host metabolite coordinates bacterial predation of macrophages

The crisis of antimicrobial resistance demands new strategies that circumvent conventional killing. Here, we show that Yersinia pseudotuberculosis intercepts host mesifurane, a mimic of quorum-sensing signal AI-2. Rather than acting through a single receptor, mesifurane is directly and independently sensed by three receptor classes, YcrA, NarX, and CusR, that converge on a "Sense, Arm, Recruit" program. YcrA drives chemotaxis toward host cells; NarX-NarP licenses T6SS-mediated killing; and CusR amplifies AI-2 production to recruit more bacteria. YcrA is conserved across Gram-negative pathogens, creating a therapeutic vulnerability. Suramin sodium, a repurposed drug blocking YcrA, disarms this circuit without inhibiting growth. In murine sepsis, suramin sodium conferred 80-90% survival against WHO critical-priority pathogens, including carbapenem-resistant A. baumannii, E. coli, and P. aeruginosa, even when delayed 8 hours post-infection, without selecting for resistance. These findings establish that disrupting sensory perception, rather than viability, provides an anti-infective strategy bypassing resistance while imposing minimal selective pressure.

microbiology↗

bioRxiv2026

The structural basis for LRRK2's activation and autoinhibition

Mutations in Leucine-Rich Repeat Kinase 2 (LRRK2) are the second most common cause of autosomal-dominant Parkinsons disease (PD), and increased LRRK2 kinase activity is also observed in idiopathic PD, making LRRK2 a major actionable therapeutic target. LRRK2 is a 286-kDa multidomain enzyme containing a Ras-like GTPase (ROC) and a kinase domain. Using cryo-EM, biochemical reconstitution, and cell-based assays, we show that the ROC GTPase governs switching between autoinhibited and active states: GTP binding promotes activation, whereas GDP binding enforces autoinhibition. Two common PD-linked mutations, G2019S and R1441C/G/H, activate LRRK2 through distinct structural mechanisms, revealing genotype-specific routes to dysregulation. These findings provide a unified framework for understanding LRRK2 regulation with broad therapeutic implications. Stabilizing the GDP-bound state may inhibit LRRK2 by maintaining autoinhibition, whereas promoting the GTP-bound state could be advantageous in specific cellular contexts, such as the lung, where increased LRRK2 kinase activity may play protective or regulatory roles.

neuroscience↗

bioRxiv2026

Glucocorticoid Programming of Erythrocyte Hypoxic Memory Enables Rapid High-Altitude Acclimatization

BackgroundRapid ascent to high altitude causes acute mountain sickness (AMS) and life-threatening pulmonary/cerebral edema, yet no prophylaxis enables immediate acclimatization. Intermittent hypoxia training (IHT) establishes a "hypoxic memory" that accelerates adaptation, to high altitude, but its cellular and molecular basis remains undefined, precluding effective pharmacological strategies. MethodsA human cohort of 18 sea-level inhibitants was equally divided into two groups, one group received IHT prior to ascent to 3,500 meters, the other group did not. Multi-omics profiling of erythrocytes and plasma, along with isotopic glucose tracing, was employed to examine the metabolic effects of IHT upon high altitude acclimatization. Preclinical studies with genetically engineered mice were used to further define the molecular and metabolic basis of IHT-induced hypoxic memory allowing rapid acclimatization to high altitude. ResultsMetabolomics revealed glucocorticoids as previously unrecognized endogenous erythroid hypoxic memory orchestrators induced by IHT that negatively correlated with AMS severity. Lipidomics and isotopic glucose tracing demonstrated that glucocorticoid signaling via the glucocorticoid receptor (GR) coordinately enhanced glucose metabolism and activated sphingosine kinase-1 (SPHK1)-driven sphingosine-1-phosphate (S1P) synthesis, pre-conditioning erythrocyte oxygen unloading and antioxidant capacity. Glucocorticoid supplementation enhanced erythrocyte SPHK1 activation and oxygen delivery, counteracting multi-tissue hypoxia and pulmonary and renal neutrophil infiltration. Conversely, erythrocyte-specific Sphk1 ablation abolished glucocorticoid-induced S1P production causing severe tissue hypoxia and exaggerated pulmonary neutrophil infiltration. ConclusionsWe establish a new function of glucocorticoids in erythrocyte metabolic plasticity to enhance oxygen delivery as a hypoxic memory mechanism for rapid adaptation to high altitude. This previously unrecognized GR-mediated reprograming of glucose and sphingolipid metabolism offers a transformative precision pharmacologic strategy for high altitude preconditioning, high altitude emergencies and hypoxia-driven diseases.

cell biology↗

bioRxiv2026

Rapid vaccine induction of macaque HIV-1 V2 Apex broadly neutralizing antibodies with immunogenetic signatures that are potentially translatable to humans

Due to the complex biology of HIV-1 broadly neutralizing antibodies (bnAbs), HIV-1 vaccines must target unmutated germline precursor antibodies with B cell receptors that have the appropriate specificity and genetic features to develop neutralization breadth. Previous work has shown that immunization or infection in macaques primes unmutated precursor antibodies that target the broadly neutralizing epitope composed of the second variable region and proximal glycans (termed V2-apex site) of HIV-1 envelope (Env). Macaque V2-apex bnAb precursors elicited thus far have homogeneous usage of the second reading frame of a diversity (D) gene found only in macaques, calling into question whether HIV-1 Env immunogens can elicit only this canonical, macaque-specific V2-apex antibody response, limiting human vaccination success. Here, we show that vaccination of rhesus macaques with Env conjugated to a ferritin nanoparticle (OPT4-scNP) rapidly elicited V2-apex bnAbs with distinct D gene segment usage and motifs that are not restricted only to macaques. After two priming immunizations, V2-apex antibodies with non-canonical HCDR3s exhibited greater neutralization potency and breadth than V2-apex antibodies with previously observed HCDR3 motifs. Following sequential boosting immunizations, a V2-apex bnAb lineage with a novel HCDR3-encoded EDGED motif increased its neutralization breadth, including neutralization of viral isolates bearing the N130 glycan, which shields the V2-apex from recognition. High-resolution structures of two members of this V2-apex bnAb lineage, called DH2050, defined a novel binding mode in which it used its EDGED motif to contact the C-strand peptide and the N160 glycan within the V2-apex site. Altogether, we define a novel bnAb binding mode to the V2 Apex and demonstrate that HIV-1 Env sequential vaccination elicits V2-apex bnAbs with immunogenetic signatures that are potentially translatable to the human immune system.

immunology↗

bioRxiv2026

Unconventional biocatalytic strategies orchestrate synthesis of the nucleoside analog sinefungin

Sinefungin is a potent nucleoside antimetabolite of S-adenosylmethionine (SAM), yet its biosynthesis has remained unclear for decades. Here we detail the identification and characterization of the complete sinefungin biosynthetic gene cluster (BGC) from Streptomyces incarnatus NRRL 8089. In vitro and in vivo analyses demonstrate that the defining carbon-carbon (C-C) bond is formed not by the long-hypothesized PLP-dependent process, but by a vitamin B12-dependent radical SAM enzyme. Using isotope-labeled cofactors and substrates, we provide evidence that the adenosyl group of sinefungin atypically originates from adenosylcobalamin via a homolytic SH2 substitution, establishing a rare instance where adenosylcobalamin is enzymatically consumed during the reaction. Furthermore, the pathway utilizes a cryptic phosphorylation-dephosphorylation strategy to control intermediate processing and substrate recognition. We also characterize two peptide aminoacyl-tRNA ligases (PEARLs) that append alanines onto the nucleoside scaffold using tRNA-activated amino acids. The PEARLs act directly on small molecules rather than macromolecular substrates, with one PEARL capable of iterative elongation. Finally, we leverage these enzymes in a reduced multi-enzyme cascade to biosynthesize sinefungin. Together, these findings redefine radical-mediated C-C bond formation and pearlin enzyme versatility, unlocking biocatalytic possibilities to produce amino acid-nucleoside conjugates. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/726688v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@10e48deorg.highwire.dtl.DTLVardef@d220ceorg.highwire.dtl.DTLVardef@167e60borg.highwire.dtl.DTLVardef@2fddec_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Substrate-dependent crosslinking by the cytochrome P450 from aminopyruvatide biosynthesis

Cytochrome P450s catalyze an array of reactions including crosslinking of aromatic side chains in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). ApyO is a cytochrome P450 that forms a C-C bond between two tyrosines in a YLY motif in the substrate ApyA, the precursor peptide of the RiPP aminopyruvatide. We utilized cell-free translation to generate ApyA variants and probe the substrate tolerance of ApyO. Through Alphafold-based modelling and in vitro assays, we show that ApyO accepts the 10 C-terminal residues of ApyA and requires a conserved Arg/Lys in the substrate. Inspired by substrate sequences in orthologous biosynthetic gene clusters, we substituted one of the tyrosine residues with a tryptophan and observed that ApyO catalyzed formation of an N-C bond between the indole of Trp and C{epsilon}2 of Tyr. ApyO unexpectedly catalyzed formation of a C-O bond between the two tyrosine residues when we substituted the leucine residue in the YLY motif with tyrosine or tryptophan. A peptide containing a biaryl linkage and C-terminal aminopyruvate displayed sub-nanomolar inhibition of select proteases with the aminopyruvate group critical for activity. Overall, this study demonstrates plasticity in the manner of macrocyclization catalyzed by the P450 ApyO.

biochemistry↗

bioRxiv2026

Dynamic dorsal body morphology encodes engineering design principles of fish propulsion and hydrodynamics

Understanding how biological shape and movement interact with surrounding fluids represents a fundamental challenge at the intersection of biology, physics, and engineering. Fish locomotion exemplifies this challenge: body morphology and swimming kinematics together determine the hydrodynamic forces and flow structures that enable efficient propulsion and maneuverability. Whereas biologists have long sought to connect morphological variation to swimming performance, traditional morphometric approaches provide limited insight into the fluid mechanical consequences of shape differences. Similarly, although computational fluid dynamics can reveal detailed flow physics, simulating hydrodynamics across diverse and dynamic morphologies remains prohibitively expensive for systematic investigation. To bridge this gap, we introduce a data-driven framework that connects fish body shape dynamics to hydro-dynamic performance through compact morphospace parameterization and reduced-order modeling. Using CFD simulations of 15 fish species from the Digital Life Project database (www.digitallife3d.org/3d-model), we generate hydrodynamic datasets capturing the shape-flow relationship. Principal Component Analysis (PCA) extracts four dominant shape parameters from dorsal body profiles, which are then integrated into an Inverse-Design with Dynamic Mode Decomposition (ID-DMD) framework to model the resulting fluid dynamics. The resulting modal analysis suggests that locomotion strategies emerge from specific shape-flow interactions. We further demonstrate the frameworks utility through single- and multi-objective shape optimization, showing how it enables efficient exploration of the morphology-hydrodynamics relationship. This approach offers a novel analysis and design tool for understanding how biological form and motion interact with fluid mechanics, with applications ranging from bio-inspired vehicle development to evolutionary biomechanics.

biophysics↗

bioRxiv2026

Role of Alanine Transaminase in Retinal Metabolic Homeostasis: Potential therapeutic target in retinal diseases

PurposeAlanine transaminases (ALT), encoded by the GPT gene, catalyzes the reversible conversion of pyruvate and glutamate to alanine and alpha-ketoglutarate, thereby correlating carbohydrate and amino acid metabolism. However, its role in the human neural retina remains unclear. This study aimed to explore the expression, localization, and metabolic function of ALT in the human neural retina and its potential involvement in retinal diseases. MethodsALT1 and ALT2 expression and localization were examined in the retinas of healthy and diabetic retinopathy (DR) donors via immunoblotting and immunofluorescence. ALT function was assessed in ex vivo human retinal explants using pharmacological inhibition with beta-chloro-L-alanine (BCLA), followed by the analyses of enzyme activity, tissue injury, and transcriptomic responses. Stable-isotope tracing with 13C-and 15N-labelled substrates combined with GC-MS was used to define ALT-dependent carbon and nitrogen fluxes in macular and peripheral retinas. Redox level (NADPH/NADP+) was also evaluated under tert-butyl hydroperoxide-induced oxidative stress. ResultsALT1 and ALT2 were both expressed in the human neural retina, with prominent localization in Muller glia and photoreceptor inner segments. ALT1 displayed a diffuse cytoplasmic distribution, whereas ALT2 demonstrated a punctate pattern consistent with mitochondrial localization. In DR retinas, ALT1 expression was spatially disorganized and heterogeneous, while ALT2 remained comparatively preserved. Inhibition of ALT with BCLA markedly reduced ALT activity without causing overt cytotoxicity or major transcriptional changes. Isotope tracing demonstrated that retinal ALT predominantly channels pyruvate-derived carbon into alanine, whereas alanine was minimally contributed to pyruvate production under basal conditions. ALT inhibition suppressed alanine synthesis and release, redirected nitrogen flux towards glutamate, glutamine, and aspartate, and uncovered distinct metabolic adaptations in macular but not peripheral retinas. Under oxidative stress, ALT inhibition induced the decrease of NADP+/NADPH ratio and LDH release, indicating improved redox balance and reduced tissue injury. ConclusionsALT is previously unrecognized as a regulator of carbon and nitrogen partitioner in the human neural retina, contributing to redox homeostasis under stress. The altered distribution of ALT1 in DR retina and the protective metabolic effects of ALT inhibition suggest ALT as a potential contributor to retinal metabolic vulnerability and a candidate therapeutic target in retinal diseases.

neuroscience↗

bioRxiv2026

A sequence-based proactive intelligence for influenza antigenic profiling improves vaccine strain selection

Seasonal influenza viruses accumulate antigenic changes, eroding population immunity and necessitating recurrent vaccine updates. Hemagglutination inhibition (HI) assays are the standard for measuring antigenic relationships between circulating and vaccine strains; however, their limited throughput constrains the scale and timeliness of surveillance. Here, we present fluProfiler, a foundation-model-based framework that learns a stable mapping from viral sequences to antigenic space and uses this representation to support influenza antigenic prediction, vaccine strain evaluation, and diversity-driven sampling. fluAgPredictor aligns hemagglutinin (HA) and neuraminidase (NA) sequence representations with HI-derived antigenicity, enabling accurate and consistent inference of pairwise antigenic distances across surveillance-aligned evaluation settings. Without prior annotation of antigenic sites, it identifies key residues in immunodominant epitopes and reveals the cooperative contributions of HA and NA to antigenic variation. Building on this antigenic-space representation, fluVacSelector provides antigenic coverage scores that are concordant with World Health Organization (WHO) vaccine recommendations while also flagging potential candidates that may offer broader coverage ahead of formal consultations. fluAgEnhancer further leverages the same representation to prioritize antigenically informative and diverse strains for experimental characterization, achieving comparable predictive accuracy with approximately 25% fewer HI measurements than random sampling. Together, these modules provide a high-throughput and interpretable complement to HI testing, converting routine genomic surveillance into a more proactive, data-driven support system for antigenic monitoring and vaccine strain selection.

bioinformatics↗

bioRxiv2026

Structure and activity of a class II lanthipeptide from a thermophilic bacterium

Lanthipeptides represent a large group of ribosomally synthesized and post-translationally modified peptides (RiPPs). They offer promising avenues for discovering new antibacterial and antifungal agents. Here, we identify and structurally analyze the product of the tla BGC, which encodes a class II lanthipeptide in the thermophilic bacterium Thermoactinomyces sp. DSM 45891. Co-expression of the lanthipeptide synthetase TlaM with its substrates in Escherichia coli resulted in modification of the two precursor peptides TlaA1 and TlaA2, which share 58% sequence identity. TlaA1 was dehydrated up to seven times, with the major products having undergone five and six dehydrations, whereas TlaA2 was dehydrated seven times. In both peptides, four thioether rings were formed with two overlapping DL-(methyl)lanthionine rings at the C-terminus. Both peptides also contain two non-overlapping DL-methyllanthionines near the N-terminus and in the center of the peptide. These peptides deviate from the general rule of stereoselective LL-(methyl)lanthionine formation from a Dhx-Dhx-Xxx-Xxx-Cys motif (Dhx = dehydroalanine or dehydrobutyrine). AspN-cleaved TlaM-modified TlaA1 displayed anti-microbial activity against a subset of bacteria including Gram-negative ESKAPE pathogens. We named the lantibiotic thermolanthin. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/716199v2_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@11b6dd0org.highwire.dtl.DTLVardef@1c6a68borg.highwire.dtl.DTLVardef@e026f4org.highwire.dtl.DTLVardef@1d7d6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Genome-wide DNA supercoiling arises from transcription and SMC activity and mediates transcriptional negative feedback

Genome-wide DNA supercoiling is closely linked to chromatin organization and gene expression, yet the mechanisms establishing genome-scale supercoiling in living cells and its functional consequences remain unclear. Here, we show that genome-wide supercoiling arises from transcription-driven asymmetric topological relaxation together with contributions from SMC complexes in human cells. During RNA polymerase elongation, human topoisomerases preferentially relax positive over negative supercoils, leading to the accumulation of negative supercoiling around genes. This imbalance enriches supercoiling at transcriptionally active regions including TAD boundaries, and promotes the emergence of large-scale topology. In parallel, SMC complexes independently shape genome-wide supercoiling, with cohesin contributing to interphase topology and condensin establishing an overall positively supercoiled mitotic genome. Functionally, the accumulation of transcription-driven negative supercoiling represses local transcription, revealing a supercoiling-mediated negative feedback mechanism. Together, these findings define the mechanistic basis of genome-scale supercoiling in human cells and establish DNA topology as an integral regulatory layer of transcription.

molecular biology↗

bioRxiv2026

HMA proteins produce 2',3'-cNMP signaling molecules and activate CNL-mediated immunity in rice

Plants deploy a sensor repertoire, usually NLRs, to perceive pathogen effectors and activate executor NLR-triggered immunity. Here we reveal that rice HMA proteins function as sensors detecting the Magnaporthe oryzae MAX effector AvrPigm to trigger broad-spectrum blast resistance mediated by the CNL PigmR. AvrPigm is conserved with multiple copies in blast genomes and targets HMA proteins, facilitating HMA translocation into the cytoplasm. Cryo-EM structure of the HPP04HMA reveals a filament-like oligomer with ssDNA/RNA bound inside the filament, which display cyclic nucleotide synthase activity to generate 2',3'-cNMP in a CNL-dependent manner. We further discovered that the LRR domains of the executor CNLs perceive 2',3'-cNMP to mount immunity. Our study thus establishes an unrecognized immunity mode with a distinct repertoire of sensor receptors that produce signaling molecules that are perceived by the LRR domains of executor NLRs to mediate immunity, shedding new light on the sensor-executor conception and immune activation in plants. HighlightsO_LIHMA proteins and CNL receptors form a new sensor-executor mode in plant immunity C_LIO_LICryo-EM reveals the filament-like structure of HMA-ssRNA/ssDNA C_LIO_LIHMA proteins are cyclic nucleotide synthetases to generate 2',3'-cNMP C_LIO_LILRR domains of CNLs perceive 2',3'-cNMP to mediate immunity C_LI

plant biology↗