Biology subjects

Zhu, L.

Publications and source records attributed to Zhu, L..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Methionine γ-lyase Traps Cofactor Pyridoxal-5'-phosphate through Specific Serine-Mediated Affinity

Pyridoxal-5'-phosphate (PLP), the ubiquitous and ancient cofactor, plays important roles in enzymatic elimination, transamination and other reactions. The catalytic efficiency of PLP-dependent enzymes is significantly higher than that of free PLP. The recruitment of PLP from the environment by the enzymes, particularly through interactions outside the active site, is the key step determining the occurrence of PLP-mediated catalysis. However, the precise mechanism by which enzymes recruit PLP remains elusive. Methionine {gamma}-lyase (MGL), a PLP-dependent enzyme, catalyzes the degradation of L-methionine, thereby suppressing cancer cell proliferation through serum or dietary methionine depletion. Here, we report the crystal structure of yMGL, which belongs to a newly identified subgroup of cystathionine {gamma}-lyases, in complex with L-methionine and PLP. Through truncating the C-terminal domain of yMGL both in vitro and in vivo, we demonstrated that this domain, outside the canonical PLP-binding domain, is essential for the specific interaction between yMGL and PLP, as well as for efficient L-methionine catabolism. A conserved Ser in the C-terminal domain, positioned at the active-site entrance of MGLs, confers specificity for PLP. These findings elucidate a previously uncharacterized mechanism of PLP recruitment by MGLs and promote rational design of MGLs with tailored cofactor selectivity and catalytic performance.

biochemistry↗

bioRxiv2025

Human ribosome interactions reframe neomycin toxicity

Aminoglycosides such as neomycin are clinically limited by toxicity, commonly attributed to the inhibition of mitoribosomes. Here, we re-evaluate this mechanism by integrating Cryo-EM and functional assays to assess neomycins binding potential in vitro with its cellular engagement and functional consequences. Cryo-EM revealed extensive multi-site binding of neomycin on both human mitochondrial and cytosolic ribosomes in vitro, including conserved regions of the decoding center. In contrast, ribosomes isolated from neomycin-treated cells show markedly remodeled occupancy patterns, with no detectable neomycin bound to the mitoribosomes and reduced occupancy at a subset of cytosolic ribosome sites. However, neomycin remained functionally active in cells, inducing widespread stop-codon readthrough while having minimal effects on global mitochondrial and cytosolic protein synthesis. These findings reveal a disconnect between structural binding potential and cellular target engagement and identify disruption of translational fidelity, rather than global translational inhibition, as a major cellular consequence of neomycin exposure.

biochemistry↗

bioRxiv2025

DrugPT: A Flexible Framework for Integrating Gene and Chemical Representations in Perturbation Modeling

Accurately modeling the transcriptional response of cells to drug perturbations is critical for drug discovery and precision medicine. Here, we propose DrugPT, a novel Transformer-based framework for predicting gene expression changes upon drug treatment. DrugPT consists of three modular components: (1) a gene representation module that encodes pre-treatment expression profiles using GPT-derived embeddings; (2) a drug representation module that captures chemical structure information using a pre-trained GPT2 model; and (3) a Transformer-based prediction module that integrates gene and drug embeddings to predict perturbed gene expression profiles. Unlike previous approaches, DrugPT formulates the prediction task as a sequence modeling problem, leveraging pre-trained language models for both gene and drug modalities. We demonstrate the architecture of DrugPT and highlight its generalizable design for encoding heterogeneous biological and chemical information. This work introduces a unified modeling framework, laying the foundation for future developments in multimodal perturbation prediction tasks.

bioinformatics↗

bioRxiv2025

A Cattle BodyMap of Transcriptome across 52 Tissues and 3 Developmental Stages Reveals New Genetic Insights into Beef Production Traits

Cattle are important livestock that provide essential meat and milk resources. However, a comprehensive analysis of gene expression, alternative splicing (AS), and RNA editing across various organs and developmental stages in cattle has not been reported. This study aims to create a comprehensive transcriptomic BodyMap across various tissues and developmental stages, integrating this information into genomic predictions of beef production traits. We created a comprehensive transcriptomic BodyMap using 400 samples collected from 52 organs of newborn, young, and adult cattle, and estimated their contributions to genetic variance and genomic predictions for 23 beef production traits in 1476 beef cattle. We cataloged the expression of 25,530 annotated genes, 28,533 novel long non-coding RNAs (lncRNAs), 215,754 AS events, and 3,093,058 A-to-I RNA-editing sites. Integrating transcriptome BodyMap with 23 beef production traits, we found lncRNAs influenced traits like rib-eye area and carcass length, while RNA editing associated with chunk roll weight and daily gain. We observed trait-relevant tissues between different stages, including the differential expressed genes of cerebellum, longissimus muscle, and testis between newborn and adult stages are more relevant to beef production traits. The tissue-specific genes and development-associated genes in several tissues could improve the reliability of genomic prediction in beef production traits. We developed Cattle BodyMap Transcriptome Database (https://cattlegenomics.online/cattle_bodymap) to retrieve, analyze, and visualize gene expression, lncRNA, splicing and RNA editing data. Our results demonstrated the potential of using transcriptome data as a valuable resource for genomic selection and breeding programs in beef cattle. Additionally, our transcriptome BodyMap serves as a valuable resource for biological interpretation, functional validation, and genomic improvement in livestock.

genomics↗

bioRxiv2025

Bmal1 expression is minimal or absent in human and mouse cerebral microglia

Microglia orchestrate immunological responses in the brain and play an important role in maintaining homeostatic brain functions. Several studies have reported clock gene expression in microglia and the circadian rhythm they drive has been linked to the modulation of immune responses and neuronal functions. In the current study, complementary approaches, including immunofluorescence, multiplexed fluorescence in situ hybridization, and liquid chromatography-mass spectrometry proteomics of isolated CD11b+ microglia, were combined with publicly available transcriptomic and epigenomic datasets to investigate the expression of the core clock gene BMAL1 in human post-mortem cortical and limbic areas as well as mouse brain. The majority of BMAL1-expressing cells were found to be neurons, with microglia representing a negligeable proportion. We also identified significantly lower chromatin accessibility or "openness" for BMAL1 gene regulatory regions (such as promoters and enhancers) in microglia compared to neurons. These regulatory regions in microglia were enriched for ETS domain transcription factor (TF) binding sites. Together, this suggests a strong role of chromatin remodeling factors in suppressing BMAL1 gene expression in microglia. Finally, while we observed a very low expression, BMAL1 TF motifs were accessible in open chromatin landscape of microglia, which may lead to downstream gene-regulatory effects upon binding, even if BMAL1 expression is constitutively low. Overall, our results reveal low or absent expression of BMAL1 in microglia and point towards potential epigenetic mechanisms regulating its expression in these cells.

neuroscience↗

bioRxiv2025

Towards the Development of Isoenergetic Peptide Nucleic Acid Based Probes Targeting Double-Stranded RNAs Through Enhancing Sequence-Specific Stacking Interactions

Peptide nucleic acid (PNA), a synthetic nucleic acid analog, exhibits substantial potential in biotechnology and therapeutic applications due to its high binding affinity and nuclease/protease resistance. Chemically modified PNAs capable of forming stable triplex structures with double-stranded RNAs (dsRNAs) under near-physiological conditions further expand their utility by enabling sequence-specific precise targeting and probing of functional RNA structural motifs. However, the presence of inverted Watson-Crick pairs (C-G and U-A) may significantly weaken the triplex formation of the dsRNA-binding PNAs (dbPNAs). Our previous work demonstrated that dbPNA P3 (composed of L, T, and Q monomers for the recognition of G-C, A-U, and C-G base pairs, respectively) can stimulate ribosomal frameshifting by binding to rHP2, a model RNA hairpin structure in an mRNA, albeit with suboptimal efficiency, due to its significantly weakened Q*C-G triple formation. We hypothesize that incorporating s2U adjacent to Q may offer unique stacking and hydrogen bonding interactions facilitating the development of isoenergetic dbPNA-based probes binding toward dsRNAs with varied sequences. In this study, we investigate how incorporating s2U adjacent to Q residues in P3 influences its binding to rHP2. Bio-layer interferometry (BLI) and non-denaturing polyacrylamide gel electrophoresis (PAGE) analyses demonstrate that substituting T with s2U at the N-terminal position adjacent to Q (P3-2QT) enhances binding affinity by [~]10-fold compared to unmodified P3, whereas C-terminal substitution (P3-TQ2) yields only a 2-fold improvement. Consistent with these findings, a cell-free dual-luciferase reporter assay reveals that P3-2QT significantly increases ribosomal frameshifting efficiency compared to P3 and P3-TQ2. Molecular dynamics simulations further indicate that P3-2QT maintains enhanced PNA-PNA stacking stability, particularly between s2U3 and Q4, suggesting a structural basis for its superior activity. Intriguingly, analogous s2U substitution in the P5 oligomer with the Q replaced by L does not confer a comparable enhancement in binding to the target RNA (rHP1) and frameshifting stimulation, highlighting the context-dependent nature of this modification. To assess the broader applicability of the s2U-Q motif, we examined its effect in dbPNAs targeting the RNA panhandle structure of influenza virus A and precursor microRNA-21, respectively. Both PAGE and BLI data confirm that s2U incorporation improves binding affinity, reinforcing the generality of this strategy. These findings underscore the potential of sequence-dependent uracil thiolation in optimizing triplex-forming dsRNA-binding PNAs, warranting further exploration of modified nucleobase designs to enhance their binding and functional properties. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/662161v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@15d86aborg.highwire.dtl.DTLVardef@1347369org.highwire.dtl.DTLVardef@852040org.highwire.dtl.DTLVardef@84b0a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThiolation of uracil upstream of Q base in PNA markedly enhances triplex binding affinity and enables isoenergetic and orthogonal targeting/activation. C_LIO_LIN-terminal s2U modification adjacent to Q residues increases PNA-dsRNA binding by [~]10-fold and significantly boosts ribosomal frameshifting efficiency. C_LIO_LIBiophysical assays and molecular dynamics simulations reveal that thiolation improves PNA stacking stability and slows dissociation, thereby enhancing functional activity toward structured RNA targets. C_LIO_LIThe general applicability of s2U modification is demonstrated with influenza A virus RNA panhandle structure and precursor micoRNA-21 targets, underscoring its broad potential for optimizing PNA-based therapeutics and biotechnological tools. C_LI

biochemistry↗

bioRxiv2025

Blockade of VCAM1 or VLA4 preserves cerebrovasculature and prevents cognitive decline late after stroke

Infarct-induced neurodegeneration occurs chronically after stroke, doubling the risk of dementia. Endothelial vascular cell adhesion molecule 1 (VCAM1) facilitates blood-brain barrier opening and immune cell diapedesis by binding very late antigen 4 (VLA4) on immune cells. We hypothesized that vascular dysfunction persists after stroke and contributes to chronic neuroinflammation and cognitive decline via signaling through the VLA4/VCAM1 axis. We used adult (3-5 month old) and middle-aged (10 month old) C57BL/6J male & female mice and a permanent middle cerebral artery occlusion stroke model. Sham surgery consisted of an identical procedure without occlusion of the artery. We quantified vascular integrity using blood vessel length, pericyte coverage of vasculature, tight junctions, and extravascular fibrinogen leakage by immunostaining. Cognitive testing was performed using both Barnes maze and novel object recognition prior to stroke, and 1 and 6 weeks after stroke, and replicated in both male and female mice. We utilized anti-VCAM1, anti-VLA4 or isotype control antibodies to block VCAM1 or VLA4 function, and then to confirm mechanisms we utilized single cell RNA sequencing on immune and endothelial cells, aptamer-based plasma proteomics, and additional immunostaining for vascular integrity. Mouse brains exhibited signs of persistent vascular dysfunction and loss of blood-brain barrier integrity at 8 weeks after stroke, compared to sham animals. We observed reduced ZO-1 tight junction and pericyte coverage of vasculature, and increased extravascular fibrinogen. Mice with stroke also developed a cognitive deficit in both Barnes maze and novel object by 6 weeks. Treatment with anti-VCAM1 or anti-VLA4 resulted in mice with stroke performing as well as sham mice treated with isotype control antibody on both the Barnes maze and novel object recognition tasks. Anti-VCAM1 and anti-VLA4 both increased expression of blood-brain barrier maintenance genes in brain endothelial cells, while only minimally altering immune cell gene expression. Immune cell infiltration was reduced by anti-VCAM1 but not anti-VLA4 in tissue sections. In contrast to this, both antibodies increased blood vessel length and pericyte vascular coverage. Finally, extravascular fibrinogen was reduced by both antibody treatments in multiple brain regions. Together, our findings establish the VLA4/VCAM1 axis as a promising target to preserve vascular integrity and prevent cognitive decline late after stroke. Our data is consistent with a model where blocking either VCAM1 or VLA4 chronically after stroke promotes new blood vessel growth and maturation and restores the blood-brain barrier to prevent infarct-induced neurodegeneration.

neuroscience↗

bioRxiv2025

Inhibiting RhoA Activation via GDP-state Stabilization to Relieve Heart Failure

High rates of heart failure (HF) morbidity and mortality have made targeting myocardial remodeling--particularly hypertrophy and fibrosis--a key therapeutic focus. RhoA, which regulates cytoskeletal reorganization and cell migration, plays a role in this process. However, RhoA has long been considered "undruggable", due to its strong binding to its endogenous substrates, GDP/GTP, and the lack of well-defined pockets for drug targeting. Here, we discovered a cryptic pocket proximate to GDP within RhoA and identified a natural product, AH001, binds here and interacts with GDP, stabilizing RhoAs interaction with its endogenous inhibitor, RhoGDI. AH001 reduced the downstream MRTFA nuclear translocation and downregulated fibrosis/hypertrophy proteins. Consequently, AH001 mitigated myocardial remodeling in multiple HF animal models, and in the 3D myocardial tissue model. Our findings highlight the therapeutic potential of inhibiting RhoA activation in myocardial remodeling, ultimately targeting HF, and offer a promising avenue for developing reversible inhibitors against undruggable GTPases.

pharmacology and toxicology↗

bioRxiv2025

Dietary fibre promotes chronic whipworm infection through direct and time-dependent modulation of innate immunity

Dietary fibre regulates the microbiome and gut health but increases murine whipworm (Trichuris muris) infection through unclear mechanisms. We show that mice fed inulin-supplemented diets exhibit dysregulated innate antimicrobial defences and altered tryptophan metabolism during T. muris infection. Inhibiting tryptophan catabolism or neutralizing IL-27 and IL-18 in inulin-fed mice restored infection resistance. Notably, inulin led to chronic infection even in microbiota-depleted mice. Removing inulin within a critical immune development window rapidly restored anti-helminth immunity, indicating direct, time-dependent modulation of mucosal immune responses. Our findings reveal a previously unrecognized, direct influence of dietary fibre on mucosal immunity to parasitic infection, independent of the microbiome, highlighting the complex interplay between diet timing and host defence.

microbiology↗

bioRxiv2025

Establishing a Digital PCR-Based Reference Measurement Procedure for Monkeypox Virus: An Inter-laboratory Assessment and Standardization Study

The accurate detection of monkeypox virus (MPXV) is crucial for effective viral diagnosis and epidemic prevention. Currently, the field lacks standardized reference methods for MPXV quantification, as well as reliable pseudovirus reference materials (RMs) to ensure quality control throughout the detection process. To address this, we developed a droplet digital PCR (ddPCR) reference measurement procedure (RMP) for precise quantification of MPXV genes B6R, which demonstrates excellent performance with a wide dynamic range (11-1.24x104 copies/L), strong linearity (R2=0.9984), and a low limit of quantitation (11 copies/L, CV[≤]25%). Repeatability tests confirmed high precision, with inter-laboratory CVs <10% across nine labs using different dPCR platforms. recovery efficiencies for B6R and F3L were [~]69%, with uncertainties incorporated into final measurements. The homogeneity assessment showed good results (CV=2.94%), and stability studies confirmed the stability of the sample during -70 {degrees}C and short-term storage (4 {degrees}C/-20 {degrees}C). Mandels statistical data shows that the reproducibility between laboratories is consistent. This validated ddPCR RMP provides metrological traceability, ensuring reliable and comparable results for MPXV diagnosis and supporting public health efforts.

molecular biology↗

bioRxiv2025

Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations

Negative selection on deleterious mutations plays a key role in shaping human genetic variation, yet the dominance effects of these mutations remain poorly understood because existing statistical methods often cannot distinguish dominance effects from the overall selective effects. In this work, we take a fundamentally different approach by leveraging the distribution of Neanderthal ancestry across the human genome. Simulations show that recessive deleterious mutations can increase archaic introgressed ancestry through heterosis in the absence of positive selection, in contrast to the depletion expected under additive effects. We use this signal to develop DominL, a machine learning classifier trained on simulations of human demography with Neanderthal introgression to identify megabase-scale genomic windows enriched with recessive mutations. DominL demonstrates robust accuracy, with particularly high power in exon-dense regions. Applied to 7 non-African populations from the 1000 Genomes Project, DominL identifies approximately 3-9% of the genome as enriched for recessive mutations, with most high-confidence regions shared across populations. Predicted regions show patterns consistent with expected signatures from recessive mutations, including weakened background selection, depletion of runs of homozygosity, and enrichment of non-additive trait-associated variants. These regions also contain genes associated with metabolic and immune-related functions.

evolutionary biology↗

bioRxiv2025

TMEDs Mediate Versatile Cargo Transport in Vesicle-dependent Unconventional Secretion

Unconventional protein secretion (UcPS) exports diverse signal peptide-lacking cargoes, yet its cargo selectivity remains poorly understood. Here, we identify TMED proteins as key regulators of vesicle-dependent UcPS, mediating selective cargo release via translocation into secretory carriers. TMED proteins act as translocators, facilitating cargo passage across lipid bilayers with assistance from HSP90 chaperones and partial cargo unfolding. Selectivity arises during translocation, where TMED cytoplasmic tails bind specific cargoes. The ER-Golgi intermediate compartment (ERGIC) is essential for TMED-mediated translocation and release. TMED homo-oligomerization enhances translocation, while hetero-tetramerization inhibits it. ERGIC localization promotes homo-oligomerization, which is further stabilized by cargo binding, forming a feed-forward mechanism to enhance translocation. These findings establish TMED proteins as central regulators of cargo diversity in UcPS, with their oligomerization and subcellular localization modulating translocation efficiency.

cell biology↗

bioRxiv2025

Heme-NO dilates arteries via mobilization of NO moieties from a vascular intracellular NO store

Nitrosyl heme (heme-NO) has recently emerged as a surrogate signaling entity for nitric oxide (NO). However, questions remain about how heme-NO signals across the cell membrane. Herein, we test the hypothesis that heme-NO signals as a nitrodilator that vasodilates by mobilizing NO moiety from a nitrodilator-activated intracellular NO store (NANOS) in the vasculature. We identify a novel mechanism for glutathione-catalyzed formation of a model compound, alb-heme-NO, and determine glutathione (GSH) as a ligand in its structure. Heme-NO complexes with plasma proteins in blood and, as such, it is impermeable to red blood cells or the vascular wall. Alb-heme-NO-mediated vasodilation, both in vitro and in vivo, is attenuated by prior depletion of the NANOS and potentiated by NANOS supplementation. Incubation with alb-heme-NO induces efflux of NO moieties from arteries. Additionally, the role of nitrosyl hemoglobin (HbNO) in mediating NO bioactivity export from erythrocytes is challenged. In conclusion, heme-NO functions as an extracellular nitrodilator via activation of the intracellular NANOS.

physiology↗

bioRxiv2025

The influence of ceftriaxone, ceftazidime-avibactam, and piperacillin-tazobactam on the gut microbiota

PurposeThe administration of antibiotics can induce dysbiosis of the gut microbiota, leading to diseases, e.g., irritable bowel syndrome, metabolic syndrome, and Clostridium difficile infection. However, the specific effects of different {beta}-lactam antibiotics on the dysbiosis of the gut microbiota remain poorly understood, particularly in human studies. MethodsThis study assessed the impacts of ceftriaxone, ceftazidime-avibactam, and piperacillin-tazobactam on the diversity, composition, and bacterial interactions within the gut microbiota at days 1, 6, and 37 after administration. ResultsAll three antibiotics significantly altered beta diversity of the gut microbiota by day 6, with ceftriaxone showing the most prolonged effects. Changes in the composition of the gut microbiota were more similar between the ceftazidime-avibactam and piperacillin-tazobactam groups and differed markedly from those in the ceftriaxone group. Consistent with beta diversity changes, bacterial interaction networks showed greater and longer-lasting disruptions of bacterial interaction in the gut microbiota in the ceftriaxone group compared to the ceftazidime-avibactam and piperacillin-tazobactam groups. ConclusionThese findings highlight distinct patterns of microbiota disruption following ceftriaxone, ceftazidime-avibactam, and piperacillin-tazobactam treatments and provide insights for mitigating dysbiosis of the gut microbiota during {beta}-lactam therapy.

microbiology↗

bioRxiv2025

Multimodal control of Cas13 activity through domain insertion at an allosteric hotspot

CRISPR-Cas13 RNA nucleases have emerged as powerful tools for programmable RNA targeting. A light-controlled RNA nuclease could be transformative by enabling researchers to selectively knock down transcripts at desired positions in a cell or tissue or at timepoints of interest. Here, we develop a set of multimodal RfxCas13d tools that can be controlled by either light or small molecule addition. Screening an RfxCas13d library containing insertions of the AsLOV2 photoswitchable domain revealed an OptoCas13d-off variant that induced target RNA cleavage in the dark and switched to an inactive state under blue light. Insertion at this same allosteric hotspot could be further exploited to generate an OptoCas13d-on with the opposite light dependence and a ChemoCas13d that is activated upon the addition of rapamycin analogs. Through biochemical assays, we showed that AsLOV2 domain switching did not substantially affect Cas13d-RNA complex formation, indicating allosteric control over Cas13d catalytic activity. We applied the OptoCas13d-on system to target several endogenous transcripts and showed that it exhibited efficient mRNA knockdown only upon blue light illumination. Overall, our results demonstrate that engineered OptoCas13d can achieve cellular RNA modulation with high spatial and temporal precision.

bioengineering↗

bioRxiv2025

Dysregulated Proline Metabolism Contributes to Subretinal Fibrosis in Neovascular AMD: Therapeutic Potential of Prolyl-4-Hydroxylase Inhibition

Subretinal fibrosis, a major cause of irreversible vision loss in neovascular age-related macular degeneration (nAMD), is driven by excessive deposition of extracellular matrix such as collagens. While proline metabolism is known to play a critical role in collagen biosynthesis and fibrosis, its involvement in subretinal fibrosis remains unclear. Here, we characterized the progression of fibrovascular lesions in JR5558 mice, observing significant molecular alterations as early as 4 weeks of age and phenotypic changes by 8 weeks. Transcriptomic and metabolomic analyses revealed elevated levels of 4-hydroxyproline, an essential component of collagen, alongside significant alterations of other fibrosis-related pathways. P4HA1, a catalytic subunit of prolyl-4-hydroxylase essential for 4-hydroxyproline biosynthesis, was prominently expressed in fibrotic lesions in retinas of JR5558 and two-stage laser-induced murine models, as well as human eyes with nAMD. Targeting P4HA1 with the small-molecule inhibitor diethyl pythiDC significantly attenuated fibrovascular lesion growth in the JR5558 murine models and reduced collagen turnover in human retinal pigment epithelium cells. Combining diethyl pythiDC with aflibercept had a stronger antifibrotic effect than monotherapies in JR5558 mice. These findings suggest a key contribution of proline metabolism, particularly proline hydroxylation, in subretinal fibrosis. Inhibiting P4HA1 with diethyl pythiDC inhibited fibrosis in the models we studied, offering a novel therapeutic strategy. Further research is warranted to explore the potential benefits of combining existing anti-angiogenic therapies with drugs that inhibit proline metabolism for the management of nAMD-associated fibrosis.

neuroscience↗

bioRxiv2025

Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking of ortho-Tyrosines

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a growing class of natural products that possess many activities that are of potential translational interest. Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), until recently termed domain of unknown function 692 (DUF692), have been gaining interest because of their involvement in a range of biochemical reactions that are remarkable from a chemical perspective. Over 13,500 putative MNIO-encoding biosynthetic gene clusters (BGCs) have been identified by sequence similarity networks (SSNs). In this study, we identified a set of precursor peptides containing a conserved FHAFRF-motif in MNIO-encoding BGCs. These BGCs follow a conserved synteny with genes encoding an MNIO, a RiPP recognition element (RRE)-containing partner protein, an arginase, and a B12-dependent radical SAM enzyme (rSAM). Using heterologous reconstitution of a representative BGC from Peribacillus simplex (pbs cluster) in E. coli, we demonstrated that the MNIO in conjunction with the partner protein catalyzes ortho-hydroxylation of each of the phenylalanine residues in the conserved FRF-motif, the arginase forms an ornithine by deguanidination of the arginine in the motif, and the B12-rSAM crosslinks the ortho-Tyr side side chains by a C-C linkage forming a novel macrocyclic molecule. Substrate scope studies suggested tolerance of the MNIO and the B12-rSAM towards substituting the Phe residues with tyrosines in the conserved motif with the position of hydroxylation and crosslinking being maintained. Overall, this study expands the diverse array of posttranslational modifications catalyzed by MNIOs and B12-rSAM enzymes. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/647296v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@37d9c8org.highwire.dtl.DTLVardef@baf547org.highwire.dtl.DTLVardef@3d0ed8org.highwire.dtl.DTLVardef@99aaee_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

A novel rat model for human Meibomian gland dysfunction and ocular rosacea

Ocular Rosacea (OR) is a common chronic inflammatory disease that affects the ocular surface and eyelids. Meibomian gland dysfunction (MGD), often associated with OR, can lead to dry eye syndrome and vision-threatening corneal complications. OR is underdiagnosed and incurable, highlighting the need for a deeper understanding of the pathogenesis of MGD associated with OR to develop targeted treatments. In this study, rat upper eyelids were exposed to UVB, a known triggering factor for rosacea, for five days. UVB exposure caused acute damage to the eyelid skin and meibomian glands (MG) together with increased oxidative stress, mitochondrial dysfunction, apoptosis, inflammation, and elevated lipid production by day 5. During the two-week healing process, inflammation and lipid hyperproduction tended to normalize, but hyperkeratinization of MG ducts persisted, and meibocyte stem cells continued to decrease. This led to MGD and was likely responsible for corneal epithelial defects observed on day 19. The progressive fibrosis in rat MG was similar to that observed in MG biopsy tissues from OR patients, suggesting that UVB causes chronic and irreversible damage to MGs. Transcriptomic intersection analysis revealed shared gene regulation patterns between UVB-induced changes in rat MG and human rosacea and MGD. Additionally, UVB altered Meibum lipid composition in ways that mimic human MGD. This model provides a valuable tool for studying the pathophysiology of MGD associated with OR and for evaluating potential treatments.

pathology↗