Biology subjects

Liao, L.

Publications and source records attributed to Liao, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Ambient-Condition Visualization of Metalloenzyme Reactive Intermediates Enabled by the SHINERS Paradigm

Reactive metal-oxygen intermediates are central to metalloenzyme catalysis, yet their low populations and short lifetimes make vibrational characterization under aqueous reaction conditions challenging. Here, we establish shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) as a powerful vibrational approach for visualizing reaction-associated metal-ligand signatures of reactive metalloenzyme states. Across the heme and non-heme iron enzymes TauD, VioC, CYP119, and TqaLNc, isotope-sensitive features provide vibrational information on reactive coordination states. In TauD and VioC, isotope-sensitive features provide vibrational characterization of Fe(IV)=O intermediates. In CYP119, an isotope-sensitive Fe(IV)=O vibration is assigned to P450 Compound I generated by m-CPBA, including under lauric-acid turnover conditions. Most notably, in TqaLNc, combined 18O- and 15N-sensitive vibrational responses support formation of the proposed (R)HN-Fe(IV)=O coordination state and the dynamic-coordination mechanism underlying selective C-N bond formation. These results demonstrate that SHINERS can serve as a powerful technique for the in situ vibrational visualization of reactive intermediates and their coordination states in metalloenzyme catalysis.

biochemistry↗

bioRxiv2026

Microfluidic-based high-throughput isolation enhances the recovery of novel strains and diversity from Arctic soil microbiome

Microbial cultivation remains essential for understanding the physiology, ecology, and biotechnological potential of environmental microbes, yet conventional plate-based methods (CPM) recover only a minute fraction of the environmental microbiome. Polar regions, particularly Arctic soils, represent unique reservoirs of "microbial dark matter" that remain challenging to cultivate, owing to oligotrophic conditions, low temperatures and freeze-thaw cycles that impose severe physiological constraints on microbial growth. Here, we report the first systematic application of microfluidic droplet technology (MDT) to Arctic active-layer soil microbiota and benchmark its performance against CPM using identical starting cell numbers, R2A medium, and incubation at 15{degrees}C. MDT achieved 6.5- to 8.1-fold higher recovery rates than CPM and improved isolation throughput by >180-fold. Near-full-length 16S rRNA gene sequencing (PacBio) revealed that MDT recovered significantly higher taxonomic richness across all taxonomic levels, with 256 genera detected in the high-cell-input group (DropAS_H) versus 211 in the corresponding plate group (PlateAS_H). Notably, MDT yielded a more even community distribution, significantly reducing the dominance of fast-growing copiotrophs such as Pseudomonas and Flavobacterium. Moreover, approximately 50% of sequences from MDT were affiliated with potential novel species (<98.46% identity to type strains), and 27% with potential novel genera (<95% identity). Strain verification by Sanger sequencing confirmed 12 of 17 isolates as candidate novel species, among which one strain represented a potential novel genus within Devosiaceae. This study demonstrates that MDT is a powerful platform for accessing the uncultured majority of polar soil microbiota and establishes a pipeline for high-throughput isolation of novel cold-adapted bacteria. IMPORTANCEArctic soils harbor a vast reservoir of microbial diversity that remains largely inaccessible due to the extreme oligotrophic conditions and low temperatures characteristic of polar environments, leading to slow growth rates and extended lag phases in most microbes. Conventional plate-based methods (CPM) inherently favor fast-growing copiotrophs while suppressing rare or slow-growing lineages. Here we demonstrate that microfluidic droplet technology (MDT) overcomes these fundamental constraints, representing its first systematic application to polar microbiology. By physically isolating individual cells into nanoliter-scale bioreactors, MDT mitigates interspecific competition, thereby releasing slow-growing and oligotrophic taxa that are otherwise outcompeted in bulk cultures. The water-in-oil emulsion format further enables extended low-temperature incubation without evaporative loss or airborne fungal contamination, issues that frequently compromise long-term plate-based cultivation of Arctic samples. Relative to CPM, MDT increased recovery rates by >6-fold and isolation throughput by >180-fold, while markedly enhanced both taxonomic richness and evenness. Exclusively recovered by MDT, the oligotrophic genus Caulobacter and numerous cold-adapted genera underscore that MDT accesses physiologically distinct fractions of the cryospheric microbiome. Furthermore, the integration of near-full-length 16S rRNA gene sequencing with MDT cultivation assessment provided substantially improved phylogenetic resolution for species-level identification and novel taxon delineation. Collectively, these findings establish MDT as a transformative platform for cryospheric culturomics, accelerating the construction of comprehensive polar strain collections essential for understanding cold-adaptation mechanisms and exploiting the biotechnological potential of Earths frozen microbiomes.

microbiology↗

bioRxiv2026

Biological characterization and host-phage interaction of a novel Pectobacterium phage

Taro (Colocasia esculenta (L.) Schott) is an important vegetable and food crop in China, but in recent years, soft rot disease has frequently occurred during its cultivation and production. This disease damages the underground corms and petiole bases of taro, causing decay in the affected parts and emitting a foul odor, leading to wilting and lodging of the entire plant. This has resulted in significant economic losses to taro production in China, along with food safety issues and ecological problems caused by excessive pesticide use, making it urgent to find a green and efficient control method. Due to its specificity and environmental safety, phage therapy exhibits advantages that chemical pesticides cannot match, representing a promising alternative to chemical pesticides for controlling pathogenic bacteria. In the preliminary work of this study, a bacterial strain was isolated from taro soft rot in Shaoguan, Guangdong, and initially identified as Pectobacterium colocasium ZXC0623. Using this strain as the host bacterium, a Pectobacterium phage was screened and named QJphage. We analyzed its physicochemical properties and obtained its biological characteristics, including optimal titer, optimal infection latency period, optimal infection multiplicity, optimal storage solvent, and resistance to ultraviolet light, pH, and chloroform. Through homologous alignment analysis, eight tail fiber proteins encoded in the QJphage genome were predicted as putative receptor-binding proteins (RBPs). To validate this prediction, the corresponding genes were cloned downstream of the egfp gene via homologous recombination, and the resulting recombinant plasmids were transformed into a prokaryotic host to express EGFP-tagged tail fiber fusion proteins. Fluorescence detection and confocal laser scanning microscopy confirmed that the protein encoded by ORF04 functions as the RBP. Furthermore, lipopolysaccharide (LPS) was knocked out in the host strain P. colocasium ZXC0623. Both{Delta} LPS1 and{Delta} LPS2 mutants formed smaller plaques compared to the wild-type strain, and the{Delta} LPS1 mutant additionally exhibited a significant reduction in plaque number, indicating that LPS serves as a receptor involved in QJphage adsorption. Finally, transcriptomic analysis during the latent period of infection focused on 20 genes predicted to be associated with phage-host receptor binding and anti-phage immune systems. The results revealed that pilin proteins act as potential reversible adsorption receptors for QJphage, while the host strain ZXC0623 also possesses a diverse repertoire of anti-phage defense systems. Collectively, QJphage exhibits stable physicochemical properties, a well-defined LPS-dependent infection mechanism, and a host with diverse defense systems, providing a foundation for the control of taro soft rot and future phage-related research. ImportancePhage therapy has emerged as a highly effective biocontrol strategy against Pectobacterium, with its specificity making it particularly valuable. A critical aspect of this approach is the identification of phage receptors. The initial step in the phage life cycle involves adsorption to the bacterial host, beginning with reversible contact followed by irreversible binding between phage receptor-binding proteins and specific bacterial surface receptors. Potential receptors include glycolipids in the Gram-negative outer membrane, capsular polysaccharides, and various membrane proteins or appendages. In this study, we first characterized the physicochemical properties of the isolated QJphage. Through integrated transcriptomic and whole-genome analyses, we demonstrated that the LPS of Pectobacterium specifically interact with the tail fiber proteins of QJphage. This research provides the first evidence revealing the molecular mechanism of interaction between Pectobacterium and its phage, establishing a foundation for developing phage-based control strategies against soft rot diseases.

microbiology↗

bioRxiv2026

An efficient and stable ascorbate/O2-driven route for L-DOPA synthesis by heme-dependent tyrosine hydroxylase

L-DOPA is a key therapeutic agent for Parkinsons disease, with growing demand due to global population aging. Here we report that heme-dependent tyrosine hydroxylase (TyrH) can utilize an ascorbate/O2 system--as an alternative to H2O2--to synthesize L-DOPA with markedly enhanced operational stability. While exogenous H2O2 rapidly inactivates TyrH within minutes, sodium ascorbate (NaAsc) enables sustained catalysis for up to 24 h, surpassing the H2O2-driven yield after only 30 min. UV-vis spectroscopy confirms that H2O2 readily degrades the heme center, whereas the heme remains intact in the presence of NaAsc. QM/MM simulations reveal that in situ generated H2O2 leads to the active species of Compound I for tyrosine hydroxylation. Through systematic optimization, we establish efficient reaction conditions (40 {micro}M TyrH, 1 mM L-Tyr, 100 mM NaAsc, pH 8.5, 40 {degrees}C), achieving >95% conversion of L-Tyr to L-DOPA within 2 h. This work not only provides a robust and sustainable biocatalytic route for L-DOPA production but also highlights the broader applicability of the ascorbate/O2 pathway in heme-enzyme catalysis.

biochemistry↗

bioRxiv2026

mSWI/SNF complex inhibition sensitizes KRAS-mutant lung cancers to targeted therapies via epithelial-mesenchymal subversion

Targeted therapies for KRAS-mutant non-small lung cancer (NSCLC) have shown promising clinical results, however, incomplete tumoral responses and the inevitable emergence of therapeutic resistance remain critical challenges. Here we identify mSWI/SNF chromatin remodeling complexes as critical determinants of (EMT)-mediated KRAS inhibitor inefficacy and resistance in KRAS G12C lung cancers. Treatment with the clinical-grade SMARCA4/2 inhibitor, FHD-286, dampens EMT-mediated acquired resistance in drug-responsive models and similarly resensitizes drug-refractory models by rewiring mSWI/SNF chromatin localization and activities that modulate epithelial transcriptional programs and cell state. Further, synergistic mSWI/SNF and KRAS inhibitor combination treatment sensitizes non-G12C KRAS-mutant NSCLC cells to pan-RAS and G12D-specific inhibitors. Finally, FHD-286 and sotorasib combination treatment results in potent anti-tumor efficacy in both G12Ci-resistant and - sensitive organoid models and in vivo patient-derived xenograft (PDX) systems. These data nominate mSWI/SNF inhibition as a combination strategy to improve KRAS inhibitor efficacy, response duration, and to mitigate emergence of resistance.

cancer biology↗

bioRxiv2026

Intermittent AP-1 activation in muscles contributes to exercise-induced health benefits

Regular physical exercise extends healthspan, yet the molecular mechanisms that translate intermittent contractile stress into lasting benefit remain incompletely understood. Using global nuclear run-on (GRO-seq) in mouse skeletal muscle after treadmill running, we profiled enhancer RNA (eRNA), a sensitive marker of enhancer activity. Activation protein-1 (AP-1), a family of pioneering factors for senescence, emerged as the top transcription factor with motif enrichment in exercise-activated enhancers. Our screen in the contracting C2C12 myotubes pinpointed cFos/JunD as the primary AP-1 factor responsible for contraction-induced transcriptional changes. Muscle-specific overexpression of A-Fos, a dominant-negative mutant of cFos, disrupted transcriptomic responses to exercise and attenuated exercise-mediated improvement in muscle functions. Interestingly, intermittent but not continuous overexpression of cFos/JunD in mouse muscles mimicked exercise-induced transcriptomic changes, increased mitochondrial volume density, enhanced muscle strength and fatigue resistance, and improved glucose tolerance. These results define a transcriptional regulatory signaling pathway linking exercise intermittency to beneficial adaptations and highlight the necessary recovery cycles in training. The paradoxical anti- and pro-aging roles of AP-1 offer insights into the timing and dynamics of stressors and stress responses in shaping senescence and healthspan.

molecular biology↗

bioRxiv2025

Recurrent RNA-lipoplex vaccination is required to sustain functional tumor-infiltrating neoantigen-specific CD8 T cells and therapeutic efficacy

Cancer vaccines induce durable, polyepitopic T cell responses, and show promising clinical benefit in adjuvant settings, yet they are largely ineffective in advanced disease. Using a clinically relevant RNA-lipoplex vaccine, we investigated the efficacy constraints in a preclinical model. Vaccination remodeled the tumor microenvironment (TME), increasing T cell infiltration and promoting a proinflammatory myeloid compartment. This was associated with complete regression of smaller, immature tumors, but only delayed growth of larger, established tumors. While vaccine-induced T cells were long-lived and functional in peripheral tissues, intratumoral T cells declined rapidly in abundance, diversity, and function, reverting to a prevaccine-like state. scRNA-seq suggested that this was driven by a pro-apoptotic program, with surviving T cells showing signatures of cellular stress and impaired activation. Importantly, recurrent vaccination replenished functional T cells in the TME and enhanced efficacy. These findings highlight the importance of optimizing vaccine schedules and tailoring therapeutic strategies to tumor stage.

immunology↗

bioRxiv2025

A single MHCII neoepitope mRNA vaccine elicits CD4 T- and B- cell responses promoting endogenous CD8 anti-tumor immunity

Recent progress in therapeutic cancer vaccines has shown promising clinical activity, especially when targeting MHC class I (MHCI) neoantigen-specific CD8+ T cell responses in post-surgical patients. To explore the role of CD4+ T cells in vaccine-dependent tumor rejection, we constructed an mRNA lipoplex vaccine encoding a single MHCII-restricted neoantigen. The vaccine elicited Tfh and Th1 cell responses while decreasing Tregs, leading to rejection of established tumors in mice. IL-21 and IFN-{gamma}, crucial for Tfh and Th1 function respectively, contributed to anti-tumor activity. B cells and neoantigen-specific antibodies were also shown to participate in vaccine efficacy. Additionally, conventional type 1 dendritic cells (cDC1s) were essential for eliciting vaccine-induced CD4+ T cells, and both cDC1s and CD4+ T cells were required to enhance endogenous CD8+ responses, which were crucial for tumor control. Our results suggest that immunizing against MHCII neoantigens alone is sufficient to orchestrate a potent and cooperative immune response against cancer.

immunology↗

bioRxiv2025

Development of a CRISPR/Cas9-induced gene editing system for Pseudoalteromona fuliginea and its applications in functional genomics

Pseudoalteromonas has been used as a model system to study cold adaptation and is of widespread interest in biotechnology and ecology. To explore its physiological responses to extreme cold, uncover functional genes, and clarify their ecological roles, efficient genetic tools are essential. However, existing genetic manipulation methods in Pseudoalteromonas rely on traditional homology-based recombination, which is inefficient and time-consuming. Consequently, improving editing efficiency is crucial for advancing both basic research and applied potential. Here, we introduced the CRISPR/Cas9 system into Pseudoalteromonas for the first time, and conducted an extensive investigation into the application of the Type II CRISPR/Cas9 system for gene editing in Pseudoalteromonas fuliginea, a representative species thriving in the frigid polar oceans. To validate the feasibility of the CRISPR/Cas system in P. fuliginea, multiple genes were selected as targets and confirmed the gene editing effects through phenotypic changes or gene expression. We have successfully achieved both gene knockouts and insertions in P. fuliginea, encompassing the deletion of genes such as fliJ, indA, and genes encoding Pf sRNAs, as well as the in vivo insertion of 3xflag and the gfp gene. The average CRISPR/Cas9 gene editing efficiency in P. fuliginea exceeded 70% (range: 73.3%-95.8%), which is significantly higher than the traditional homology-based approach (less than 0.1%). In summary, we developed an efficient CRISPR/Cas9-based editing system in P. fuliginea, which can be utilized to accelerate the development of Pseudoalteromonas as a model system for addressing fundamental questions related to extreme environmental adaptation and to fulfill its potential biotechnological applications. IMPORTANCEPseudoalteromonas fuliginea is a marine bacterium with great potential for ecological and biotechnological research, yet its genetic manipulation has long been a technical challenge. In this study, we developed a gene editing system based on CRISPR technology that enables efficient and precise genome modification in this organism. Using this system, we successfully deleted, inserted, and tagged multiple genes, including regulatory and non-coding elements, with high success rates. Notably, several of these genes are linked to key traits such as motility and stress response, which contribute to microbial adaptation in polar environments. This tool allows researchers to directly test gene function and study microbial adaptation in cold marine environments. The ability to perform reliable genetic edits in Pseudoalteromonas fuliginea opens new possibilities for its use as a model organism and will support future advances in microbial ecology, environmental microbiology, and marine biotechnology.

molecular biology↗

bioRxiv2025

Biodegradable Poly(β-amino amide)s Enable Efficient RNA Delivery and Spleen Targeting

RNA therapeutics are emerging as transformative modalities in clinical applications and have become a key area in life science research. While lipid nanoparticles (LNPs) have become the leading platform for RNA delivery in preventive and therapeutic products, they still face significant challenges in achieving efficient extrahepatic delivery and maintaining long term shelf stability. Here we report the development of a series of biodegradable poly({beta}-amino amide) (PBAA) polymers, detailing their design, synthesis, and performance as gene delivery vehicles both in vitro and in vivo. These cationic polymers, featuring interspersed trialkylamine motifs, provide a readily tunable functional handle and facilitate complexation with gene cargo. The redox-sensitive disulfide motifs introduce a redox-responsive decomposition pathway for the polymer backbone, triggering cargo release during intracellular delivery. The results herein demonstrate that these polymers offer remarkable efficiency in encapsulating and delivering translation-competent cargos, including mRNA and CRISPR-Cas based gene editing tools. Notably, a dodecyl modified PBAA transporter has achieved over 97% gene editing efficiency in vitro, and over 97% spleen-targeting selectivity in a murine model. Additionally, it produces stable nanoparticles that maintain their physicochemical properties at 4 {degrees}C for up to two weeks without addition of excipients such as PEG, offering a cost-effective solution for RNA therapeutics supply chains. As the transformative impact of RNA and other nucleic acids continues to build within the pharmaceutical industry and beyond, it is imperative that the supporting technologies evolve in stride to maximize said impact. The tunable and biodegradable PBAA polymer designs presented herein are illustrative examples of how high-level functional performance can be acheived in conjunction with the critical targeting, formulation, and operational simplicity needed of state-of-the-art transfection and delivery technologies.

biochemistry↗

bioRxiv2025

A dWDR45 knock-out Drosophila model to decipher the role of autophagy in BPAN

Beta-propeller protein-associated neurodegeneration (BPAN) is a rare neurological disorder characterized by severe cognitive and motor impairments. BPAN is caused by de novo pathogenic variants in the WDR45 gene on the X chromosome. WDR45 gene encodes the protein WDR45/WIPI4, a known regulator of autophagy. A defective autophagy has been observed in cellular models of BPAN disease and is associated with neurological dysfunctions in wdr45 knockout (KO) mice. However, it remains unclear whether the autophagic defect directly contributes to all WDR45 loss-induced phenotypes or whether other WDR45-dependent cellular functions are involved. To investigate this, we generated a CRISPR/Cas9-mediated KO of CG11975 (dwdr45 KO), the Drosophila homolog of WDR45. Our analysis revealed that dwdr45 KO flies display BPAN-like phenotypes, including impaired locomotor function, seizure-like behavior, autophagy dysregulation and iron dyshomeostasis. Additionally, dwdr45 KO flies exhibit shortened lifespan compared to control flies. These findings demonstrate that dwdr45 KO fly is a relevant in-vivo model for investigating the key cellular and molecular mechanisms underlying BPAN-associated phenotypes. Here we showed that induction of autophagy in dwdr45 KO flies improved both the shortened lifespan and the seizure-like behavior, but did not restore locomotor function. This suggests that defective autophagy contributes to some, but not all, aspects of the phenotypes resulting from loss of dWdr45 function.

cell biology↗

bioRxiv2024

Excitatory and Inhibitory Effects of Saphenous Nerve Stimulation on Two Different Bladder Conditons: Underactivity and Overactivity

BackgroundThis study aimed at exploring the effects of saphenous nerve stimulation (SNS) on treating both overactive bladder (OAB) and underactive bladder (UAB). MethodIn 6 -chloralose anesthetized cats, bipolar nerve cuff electrodes were implanted on the saphenous nerve and pudendal nerve. UAB was induced by pudendal nerve stimulation (PNS) at 5Hz, 2 threshold (T) and OAB was induced by infusion of 0.25% acetic acid (AA). Multiple cystometrograms (CMGs) were performed to investigate the effects of SNS on pathological bladder at 1Hz and 20Hz, respectively. ResultsApplication of PNS (5Hz, 2T) induced UAB by significantly increasing the bladder capacity (BC) to 156.3%{+/-}9.8% of control level, while combination of PNS and SNS (1Hz, 2T) applied during CMGs normalized the bladder underactivity by significantly reducing the BC to 93.6%{+/-}9.5% (P =0.026). Moreover, the BC was reduced to 64.1%{+/-}5.4% of control after infusion of AA, and SNS at 20Hz, 6T significantly increased the BC back to 93.4%{+/-}6.3% (P =0.005). No post-stimulation effect of SNS was detected at both 1Hz and 20Hz. However, there were no significant changes of contraction amplitude and duration during stimulation. ConclusionIn this study, we confirmed the frequency-dependence of SNS in regulating pathological bladder in cats. It provided experimental evidence for treating both OAB and UAB using SNS in clinic.

physiology↗

bioRxiv2024

Unravelling an Efficient O2/Reductant-Dependent Catalytic Route in Heme Peroxygenases for Sustainable Applications

Heme peroxygenases are attractive biocatalysts for incorporating oxygen into the organic molecules using H2O2 as oxygen source under mild conditions. However, their practical applications are hindered by irreversible oxidative inactivation caused by exogenous H2O2 usage. Herein, we report a novel catalytic pathway in heme peroxygenases that relies on O2 and small-molecule reductants such as ascorbate acid (AscA), dehydroascorbic acid (DHA), gallic acid (GA), or pyrogallol (PA) to drive reactions. For reactions of unspecific peroxygenase (UPO) with either AscA or DHA, experimental and computational studies revealed that DHAA (the hydrated form of DHA) is the actual co-substrate responsible for activating oxygen to generate oxyferryl heme (compound I, Cpd I) as the oxygenation species. Subsequently, we demonstrate the universality of this O2/reductant-dependent route across various heme peroxygenases, highlighting its biological significance as monooxygenases. Compared to the conventional H2O2-dependent process, this innovative route can efficiently eliminate the excessive production of H2O2, thereby preventing the heme destruction and related enzyme inactivation. Finally, scale-up reactions were performed for the preparations of chiral, value-added products with unprecedented productivity, underscoring the great synthetic capabilities of the developed peroxygenase technology, which paves the way for sustainable and practical applications in various chemical transformations.

bioengineering↗

bioRxiv2023

Identification of a Novel Ferroptosis Inducer with Dual Modulatory Effects on GPX4 Activity and Stability

Ferroptosis is a unique form of intracellular iron-dependent cell death that differs from apoptosis, necrosis, and autophagy. GPX4, an antioxidant defense enzyme, plays a pivotal role as regulator of ferroptosis. Extensive researches suggest that targeting GPX4 holds promise for cancer therapy. However, the current GPX4 inhibitors face challenges due to unfavorable drug-like properties, which hinder their progress in clinical development. In this study, we identified a novel inhibitor called MI-2, demonstrating potent ferroptosis-inducing capacity. Mechanistically, MI-2 effectively inhibits the activity of GPX4 by direct interaction. Furthermore, MI-2 promotes the degradation of GPX4 through its well-established target, MALT1. In multiple cancer models, MI-2 has demonstrated synergistic effects when combined with sorafenib or regorafenib, resulting in enhanced ferroptosis induction. These findings highlight the dual modulatory effects of MI-2 on GPX4 activity and stability, offering a promising starting point for the development of drug-like GPX4 inhibitors with translational potential.

cell biology↗

bioRxiv2023

SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution

BackgroundUnderstanding cellular heterogeneity within tissues hinges on knowledge of their spatial context. However, it is still challenging to accurately map cells to their spatial coordinates. ResultsWe present SC2Spa, a deep learning-based approach that learns intricate spatial relationships from spatial transcriptomics (ST) data. Benchmarking tests show that SC2Spa outperformed other predictors and accurately detected tissue architecture from transcriptome. SC2Spa successfully mapped single cell RNA sequencing (scRNA-seq) to Visium assay, providing an approach to enhance the resolution for low resolution ST data. Our test showed that SC2Spa performs well for various ST technologies and robust to spatial resolution. In addition, SC2Spa can suggest spatially variable genes that cannot be identified from previous approaches. ConclusionsSC2Spa is a robust and accurate approach to provide single cells with their spatial location and identify spatially meaningful genes.

bioinformatics↗

bioRxiv2023

Cyclic di-GMP interact with putrescine via a PilZ domain receptor YcgR

The cell motility is one of the key pathogenic factors that contribute to the virulence of Dickeya oryzea, which is a prevalent bacterial pathogen capable of infecting a range of crops and plants. We showed recently that the bacterial second messenger c-di-GMP, and the putrescine-mediated quorum sensing (QS) system, are both involved in the regulation of the bacterial motility in D. oryzea EC1. In this study, we set to determine whether and how there two signaling mechanisms work together to modulate the bacterial motility. The results showed that the second messenger signaling system interacts with the putrescine QS system via the c-di-GMP receptor YcgR, which could promote the activity of SpeA, the rate-limiting enzyme in the putrescine biosynthesis pathway, thereby increasing the intracellular putrescine levels. However, it was shown that this facilitative effect could be inhibited by c-di-GMP molecules. In addition, we demonstrated the dominance of c-di-GMP over putrescine in the regulation of bacterial motility. The findings from this study provide the first insight into the interaction between c-di-GMP and putrescine in bacteria and provide a valuable reference for the study of intracellular second messenger system and polyamine-mediated quorum sensing system in other bacteria. ImportanceDickea oryzea is a major bacterial pathogen capable of infesting many plants and crops, causing significant economic damage to rice and banana production especially. Bacterial motility is a key pathogenic factor of D. oryzea to compete for food resources and infect their host species, which is negatively regulated by c-di-GMP and positively regulated by putrescine, respectively. However, the connection between c-di-GMP and putrscine in regulating the motility of D.oryzea is not understood. Here we revealed the link and the mechanism of interaction between them, showing that c-di-GMP interact with putrescine via a receptor of c-di-GMP. The significance of our research is in providing the first insight into the interaction between c-di-GMP and putrescine and the methods and experimental designs in our study will provide a valuable reference for subsequent studies on the link between c-di-GMP and putrescine in other bacteria and even the regulatory mechanisms of complex bacterial motility networks, respectively.

pathology↗

bioRxiv2022

Immortalized bovine satellite cells for cultured meat applications

For cultured meat to succeed at scale, muscle cells from food-relevant species must be expanded in vitro in a rapid and reliable manner to produce millions of metric tons of biomass annually. Toward this goal, genetically immortalized cells offer substantial benefits over primary cells, including rapid growth, escape from cellular senescence, and consistent starting cell populations for production. Here, we develop genetically immortalized bovine satellite cells (iBSCs) via constitutive expression of bovine Telomerase reverse transcriptase (TERT) and Cyclin-dependent kinase 4 (CDK4). These cells achieve over 120 doublings at the time of publication and maintain their capacity for myogenic differentiation. They therefore offer a valuable tool to the field, enabling further research and development to advance cultured meat.

cell biology↗

bioRxiv2022

Targeting of plasmodesmal proteins requires unconventional signals

Cellular signaling relies on precise spatial localization and dynamic interactions of proteins within the subcellular compartment or niches, including cell-cell contact sites and connections. In plants, both endogenous and pathogenic proteins gained the ability to target plasmodesmata, the membrane-lined cytoplasmic connections, to regulate or exploit cellular signaling across cell wall boundaries. Those include the receptor-like membrane protein PDLP5, a potent regulator of plasmodesmal permeability that generates feed-forward or -back signals vital for plant immunity and root development. However, little is known about what molecular features determine the plasmodesmal association of PDLP5 or other proteins. Notably, although these proteins each have the ability to target plasmodesmata, no protein motifs or sequences have been identified indicative of targeting signals. To address this knowledge gap, we combined machine learning and targeted mutagenesis approaches. Here we report that PDLP5 and its closely related proteins carry novel targeting signals comprising short stretches of amino acid residues. As for PDLP5, it contains two non-redundant, tandemly arranged signals, either of which is sufficient for both localization and biological function regulating viral movement. Strikingly, plasmodesmal targeting signals exhibit little conservation in sequence but are located similarly proximal to the membrane. These novel unconventional features appear to be a common theme in plasmodesmal targeting.

plant biology↗