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Li, Y.-L.

Publications and source records attributed to Li, Y.-L..

At least 19 recordsLinked to original sources

Annual life-history strategy hitchhikes low-light adaptation in a clonal seagrass

While life-history strategies are typically fixed within species, evolutionary transitions between perenniality and annuality can occur. In clonal seagrasses, annual and perennial plants often coexist in the same population, providing a unique model for studying the genetic basis of this transition. Two seagrass Zostera marina populations in South Korea display a striking dichotomy: shallow-water sub-populations follow a typical perennial strategy, whereas their deep-water counterparts are annual. Here we show that this shift from perenniality to annuality, potentially caused by the SAPK7 gene, is genetically coupled with the CAO gene, which is under strong positive selection for low-light adaptation. The up-regulation of the SAPK7 gene triggers early flowering in seedlings, before the formation of any lateral shoots via asexual reproduction. In this special case where the genet contains only one ramet, the post-reproductive death of the ramet is equivalent to the death of the whole genet, which explains the annual phenotype. Our findings reveal a mechanistic example where annuality overcomes perenniality by hitchhiking on a positively selected gene. Given that the ancestral state of plants is perennial, this coupling of annuality with beneficial alleles may represent one of the pathways for the repeated evolution of annual life histories across flowering plants.

evolutionary biology↗

Differential pairings of MAT1-1-1 and MAT1-2-1 protein variants with heteromorphic tertiary structures produced by Ophiocordyceps sinensis strains

The MAT_HMGbox domain in the MAT1-1-1 protein and the HMG-box_ROX1-like domain in the MAT1-2-1 protein play essential roles in DNA binding and regulating the transcription of genes that control sexual reproduction in Ophiocordyceps sinensis. Previous studies have reported differential occurrences, differential transcription, and alternative splicing of the MAT1-1-1, MAT1-2-1, and pheromone receptor genes in Hirsutella sinensis (Genotype #1 among 17 genome-independent genotypes of O. sinensis fungi). In this study, we further demonstrated that the DNA-binding domains of the paired MAT1-1-1 and MAT1-2-1 proteins derived from each of the 20 purportedly "pure" O. sinensis strains exhibit heteromorphic tertiary structures, as predicted by AlphaFold 3D structural modeling. These differentially paired mating proteins are characterized by different truncations, diverse 1-4 amino acid substitutions at distinct sites, altered hydrophobicity and secondary structures, and heteromorphic tertiary structures, indicating divergency in the fungal origins of the mating proteins within the mycologically and genetically impure O. sinensis strains. Our findings support the self-sterility hypothesis for O. sinensis and likely ensure the fidelity and genetic diversity of heterothallic or hybrid reproduction during the lifecycle of the Cordyceps sinensis insect-fungal complex.

biochemistry↗

Cytoskeleton Regulates Cytoophidium Dynamics in Drosophila Ovaries

Cytoophidia are filamentous structures composed of CTP synthase (CTPS) and were initially discovered in ovarian cells of Drosophila. As a highly conserved membraneless organelle present across all three domains of life, cytoophidia display dynamic behaviors that are crucial for cellular homeostasis and function. Previous research has shown that cytoophidia are actively transported from nurse cells to oocytes, implicating their potential role in Drosophila oogenesis. Nevertheless, the molecular and cellular mechanisms governing cytoophidium dynamics remain largely unclear. In this study, we employ live-cell imaging to systematically characterize the spatiotemporal dynamics of cytoophidia and to explore the underlying regulatory mechanisms. Our findings demonstrate that cytoophidium dynamics are dependent on the cytoskeletal components-- microtubules, microfilaments (actin filaments), and myosin II. Notably, disruption of either microtubules or microfilaments resulted in the disassembly or depolymerization of large cytoophidia (macro-cytoophidia), highlighting an essential role of the cytoskeleton in maintaining cytoophidium integrity and assembly. Together, these results indicate that microtubules, microfilaments, and myosin II play pivotal roles in regulating cytoophidium dynamics. This study provides new insights into the mechanisms underlying cytoophidium transport and assembly, and lays a foundation for further investigation of their functional significance in Drosophila oogenesis.

cell biology↗

Altered stereostructures of the DNA binding domains in the mutant mating proteins of Ophiocordyceps sinensis and the Cordyceps sinensis insect-fungal complex

The MAT_HMGbox and HMG-box_ROX1-like domains of the MAT1-1-1 and MAT1-2-1 proteins, respectively, play essential roles in DNA binding and the downstream regulation of gene transcription that controls sexual reproduction in Ophiocordyceps sinensis. Alternative splicing, differential occurrence and transcription of the MAT1-1-1 and MAT1-2-1 genes have been revealed in Hirsutella sinensis (Genotype #1 of the 17 O. sinensis genotypes), suggesting the occurrence of self-sterility under heterothallic or hybrid outcrossing. This study demonstrates that the MAT_HMGbox domains of MAT1-1-1 proteins in wild-type Cordyceps sinensis isolates cluster into 5 clades with or without branches in the Bayesian clustering tree and belong to diverse 3D structural morphs under 19 AlphaFold codes. The HMG-box_ROX1-like domains of MAT1-2-1 proteins cluster into 2 clades with branches in the Bayesian clustering tree and belong to diverse 3D structural morphs under 25 AlphaFold codes. Correlation analysis reveals that 1-3 amino acid substitutions at various sites in the DNA-binding domains of the mutant mating proteins result in alterations in the hydrophobicity and the secondary and tertiary structures of the DNA-binding domains of the proteins. Fungal origin analysis reveals heterospecific fungal sources or genome-independent, genotypic sources of the mating proteins with stereostructure variations in the wild-type C. sinensis isolates that represent the changed functionalities of the proteins in regulating and ensuring the accuracy and genetic diversity of the heterothallic and hybrid sexual reproductive processes of O. sinensis during the lifecycle of the C. sinensis insect-fungi complex.

biochemistry↗

Multiple-level organizational logic of the locus coeruleus-norepinephrine system in structure and function

The locus coeruleus (LC) regulates various neural processes through a limited number of norepinephrine (NE)-releasing neurons with widespread axon projections. However, how the LC is organized to exert brain-wide regulatory functions remain elusive. Utilizing larval zebrafish as a whole-brain-scale model, we reveal that morphologically heterogenous but physiologically comparable LC-NE neurons assemble complementarily to implement region-specific regulation of brain-wide neural dynamics. Individual LC-NE neurons exhibit diverse axon projections with ipsilateral bias and region preference, but share comparable electrophysiological properties, sensory responses and neural function-related genes expression. Moreover, population LC-NE neurons display bilaterally symmetrical yet regionally different axon projections and fire synchronously, causing regionally patterned NE release. Along with the regional comparability of NE receptor expression, these enable the LC to tune brain-wide neural dynamics in an inverted-U manner with region difference. Thus, our study provides a comprehensive understanding of the organizational logic of the LC system.

neuroscience↗

Locust cGAS-like receptors recognize derivatives of a Gypsy retrotransposon to synergize with RNAi against viral invasion

The co-option of transposable elements (TEs) as immune sentinels represents an evolutionarily conserved strategy across metazoans, yet the molecular mechanisms linking retrotransposon reactivation to antiviral defense remain enigmatic. Here, we identify LmGypsy, a long terminal repeat (LTR) retrotransposon in Locusta migratoria, as a critical mediator of biphasic antiviral immunity against Acrididae reovirus (ARV). ARV infection triggers selective de-repression of LmGypsy, which orchestrates dual antiviral pathways: (1) its encoded reverse transcriptase synthesizes viral DNA (vDNA) from ARV RNA, fueling RNA interference (RNAi)-mediated viral RNA degradation through Dicer-2-dependent vsiRNA biogenesis; (2) LmGypsy-derived nucleic acids activate cGAS-like receptors (LmcGASs) and induce immune responses. Strikingly, vDNA persists in infected locusts from 24 h post-infection until host death, suggesting a role in sustaining antiviral activity akin to immune memory mechanisms observed in Diptera. This study provides the first evidence that insect cGAS homologs function as retrotransposon sensors, mirroring mammalian cGAS-STING recognition of endogenous retroviral elements. Our findings redefine retrotransposons as central hubs in arthropod antiviral immunity, bridging RNAi and nucleic acid-sensing pathways to establish a coordinated defense network. These results illuminate conserved principles of TE-immune crosstalk and highlight LmGypsy as a paradigm for understanding host-transposon coevolution in antiviral contexts.

immunology↗

Calcium Homeostasis Modulator 2 Constitutes an ATP-regulation Pore in Mitochondria

Recent structural analyses showed that the calcium homeostasis modulator-2 (CALHM2) forms a mega channel, but its cellular location and endogenous function are yet unknown. We found that native CALHM2 resides on the mitochondrial inner membrane and constitutes an ATP-regulated ATP release channel. CALHM2 knockdown/knockout decreases cytosolic ATP concentration, and thereby compromises energy-sensitive processes, such as intracellular Ca2+ handling. However, CALHM2 loss-of-function elevates ATP concentration in the mitochondrial matrix, dephosphorylates key enzymes in the mammalian target of rapamycin (mTOR) pathway, and promotes longevity in CALHM2 knockout mice. These findings reveal that CALHM2 constitutes a novel regulator of mitochondrial metabolism, which may have important implications in aging and diseases.

cell biology↗

Cytoophidium complexes resonate with cell fates

Metabolism is a fundamental characteristic of life. In 2010, we discovered that the metabolic enzyme CTP synthase (CTPS) can assemble a snake like structure inside cells, which we call the cytoophidium. Including CTPS, an increasing number of metabolic enzymes have been found to form cytoophidia in cells. However, the distribution and relationship among cytoophidia formed by different metabolic enzymes remain elusive. Here we investigate five metabolic enzymes that can form cytoophidia, namely Asn1, Bna5, CTPS (ie. Ura7), Glt1, and Prs5 in Saccharomyces cerevisiae. We find that multiple cytoophidia can be assembled into cytoophidium complexes by docking one after another. Glt1 cytoophidia tend to assemble in non-quiescent cells, while CTPS cytoophidia are more abundant in quiescent cells and form complexes with Prs5 and Asn1 cytoophidia. Blocking CTPS cytoophidium assembly can lead to a non-quiescent phenotype and increase the assembly of Glt1 cytoophidia, Bna5 cytoophidia, and cytoophidium complexes. Blocking CTPS cytoophidium assembly also inhibits the NAD biosynthesis pathway, which includes Bna5 and Sir2. Consistent with this result, the non-quiescent phenotype caused by blocking CTPS cytoophidium assembly can be rescued by blocking Glt1 cytoophidium assembly, supplementing nicotinic acid, or overexpressing Sir2. Our results indicate that the assembly of cytoophidium complexes with different compositions resonates with distinct cell fates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/614056v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1a297bcorg.highwire.dtl.DTLVardef@197c0aforg.highwire.dtl.DTLVardef@1eb46e8org.highwire.dtl.DTLVardef@17c2e6e_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIMultiple cytoophidia can be assembled into cytoophidium complexes by docking one after another. C_LIO_LICTPS cytoophidia blockage impedes quiescence and boosts Glt1-Bna5 cytoophidium complex. C_LIO_LIGlt1 cytoophidium blockage restores quiescence and Bna5 inhibition in NAD pathway. C_LIO_LIActivating NAD utilizing SIR2 rescues CTPS cytoophidium blockage induced non-quiescence. C_LI

cell biology↗

Differential cytoophidium assembly between Saccharomyces cerevisiae and Schizosaccharomyces pombe

The de novo synthesis of cytidine 5-triphosphate (CTP) is catalyzed by the enzyme CTP synthase (CTPS), which is known to form cytoophidia across all three domains of life. In this study, we use the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as model organisms to compare cytoophidium assembly under external environmental and intracellular CTPS alterations. We observe that under low and high temperature conditions, cytoophidia in fission yeast gradually disassembled, while cytoophidia in budding yeast remain unaffected. The effect of pH changes on cytoophidia maintenance in the two yeast species is different. When cultured in the yeast saturated cultured medium, cytoophidia in fission yeast disassemble, while cytoophidia in budding yeast gradually form. Overexpression of CTPS leads to the presence and maintenance of cytoophidia in both yeast species from the log phase to the stationary phase. In summary, our results demostrate differential cytoophidium assembly between Saccharomyces cerevisiae and Schizosaccharomyces pombe, the two most studied yeast species.

cell biology↗

Receptor tyrosine kinases CAD96CA and FGFR1 function as the cell membrane receptors of insect juvenile hormone

Juvenile hormone (JH) is important to maintain insect larval status; however, its cell membrane receptor has not been identified. Using the lepidopteran insect Helicoverpa armigera (cotton bollworm), a serious agricultural pest, as a model, we determined that receptor tyrosine kinases (RTKs) cadherin 96ca (CAD96CA) and fibroblast growth factor receptor homologue (FGFR1) function as JH cell membrane receptors by their roles in JH-regulated gene expression, larval status maintaining, rapid intracellular calcium increase, phosphorylation of JH intracellular receptor MET1 and cofactor Taiman, and high affinity to JH III. Gene knockout of Cad96ca and Fgfr1 by CRISPR/Cas9 in embryo and knockdown in various insect cells, and overexpression of CAD96CA and FGFR1 in mammalian HEK-293T cells all supported CAD96CA and FGFR1 transmitting JH signal as JH cell membrane receptors.

developmental biology↗

Cytoophidia influence cell cycle and size in Schizosaccharomyces pombe

CTP synthase (CTPS) forms cytoophidia in all three domains of life. Here we focus on the function of cytoophidia in cell proliferation using Schizosaccharomyces pombe as a model system. We find that converting His359 of CTPS into Ala359 leads to cytoophidium disassembly. By reducing the level of CTPS protein or specific point mutations, the loss of cytoophidia prolongs the G2 phase and expands cell size. In addition, the loss-filament mutant of CTPS leads to a decrease in the expression of genes related to G2/M transition and cell growth, including slm9. The overexpression of slm9 alleviates the G2 phase elongation and cell size enlargement induced by CTPS loss-filament mutant. Overall, our results connect cytoophidia with cell cycle and cell size control in Schizosaccharomyces pombe.

cell biology↗

Altered GC- and AT-biased genotypes of Ophiocordyceps sinensis in the stromal fertile portions and ascospores of natural Cordyceps sinensis

ObjectiveTo examine multiple genotypes of Ophiocordyceps sinensis in a semi-quantitative manner in the stromal fertile portion (SFP) densely covered with numerous ascocarps and ascospores of natural Cordyceps sinensis and to outline the dynamic alterations of the coexisting O. sinensis genotypes in different developmental phases. MethodsMature Cordyceps sinensis specimens were harvested and continuously cultivated in our laboratory (altitude 2,254 m). The SFPs (with ascocarps) and fully and semi-ejected ascospores were collected for histological and molecular examinations. Biochip-based single nucleotide polymorphism (SNP) MALDI-TOF mass spectrometry (MS) was used to genotype multiple O. sinensis mutants in the SFPs and ascospores. ResultsMicroscopic analysis revealed distinct morphologies of the SFPs (with ascocarps) before and after ascospore ejection and SFP of developmental failure, which, along with the fully and semi-ejected ascospores, were subjected to SNP MS genotyping analysis. Mass spectra showed the coexistence of GC- and AT-biased genotypes of O. sinensis that were genetically and phylogenetically distinct in the SFPs before and after ejection and of developmental failure and in fully and semi-ejected ascospores. The intensity ratios of MS peaks were dynamically altered in the SFPs and the fully and semi-ejected ascospores. Mass spectra also showed transversion mutation alleles of unknown upstream and downstream sequences with altered intensities in the SFPs and ascospores. Genotype #5 of AT-biased Cluster-A maintained a high intensity in all SFPs and ascospores. An MS peak with a high intensity containing AT-biased Genotypes #6 and #15 in pre-ejection SFPs was significantly attenuated after ascospore ejection. The abundance of Genotypes #5-6 and #16 of AT-biased Cluster-A was differentially altered in the fully and semi-ejected ascospores that were collected from the same Cordyceps sinensis specimens. ConclusionMultiple O. sinensis genotypes coexisted in different combinations with altered abundances in the SFPs prior to and after ejection, the SFP of developmental failure, and the two types of ascospores of Cordyceps sinensis, demonstrating their genomic independence. Metagenomic fungal members present in different combinations and with dynamic alterations play symbiotic roles in different compartments of natural Cordyceps sinensis.

molecular biology↗

Super-resolution imaging reveals dynamic skeletal cytoophidia

CTP synthase (CTPS) can form filamentous structures termed cytoophidia in cells from all three domains of life. In order to study the mesoscale structure of cytoophidia, we perform fluorescence recovery after photobleaching (FRAP) and stimulated emission depletion (STED) microscopy in human cells. By using EGFP dimeric tag, as a tool to explore the physical properties of cytoophidia, we find that cytoophidia are dynamic and reticular. The reticular structure of CTPS cytoophidia may provide space for other components such as IMPDH. In addition, we observe CTPS granules with tentacles.

biophysics↗

Structural basis of human PRPS2 filaments

PRPP synthase (PRPS) transfers the pyrophosphate groups from ATP to ribose-5-phosphate to produce 5-phosphate ribose-1-pyrophosphate (PRPP), a key intermediate in the biosynthesis of several metabolites including nucleotides, dinucleotides and some amino acids. There are three PRPS isoforms encoded in human genome. While hPRPS1 and hPRPS2 are expressed in most tissues, hPRPS3 is exclusively expressed in testis. Although hPRPS1 and hPRPS2 share 95% sequence identity, hPRPS2 has been shown to be less sensitive to allosteric inhibition and specifically upregulated in certain cancers in the translational level. Recent studies demonstrate that PRPS can form a subcellular compartment termed the cytoophidium in multiple organisms across prokaryotes and eukaryotes. Forming the cytoophidium is considered as a distinctive mechanism involving the polymerization of the protein. In order to investigate the function and molecular mechanism of hPRPS2 polymerization, we solve the polymer structure of hPRPS2 at 3.08[A] resolution using cryo-Electron Microscopy (cryo-EM). hPRPS2 hexamers stack into polymers in the conditions with the allosteric/competitive inhibitor ADP. The binding modes of ADP at the canonical allosteric site and at the catalytic active site are clearly determined. A point mutation disrupting the inter-hexamer interaction prevents hPRPS2 polymerization and results in significantly reduced catalytic activity. Our findings suggest that the regulation of hPRPS2 polymer is distinct from E. coli PRPS polymer and provide new insights to the regulation of hPRPS2 with structural basis.

biochemistry↗

Differential coexistence of multiple genotypes of Ophiocordyceps sinensis in the stromata, ascocarps and ascospores of natural Cordyceps sinensis

ObjectiveTo examine the differential occurrence of Ophiocordyceps sinensis genotypes in the stroma, stromal fertile portion (SFP) densely covered with numerous ascocarps, and ascospores of natural Cordyceps sinensis. MethodsImmature and mature C. sinensis specimens were harvested. Mature C. sinensis specimens were continuously cultivated in our laboratory (altitude 2,200 m). The SFPs (with ascocarps) and ascospores of C. sinensis were collected for microscopic and molecular analyses using species-/genotype-specific primers. Sequences of mutant genotypes of O. sinensis were aligned with that of Genotype #1 Hirsutella sinensis and compared phylogenetically using a Bayesian majority-rule method. ResultsFully and semiejected ascospores were collected from the same specimens. The semiejected ascospores tightly adhered to the surface of the asci as observed by the naked eye and under optical and confocal microscopies. The multicellular heterokaryotic ascospores showed uneven staining of nuclei. The immature and mature stromata, SFPs (with ascocarps) and ascospores were found to differentially contain several GC- and AT-biased genotypes of O. sinensis, Samsoniella hepiali, and an AB067719-type fungus. The genotypes within AT-biased Cluster-A in the Bayesian tree occurred in all compartments of C. sinensis, but those within AT-biased Cluster-B were present in immature and mature stromata and SPFs but absent in the ascospores. Genotype #13 of O. sinensis was present in semi-ejected ascospores and Genotype #14 in fully ejected ascospores. GC-biased Genotypes #13-14 featured large DNA segment substitutions and genetic material recombination between the genomes of the parental fungi (H. sinensis and the AB067719-type fungus). These ascosporic offspring genotypes combined with varying abundances of S. hepiali in the 2 types of ascospores participated in the control of the development, maturation and ejection of the ascospores. ConclusionMultiple genotypes of O. sinensis coexist differentially in the stromata, SFPs and 2 types of C. sinensis ascospores, along with S. hepiali and the AB067719-type fungus. The fungal components in different combinations and their dynamic alterations in the compartments of C. sinensis during maturation play symbiotic roles in the lifecycle of natural C. sinensis.

molecular biology↗

The trifecta of disease avoidance, silique shattering resistance and flowering period elongation achieved by the BnaIDA editing in Brassica napus

Rapeseed (Brassica napus) oil is a main vegetable oil source in the world. The devastating disease of stem rot caused by the necrotrophic fungus Sclerotinia sclerotiorum and pod shattering led to a great yield loss in Brassica napus. S.sclerotiorum infects the rapeseed by the detached floral petals, in which the released ascospores land and germinate as mycelium, then the petals fall on the leaves at lower part of the rapeseed and heavily attacks the leaves and stems. The prevention of petal-shedding is a promising approach to avoid the stem rot damage, moreover, longer period of flowering time will bring rapeseed flower tourism a huge economic benefit. Notably, IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and IDA-LIKE(IDL) protein control floral organ abscission in Arabidopsis thaliana. In our study, the precisely editing of two IDA homologues genes using CRISPR/Cas9 system in Brassica napus caused the petal attaching to the flower till pod mature and enhancing the silique dehiscence resistance. Incubating the S.sclerotiorum to petal showed the edited rapeseed avoiding the infection of S.sclerotiorum RNA-Seq analysis demonstrated that in the editted plant, the genes involed in IDA pathway were regulated, while other genes keep unaltered. Investigation of agronomic traits showed that no positive the agronimic traits was introduced in editted plant. Our study demonstrated that mutation of two BnaIDAs creating a promising germplasm for disease avoidance, siliques shattering resistance and flowering period elongation which will contribute great to rapeseed industry.

plant biology↗

A serotonergic axon-cilium synapse drives nuclear signaling to maintain chromatin accessibility

Chemical synapses between axons and dendrites mediate much of the brains intercellular communication. Here we describe a new kind of synapse - the axo-ciliary synapse - between axons and primary cilia. By employing enhanced focused ion beam - scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between the serotonergic axons arising from the brainstem, and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, 5-hydroxytryptamine receptor 6 (HTR6), whose mutation is associated with learning and memory defects. Using a newly developed cilia-targeted serotonin sensor, we show that optogenetic stimulation of serotonergic axons results in serotonin release onto cilia. Ciliary HTR6 stimulation activates a non-canonical Gq/11-RhoA pathway. Ablation of this pathway results in nuclear actin and chromatin accessibility changes in CA1 pyramidal neurons. Axo-ciliary synapses serve as a distinct mechanism for neuromodulators to program neuron transcription through privileged access to the nuclear compartment.

cell biology↗

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.

biophysics↗