Biology subjects

Zhang, Y.-Z.

Publications and source records attributed to Zhang, Y.-Z..

15 recordsLinked to original sources

bioRxiv2026

Architecture and Energy Transfer of the Bacterial Photosynthetic Unit

In phototrophic organisms, pigment-protein membrane complexes are densely packed to form photosynthetic units (PSUs) that capture solar energy and convert it into chemical energy. Although the structures of many individual photosynthetic complexes have been resolved, how they are arranged and interact with others within photosynthetic membranes to enable efficient excitation energy transfer (EET) remains poorly understood. Here, we report cryo-electron microscopy structures of PSU supercomplex assemblies from the phototrophic a-proteobacterium Rhodovulum viride, including an RC-LH1 core associated with one or two peripheral LH2 complexes and a curved LH2 tetramer. These membrane-derived assemblies define the relative positions and orientations of neighboring photosynthetic complexes and place their pigment arrays in proximity across antenna-antenna and antenna-core interfaces. Structure-based simulations identify potential EET pathways within the PSU assemblies and reveal rapid energy transfer across both LH2-LH2 and LH2-LH1 interfaces. Collectively, these findings provide insights into the assembly and structural modularity of bacterial PSUs and elucidate how the lateral organization of membrane protein complexes facilitates efficient energy transfer. This work extends structural studies of bacterial photosynthesis from individual complexes to their native higher-order assembly, providing a framework for understanding how photosynthetic supercomplex organization shapes energy migration and for guiding the design of artificial photosynthesis.

biochemistry↗

bioRxiv2026

Structure and energy transfer of a minimal PSI-LHCI supercomplex with FNR binding from a terrestrial eustigmatophyte

Soil microalgae endure harsh terrestrial stressors, such as intense light. Eustigmatophytes are an independent evolutionary branch within stramenopiles and occupy diverse aquatic and terrestrial environments, but the structural organization of their photosynthetic apparatus remains poorly understood. Here, we determined the cryo-electron microscopy structure of a photosystem I-light-harvesting complex I (PSI-LHCI) supercomplex bound with ferredoxin-NADP+ oxidoreductase (FNR) from the terrestrial eustigmatophyte Vischeria stellata at 2.44 [A] resolution. The supercomplex contains a monomeric PSI core associated with only three LHCI subunits, representing the smallest PSI-LHCI reported among structurally characterized red-lineage PSI complexes composed of violaxanthin-Chl a proteins (VCPs). The three VCPIs with distinct structure features and arrangements form a compact belt along the PsaL-PsaI-PsaM side of PSI. The structure also resolves a 43-residue N-terminal segment of FNR (FNR-N) bound to the PSI stromal surface, which is stabilized by both a eustigmatophyte-conserved insertion in PsaL and the N-terminal region of PsaD. In contrast, the catalytic region of FNR was not resolved, suggesting conformational flexibility. Computational simulations indicate potential excitation-energy-transfer pathways connecting the three VCPI subunits to the PSI core and highlight lineage-specific pigments that maintain energetic connectivity within the exceptionally compact antenna. Our analysis further reveals conservation of FNR tethering despite pronounced diversification of antenna size and organization. These findings uncover a modular evolutionary principle in which PSI acceptor-side organization is retained while the light-harvesting antenna is extensively remodeled, providing a framework for understanding the diversification of photosynthetic energy conversion across ecological transitions.

plant biology↗

bioRxiv2025

Machine learning-based definition of cellular senescence reveals pro-senescence potential implication in lung adenocarcinoma

Despite growing evidence implicating cellular senescence in tumor progression, methodological challenges in objectively quantifying senescent cell burden across cancer types continue to limit mechanistic studies and clinical translation. To address this, we developed the Predictive Cellular Senescence Model (PreCSenM), a machine learning-based tool that assigns a CS score by integrating senescence-associated features across 888 samples. Benchmarking analyses confirmed that PreCSenM markedly outperforms existing methodologies in reliably predicting senescent states within both normal and cancerous transcriptomic datasets. In lung adenocarcinoma (LUAD), PreCSenM identified the CS score as a robust predictor of clinical outcomes. Multi-omics analyses further revealed that lower CS levels correlate with decreased genomic stability and enhanced immune responses, aligning with clinical observations. Notably, drug discovery using PreCSenM identified histone deacetylase inhibitors (HDACis) as potent inducers of CS in LUAD. Transcriptional and epigenetic profiling of HDACi-treated cells pinpointed FOSB as a core transcription factor driving CS, and FOSB knockdown blocked HDACi-induced senescence. Overall, our study establishes PreCSenM as a multidimensional senescence quantification tool, bridging computational prediction with clinical relevance and mechanistic validation to enable senescence-directed therapies in precision oncology.

bioinformatics↗

bioRxiv2025

Sustained cross-species transmission of gammacoronavirus in wild birds reveled by viral characterization in China

Gammacoronavirus ({gamma}-CoV) primarily infects poultry, wild birds, and marine mammals. The widespread distribution and circulation of {gamma}-CoV in the ecological environment may lead to sustained transmission and economic loss. To better understand the diversity of {gamma}-CoV in wild birds, we collect 482 wild-bird fecal samples from Yunnan, encompassing fourteen bird species. We detected twelve {gamma}-CoV positive samples in five bird species, with the characterization of five complete genomes - HNU5-1, HNU5-2, HNU5-3, HNU6-1, and HNU6-2-indicating that these genomes represent two viral species. The HNU5 strains were derived from Black-headed gull (Chroicocephalus ridibundus), while the HNU6 strains were came from Mallard (Anas platyrhynchos), and both of those were recombinant. The HNU5 strain exhibited the highest sequence identity (95.45%) with a {gamma}-CoV strain isolated from Numenius phaeopus (GenBank accession: PP845452). Similarly, the HNU6 strain showed 95.18% nucleotide identity with a {gamma}-CoV strain (GenBank accession: PP845437) derived from Anas platyrhynchos. Taxonomic analysis confirmed that HNU6s belong to the Gammacoronavirus anatis species, while HNU5s attributed to a new species. Cross-species analysis revealed active host-switching events among {gamma}-CoVs, indicating potential transmission of {gamma}-CoVs from marine mammals to wild bird, from wild bird to poultry, and inter-wild bird and inter-poultry transmission. In summary, we report five new {gamma}-CoV strains in wild birds and outline the cross-species transmission of {gamma}-CoVs. Our findings link {gamma}-CoV hosts across different natural environments and provide new insights for exploring {gamma}-CoVs.

microbiology↗

bioRxiv2025

Structural basis for the RC-LH1 supercomplex of Dinoroseobacter shibae for anaerobic anoxygenic photosynthesis

Aerobic anoxygenic phototrophic (AAP) bacteria are essential for oceanic carbon cycling. However, the architecture and structural adaptations of their photosynthetic systems to ensure adequate light harvesting, electron transport, and oxidative resilience in oxygen-rich environments remain poorly understood. In this study, we present the 2.4-[A] cryo-EM structure of the reaction center-light-harvesting 1 (RC-LH1) supercomplex from Dinoroseobacter shibae DFL-12, a marine AAP bacterial symbiont of benthic dinoflagellates. This RC-LH1 supercomplex features a closed LH1 ring comprising 17 {beta}-subunits, each containing two spheroidenones per {beta}-heterodimer--a previously unreported configuration in phototrophic bacteria. The cytochrome subunit of the RC is truncated to three hemes, in contrast to the four-heme configuration found in anaerobic relatives. The structure also reveals elongated bacteriochlorophyll (BChl) spacing, accounting for its blue-shifted absorption maximum that is optimized for low-light benthic environments. Furthermore, we identify a previously unknown protein-LRC (Light-Respiratory Connector), which structurally bridges the RC and LH1 components and exhibits homology to NADH oxidoreductase subunit E, suggesting a functional coupling between photochemical and respiratory electron transport. Collectively, these specific structural features allow AAP bacteria to balance anoxygenic photosynthesis and protection against oxidative damage, providing a mechanistic framework for them to thrive in oxygenated marine environments. Our study provides insights into the structural and functional variability of bacterial photosynthesis in response to oxygenated marine environments.

biochemistry↗

bioRxiv2024

Crystal structure and catalytic mechanism of PL35 family glycosaminoglycan lyases with an ultrabroad substrate spectrum

Recently, a new class of glycosaminoglycan (GAG) lyases (GAGases) belonging to PL35 family has been discovered with an ultrabroad substrate spectrum that can degrade three types of uronic acid-containing GAGs (hyaluronic acid, chondroitin sulfate and heparan sulfate) or even alginate. In this study, the structures of GAGase II from Spirosoma fluviale and GAGase VII from Bacteroides intestinalis DSM 17393 were determined at 1.9 and 2.4 [A] resolution, respectively, and their catalytic mechanism was investigated by the site-directed mutant of their crucial residues and molecular docking assay. Structural analysis showed that GAGase II and GAGase VII consist of an N-terminal (/)6 toroid multidomain and a C-terminal two-layered {beta}-sheet domain with Mn2+. Notably, although GAGases share similar folds and catalytic mechanisms with some GAG lyases and alginate lyases, they exhibit higher structural similarity with alginate lyases than GAG lyases, which may present a crucial structural evidence for the speculation that GAG lyases with (/)n toroid and antiparallel {beta}-sheet structures arrived by a divergent evolution from alginate lyases with the same folds. Overall, this study not only solved the structure of PL35 GAG lyases for the first time and investigated their catalytic mechanism, especially the reason why GAGase III can additionally degrade alginate, but also provided a key clue in the divergent evolution of GAG lyases that originated from alginate lyases.

biochemistry↗

bioRxiv2020

Novel enzyme for dimethyl sulfide-releasing in bacteria reveals a missing route in the marine sulfur cycle

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule and plays important roles in the global sulfur cycle. Cleavage of DMSP produces volatile dimethyl sulfide (DMS), which has impacts on the global climate. Multiple pathways for DMSP catabolism have been identified. Here we identified yet another novel pathway, the ATP DMSP lysis pathway. The key enzyme, AcoD, is an ATP-dependent DMSP lyase. AcoD belongs to the acyl-CoA synthetase superfamily, which is totally different from other DMSP lyases, showing a new evolution route. AcoD catalyses the conversion of DMSP to DMS by a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. AcoD is widely distributed in many bacterial lineages including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Firmicutes, revealing this new pathway plays important roles in global DMSP/DMS cycles.

ecology↗

bioRxiv2020

Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis

Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a new mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 (AGO5) and We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.

plant biology↗

bioRxiv2020

Meta-transcriptomic identification of divergent Amnoonviridae in fish

Tilapia lake virus (TiLV) has caused mass mortalities in farmed and wild tilapia with serious economic and ecological consequences. Until recently, this virus was the sole member of the Amnoonviridae, a family within the order Articulavirales comprising segmented negative-sense RNA viruses. We sought to identify additional viruses within the Amnoonviridae through total RNA sequencing (meta-transcriptomics) and data mining of published transcriptomes. Accordingly, we sampled marine fish species from both Australia and China and discovered two new viruses within the Amnoonviridae, tentatively called Flavolineata virus and Piscibus virus, respectively. In addition, by mining vertebrate transcriptome data we identified nine additional virus transcripts matching to multiple genomic segments of TiLV in both marine and freshwater fish. These new viruses retained sequence conservation with the distantly related Orthomyxoviridae in the RdRp subunit PB1, but formed a distinct and diverse phylogenetic group. These data suggest that the Amnoonviridae have a broad host range within fish and that greater animal sampling will identify additional divergent members of the Articulavirales.

microbiology↗

bioRxiv2020

Extensive Genetic Diversity and Host Range of Rodent-borne Coronaviruses

To better understand the genetic diversity, host association and evolution of coronaviruses (CoVs) in China we analyzed a total of 696 rodents encompassing 16 different species sampled from Zhejiang and Yunnan provinces. Based on the reverse transcriptase PCR-based CoV screening CoVs of fecal samples and subsequent sequence analysis of the RdRp gene, we identified CoVs in diverse rodent species, comprising Apodemus agrarius, Apodemus latronum, Bandicota indica, Eothenomys miletus, E. eleusis, Rattus andamanesis, Rattus norvegicus, and R. tanezumi. Apodemus chevrieri was a particularly rich host, harboring 25 rodent CoVs. Genetic and phylogenetic analysis revealed the presence of three groups of CoVs carried by a range of rodents that were closely related to the Lucheng Rn rat coronavirus (LRNV), China Rattus coronavirus HKU24 (ChRCoV_HKU24) and Longquan Rl rat coronavirus (LRLV) identified previously. One newly identified A. chevrieri-associated virus closely related to LRNV lacked an NS2 gene. This virus had a similar genetic organization to AcCoV-JC34, recently discovered in the same rodent species in Yunnan, suggesting that it represents a new viral subtype. Notably, additional variants of LRNV were identified that contained putative nonstructural NS2b genes located downstream of the NS2 gene that were likely derived from the host genome. Recombination events were also identified in the ORF1a gene of Lijiang-71. In sum, these data reveal the substantial genetic diversity and genomic complexity of rodent-borne CoVs, and greatly extend our knowledge of these major wildlife virus reservoirs.

genetics↗

bioRxiv2020

Structural visualization of septum formation in Staphylococcus warneri using atomic force microscopy

Cell division of Staphylococcus adopts a "popping" mechanism that mediates extremely rapid separation of the septum. Elucidating the structure of the septum is crucial for understanding this exceptional bacterial cell division mechanism. Here, the septum structure of Staphylococcus warneri is extensively characterized using high-speed time-lapse confocal microscopy, atomic force microscopy, and electron microscopy. The cells of S. warneri divide in a fast "popping" manner on a millisecond timescale. Our results show that the septum is composed of two separable layers, providing a structural basis for the ultrafast daughter cell separation. The septum is formed progressively toward the center with non-uniform thickness of the septal disk in radial directions. The peptidoglycan on the inner surface of double-layered septa is organized into concentric rings, which are generated along with septum formation. Moreover, this study signifies the importance of new septum formation in initiating new cell cycles. This work unravels the structural basis underlying the "popping" mechanism that drives Staphylococcus cell division and reveals a generic structure of the bacterial cell. IMPORTRANCEThis work shows that the septum of Staphylococcus warneri is composed of two layers and the peptidoglycan on the inner surface of the double-layered septum is organized into concentric rings. Moreover, new cell cycles of Staphylococcus could be initiated before the previous cell cycle is complete. This work advances our knowledge about a basic structure of bacterial cell and provides the double layered structural information of septum for the bacterium that divide with the "popping" mechanism.

biophysics↗

bioRxiv2020

Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China

Emerging and re-emerging infectious diseases, such as SARS, MERS, Zika and highly pathogenic influenza present a major threat to public health1-3. Despite intense research effort, how, when and where novel diseases appear are still the source of considerable uncertainly. A severe respiratory disease was recently reported in the city of Wuhan, Hubei province, China. At the time of writing, at least 62 suspected cases have been reported since the first patient was hospitalized on December 12nd 2019. Epidemiological investigation by the local Center for Disease Control and Prevention (CDC) suggested that the outbreak was associated with a sea food market in Wuhan. We studied seven patients who were workers at the market, and collected bronchoalveolar lavage fluid (BALF) from one patient who exhibited a severe respiratory syndrome including fever, dizziness and cough, and who was admitted to Wuhan Central Hospital on December 26th 2019. Next generation metagenomic RNA sequencing4 identified a novel RNA virus from the family Coronaviridae designed WH-Human-1 coronavirus (WHCV). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that WHCV was most closely related (89.1% nucleotide similarity similarity) to a group of Severe Acute Respiratory Syndrome (SARS)-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) previously sampled from bats in China and that have a history of genomic recombination. This outbreak highlights the ongoing capacity of viral spill-over from animals to cause severe disease in humans.

pathology↗

bioRxiv2019

CsHscB as a novel TLR2 agonist from carcinogenic liver fluke Clonorchis sinensis modulates host immune response

Clonorchis sinensis-a fluke dwelling on the intrahepatic bile ducts causes clonorchiasis. During C. sinensis infection, worm-host interaction results in activation of PRRs and further triggers immune responses which determine the outcome of infection. However, the mechanisms by which pathogen-associated molecules patterns from C. sinensis interacted with TLRs were poorly understood. In the present study, we identified a [~]34 kDa lipoprotein CsHscB from C. sinensis which physically bound with TLR2. We also found that recombinant CsHscB (rCsHscB) potently activated macrophage to express various proteins including TLR2, CD80, MHCII, and cytokines like IL-6, TNF-, and IL-10 in a TLR2-dependent manner but rCsHscB failed to induce IL-10 in macrophages from Tlr2-/- mice. Moreover, ERK1/2 activation was required for rCsHscB-induced IL-10 production in macrophages. In vivo study revealed that rCsHscB triggered a high induction of IL-10 in the wild-type (WT) but not in Tlr2-/- mice. Our data thus demonstrate that rCsHscB from C. sinensis is an unidentified TLR2 agonist with immune regulatory activities, and may have some therapeutic implications in future beyond parasitology.

immunology↗

bioRxiv2018

Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products

Marine phytoplankton contributes to about one half of global primary production, and a significant proportion of their photosynthetically fixed organic carbon is released after viral infection as dissolved organic matter (DOM). This DOM pool is known to be consumed by heterotrophic microorganisms; however, its impact on the uninfected co-occurring phytoplankton remains largely unknown. Here, we conducted transcriptomic analyses to study the effects of viral lysis products on the unicellular cyanobacterium Prochlorococcus, which is the most abundant photosynthetic organism on Earth. While Prochlorococcus growth was not affected by viral lysis products, many tRNAs increased in abundance, which was also seen after amino acid addition, suggesting that amino acids are one of the compounds in viral lysis products that affected the expression of tRNA genes. The decreased transcript abundances of N metabolism genes also suggested that Prochlorococcus responded to organic N compounds, consistent with abundant amino acids in viral lysis products. The addition of viral lysis products to Prochlorococcus reduced the maximum photochemical efficiency of photosystem II and CO2 fixation while increased its respiration rate, consistent with differentially expressed genes related to photosynthesis and respiration. One of the highest positive fold-changes was observed for the 6S RNA, a non-coding RNA functioning as a global transcriptional regulator in bacteria. The high level of 6S RNA might be responsible for some of the observed transcriptional responses. Taken together, our results revealed the transcriptional regulation of Prochlorococcus in response to viral lysis products and suggested its metabolic potential to utilize organic N compounds.\n\nImportancePhotosynthetic microorganisms called phytoplankton are abundant in the oceans and contribute to about one half of global CO2 fixation. Phytoplankton are frequently infected by viruses and after infection their organic carbon is released into the ocean as dissolved organic matter (DOM). Marine DOM is important for the marine food web because it supports the growth of heterotrophic microorganisms. However, the impact of viral DOM on the uninfected phytoplankton is largely unknown. In this study, we conducted transcriptomic analyses and identified many differentially expressed genes when viral DOM was added to the marine cyanobacterium Prochlorococcus. One effect of viral DOM is that the carbon fixation of Prochlorococcus was reduced by ~16%, which might affect carbon cycling in the worlds oceans since Prochlorococcus is the most abundant photosynthetic organism on Earth.

microbiology↗

bioRxiv2017

An overexpressed Q allele leads to increased spike density and improved processing quality

Spike density and processing quality are important traits during the evolution of wheat, which is controlled by multiple gene loci. The associated gene loci have been heavily studied with slow progress. A common wheat mutant with extremely compact spikes and good processing quality was isolated. The gene (Qc1) responsible for the mutant phenotype was mapped and cloned, and the cellular mechanism for the mutant phenotype was investigated. Qc1 originated from a point mutation that interferes with the miR172-directed cleavage of the Q gene, leading to its overexpression. Qc1 reduces the longitudinal cell size of rachises, resulting in an increased spike density. Qc1 increases the number of vascular bundles, which suggests a higher efficiency in the transportation of assimilates in the spikes of the mutant than in the WT. This could account for the improved processing quality. The effects of Qc1 on spike density and wheat processing quality were confirmed by the identification of nine common wheat mutants having four different Qc alleles. These results deepen our understanding of the key role of Q gene, one of the most important domestication gene for wheat, and provide new insights for the potential application of Qc allele in wheat breeding.

genetics↗