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Systemically functional characterization of regiospecific flavonoid O-methyltransferases from Glycine max

Synthetic and Systems Biotechnology 2024年第2期9卷 340-348页

作者： Bingtong Feng Yuguo Jiang Xiaodong Li Yan Wang Ziyu Ren Jian Lu Xing Yan Zhihua Zhou Pingping Wang Life Science and Technology College Guangxi UniversityNanningGuangxi530004China CAS-Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai200032China University of Chinese Academy of Sciences Beijing100049China The College of Life Sciences Shanghai Normal UniversityShanghai200234China

Plants produce diverse flavonoids for defense and stress resistance,most of which have health benefits and are widely used as food additives and *** of the free hydroxyl groups of flavonoids,catalyzed by S-adenosyl-l-methionine-dependent O-methyltransferases(OMTs),significantly affects their physicochemical properties and ***(Glycine max)contain a rich pool of O-methylated ***,the OMTs responsible for flavonoid methylation in *** remain largely *** screened the *** genome and obtained 22 putative OMT-encoding genes that share a broad spectrum of amino acid identities(25–96%);among them,19 OMTs were successfully cloned and heterologously expressed in Escherichia *** used the flavonoids containing the free 3,5,7,8,3′,4′hydroxyl group,such as flavones(luteolin and 7,8-dihydroxyflavone),flavonols(kaempferol and quercetin),flavanones(naringenin and eriodictyol),isoflavonoids(daidzein and glycetein),and caffeic acid as substrates,and 15 OMTs were proven to catalyze at least one *** methylation activities of these GmOMTs covered the 3,7,8,3′,4′-hydroxyl of flavonoids and 7,4′-hydroxyl of *** systematic characterization of *** flavonoid OMTs provides insights into the biosynthesis of methylated flavonoids in soybeans and OMT bioparts for the production of methylated flavonoids via synthetic biology.

关键词： Flavonoids O-methyltransferases Glycine max Functional characterization

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Cytochrome P450s in algae:Bioactive natural product biosynthesis and light-driven bioproduction

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Acta Pharmaceutica Sinica B 2022年第6期12卷 2832-2844页

作者： Shanmin Zheng Jiawei Guo Fangyuan Cheng Zhengquan Gao Lei Du Chunxiao Meng Shengying Li Xingwang Zhang School of Life Sciences Shandong University of TechnologyZibo 255000China State Key Laboratory of Microbial Technology Shandong UniversityQingdao 266237China School of Pharmacy Binzhou Medical UniversityYantai 264003China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China

Algae are a large group of photo synthetic organisms responsible for approximately half of the earth’s total *** addition to their fundamental ecological roles as oxygen producers and as the food base for almost all aquatic life,algae are also a rich source of bioactive natural products,including several clinical *** P450 enzymes(P450s) are a superfamily of biocatalysts that are extensively involved in natural product biosynthesis by mediating various types of *** the post-genome era,a growing number of P450 genes have been discovered from algae,indicating their important roles in algal ***,the functional studies of algal P450s remain *** from the recent technical advances in algae cultivation and genetic manipulation,the researches on P450s in algal natural product biosynthesis have been approaching to a new ***,some photoauto trophic algae have been developed into "photo-bioreactors" for heterologous P450s to produce high-value added pharmaceuticals and chemicals in a carbon-neutral or carbon-negative ***,we comprehensively review these advances of P450 studies in algae from 2000 to 2021.

关键词： Natural product biosynthesis Algal pharmaceuticals Cytochrome P450 enzymes Algae Light-driven bioproduction

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ATP promotes protein coacervation through conformational compaction

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Journal of Molecular Cell Biology 2024年第8期16卷 46-57页

作者： Yueling Zhu Shiyan Lin Lingshen Meng Min Sun Maili Liu Jingyuan Li Chun Tang Zhou Gong State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics Innovation Academy for Precision Measurement Science and TechnologyChinese Academy of SciencesWuhan 430071China University of Chinese Academy of Sciences Beĳing 100049China Zhejiang Province Key Laboratory of Quantum Technology and Device School of PhysicsZhejiang UniversityHangzhou 310058China College of Chemistry and Molecular Engineering Beĳing National Laboratory for Molecular Sciences&Center for Quantitative BiologyPKU-Tsinghua Center for Life SciencesPeking UniversityBeĳing 100871China

Adenosine triphosphate(ATP)has been recognized as a hydrotrope in the phase separation process of intrinsically disordered proteins(IDPs).Surprisingly,when using the disordered Arg-Gly/Arg-Gly-Gly(RG/RGG)rich motif from the HNRNPG protein as a model system,we discover a biphasic relationship between the ATP concentration and IDP phase *** show that,at a relatively low ATP concentration,ATP dynamically interacts with the IDP,which neutralizes protein surface charges,promotes intermolecular interactions,and consequently promotes phase *** further demonstrate that ATP induces a compact conformation of the IDP,accounting for the reduced solvent exchange rate and lower compression ratio during phase *** ATP concentration increases,its hydrotropic properties emerge,leading to the dissolution of the phase-separated *** finding uncovers a complex mechanism by which ATP molecules modulate the structure,interaction,and phase separation of IDPs and accounts for the distinct phase separation behaviors of the charge-rich RGG motif and other low-complexity IDPs.

关键词： intrinsically disordered protein phase separation ATP conformational compaction HNRNPG

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The third dimension of alpine plant leaf traits is related to cold-tolerance

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Plant Diversity 2025年第1期47卷 159-165页

作者： Yuan Wang Ji Suonan Kun Liu Yanni Gao Sihao Zhu Qian Liu Ning Zhao State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems College of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina College of Life Sciences Qinghai Normal UniversityXiningChina College of Ecology Lanzhou UniversityLanzhouChina State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment Chinese Research Academy of Environmental SciencesBeijingChina State Key Laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijingChina

Alpine plants possess unique traits to adapt alpine *** leaf trait relationships of alpine plants can be captured by the two trait dimensions of organ size and resource economics is *** hypothesized that,beyond the trait dimensions of leaf size and resource economics,nonstructured carbohydrates(NSC)would reflect a dimension of cold-tolerance in alpine *** test this hypothesis,we measured 12 leaf traits critical to leaf construction and growth in 143 species across 7 sites ranging from alpine steppes to alpine meadows along an environmental gradient on the Tibetan ***,a cold resistance experiment was conducted at one of these sites to estimate the lethal temperature causing 50%frost damage(LT_(50))of 11 alpine *** majority of variations in 12 leaf traits of alpine plants were captured by three trait axes,in which leaf carbon(LCC)and NSC(including leaf starch;LSC and leaf soluble sugars;LSS)were clustered in a new dimension(PC3)beyond leaf size and structure,and resource *** LCC,LSC and LSS all showed negative correlations with mean annual temperature,a significant negative correlation was only found between LSS and LT_(50).It indicated that PC3 was able to reflect the cold-tolerance of alpine plants to some extent,in which LSS was the most critical *** storage and transformation of NSC under stressful conditions could reflect a dimension of long-term metabolic adaptation and cold-tolerance,which is an extension of the resource-utilization strategy beyond construction cost and growth.

关键词： Non-structured carbohydrates Resource economics Stress resistance Trait relationships The lethal temperature causing 50%frost damage(LT50)

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Enhancing the interlamellar carrier transfer via oxygen-containing groups in layer-stacked carbon nitride nanorod for superior photocatalytic disinfection

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science China Chemistry 2025年

作者： Fengming Hou Wei Wei Ruirui Hou Rujing Shen Xianghong Niu Zhipeng Guo Yihang Li Xiuyun Zhang Ang Wei State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM) College of Chemistry and Life Science Nanjing University of Posts & Telecommunications College of Physics and Electronic Information Engineering Guilin University of Technology College of Physics Science and Technology Yangzhou University

Layered polymer suffers from a transfer barrier of photogenerated carriers resulting from the lack of interlamellar connection channels and intralayer disorder. Herein, a layer-stacked crystalline carbon nitride nanorod resembling an accordion(A-CNR)grafted abundant interlamellar oxygen-containing groups is ingeniously designed to break through the transfer barrier between layers without inserting any extra impurities. Density functional theory reveals that electrons are enriched near the oxygencontaining groups, promoting the extension and coupling of interlayer electron clouds. This reduces the interlamellar electrostatic potential barrier from 5.38 to 2.74 eV. Remarkably, the groups not only establish interlayer bridges but also guide carriers to the bridge entrance, further enhancing interlayer carrier transfer. Additionally, the intralayer carrier separation and transfer are also improved, profiting from the asymmetrical charge distribution and high crystallinity. A-CNR exhibits impressive photoelectric properties and photocatalytic water disinfection capability. Within 18 min irradiation, over 10～6 colony-forming units(CFU)/mL of bacteria are completely inactivated. Moreover, A-CNR can be dispersed in water over a long period benefiting from the introduced oxygen-containing groups, making it suitable for photocatalysis in the aqueous phase. The work provides a feasible and effective strategy to overcome the inherent barrier of layered polymeric photocatalysts.

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Panoramic comparison between NK cells in healthy and cancerous liver through single-cell RNA sequencing

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Cancer Biology & Medicine 2022年第9期19卷 1334-1351页

作者： Huan Liu Ronghua Zhao Rongrong Qin Haoyu Sun Qiang Huang Lianxin Liu Zhigang Tian Björn Nashan Cheng Sun Rui Sun The First Affiliated Hospital of USTC Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230001China The CAS Key Laboratory of Innate Immunity and Chronic Disease School of Basic Medical SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China Institute of Immunology University of Science and Technology of ChinaHefei 230027China

Objective:NK cells play crucial roles in the immune defense mechanisms against viral infections and transformed ***,the developmental progression,transcriptomic landscape,and functional subtypes of liver NK cells are not well *** carcinoma(HCC)accounts for approximately 80%of primary liver cancer worldwide,yet the biological characteristics of NK cells in the HCC environment are ***,we aimed to determine these cells’roles in tumorigenesis and ***:We compared the single-cell RNA sequencing profiles of NK cells purified from blood(n=1),healthy liver tissues(n=3),HCC tumor tissues(n=4),and peritumor liver tissues(n=1)to identify NK cell ***,we performed bioinformatics analysis by using The Cancer Genome Atlas(TCGA)data to identify prognostic biomarkers simultaneously overexpressed in the blood and tumor tissues of patients with ***:Transcriptomic analysis revealed 5 NK cell subsets(L1-NK-CD56bright,L2-NK-CD56dim,L3-NK-HLA,L4-LrNK-FCGR3A,and L5-LrNK-XCL1)in the healthy liver ***,the transitional L3 subset and the CXCR6+CD16+L4 subset with strong anti-tumor activity were absent in the HCC and peritumor liver ***,4 common prognosis-associated genes(RHOB,TALDO1,HLA-DPA1,and TKT)were significantly overexpressed in the paired tumor tissue and ***:Our study revealed 5 specific subsets of NK cells in healthy human liver ***,only 3 of the 5 NK cell subsets were present in HCC and peritumor *** cytotoxic NK cell subsets were absent in HCC ***,we identified 4 potential non-invasive prognostic biomarkers in patients with HCC.

关键词： Hepatocellular carcinoma natural killer cell single-cell RNA sequencing heterogeneity prognosis

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Adsorption and desorption behavior under coal–water–gas coupling conditions of high- and low-rank coal samples

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Frontiers of Earth science 2023年第1期17卷 145-157页

作者： Chen GUO Jiang GOU Dongmin MA Yuan BAO Qingmin SHI Jiahao MENG Junzhe GAO Lingling LU College of Geology and Environment Xi’an University of Science and TechnologyXi’an 710054China Shaanxi Provincial Key Laboratory of Geological Support for Coal Green Exploitation Xi’an 710054China Geological Research Institute for Coal Green Mining Xi’an University of Science and TechnologyXi’an 710054China Aerophoto Grammetry and Remote Sensing Bureau China National Administration of Coal GeologyXi’an 710100China

High-and low-rank coalbed methane(CBM)are both important fields of CBM development in China,but their formation and production mechanisms differ *** adsorption/desorption behavior of high-and low-rank coals under the coupling of coal–water–gas was investigated using two series of *** samples from Zhangjiamao(ZJM)coal mine,Ordos basin,and Sihe(SH)coal mine,Qinshui basin,were tested by isothermal adsorption–desorption experiment,natural imbibition experiment,nuclear magnetic resonance,mercury injection porosimetry,contact angle test,and permeability *** adsorption and desorption experiments under dry,equilibrium water,and saturated water,were performed to explore the differences between the adsorption and desorption *** results show that the wettability and permeability of the ZJM low-rank coal sample was considerably higher than that of the SH high-rank coal *** imbibition process of the ZJM sample exhibited a high imbibition rate and high total-imbibition volume,whereas the SH sample exhibited a slow imbibition rate and low total-imbibition *** ZJM sample had a complex pore structure and diverse pore-size distribution with a lower mercury withdrawal efficiency at 59.60%,whereas the SH sample had a relatively uniform pore-size distribution with a higher mercury withdrawal efficiency at 97.62%.The response of adsorption and desorption of the ZJM sample to water was more significant than that of the SH *** desorption hysteresis of the ZJM sample was stronger than that of the SH sample and was more prominently affected by water,which was consistent with its strong wettability and complex pore-throat configuration.A comprehensive adsorption and desorption mode was constructed for high-and low-rank coal samples under coal–water–gas coupling *** research results are important to enrich the geological theory of high-and low-rank CBM and to guide efficient CBM recovery.

关键词： coalbed methane adsorption-desorption desorption hysteresis wettability pore structure coal-water-gas coupling

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Advancing Template-Based Flexible Docking of P450-Heme Complexes via JAX MD

Advancing Template-Based Flexible Docking of P450-Heme Compl...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Guo, Rongxu Chen, Cheng Sang, Jiaheng Cui, Guishan Zhang, Fa Cui, Xuefeng Li, Shengying Shandong University School of Computer Science and Technology Qingdao China Shandong University School of Life Science Qingdao China Yanbian University College of Geography and Ocean Sciences Yanji China Beijing Institute of Technology School of Medical Technology Beijing China Shandong University State Key Laboratory of Microbial Technology Qingdao China

ISBN: (纸本)9798350386226

AlphaFold2 has advanced protein structure prediction but often overlooks complexes with essential ligands, crucial for understanding protein-ligand interactions relevant to drug design. AlphaFill was developed to integrate ligands and ions from experimental structures into predicted models. However, many resulting complexes lack precise spatial constraints, leading to clashes between filled heme atoms and the P450 structure, as well as discrepancies in the key Fe-S ***, we propose FlexFill, a rapid flexible docking algorithm based on JAX MD. Specifically, FlexFill takes the predicted P450 structure as input to generate the P450-heme complex structure. During the docking process, we leverage JAX MD to account for the structural flexibility of P450. Unlike traditional molecular dynamics methods, we developed a customized energy function that focuses on the atoms near the pocket, significantly reducing runtime while satisfying spatial *** results indicate that AlphaFill experienced almost 50% structural crashes, while FlexFill exhibited a substantially lower rate at less than 5%. Furthermore, FlexFill is 25% faster than AlphaFill, with further speed improvements by removing redundant entries from the template library. These observations suggest that FlexFill is capable of generating high-fidelity P450heme complexes and has the ability to flexibly dock a diverse array of protein-ligand complexes. Code and pre-trained model are released at https://***/xfcui/FlexFill. © 2024 IEEE.

关键词： Molecular docking

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Reference surface self-calibration stitching algorithm based on Legendre polynomials for testing synchrotron radiation flat mirrors 8

Reference surface self-calibration stitching algorithm based...

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8th Asia Pacific Conference on Optics Manufacture, APCOM 2023 and 3rd International Forum of Young Scientists on Advanced Optical Manufacturing, YSAOM 2023

作者： Liu, Yong Gao, Xibo Hu, Zubo Xue, Shuai Chen, Shanyong Huang, Cheng Du, Chunyang Hu, Hao Dai, Yifan Peng, Xiaoqiang Wang, Linfeng College of Intelligence Science and Technology National University of Defense Technology Changsha Hunan410073 China Hunan Key Laboratory of Ultra-Precision Machining Technology Changsha Hunan410073 China Laboratory of Science and Technology on Integrated Logistics Support National University of Defense Technology Changsha Hunan410073 China State Key of High Performance Complex Manufacturing Central South University Changsha Hunan410073 China

ISBN: (纸本)9781510672673

X-ray mirrors play a critical role in transmitting and focusing beams in advanced light source devices like synchrotron radiation (SR) and free electron laser (FEL) light sources. The Root-Mean-Square (RMS) value of surface shape accuracy required for these mirrors is typically sub-micro radian/sub-nanometer, and their aperture can be hundreds of millimeters or even meters. To achieve this accuracy, deterministic figuring is required and surface figure error is the premise. Interferometric stitching test is commonly utilized. However, interferometric test obtains the surface figure error relative to the reference surface. To obtain the absolute surface figure error of X-ray mirrors, it is crucial to obtain the surface figure error of the reference surface before or during stitching measurement and separate it from the stitching result. To achieve this, a reference surface self-calibration interferometric stitching algorithm based on Legendre polynomial fitting is reported. The algorithm fits the reference surface by orthogonal Legendre polynomials in the rectangular domain, and the polynomial coefficients are expressed as interlocking terms in the stitching algorithm. The fitting coefficients are optimized and fitted together with the free compensation terms, i. *** translation and tilt terms. The paper established the theoretical model of the algorithm and conducted simulations on an X-ray mirror with a length of 300 mm. A two dimensional stitching interferometry device was built. An X-ray mirror with a length of 300 mm was tested utilizing the proposed method. The short-Term repeatability was preliminarily analyzed. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.

关键词： Synchrotron radiation

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AtMCM10 promotes DNA replication-coupled nucleosome assembly in Arabidopsis

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Journal of Integrative Plant Biology 2023年第1期65卷 203-222页

作者： Xinjie Zhao Jingyi Wang Dan Jin Jinkui Cheng Hui Chen Zhen Li Yu Wang Huiqiang Lou Jian-Kang Zhu Xuan Du Zhizhong Gong State Key Laboratory of Plant Physiology and Biochemistry College of Biological Sciences China Agricultural UniversityBeijing 100193 China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences The Chinese Academy of Agricultural SciencesBeijing 100081 China State Key Laboratory of Agro-Biotechnology College of Biological Sciences China Agricultural UniversityBeijing 100193 China Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes Institute of Plant and Food ScienceSchool of Life ScienceDepartment of Biology Southern University of Science and TechnologyShenzhen 518055 China Department of Biochemistry and Molecular Biology International Cancer Center Shenzhen University Medical SchoolShenzhen 518060 China Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging National-Regional Key Technology Engineering Laboratory for Medical UltrasoundSchool of Biomedical Engineering Shenzhen University Medical SchoolShenzhen 518060 China School of Life Science Institute of Life Science and Green Development Hebei UniversityBaoding 071002 China

Minichromosome Maintenance protein 10(MCM10)is essential for DNA replication initiation and DNA elongation in yeasts and *** the functions of MCM10 in DNA replication and repair have been well documented,the detailed mechanisms for MCM10 in these processes are not well ***,we identified AtMCM10 gene through a forward genetic screening for releasing a silenced marker *** plant MCM10 possesses a similar crystal structure as animal MCM10,AtMCM10 is not essential for plant growth or development in ***10 can directly bind to histone H3-H4 and promotes nucleosome assembly in *** nucleosome density is decreased in Atmcm10,and most of the nucleosome density decreased regions in Atmcm10 are also regulated by newly synthesized histone chaperone Chromatin Assembly Factor-1(CAF-1).Loss of both AtMCM10 and CAF-1 is embryo lethal,indicating that AtM CM10 and CAF-1 are indispensable for replication-coupled nucleosome ***10 interacts with both new and parental ***10 mutants have lower H3.1abundance and reduced H3K27me1/3 levels with releasing some silenced *** propose that AtM CM10 deposits new and parental histones during nucleosome assembly,maintaining proper epigenetic modifications and genome stability during DNA replication.

关键词： AtMCM10 H3K27me1 nucleosomes assembly

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