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Structural and functional insights into the 20-O-methyltransferase of SARS-CoV-2

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Virologica Sinica 2024年第4期39卷 619-631页

作者： Jikai Deng Feiyu Gong Yingjian Li Xue Tan Xuemei Liu Shimin Yang Xianying Chen Hongyun Wang Qianyun Liu Chao Shen Li Zhou Yu Chen State Key laboratory of Virology RNA InstituteCollege of Life Sciences and Frontier Science Center for Immunology and MetabolismWuhan UniversityWuhan430072China Animal Bio-Safety Level III laboratory/Institute for Vaccine research Wuhan University School of MedicineWuhan430071China

A unique feature of coronaviruses is their utilization of self-encoded nonstructural protein 16(nsp16),20-Omethyltransferase(20-O-MTase),to cap their RNAs through ribose 20-O-methylation *** process is crucial for maintaining viral genome stability,facilitating efficient translation,and enabling immune *** considerable advances in the ultrastructure of SARS-CoV-2 nsp16/nsp10,insights into its molecular mechanism have so far been *** this study,we systematically characterized the 20-O-MTase activity of nsp16 in SARS-CoV-2,focusing on its dependence on nsp10 *** observed cross-reactivity between nsp16 and nsp10 in various coronaviruses due to a conserved interaction ***,a single residue substitution(K58T)in SARS-CoV-2 nsp10 restricted the functional activation of MERS-CoV ***,the cofactor nsp10 effectively enhanced the binding of nsp16 to the substrate RNA and the methyl donor Sadenosyl-L-methionine(SAM).Mechanistically,His-80,Lys-93,and Gly-94 of nsp10 interacted with Asp-102,Ser-105,and Asp-106 of nsp16,respectively,thereby effectively stabilizing the SAM binding ***-43 of nsp10 interacted with Lys-38 and Gly-39 of nsp16 to dynamically regulate the RNA binding pocket and facilitate precise binding of RNA to the nsp16/nsp10 *** assessing the conformational epitopes of nsp16/nsp10 complex,we further determined the critical residues involved in 20-O-MTase ***,we utilized an in vitro biochemical platform to screen potential inhibitors targeting 20-O-MTase ***,our results significantly enhance the understanding of viral 20-O methylation process and mechanism,providing valuable targets for antiviral drug development.

关键词： SARS-CoV-2 nsp16/nsp10 20-O-Methyltransferase 3-Dimensional structure Molecular mechanism Inhibitors

Recent advances in genome-scale engineering in Escherichia coli and their applications

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Engineering Microbiology 2024年第1期4卷 28-38页

作者： Hui Gao Zhichao Qiu Xuan Wang Xiyuan Zhang Yujia Zhang Junbiao Dai Zhuobin Liang Institute of Molecular Physiology Shenzhen Bay LaboratoryShenzhen 518132China CAS Key laboratory of Quantitative Engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics.Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Regenerative Medicine Program Bellvitge Institute for Biomedical Research(IDIBELL)and Program for Clinical Translation of Regenerative Medicine in Catalonia(P-CMRC)L’Hospitalet de LlobregatBarcelona 08908Spain Faculty of Pharmacy and Food Science Barcelona UniversityBarcelona 08028Spain College of Life Sciences Northwest A&F UniversityShaanxi 712100China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Owing to the rapid advancement of genome engineering technologies,the scale of genome engineering has expanded *** editing has progressed from one genomic alteration at a time that could only be employed in few species,to the simultaneous generation of multiple modifications across many genomic loci in numerous *** development and recent advances in multiplex automated genome engineering(MAGE)-associated technologies and clustered regularly interspaced short palindromic repeats and their associated protein(CRISPR-Cas)-based approaches,together with genome-scale synthesis technologies offer unprecedented opportunities for advancing genome-scale engineering in a broader *** approaches provide new tools to generate strains with desired phenotypes,understand the complexity of biological systems,and directly evolve a genome with novel ***,we review the recent major advances in genome-scale engineering tools developed for Escherichia coli,focusing on their applications in identifying essential genes,genome reduction,recoding,and beyond.

关键词： Genome-scale engineering E.coli Recombineering CRISPR-Cas

Application of Fusobacterium nucleatum as a biomarker in gastrointestinal malignancies

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World Journal of Gastrointestinal Oncology 2024年第6期16卷 2271-2283页

作者： Long-Chen Yu Ya-Ping Li Yue-Ming Xin Mai Mao Ya-Xin Pan Yi-Xuan Qu Zheng-Dong Luo Yi Zhang Xin Zhang Department of Clinical laboratory Qilu Hospital of Shandong UniversityShandong Engineering Research Center of Biomarker and Artificial Intelligence ApplicationJinan 250012Shandong ProvinceChina

The morbidity and mortality of gastrointestinal(GI)malignancies are among the highest in the world,posing a serious threat to human *** of the insidious onset of the cancer,it is difficult for patients to be diagnosed at an early stage,and it rapidly progresses to an advanced stage,resulting in poor treatment and *** nucleatum(***)is a gram-negative,sporefree anaerobic bacterium that primarily colonizes the oral cavity and is implicated in the development of colorectal,esophageal,gastric,and pancreatic cancers via various intricate *** development in novel research suggests that *** may function as a biomarker in GI *** the abundance of *** in stool,saliva,and serum samples of patients may aid in the diagnosis,risk assessment,and prognosis monitoring of GI *** editorial systematically describes the biological roles and mechanisms of *** in GI malignancies focusing on the application of *** as a biomarker in the diagnosis and prognosis of GI malignancies to promote the clinical translation of *** and GI tumors-related research.

关键词： Gastrointestinal malignancies Fusobacterium nucleatum Biomarker Diagnosis Prognosis

Scalable synthesis of lipid nanoparticles for nucleic acid drug delivery using an isometric channel-size enlarging strategy

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Nano research 2024年第4期17卷 2899-2907页

作者： Zesen Ma Haiyang Tong Sijin Lin Li Zhou Demeng Sun Baoqing Li Changlin Tian Jiaru Chu Department of Precision Machinery and Precision Instrumentation University of Science and Technology of ChinaHefei 230027China Key laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes University of Science and Technology of ChinaHefei 230027China Science Island Branch Graduate SchoolUniversity of Science and Technology of ChinaHefei 230026China Anhui Provincial Key laboratory of High Field Magnetic Resonance imaging High Magnetic Field LaboratoryHefei Institute of Physical ScienceChinese Academy of SciencesHefei 230031China Anhui Provincial Engineering laboratory of Peptide Drugs University of Science and Technology of ChinaHefei 230027China School of Biomedical Engineering Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaSuzhou 215127China

Lipid nanoparticles(LNPs)have emerged as highly effective delivery systems for nucleic acid-based ***,the broad clinical translation of LNP-based drugs is hampered by the lack of robust and scalable synthesis techniques that can consistently produce formulations from early development to clinical *** this work,we proposed a method to achieve scalable synthesis of LNPs by scaling inertial microfluidic mixers isometrically in three ***,a theoretical predictive method,which controls the mixing time to be equal across different chips,is developed to ensure consistent particle size and size distribution of the synthesized *** loaded with small interfering RNA(siRNA)were synthesized at different flow rates,exhibiting consistent physical properties,including particle size,size distribution and encapsulation *** work provides a practical approach for scalable synthesis of LNPs consistently,offering the potential to accelerate the transition of nucleic acid drug development into clinical application.

关键词： lipid nanoparticles nucleic acid delivery microfluidics scalable synthesis consistent particle size

The essential roles of m^(6)A modification in osteogenesis and common bone diseases

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Genes & Diseases 2024年第1期11卷 335-345页

作者： Yuxi Gu Yidan Song Yihua Pan Jun Liu State Key laboratory of Oral Diseases&National Clinical research Center for Oral Diseases Department of OrthodonticsWest China Hospital of StomatologySichuan UniversityChengduSichuan 610041China

N6-methyladenosine(m^(6)A)is the most prevalent modification in the eukaryotic transcriptome and has a wide range of functions in coding and noncoding *** affects the fate of the modified RNA,including its stability,splicing,and translation,and plays an important role in post-transcriptional *** play a key role in supporting and pro-tecting muscles and other organs,facilitating the movement of the organism,ensuring blood production,*** diseases such as osteoarthritis,osteoporosis,and bone tumors are serious public health *** processes of bone development and osteogenic differen-tiation require the precise regulation of gene expression through epigenetic mechanisms including histone,DNA,and RNA *** a reversible dynamic epigenetic mark,m^(6)A modifications affect nearly every important biological process,cellular component,and molecular function,including skeletal development and *** recent years,studies have shown that m^(6)A modification is involved in osteogenesis and bone-related *** this review,we summarized the proteins involved in RNA m^(6)A modification and the latest progress in elucidating the regulatory role of m^(6)A modification in bone formation and stem cell direc-tional *** also discussed the pathological roles and potential molecular mech-anisms of m^(6)A modification in bone-related diseases like osteoporosis and osteosarcoma and suggested potential areas for new strategies that could be used to prevent or treat bone de-fects and bone diseases.

关键词： Bone diseases m^(6)A modification Osteogenesis Regulatory role Stem cells

The RNA binding protein EHD6 recruits the m^(6)A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering

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Molecular Plant 2024年第6期17卷 935-954页

作者： Song Cui Peizhe Song Chaolong Wang Saihua Chen Benyuan Hao Zhuang Xu Liang Cai Xu Chen Shanshan Zhu Xiangchao Gan Hui Dong Yuan Hu Liang Zhou Haigang Hou Yunlu Tian Xi Liu Liangming Chen Shijia Liu Ling Jiang Haiyang Wang Guifang Jia Shirong Zhou Jianmin Wan State Key laboratory for Crop Genetics&Germplasm Enhancement and Utilization Zhongshan Biological Breeding LaboratoryNational Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjing 210095China State Key laboratory for Crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking-Tsinghua Center for Life SciencesBeijing Advanced Center of RNA BiologyPeking UniversityBeijingChina Jiangsu Key laboratory of Crop Genomics and Molecular Breeding Agricultural College of Yangzhou UniversityYangzhou 225009China Max Planck Institute for Plant Breeding research Carl-von-Linne´-Weg 1050829 KolnGermany

N6-Methyladenosine(m^(6)A)is one of the most abundant modifications of eukaryotic mRNA,but its comprehensive biological functionality remains further *** this study,we identified and characterized a new flowering-promoting gene,EARLY HEADING DATE6(EHD6),in ***6 encodes an RNA recognition motif(RRM)-containing RNA binding protein that is localized in the non-membranous cytoplasm ribonucleoprotein(RNP)granules and can bind both m^(6)A-modified RNA and unmodified RNA *** found that EHD6 can physically interact with YTH07,a YTH(YT521-B homology)domain-containing m^(6)A *** showed that their interaction enhances the binding of an m^(6)A-modified RNA and triggers relocation of a portion of YTH07 from the cytoplasm into RNP granules through phase-separated *** these condensates,the mRNA of a rice flowering repressor,CONSTANS-like 4(OsCOL4),becomes sequestered,leading to a reduction in its protein abundance and thus accelerated flowering through the Early heading date 1 *** together,these results not only shed new light on the molecular mechanism of efficient m^(6)A recognition by the collaboration between an RNA binding protein and YTH family m^(6)A reader,but also uncover the potential for m^(6)A-mediated translation regulation through phaseseparated ribonucleoprotein condensation in rice.

关键词： N6-methyladenosine m^(6)A EHD6 YTH domain-containing protein phase separation heading date

m^(1)A inhibition fuels oncolytic virus-elicited antitumor immunity via downregulating MYC/PD-L1 signaling

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International Journal of Oral Science 2024年第3期16卷 486-498页

作者： Shujin Li Tian Feng Yuantong Liu Qichao Yang An Song Shuo Wang Jun Xie Junjie Zhang Bifeng Yuan Zhijun Sun State Key laboratory of Oral&Maxillofacial Reconstruction and Regeneration Key Laboratory of Oral Biomedicine Ministry of EducationHubei Key Laboratory of StomatologySchool&Hospital of StomatologyFrontier Science Center for Immunology and MetabolismTaikang Center for Life and Medical SciencesWuhan UniversityWuhanChina School of Public Health Wuhan UniversityWuhanChina State Key laboratory of Virology Medical Research InstituteWuhan UniversityWuhanChina Department of Oral Maxillofacial-Head Neck Oncology School and Hospital of StomatologyWuhan UniversityWuhanChina

N^(1)-methyladenosine(m^(1)A)RNA methylation is critical for regulating mRNA translation;however,its role in the development,progression,and immunotherapy response of head and neck squamous cell carcinoma(HNSCC)remains largely *** Tgfbr1 and Pten conditional knockout(2cKO)mice,we found the neoplastic transformation of oral mucosa was accompanied by increased m^(1)A modification *** of m^(1)A-associated genes identified TRMT61A as a key m^(1)A writer linked to cancer progression and poor ***,TRMT61A-mediated tRNA-m^(1)A modification promotes MYC protein synthesis,upregulating programmed death-ligand 1(PD-L1)***,m^(1)A modification levels were also elevated in tumors treated with oncolytic herpes simplex virus(oHSV),contributing to reactive PD-L1 *** m^(1)A inhibition sustained oHSV-induced antitumor immunity and reduced tumor growth,representing a promising strategy to alleviate *** findings indicate that m^(1)A inhibition can prevent immune escape after oHSV therapy by reducing PD-L1 expression,providing a mutually reinforcing combination immunotherapy approach.

关键词： immunity sustained representing

M2-type macrophage membrane-mediated delivery of Carvedilol nanocomplex for acute liver failure treatment and remodeling inflammatory microenvironment

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Nano research 2024年第7期17卷 6362-6375页

作者： Mingge Shang Yaohui Zhang Junjie Qian Wenchao Wang Xizhi Yu Jiacheng Huang Lin Zhou Shusen Zheng Division of Hepatobiliary and Pancreatic Surgery Department of SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003China NHC Key laboratory of Combined Multi-organ Transplantation Key Laboratory of Organ TransplantationHangzhou 310003China Key laboratory of the diagnosis and treatment of organ Transplantation Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic CancerChinese Academy of Medical Sciences(2019RU019)Hangzhou 310003China State Key laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious DiseasesHangzhou 310003China Department of Thyroid Surgery The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310003China Shulan(Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College Hangzhou 310000China

Interactions of hepatic macrophages with local inflammatory microenvironment is the key factor promoting the development of acute liver failure(ALF).Hence,reprogramming pro-inflammatory M1 into anti-inflammatory M2 phenotype may offer a promising strategy for treating ALF by targeting *** group found Carvedilol possessed potential anti-inflammatory property previously,which had been scarcely reported in *** present a synergy strategy to induce macrophages into the phenotype M2-type anti-inflammatory macrophages with interleukin-4(IL-4)and IL-10 at *** Carvedilol is loaded on the macrophage membrane-camouflaged biomimetic nano-platform(termed as M2M@CNP)to evade reticuloendothelial system(RES)and afford Carvedilol delivery to the inflammatory environment with overproduced reactive oxygen species(ROS),further prolonging its circulation and *** released Carvedilol produced anti-inflammatory,antioxidant and anti-apoptosis effects,combining local M2-type cell membranes(M2-CM)inhibited pro-inflammatory cytokines and ROS levels,which in turn promoted and amplified M1 to M2 phenotype polarization *** study offers new insights into the rational design of biomimetic nanosystems for safe and effective ALF therapy to accelerate the clinical translation.

关键词： acute liver failure hepatic drug delivery M2 macrophage-camouflaged nanoplatform inflammatory microenvironment macrophage polarization

Phase separation of GRP7 facilitated by FERONIAmediated phosphorylation inhibits mRNA translation to modulate plant temperature resilience

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Molecular Plant 2024年第3期17卷 460-477页

作者： Fan Xu Long Wang Yingbin Li Junfeng Shi Dorothee Staiger Feng Yu state Key laboratory of Chemo/Biosensing and Chemometrics College of Biologyand Hunan Key Laboratory of Plant Functional Genomics and Developmental RegulationHunanUniversityChangsha 410082P.R.China State Key laboratory of Hybrid Rice Hunan Agricultural Biotechnology Research InstituteHunan Academy of Agricultural SciencesChangsha 410125P.R.China RNA Biology and Molecular Physiology Faculty of BiologyBielefeld University33615 BielefeldGermany

Changes in ambient temperature profoundly affect plant growth and ***,the molecu-larbasis of plant acclimation to temperature fluctuation is of great *** this study,we discovered that GLYCINE-RICH RNA-BINDING PROTEIN 7(GRP7)contributes to cold and heat tolerance in Arabidopsis *** found that exposure to a warm temperature rapidly induces GRP7 condensates in planta,which can be reversed by transfer to a lower *** biology and biochemical assays revealed that GRP7 undergoes liquid-liquid phase separation(LLPS)in vivo and in *** of GRP7 in the cyto-plasm contributes to the formation of stress granules that recruit RNA,along with the translation machinery component eukaryotic initiation factor 4E1(elF4E1)and the mRNA chaperones COLD SHOCK PROTEIN 1(CSP1)and CSP3,to inhibit ***,natural variations in GRP7 affecting the residue phos-phorylated by the receptorkinase FERONIA alter its capacity to undergo LLPS and correlate with the adap-tation of some Arabidopsis accessions to a widertemperature *** together,ourfindings illustrate the role of translational control mediated by GRP7 LLPS to confer plants with temperature resilience.

关键词： fluctuating temperature glycine-rich RNA-binding protein phase separation cold shock proteins translation