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Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012–2014

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Virologica Sinica 2022年第6期37卷 883-893页

作者： Jun Wang Jian Xiao Zheng Zhu Siyuan Wang Lei Zhang Zhaojun Fan Yali Deng Zhihong Hu Fang Peng Shu Shen Fei Deng State Key laboratory of Virology and National virus Resource Center Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China Xinjiang Key laboratory of Biological Resources and Genetic Engineering College of Life Science and TechnologyXinjiang UniversityUrumqi830046China China Center for Type Culture Collection(CCTCC) College of Life SciencesWuhan UniversityWuhan430072China Natisonal Emerging Infectious Diseases Laboratories Boston UniversityBostonMA 02118United States Department of Biochemistry Boston University School of MedicineBostonMA 02118United States

Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses,which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012–2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity,they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein(rep)-encoding single-stranded(CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity,complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils,Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.

关键词： Arctic soil Antarctica animal feces Metagenomics virus diversity

A cell-based large-scale screening of natural compounds for inhibitors of SARS-CoV-2

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Signal Transduction and Targeted Therapy 2020年第1期5卷 667-669页

作者： Zhe-Rui Zhang Ya-Nan Zhang Xiao-Dan Li Hong-Qing Zhang Shu-Qi Xiao Fei Deng Zhi-Ming Yuan Han-Qing Ye Bo Zhang Key laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyCenter for Biosafety Mega-ScienceChinese Academy of Sciences430071 WuhanChina University of Chinese Academy of Sciences 100049 BeijingChina Hunan Normal University School of Medicine410081 ChangshaChina State Key laboratory of Virology and National virus Resource Center Wuhan Institute of VirologyChinese Academy of Sciences430071 WuhanHubeiChina

Dear Editor,Coronavirus disease 2019(COVID-19),caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),has spread rapidly and developed into a global pandemic since its outbreak in December 2019.Currently,there is no antiviral treatment available for human use.Numerous compounds,such as remdesivir and chloroquine,have been reported to inhibit SARS-CoV-2 replication effectively in vitro,but for most of them,the in vivo efficacies against SARS-CoV-2 are still under clinical studies,and for chloroquine,a drug with prominent in vitro antiviral activity,it has been found no beneficial effect for COVID-19 patients in the recent largest study.It is thus urgent to speed up large-scale screening to discover drug candidates to treat COVID-19.

关键词： acute respiratory compounds

A new anterograde trans-synaptic tracer based on Sindbis virus

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Neural Regeneration Research 2022年第12期17卷 2761-2764页

作者： Xiang-Wei Shi Fan Jia Pei Lyu Fu-Qiang Xu State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics Key Laboratory of Magnetic Resonance in Biological SystemsWuhan Center for Magnetic ResonanceInnovation Academy for Precision Measurement Science and TechnologyChinese Academy of SciencesWuhanHubei ProvinceChina Guangdong Provincial Key laboratory of Brain Connectome and Behavior CAS Key Laboratory of Brain Connectome and Manipulationthe Brain Cognition and Brain Disease Institute(BCBDI)Translational Research Center for the Nervous System(TRCNS)Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research InstitutionsShenzhenGuangdong ProvinceChina NMPA Key laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products Key Laboratory of Quality Control Technology for Virus-Based TherapeuticsGuangdong Provincial Medical Products AdministrationShenzhen Key Laboratory of Viral Vectors for BiomedicineShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong ProvinceChina University of Chinese Academy of Sciences BeijingChina Wuhan National laboratory for Optoelectronics Huazhong University of Science and TechnologyWuhanHubei ProvinceChina

Mapping neural circuits is critical for understanding the structure and function of the nervous system.Engineered viruses are a valuable tool for tracing neural circuits.However,current tracers do not fully meet the needs for this approach because of various drawbacks,such as toxicity and characteristics that are difficult to modify.Therefore,there is an urgent need to develop a new tracer with low toxicity and that allows for long-term studies.In this study,we constructed an engineered Sindbis virus(SINV)expressing enhanced green fluorescent protein(EGFP)reporter gene(SINV-EGFP)and found that it had no significant difference in biological characterization compared with the wild-type Sindbis virus in BHK-21 cells and neurons in vitro.We injected the virus into the visual circuit of mouse brain and found that the virus infected neurons in the local injected site and anterogradely spread in the neural circuits.Although the efficiency of transmission was limited,the findings demonstrate that SINV can be used as a new anterograde tracer to map neural circuits in mouse brain and that it spreads exclusively in the anterograde direction.Further,use of SINV in mouse brain research will provide longer time windows for circuit tracing than is possible with herpes simplex virus and vesicular stomatitis virus tracers.

关键词： anterograde lateral geniculate nucleus mouse brains neural circuit neurons retina Sindbis virus superior colliculus synapse tracer

N-gamboyl Gemcitabine Inhibits Tumor Cells Proliferation and Migration

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Journal of Donghua University(English Edition) 2023年第4期40卷 377-383页

作者：裴屹斐邓敏姜玉新邵志宇王红声 Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine College of Biological Science and Medical EngineeringDonghua UniversityShanghai 201620China College of Chemistry and Chemical Engineering Donghua UniversityShanghai 201620China The First Hospital of Jiaxing Jiaxing Key Laboratory of Virus-Related Infectious DiseasesJiaxing UniversityJiaxing 314001China

Gambogic acid(GA) is a natural substance with a good antitumor effect, but it is too lipophilic to be metabolized and excreted, thus accumulating in the body. Gemcitabine(GEM), one of the first-line antitumor drugs, has high hydrophilicity, which greatly shortens its half-life in vivo. We previously reported a compound named N-gamboyl gemcitabine(GAG), derived from the condensation of GEM and GA, whose hydrophilicity is better than GA and stability is better than GEM. Here, the antitumor performance of GAG was investigated for the first time by using several common tumor cell lines as tumor models. The results of in vitro study showed that GAG significantly inhibited the proliferation and migration of the tumor cells. The IC50 values of GAG for the tumor cells were lower than those of GEM and GA. The present study suggests that GAG has a promising potential to be developed into a broad-spectrum antitumor drug.

关键词： N-gamboyl gemcitabine(GAG) gambogic acid(GA) gemcitabine(GEM) antitumor

Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements

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Molecular Plant 2020年第6期13卷 851-863页

作者： Le Xu Kun Yuan Meng Yuan Xiangbing Meng Min Chen Jianguo Wu Jiayang Li Yijun Qi Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China Key laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Vector-borne virus Research Center State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Province Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhou 350002China

Tillering is a major determinant of rice plant architecture and grain yield.Here,we report that depletion of rice OsNRPD1a and OsNRPD1b,two orthologs of the largest subunit of RNA polymerase IV,leads to a high-tillering phenotype,in addition to dwarfism and smaller panicles.OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements(TEs)including miniature inverted-repeat TEs(MITEs).Interestingly,many genes are regulated either positively or negatively by TE methylation.Among them,OsMIR156d and OsMIR156j,which promote rice tillering,are repressed by CHH methylation at two MITEs in the promoters.By contrast,D14,which suppresses rice tillering,is activated by CHH methylation at an MITE in its downstream.Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.

关键词： RdDM siRNA MITEs OsMIR156 D14 tiller

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Preface

Virologica Sinica 2019年第2期34卷 117-118页

作者： Zhi-Ming Zheng Ke Lan Eric O. Freed Zheng-Li Shi Tumor virus RNA Biology Section. RNA Biology laboratory Center for Cancer Research. National Cancer Institute NIH. Frederick MD 21702 USA State Key laboratory of Virology College of Life Sciences Wuhan University Wuhan 430072 China virus-Cell Interaction Section HIV Dynamics and Replication Program Center for Cancer Research National Cancer Institute Frederick. MD 21702 USA Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China

Viral infections remain a global threat to world health in the twenty-first century. They are caused by both DNA and RNA viruses and can manifest as acute or chronic infections, in some cases causing epidemics or even global pandemics.Persistent viral infections lead to host immunodeficiency and the development of ~12% of human cancers worldwide.

关键词： Viral infections twenty-first century cancers worldwide

Genome Analysis of Dasineura jujubifolia Toursvirus 2,A Novel Ascovirus

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Virologica Sinica 2020年第2期35卷 134-142页

作者： Jun Wang Minglu Yang Haibing Xiao Guo-Hua Huang Fei Deng Zhihong Hu State Key laboratory of Virology and National virus Resource Center Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China Tarim University Alar 843300China Hunan Provincial Key laboratory for Biology and Control of Plant Diseases and Insect Pests Institute of VirologyHunan Agricultural UniversityChangsha 410128China

So far,ascoviruses have only been identified from Lepidoptera host insects and their transmission vectors-endoparasitic wasps.Here,we reported the first finding of a complete novel ascovirus genome from a Diptera insect,Dasineura jujubifolia.Initially,sequence fragments with homology to ascoviruses were incidentally identified during metagenomic sequencing of the mitochondria of D.jujubifolia(Cecidomyiidae,Diptera)which is a major pest on Ziziphus jujuba.Then a full circular viral genome was assembled from the metagenomic data,which has an A+T percentage of 74%and contains 142,600 bp with 141 open reading frames(ORFs).Among the 141 ORFs,37 were conserved in all sequenced ascoviruses(core genes)including proteins predicted to participate in DNA replication,gene transcription,protein modification,virus assembly,lipid metabolism and apoptosis.Multi-gene families including those encode for baculovirus repeated open reading frames(BROs),myristylated membrane proteins,RING/U-box E3 ubiquitin ligases,and ATP-binding cassette(ABC)transporters were found in the virus genome.Phylogenetic analysis showed that the newly identified virus belongs to genus Toursvirus of Ascoviridae,and is therefore named as Dasineura jujubifolia toursvirus 2(DjTV-2a).The virus becomes the second reported species of the genus after Diadromus pulchellus toursvirus 1(DpTV-1a).The genome arrangement of DjTV-2a is quite different from that of DpTV-1a,suggesting these two viruses separated in an early time of evolution.The results suggest that the ascoviruses may infect a much broader range of hosts than our previous knowledge,and shed lights on the evolution of ascoviruses and particularly on that of the toursviruses.

关键词： Dasineura jujubifolia toursvirus 2(DjTV-2a) Ascovirus Toursvirus

Viral Tools for Neural Circuit Tracing

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Neuroscience Bulletin 2022年第12期38卷 1508-1518页

作者： Qing Liu Yang Wu Huadong Wang Fan Jia Fuqiang Xu The Brain Cognition and Brain Disease Institute(BCBDI) Shenzhen Key Laboratory of Viral Vectors for BiomedicineShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research InstitutionsNMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal ProductsShenzhen Key Laboratory of Quality Control Technology for Virus-Based TherapeuticsGuangdong Provincial Medical Products AdministrationShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics Key Laboratory of Magnetic Resonance in Biological SystemsWuhan Center for Magnetic ResonanceInnovation Academy for Precision Measurement Science and TechnologyChinese Academy of SciencesWuhan 430071China Center for Excellence in Brain Science and Intelligence Technology Chinese Academy of SciencesShanghai 200031China University of Chinese Academy of Sciences Beijing 100049China

Neural circuits provide an anatomical basis for functional networks.Therefore,dissecting the structure of neural circuits is essential to understanding how the brain works.Recombinant neurotropic viruses are important tools for neural circuit tracing with many advantages over non-viral tracers:they allow for anterograde,retrograde,and trans-synaptic delivery of tracers in a cell type-specific,circuit-selective manner.In this review,we summarize the recent developments in the viral tools for neural circuit tracing,discuss the key principles of using viral tools in neuroscience research,and highlight innovations for developing and optimizing viral tools for neural circuit tracing across diverse animal species,including nonhuman primates.

关键词： Neural circuit Viral tool Anterograde Retrograde Trans-synaptic

Structure basis for allosteric regulation of lymphocytic choriomeningitis virus polymerase function by Z matrix protein

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Protein & Cell 2023年第9期14卷 703-707页

作者： Lu Liu Panpan Wang Aijun Liu Leike Zhang Liming Yan Yu Guo Gengfu Xiao Zihe Rao Zhiyong Lou MOE Key laboratory of Protein Science School of MedicineTsinghua UniversityBeijing 100084China School of Life Sciences Peking UniversityBeijing 100080China Kobilka Institute of Innovative Drug Discovery School of Life and Health SciencesThe Chinese University of Hong KongShenzhen 518100China State key laboratory of Virology and National virus Resource Center Wuhan Institute of VirologyCenter for Biosafety Mega-ScienceChinese Academy of SciencesWuhan430071China State Key laboratory of Medicinal Chemical Biology College of Life Sciences and College of PharmacyNankai UniversityTianjin 300350China National laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100105China Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology ShanghaiTech UniversityShanghai 200120China Innovation Center for Pathogen Research Guangzhou LaboratoryGuangzhou 510005China

DearEditor,The Arenaviridae family(recently assigned to the Bunyavirales order)is a group of emerging viruses that include causative agents of severe hemorrhagic fevers with high mortality in humans(de la Torre,2009).Lymphocytic choriomeningitis virus(LCMV)is the prototypic member of the Arenaviridae family and belongs to the Old World(OW)arenavirus together with Lassa virus(LASV),which are distinct from the New World(NW)arenavirus[e.g.Machupo virus(MACV)and Junin virus(JUNV)].LCMV infection in the fetus and newborm results in severe impairment of brain development associated with sensory loss and mental retardation and is also known to be associated with severe systemic infection with high mortality in transplantation patients(Palacios et al.,2008).

关键词： lymphocytic mortality fetus