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Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods

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Marine Life science & Technology 2021年第2期3卷 231-242页

作者： Haining Hu Vengadesh Perumal Natarajan Fengping Wang State Key Laboratory of microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China school of Oceanography Shanghai Jiao Tong UniversityShanghai200240China

The archaea that can be readily cultivated in the laboratory are only a small fraction of the total diversity that exists in *** molecular ecology methods,such as metagenomic sequencing,can provide valuable information independent of cell cultivation,it is only through cultivation-based experiments that they may be fully characterized,both for their physiological and ecological ***,we report our efforts towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation ***,cells were retrieved from the sediment samples through a cell extraction procedure and the sediment-free mixed cells were then divided into different size-range fractions by successive filtration through 0.8µm,0.6µm and 0.2µm *** 16S rRNA gene analyses indicated noticeable retention of different archaeal groups in different *** each fraction,supplementation with a variety of defined substrates(e.g.,methane,sulfate,and lignin)and stepwise dilutions led to highly active enrichment cultures of several archaeal groups with Bathyarchaeota most prominently ***,using a roll-bottle technique,three co-cultures consisting of Bathyarchaeota(subgroup-8)and a bacterial species affiliated with either Pseudomonas or Glutamicibacter were *** results demonstrate that a combination of cell extraction,size fractionation,and roll-bottle isolation methods could be a useful protocol for the successful enrichment and isolation of numerous slow-growing archaeal groups from marine sediments.

关键词： microbial cultivation Marine sediments Uncultivated archaea Co-culture Bathyarchaeota

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A Potential Disease Susceptibility Gene CsLOB of Citrus Is Targeted by a Major Virulence Effector PthA of Xanthomonas citri subsp, citri

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molecular Plant 2014年第5期7卷 912-915页

作者： Zheng Li Lifang Zou Gang Ye Li Xiong Zhiyuan Ji Muhammad Zakria Ni Hong Guoping Wang Gongyou Chen school of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China State Key Laboratory of microbial Metabolism School of Life Science &Biotechnology Shanghai Jiao Tong University Shanghai 200240 China National Key Laboratory of Agromicrobiology Huazhong Agricultural University Wuhan Hubei 430070 China

Dear Editor, Citrus bacterial canker （CBC）, one of the most destructive diseases of citrus, has a severe economic impact on citrus industries in tropical and subtropical countries （Das, 2003）. It has been widely known that Xanthomonas citri subsp, citri （Xcc） causes the CBC by transferring the type-Ill effectors （T3SEs） to the interior of the plant cell through type-Ill secretion system （T3S） to modulate transcription of host plants to trigger CBC disease （Schaad et al., 2006）. Pathotype A,

关键词： CITRUS canker CITRUS fruit industry NUCLEOTIDES PATHOGENIC microorganisms MUTAGENESIS

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A SPX domain vacuolar transporter links phosphate sensing to homeostasis in Arabidopsis

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molecular Plant 2022年第10期15卷 1590-1601页

作者： Mingda Luan Fugeng Zhao Guangfang Sun Min Xu Aigen Fu Wenzhi Lan Sheng Luan Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of EducationProvincial Key Laboratory of BiotechnologyCollege of Life SciencesNorthwest UniversityXi'an 710069China Institute of Future Agriculture Northwest Agriculture and Forestry UniversityYanglingShaanxi 712100China school of Life sciences Nanjing UniversityNanjingJiangsu 210023China Department of Plant and microbial Biology University of CaliforniaBerkeleyBerkeleyCA 94720USA

Excess phosphate(Pi)is stored into the vacuole through Pi transporters so that cytoplasmic Pi levels remain stable in plant *** hypothesized that the vacuolar Pi transporters may harbor a Pi-sensing mechanism so that they are activated to deliver Pi into the vacuole only when cytosolic Pi reaches a threshold high *** tested this hypothesis using Vacuolar Phosphate Transporter 1(VPT1),a SPX domain-containing vacuolar Pi transporter,as a *** studies have defined SPX as a Pi-sensing module that binds inositol polyphosphate signaling molecules(InsPs)produced at high cellular Pi *** showed here that Pi-deficient conditions or mutation of the SPX domain severely impaired the transport activity of *** further identified an auto-inhibitory domain in VPT1 that suppresses its transport *** together the results from detailed structure-function analyses,our study suggests that VPT1 is in the auto-inhibitory state when Pi status is low,whereas at high cellular Pi status InsPs are produced and bind SPX domain to switch on VPT1 activity to deliver Pi into the *** thus provides an auto-regulatory mechanism for VPT1-mediated Pi sensing and homeostasis in plant cells.

关键词： VPT1 Pi signaling autoinhibition transport activity inositol phosphates

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p38γ regulates UV-induced checkpoint signaling and repair of UV-induced DNA damage

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Protein & Cell 2010年第6期1卷 573-583页

作者： Chia-Cheng Wu Xiaohua Wu Jiahuai Han Peiqing Sun Department of Immunology and microbial science The Scripps Research Institute10550 N.Torrey Pines Road.La JollaCA 92037USA Department of molecular and Experimental Medicine The Scripps Research Institute10550 N.Torrey Pines Road.La JollaCA 92037USA Key Laboratory of Ministry of Education for Cell Biology and Tumor Cell Engineering School of Life SciencesXiamen UniversityXiamen 361005China Dempartment of molecular Biology The Scripps Research Institute10550 N.Torrey Pines Road.La JollaCA 92037USA

In eukaryotic cells,DNA damage triggers activation of checkpoint signaling pathways that coordinate cell cycle arrest and repair of damaged *** DNA damage responses serve to maintain genome stability and prevent accumulation of genetic mutations and development of *** p38 MAPK was previously implicated in cellular responses to several types of DNA ***,the role of each of the four p38 isoforms and the mechanism for their involvement in DNA damage responses remained poorly *** this study,we demonstrate that p38γ,but not the other p38 isoforms,contributes to the survival of UV-treated *** of p38γsensitizes cells to UV exposure,accompanied by prolonged S phase cell cycle arrest and increased rate of *** investigation reveal that p38γis essential for the optimal activation of the checkpoint signaling caused by UV,and for the efficient repair of UVinduced DNA *** findings have established a novel role of p38γin UV-induced DNA damage responses,and suggested that p38γcontributes to the ability of cells to cope with UV exposure by regulating the checkpoint signaling pathways and the repair of damaged DNA.

关键词： p38γ DNA damage UV DNA repair checkpoint signaling

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Insights into microbiota community dynamics and flavor development mechanism during golden pomfret(Trachinotus ovatus)fermentation based on single-molecule real-time sequencing and molecular networking analysis

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Food science and Human Wellness 2024年第1期13卷 101-114页

作者： Yueqi Wang Qian Chen Huan Xiang Dongxiao Sun-Waterhouse Shengjun Chen Yongqiang Zhao Laihao Li Yanyan Wu Key Laboratory of Aquatic Product Processing Ministry of Agriculture and Rural Affairs of The People’s Republic of ChinaNational R&D Center for Aquatic Product ProcessingSouth China Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510300China Co-Innovation Center of Jiangsu Marine Bio-industry Technology Jiangsu Ocean UniversityLianyungang 222005China school of Chemical sciences The University of AucklandAuckland 92019New Zealand Collaborative Innovation Center of Seafood Deep Processing Dalian Polytechnic UniversityDalian 116034China

Popular fermented golden pomfret(Trachinotus ovatus)is prepared via spontaneous fermentation;however,the mechanisms underlying the regulation of its flavor development remain *** study shows the roles of the complex microbiota and the dynamic changes in microbial community and flavor compounds during fish ***-molecule real-time sequencing and molecular networking analysis revealed the correlations among different microbial genera and the relationships between microbial taxa and volatile *** underlying flavor development were also elucidated via KEGG based functional ***,Shewanella,and Staphylococcus were the dominant microbial ***-nine volatile compounds were detected in the fermented fish samples,with thirteen identified as characteristic volatile compounds(ROAV>1).Volatile profiles resulted from the interactions among the microorganisms and derived enzymes,with the main metabolic pathways being amino acid biosynthesis/metabolism,carbon metabolism,and glycolysis/*** study demonstrated the approaches for distinguishing key microbiota associated with volatile compounds and monitoring the industrial production of high-quality fermented fish products.

关键词： Fermented golden pomfret Microbiota community Volatile compound Co-occurrence network Metabolic pathway

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Impact of oxygen supply on production of terpenoids by microorganisms: State of the art

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Chinese Journal of Chemical Engineering 2021年第2期34卷 46-53页

作者： Ting-Ting Liu Han Xiao Jian-Hui Xiao Jian-Jiang Zhong State Key Laboratory of microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental SciencesLaboratory of Molecular Biochemical Engineering and Advanced Fermentation TechnologyDepartment of BioengineeringSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Zunyi Municipal Key Laboratory of Medicinal Biotechnology Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyi 563003China

Terpenoids are a class of high value-added natural products with a variety of biological *** engineered microorganisms,such as those of Escherichia coli and Saccharomyces cerevisiae,have merits in producing plant or fungus-derived terpenoids,due to their mature genetic manipulation,simple nutrient demand and fast ***,as a key environmental factor,is particularly important to microbial metabolism and growth,and suitable oxygen supply is viewed as a prerequisite for realizing highly efficient production of terpenoids by engineered *** this article,the role of oxygen in regulating terpenoid bioproduction is overviewed from the viewpoints of cellular carbon metabolism,energy metabolism and terpenoid *** on adjusting oxygen availability to microorganisms,including genetic modification of cellular metabolism related with oxygen utilization,are summarized and discussed,to provide helpful information for further improvement of terpenoid biosynthesis by microbes.

关键词： Terpenoid Microorganisms Oxygen supply Chassis modification

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The Tara Oceans Project:New Opportunities and Greater Challenges Ahead

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Genomics, Proteomics & Bioinformatics 2015年第5期13卷 275-277页

作者： Houjin Zhang Kang Ning school of Life science and Technology Huazhong University of Science and Technology

In the May 22, 2015 issue of science magazine, several articles （including the editorial, research papers, and perspectives） were published on the Tara Oceans Project and studies related to ocean microbes [1-8]. This represents truly a milestone for studies in both ocean ecology and microbial communities. As stated on the European molecular Biology Laboratory （EMBL） website （http：//***/tara-oceans/start/）：＂Tara Oceans results reveal climate change insights, and a treasure trove of novel species and genes.＂

关键词： Project The Tara Oceans Project data

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Structural analysis of receptor-like kinase SOBIR1 reveals mechanisms that regulate its phosphorylation-dependent activation

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Plant Communications 2022年第2期3卷 34-51页

作者： Xue Wei Yulu Wang Su Zhang Tianyi Gu Gabryel Steinmetz Haiyan Yu Guoguang Guo Xin Liu Shilong Fan Fengzhong Wang Yangnan Gu Fengjiao Xin Laboratory of Biomanufacturing and Food Engineering Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China Beijing Advanced Innovation Center for Tree Breeding by molecular Design Beijing Forestry UniversityBeijing 100083China Department of Plant and microbial Biology University of CaliforniaBerkeleyCA 94720USA Innovative Genomics Institute University of CaliforniaBerkeleyCA 94720USA Key Laboratory of Ministry of Education for Protein science School of Life SciencesTsinghua UniversityBeijing 100084China Hefei National Laboratory for Physical sciences at the Microscale and school of Life sciences University of Science and Technology of ChinaHefeiAnhui 230026China The Center of Protein science Tsinghua UniversityBeijing 100084China

Plant leucine-rich repeat(LRR)receptor-like kinases(RLKs)and LRR receptor-like proteins(RLPs)comprise a large family of cell surface receptors that play critical roles in signal perception and *** LRR-RLKs and LRR-RLPs rely on regulatory LRR-RLKs to initiate downstream signaling *** INSENSITIVE 1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3(BAK1/SERK3)and SUPPRESSOR OF BIR1-1(SOBIR1)are important and extensively studied regulatory LRR-RLKs with distinct *** the regulatory mechanism of BAK1 activation has been studied in detail,the activation mechanism of SOBIR1 remains poorly ***,the crystal structures of the catalytically inactive kinase domain of SOBIR1(SOBIR1-KD)from Arabidopsis thaliana were determined in complexes with AMP-PNP and Mg^(2+).The results show that SOBIR1-KD contains a uniquely long β3-αC loop and adopts an Src-like inactive conformation with an unusual architecture at the activation segment,which comprises three *** studies revealed that SOBIR1 is transphosphorylated by BAK1 following its autophosphorylation via an intermolecular mechanism,and the phosphorylation of Thr529 in the activation segment and the β3-αC loop are critical for SOBIR1 *** functional analysis confirmed the importance of Thr529 and the β3-αC loop for the SOBIR1-induced cell death response in Nicotiana *** together,these findings provide a structural basis for the regulatory mechanism of SOBIR1 and reveal the important elements and phosphorylation events in the special stepwise activation of SOBIR1-KD,the first such processes found in regulatory LRR-RLKs.

关键词： LRR-RLK SOBIR1 crystal structure unusual architecture autophosphorylation stepwise activation

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Heparin mimetics as potential intervention for COVID-19 and their bio-manufacturing

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Synthetic and Systems Biotechnology 2023年第1期8卷 11-19页

作者： Lan Jiang Tianji Zhang Hongzhong Lu Saijuan Li Kangjie Lv Alex Tuffour Lixin Zhang Kan Ding Jin-Ping Li Hongmei Li Xueting Liu Department of Cardiothoracic Surgery Children’s Hospital of Nanjing Medical UniversityNanjing210093China State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghai200237China Division of Chemistry and Analytical science Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market RegulationNational Institute of MetrologyBeijing100029China State Key Laboratory of microbial Metabolism and school of Life sciences and Biotechnology Shanghai Jiao Tong UniversityShanghai200240China Glycochemistry&Glycobiology Lab Key Laboratory of Receptor ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China International Research Center for Soft Matter Beijing University of Chemical TechnologyBeijing100029China Department of Medical Biochemistry and Microbiology University of UppsalaUppsalaSweden

The COVID-19 pandemic has caused severe health problems worldwide and unprecedented decimation of the global ***,after more than 2 years,many populations are still under pressure of ***,a broader perspective in developing antiviral strategies is still of great *** by the observed multiple benefits of heparin in the treatment of thrombosis,the potential of low molecular weight heparin(LMWH)for the treatment of COVID-19 have been *** applications found that LMWH decreased the level of inflammatory cytokines in COVID-19 patients,accordingly reducing ***,several in vitro studies have demonstrated the important roles of heparan sulfate in SARS-CoV-2 infection and the inhibitory effects of heparin and heparin mimetics in viral *** clinical observations and designed studies argue for the potential to develop heparin mimetics as anti-SARS-CoV-2 drug *** this review,we summarize the properties of heparin as an anticoagulant and the pharmaceutical possibilities for the treatment of virus infection,focusing on the perspectives of developing heparin mimetics via chemical synthesis,chemoenzymatic synthesis,and bioengineered production by microbial cell *** ultimate goal is to pave the eminent need for exploring novel compounds to treat coronavirus infection-caused diseases.

关键词： Heparin Biosynthesis Biological activities Bio-production

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Back to science in Searching for SARS-CoV-2 Origins

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China CDC weekly 2023年第14期5卷 315-317页

作者： William J Liu Wenwen Lei Xiaozhou He Peipei Liu Qihui Wang Zhiqiang Wu Yun Tan Shuhui Song Gary Wong Jian Lu Jingkun Jiang Qiang Wei Mingkun Li Juncai Ma Xiaozhong Peng Yixue Li Baoxu Huang Yigang Tong Jun Han Guizhen Wu NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijingChina NHC Key Laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijingChina Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational MedicineRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina Beijing Institute of Genomics Chinese Academy of Sciencesand China National Center for BioinformationBeijingChina Laboratory of molecular Virology and Immunology Institut Pasteur of ShanghaiChinese Academy of SciencesShanghaiChina State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijingChina school of Environment Tsinghua UniversityBeijingChina National Pathogen Resource Center Chinese Center for Disease Control and Prevention(China CDC)BeijingChina microbial Resource and Big Data Center Chinese National Microbiology Data Center(NMDC)Institute of MicrobiologyChinese Academy of SciencesBeijingChina State Key Laboratory of Medical molecular Biology Department of Molecular Biology and BiochemistryInstitute of Basic Medical SciencesMedical Primate Research CenterNeuroscience CenterChinese Academy of Medical SciencesSchool of Basic MedicinePeking Union Medical CollegeBeijingChina school of Life science and Technology ShanghaiTech UniversityShanghaiChina Bio-Med Big Data Center Key Laboratory of Computational BiologyCAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina China Animal Health and Epidemiology Center Qingdao CityShandong ProvinceChi

In recent decades,emerging and re-emerging human-infecting pathogens have been represented as huge threats to public health and have become a global concern(1).After outbreaks of two coronaviruses(CoVs),severe acute respiratory syndrome coronavirus(SARS-CoV)and Middle East respiratory syndrome coronavirus(MERS-CoV),severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)became the first-known pandemic hastening CoV with tremendous wrecking to the world(2).The origin tracing of these emerging pathogens is of great significance in infectious disease prevention and control(3–4).The origin of SARS-CoV-2 remains elusive after the more than 3-year pandemic,though scientists around the world are making great *** the experience of studying many other infectious pathogens,origin tracing is systematic and time-consuming *** supposed origins of many infectious pathogens are still in debate,including SARS-CoV and human immunodeficiency virus,etc(5).

关键词： prevention respiratory acute

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