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Developing a microﬂuidic-based epicPCR reveals diversepotential hosts of the mcrA gene in marine cold seep

mLife 2025年第1期4卷 70-82页

作者： Wenli Shen Danrui Wang Jiangtao Li Yue Liu Yinzhao Wang Xingsheng Yang Xi Peng Bingliang Xie Lei Su Ziyan Wei Qing He Zhiyi Wang Kai Feng Wenbin Du Ye Deng CAS Key Laboratory of Environmental Biotechnology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijingChina Institute for MarineScience and Technology Shandong UniversityQingdaoChina Soil Ecology Lab Nanjing Agricultural UniversityNanjingChina State Key Laboratory of Marine Geology Tongji UniversityShanghaiChina College of Environmental Science and Engineering Liaoning Technical UniversityFuxinChina Microbiology Division School of LifeSciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy ofSciencesBeijingChina Savaid Medical School University of the Chinese Academy of SciencesBeijin

Anaerobic methanotrophic(ANME)microbes play a crucial role in the bioprocess of anaerobic oxidation of methane(AOM).However,due to their unculturable status,their diversity is poorly *** this study,we established a microﬂuidics-based epicPCR(Emulsion,Paired Isolation,and Concatenation PCR)to fuse the 16S rRNA gene and mcrA gene to reveal thediversity of ANME microbes(mcrA gene hosts)in three sampling push-cores from the marine cold seep.A total of 372516Samplicon sequence variants(ASVs)of the mcrA gene hosts were detected,and classiﬁed into 78 genera across 23 *** all samples,the dominant phyla with high relative abundance(>10%)were the well-known Euryarchaeota,and somebacterial phyla such as Campylobacterota,Proteobacteria,and Chloroﬂexi;however,the speciﬁcity of these associations wasnot veriﬁ*** addition,the compositions of the mcrA gene hosts were signiﬁcantly different in different layers,where thearchaeal hosts increased with the depths of sediments,indicating the carriers of AOM were divergent in ***,the consensus phylogenetic trees of the mcrA gene and the 16S rRNA gene showed congruence in archaea not in bacteria,suggesting the horizontal transfer of the mcrA gene may occur among host ***,some bacterial metagenomeswere found to contain the mcrA gene as well as other genes that encode enzymes in the AOM pathway,which prospectivelypropose the existence of ANME *** study describes improvements for a potential method for studying the diversityof uncultured functional microbes and broadens our understanding of the diversity of ANMEs.

关键词： anaerobic oxidation of methane cold seep epicPCR mcrA gene

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Structural overview and perspectives of the nuclear receptors,a major family as the direct targets for small-molecule drugs

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生物化学与生物物理学报（英文版） 2022年第1期54卷 12-24页

作者： Fengwei Li Chun Song Youming Zhang Dalei Wu Helmholtz International Lab State Key Laboratory of Microbial TechnologyShandong UniversityQingdao 266237China

The nuclear receptors(NRs)are an evolutionarily related family of transcription factors,which share certain common structural characteristics and regulate the expressions of various genes by recognizing different response *** play important roles in cell differentiation,proliferation,survival and apoptosis,rendering them indispensable in many physiological activities including growth and *** a result,dysfunctions of NRs are closely related to a variety of diseases,such as diabetes,obesity,infertility,inflammation,the Alzheimer's disease,cardiovascular diseases,prostate and breast ***,small-molecule drugs directly targeting NRs have been widely used in the treatment of above *** we summarize recent progress in the structural biology studies of NR family *** with the dozens of structures of isolated DNA-binding domains(DBDs)and the striking more than a thousand of structures of isolated ligand-binding domains(LBDs)accumulated in the Protein Data Bank(PDB)over thirty years,by now there are only a small number of multi-domain NR complex structures,which reveal the integration of different NR domains capable of the allosteric signal transduction,or the detailed interactions between NR and various coregulator *** the other hand,the structural information about several orphan NRs is still totally unavailable,hindering the further understanding of their *** fast development of new technologies in structural biology will certainly help us gain more comprehensive information of NR structures,inspiring the discovery of novel NR-targeting drugs with a new binding site beyond the classic LBD pockets and/or a new mechanism of action.

关键词： drug target nuclear receptor small-molecule drug structure

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Synergistic effects of cellobiose dehydrogenase and manganese-dependent peroxidases during lignin degradation

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Chinese Science Bulletin 2001年第23期46卷 1956-1962页

作者： HUANG Feng FANG Jing LU Xuemei GAO Peiji CHEN Jiaxiang State Key Laboratory of Microbial Technology Shandong UniversityJinan 250100China State Key Lab of Pulp and Paper Engineering South China University of TechnologyGuangzhou 510641China

The synergistic effects of cellobiose dehydro-genase (CDH) and manganese-dependent peroxidases (MnP) on the degradation of kraft pulp cellulolytic enzyme lignin (CEL) were investigated. Addition of CDH significantly increased the amount of water-soluble products reduced from CEL by MnP. CDH facilitated the reduction of the contents of methoxyl, carboxyl, phenolic hydroxyl and total hydroxyl groups of CEL by MnP. 1H-NMR analysis showed that addition of CDH also decreased further the amount of protons of CEL degraded by MnP. The results proved for the first time that CDH could promote degradation of lignin by MnP and suggest that CDH could not only promote degradation of cellulose but also is an important part of the lignin biodeg-radation system.

关键词： cellobiose dehydrogenase manganese-dependent per- oxidase lignin degradation.

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A Novel Method for Fabrication of a Glass-Electrode-Based Lipase Sensor

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Chinese Chemical Letters 2001年第5期12卷 453-456页

作者： Xi Rong HUANG Yue Zhong LI Guo Liang YANG Li Li LIU Yin Bo QU Wen Juan ZHANG State Key Lab of Microbial Technology of China Shandong UniversityJinan 250100 Key Lab for Colloid and Inferface Chemistry of the Education Ministry of China Shandong UniversityJinan 250100

Based on an unusual reversible sol-gel transition phenomenon. a novel method for the fabrication of a lipase electrode was developed. The response characteristics of the biosensor was studied by potentiometric technique using olive oil as substrate. After optimization, the lipase electrode demonstrated high activity and good stability.

关键词： Lipase microemulsion-based gel biosensor response characteristics.

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Establishment and improvement of genetic manipulation tools for Fusobacterium nucleatum

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Engineering Microbiology 2025年第1期5卷

作者： Guan, Zhiwei Wang, Hailong Feng, Qiang School of Life Science Qilu Normal University Shandong Jinan 250200 China Department of Human Microbiome Cheeloo College of Medicine School and Hospital of Stomatology Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases Shandong Jinan 250012 China State Key Laboratory of Microbial Technology Institute of Microbial Technology Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology Shandong University Shandong Qingdao 266237 China Shandong University-BOP Joint Oral Microbiome Laboratory Shandong Jinan 250012 China

An imbalance in oral microbial homeostasis is significantly associated with the onset and progression of several systemic diseases. Fusobacterium nucleatum, a ubiquitous periodontitis-causing bacterium in the oral cavity, is frequently detected in focal sites and contributes to the pathogenesis of many extraoral diseases, including cancers, cardiovascular diseases, and adverse pregnancy outcomes (APOs). F. nucleatum is one of the few oral anaerobes that can be cultured purely in vitro and is a ‘model species’ for studying the impact of oral health on systemic health. The establishment and development of genetic manipulation tools for F. nucleatum and the construction of pathogenic gene-disrupted strains are important strategies for studying the pathogenicity of F. nucleatum. Here, we review the establishment and development of the genetic manipulation systems for F. nucleatum and summarize the characteristics of various genetic manipulation tools, such as suicide plasmid-based systems for gene inactivation, replicable plasmid-based systems controlling gene expression, and transposon-based random mutagenesis systems. Notably, we summarize and analyze their applications in the study of the pathogenic mechanisms of F. nucleatum. We hope to provide reference information and ideas for future research on genetic manipulation tools and the pathogenic mechanisms of F. nucleatum and other Fusobacterium species. © 2025 The Author(s)

关键词： Crispr interference Fusobacterium nucleatum Gene inactivation Genetic manipulation tool Natural competence Restriction-modification system

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Current strategies and progress for targeting the"undruggable"transcription factors

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中国药理学报（英文版） 2022年第10期43卷 2474-2481页

作者： Jing-jing Zhuang Qian Liu Da-lei Wu Lu Tie Marine College Shandong UniversityWeihai 264209China Helmholtz International Lab State Key Laboratory of Microbial TechnologyShandong UniversityQingdao 266237China Department of Pharmacology School of Basic Medical SciencesPeking University and Beijing Key Laboratory of Tumor Systems BiologyPeking UniversityBeijing 100191China Helmholtz International Lab State Key Laboratory of Microbial TechnologyShandong UniversityQingdao 266237China

Transcription factors(TFs)specifically bind to DNA,recruit cofactor proteins and modulate target gene expression,rendering them essential roles in the regulation of numerous biological ***,mutated or dysregulated TFs are involved in a variety of human *** multiple signaling pathways ultimately converge at TFs,targeting these TFs directly may prove to be more specific and cause fewer side effects,than targeting the upfront conventional targets in these *** these features together endue TFs with great potential and high selectivity as therapeutic drug ***,TFs have been historically considered"undruggable",mainly due to their lack of structural information,especially about the appropriate ligand-binding sites and protein-protein interactions,leading to relatively limited choices in the TF-targeting drug *** this review,we summarize the recent progress of TF-targeting drugs and highlight certain strategies used for targeting TFs,with a number of representative drugs that have been approved or in the clinical trials as *** approaches in targeting TFs directly or indirectly have been *** direct strategies include aiming at defined binding pockets,proteolysis-targeting chimaera(PROTAC),and mutant protein *** contrast,the indirect ones comprise inhibition of protein-protein interactions between TF and other proteins,blockade of TF expression,targeting the post-translational modifications,and targeting the TF-DNA *** more comprehensive structural information about TFs revealed by the powerful cryo-electron microscopy technology and predicted by machine-learning algorithms,plus more efficient compound screening platforms and a deeper understanding of TF-disease relationships,the development of TF-targeting drugs will certainly be accelerated in the near future.

关键词： transcription factor drug discovery undruggable PROTAC protein-protein interaction post-translational modification

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Function of the iron-binding chelator produced by Coriolus versicolor in lignin biodegradation

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Science China(Life Sciences) 2008年第3期51卷 214-221页

作者： WANG Lu1, YAN WenChao1, CHEN JiaChuan2, HUANG Feng1,2 & GAO PeiJi1 1 state key laboratory of microbial technology, Shandong University, Jinan 250100, China 2 Shandong key lab of Pulp and Paper Engineering, Shandong Institute of Light Industry, Jinan 250100, China State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China Shandong Key Lab of Pulp Paper Engineering Shandong Institute of Light Industry Jinan 250100 China

An ultrafiltered low-molecular-weight preparation of chelating compounds was isolated from a wood-containing culture of the white-rot basidiomycete Coriolus versicolor. This preparation could chelate Fe3+ and reduce Fe3+ to Fe2+, demonstrating that the substance may serve as a ferric chelator, oxygen-reducing agent, and redox-cycling molecule, which would include functioning as the electron transport carrier in Fenton reaction. Lignin was treated with the iron-binding chelator and the changes in structure were investigated by 1H-NMR, 13C-NMR, difference spectrum caused by ionization under alkaline conditions and nitrobenzene oxidation. The results indicated that the iron-binding chelator could destroy the β-O-4 bonds in etherified lignin units and insert phenolic hydroxyl groups. The low-molecular-weight chelator secreted by C. versicolor resulted in new phenolic substructures in the lignin polymer, making it susceptible to attack by laccase or manganese peroxidase. Thus, the synergic action of the iron-binding chelator and the lignocellulolytic enzymes made the substrate more acces- sible to degradation.

关键词： Coriolus versicolor lignin degradation iron binding chelator

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Dammarane-type triterpenoid saponins isolated from Gynostemma pentaphyllum ameliorate liver fibrosis via agonizing PP2Cαand inhibiting deposition of extracellular matrix

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Chinese Journal of Natural Medicines 2023年第8期21卷 599-609页

作者： LIU Yue YANG Yating WANG Hanghang LI Han LV Qi WANG Xiachang WU Dalei HU Lihong ZHANG Yinan Jiangsu Key Laboratory for Functional Substances of Chinese Medicine School of PharmacyNanjing University of Chinese MedicineNanjing 210023China Helmholtz International Lab State Key Laboratory of Microbial TechnologyShandong UniversityQingdao 266237China

Gypenosides,structurally analogous to ginsenosides and derived from a sustainable source,are recognized as the principal active compounds found in Gynostemma pentaphyllum,a Chinese medicinal plant used in the treatment of the metabolic *** bioactive tracking isolation of the plants collected from different regions across China,we obtained four new gypenosides(1−4),together with nine known gypenosides(5−13),from the methanol extract of the *** structures of new gypenosides were elucidated by one-dimensional(1D)and two-dimensional(2D)nuclear magnetic resonance(NMR)spectra,complemented by chemical degradation *** comprehensive evaluation involving COL1A1 promoter assays and PP2Cαactivity assays,we established a definitive structure-activity relationship for these dammarane-type triterpenoids,affirming the indispensability of the C-3 saccharide chain and C-17 lactone ring in effectively impeding extracellular matrix(ECM)deposition within hepatic stellate *** in vivo study on the CCl4-induced liver damage mouse model corroborated that compound 5 significantly ameliorated the process of hepatic fibrosis by oral *** results underscore the potential of dammarane-type triterpenoids as prospective antifibrotic leads and highlight their prevalence as key molecular frameworks in the therapeutic intervention of chronic hepatic disorders.

关键词： Dammarane-type triterpenoid Gypenoside Liver fibrosis Extracellular matrix

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Rearranged 19-nor-7,8-seco-labdane diterpenoids and Diels-Alder cycloadducts from the Chinese liverwort Pallavicinia ambigua:Structural elucidation,photoinduced rearrangement,and cytotoxic activity

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Chinese Chemical Letters 2024年第3期35卷 415-418页

作者： Chunyang Zhang Yuelan Li Zhaojun Chu Shuangzhi Yuan Yanan Qiao Jiaozhen Zhang Lin Li Yueqing Zhang Ruifeng Tian Yajie Tang Hongxiang Lou Department of Natural Products Chemistry Key Lab of Chemical Biology(MOE)School of Pharmaceutical SciencesShandong UniversityJi'nan 250012China State Key Laboratory of Microbial Technology Shandong UniversityQingdao 266237China

Two distinctive rearranged 19-nor-7,8-seco-labdane diterpenoids(1 and 2)with a novel tetracyclo[5.2.1.0^(2,5.)0^(4,10)]decane skeleton,a derivative of the open tetrahydrofuran ring(7),three dimeric compounds(8-10),and four revised homologs(3-6)were obtained from Chinese liverwort Pallavicinia *** structures were identified via combined analysis of their spectroscopic data,single-crystal X-ray diffraction patterns,and ECD *** light-driven conversion of compound 5 to compounds 1-4 demonstrated that photochemically induced postmodification involved in biosynthesis is an important way to diversify natural structures.A preliminary cytotoxicity assay revealed that compound 5 showed significant inhibition in the human prostate cancer(PC-3)cell line via an apoptotic pathway.

关键词： Liverwort Pallavicinia ambigua 19-nor-7 8-seco-labdan diterpenoid Photoinduced rearrangement Cytotoxic activity

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Increase Renaturation Yield of Reteplase Using the Recombinant Human Protein Disulfide Isomerase

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High technology Letters 2004年第1期10卷 49-51页

作者：赵友春 Wang Ge Kong Yang WANG Yanbing Zhang Changkai Chen Chao Liang Bufeng State Key Lab. of Microbial Technology Shandong University Jinan 250100 P.R. China Department of Science & Technology of Shandong Province Jinan 250011 P.R.China Shandong Younglong Biotechnology Co. Jinan 250100 P.R. China State Key Lab. of Microbial Technology Shandong University Jinan 250100 P.R. China

Reteplase, the recombinant type of novel tissue plasminogen activator (t-PA) variant, is a promising thrombolytics in clinics. Expressed in the form of an inclusion body, reteplase consists of about 40 % of the total intracellular proteins of Escherichia coli. The recombinant human protein disulfide isomerase (rhPDI) is used to increase the chance for the correct matching of the 18 hydrosulfide groups of the reteplase molecule in the renaturation process and it increase is the reteplase renaturation yield from 1%～2% to 15%～20% with a the purity aboue 99% and the specific activity of 5(105 IU/mg is reached. This novel method can reduce significantly the cost of production.

关键词：人体组织血浆酶原催化剂硫蛋白异构酶重建复活产量心脑血管疾病溶血栓剂

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