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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu Michael H Perlin David Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale Paweł Łabaj Nicolás Rascovan Nur Hazlin Hazrin-Chong Soojin Jang Haruo Suzuki Marina Nieto-Caballero Bharath Prithiviraj Patrick K H Lee Agnieszka Chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher E Mason Tieliu Shi Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Performance and Cloud Computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen Research Center Bogotá110311Colombia Applied Environmental Metagenomics and Infectious Diseases Research(AEMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska Centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of Environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of Energy and Environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban *** address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based *** findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical *** also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel *** study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment

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Marine Life Science & Technology 2024年第1期6卷 126-142页

作者： Elisa Banchi Erwan Corre Paola Del Negro Mauro Celussi Francesca Malfatti National Institute of Oceanography and Applied Geophysics OGS TriesteItaly FR2424 Station Biologique de RoscoffPlateforme ABiMS(Analysis and Bioinformatics for Marine Science)Sorbonne Universite CNRS29680 RoscoffFrance Department of Life Sciences University of TriesteTriesteItaly

Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from‘omics’***,we characterized metagenome-assembled-genomes(MAGs)from the surface sediment microbes of the Venice Lagoon(northern Adriatic Sea)in distinct sub-basins exposed to various natural and anthropogenic *** were explored for biodiversity,major marine metabolic processes,anthropogenic activity-related functions,adaptations at the microscale,and biosynthetic gene *** from 126 MAGs,a non-redundant dataset of 58 was compiled,the majority of which(35)belonged to(Alpha-and Gamma-)*** the broad microbial metabolic repertoire(including C,N,and S metabolisms)the potential to live without oxygen emerged as one of the most important *** was also found as a successful *** analysis showed that different MAGs encoded the same metabolic patterns(e.g.,C fixation,sulfate oxidation)thus suggesting metabolic *** and toxic compounds resistance genes were coupled,a condition that could promote the spreading of these genetic *** showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular *** results highlighted that bacteria living in an impacted environment,such as the surface sediments of the Venice Lagoon,may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites,promoting ecosystem resilience and stability toward environmental pressures.

关键词： Antibiotic resistance PAHs biosynthetic gene clusters Microscale Mobilome Resistome

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Targeted genome mining for microbial antitumor agents acting through DNA intercalation

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Synthetic and Systems Biotechnology 2023年第3期8卷 520-526页

作者： Zhijie Zhao Guiyun Zhao Yi Chai Wei Li Kaihui Song Wenbin Zhao Hairong Li Miaolian Wu Zhan Zhou Yi-Ling Du The Fourth Affiliated Hospital and Department of Microbiology School of MedicineZhejiang UniversityHangzhou310058China Yong Loo Lin School of Medicine National University of SingaporeSingapore Innovation Institute for Artificial Intelligence in Medicine College of Pharmaceutical SciencesZhejiang UniversityHangzhou310058China The Fourth Affiliated Hospital School of MedicineZhejiang UniversityYiwu322000China Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering Hangzhou310058China

Microbial natural products have been one of the most important sources for drug *** the current postgenomic era,sequence-driven approaches for natural product discovery are becoming increasingly ***,we develop an effective genome mining strategy for the targeted discovery of microbial metabolites with antitumor *** method employs uvrA-like genes as genetic markers,which have been identified in the biosynthetic gene clusters(BGCs)of several chemotherapeutic drugs of microbial origin and confer self-resistance to the corresponding *** systematic genomic analysis of gifted actinobacteria genera,identification of uvrA-like gene-containing BGCs,and targeted isolation of products from a BGC prioritized for metabolic analysis,we identified a new tetracycline-type DNA intercalator *** results thus provide a new genome mining strategy for the efficient discovery of antitumor agents acting through DNA intercalation.

关键词： Genome mining Microbial natural product DNA intercalator UvrA-like protein biosynthetic gene clusters Tetracycline

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Oryzalexin S biosynthesis:a cross-stitched disappearing pathway

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aBIOTECH 2023年第1期4卷 1-7页

作者： Le Zhao Richard Oyagbenro Yiling Feng Meimei Xu Reuben J.Peters Roy J.Carver Department of Biochemistry Biophysics and Molecular BiologyIowa State UniversityAmesIA50011USA

Rice produces many diterpenoid phytoalexins and,reflecting the importance of these natural products in this important cereal crop plant,its genome contains three biosynthetic gene clusters(BGCs)for such *** chromosome 4 BGC(c4BGC)is largely associated with momilactone production,in part due to the presence of the initiating syn-copalyl diphosphate(CPP)synthase gene(OsCPS4).Oryzalexin S is also derived from ***,the relevant subsequently acting syn-stemarene synthase gene(OsKSL8)is not located in the *** of oryzalexin S further requires hydroxylation at carbons 2 and 19(C2 and C19),presumably catalyzed by cytochrome P450(CYP)*** it is reported the closely related CYP99A2 and CYP99A3,whose genes are also found in the c4BGC catalyze the necessary C19-hydroxylation,while the closely related CYP71Z21 and CYP71Z22,whose genes are found in the recently reported chromosome 7 BGC(c7BGC),catalyze subsequent hydroxylation at C2α.Thus,oryzalexin S biosynthesis utilizes two distinct BGCs,in a pathway cross-stitched together by ***,in contrast to the widely conserved c4BGC,the c7BGC is subspecies(ssp.)specific,being prevalent in *** and only rarely found in the other major ***,while the closely related syn-stemodene synthase OsKSL11 was originally considered to be distinct from OsKSL8,it has now been reported to be a *** derived allele at the same genetic ***,more detailed analysis indicates that OsKSL8(j)is being replaced by OsKSL11(OsKSL8i),suggesting introgression from *** to(sub)tropical japonica,with concurrent disappearance of oryzalexin S production.

关键词： biosynthetic gene clusters Phytoalexins Diterpenoids Rice evolution

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Coordinated regulation for nature products discovery and overproduction in Streptomyces

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Synthetic and Systems Biotechnology 2020年第2期5卷 49-58页

作者： Qun Zhou Shuqing Ning Yunzi Luo Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China Collaborative Innovation Center of Chemical Science and Engineering(Tianjin) Tianjin UniversityTianjin300072China

Streptomyces is an important treasure trove for natural products *** recent years,many scientists focused on the genetic modification and metabolic regulation of Streptomyces to obtain diverse bioactive compounds with high *** review summarized the commonly used regulatory strategies for natural products discovery and overproduction in Streptomyces from three main aspects,including regulator-related strategies,promoter engineering,as well as other strategies employing transposons,signal factors,or feedback *** is expected that the metabolic regulation network of Streptomyces will be elucidated more comprehensively to shed light on natural products research in the future.

关键词： gene expression regulation Natural products Streptomyces biosynthetic gene clusters

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Development of fungal cell factories for the production of secondary metabolites:Linking genomics and metabolism

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Synthetic and Systems Biotechnology 2017年第1期2卷 5-12页

作者： Jens Christian Nielsen Jens Nielsen Chalmers University of Technology Kemivagen 10Sweden

The genomic era has revolutionized research on secondary metabolites and bioinformatics methods have in recent years revived the antibiotic discovery process after decades with only few new active molecules being *** computational tools are driven by genomics and metabolomics analysis,and enables rapid identification of novel secondary *** translate this increased discovery rate into industrial exploitation,it is necessary to integrate secondary metabolite pathways in the metabolic engineering *** this review,we will describe the novel advances in discovery of secondary metabolites produced by filamentous fungi,highlight the utilization of genome-scale metabolic models(GEMs)in the design of fungal cell factories for the production of secondary metabolites and review strategies for optimizing secondary metabolite production through the construction of high yielding platform cell factories.

关键词： Secondary metabolism Fungi biosynthetic gene clusters Genome mining Metabolic modeling Cell factories

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Unlocking plant metabolic diversity: A (pan)- genomic view

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Plant Communications 2022年第2期3卷 112-120页

作者： Xuan Zhou Zhenhua Liu Joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Collaborative Innovation Center of Agri-Seeds School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China

Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life ***,unlocking this metabolic diversity is significantly impeded by the size,complexity,and abundant repetitive elements of typical plant *** genome sequencing becomes routine,we anticipate that links between metabolic diversity and genetic variation will be *** addition,an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi;gene clusters for various classes of compounds have also been found in plants,and many are associated with important agronomic *** present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic *** also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.

关键词： metabolic diversity gene and genome duplication biosynthetic gene clusters genomic structural variations pan-genomics

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Metabolic engineering of Streptomyces to enhance the synthesis of valuable natural products

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Engineering Microbiology 2022年第2期2卷 29-36页

作者： Zuwei Xu Lihao Ji Wenxiu Tang Liang Guo Cong Gao Xiulai Chen Jia Liu Guipeng Hu Liming Liu State Key Laboratory of Food Science and Technology Jiangnan UniversityWuxi 214122China School of Life Sciences and Health Engineering Jiangnan UniversityWuxi 214122China

The mycelial bacterium Streptomyces is a workhorse for producing natural products,serving as a key source of drugs and other valuable ***,its complicated life cycle,silent biosynthetic gene clusters(BGCs),and poorly characterized metabolic mechanisms limit efficient production of natural ***-fore,a metabolic engineering strategy,including traditional and emerging tools from different disciplines,was developed to further enhance natural product synthesis by ***,current trends in systems metabolic engineering,including tools and strategies,are ***,this review focuses on recent developments in the selection of methods for regulating the Streptomyces life cycle,strategies for the activation of silent gene clusters,and the exploration of regulatory mechanisms governing antibiotic ***,future challenges and prospects are discussed.

关键词： Streptomyces Natural products Metabolic engineering Life cycle biosynthetic gene clusters

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