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Cobalamin-dependent radical S-adenosyl-L-methionine protein functions with a partner to successively methylate tricyclic indole alkaloid for chuangxinmycin maturation and derivatization

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Science China Chemistry 2025年第1期68卷 308-316页

作者： Sili Wang Jiancheng Huang Yanan Du Wei Huang Yufeng Xue Xiaokun Xu Guannan Zhong Yuanyuan Shi Bin Hong Xiaoying Bian Wen Liu State key laboratory of Chemical Biology Shanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200032China State key laboratory of microbial Technology Shandong UniversityQingdao 266237China National Health Commission(NHC)key laboratory of biotechnology for microbial Drugs Institute of Medicinal BiotechnologyChinese Academy of Medical Science&Peking Union Medical CollegeBeijing 100050China

Cobalamin(Cbl)-dependent radical S-adenosyl-L-methionine(SAM)proteins constitute the largest collection of the radical SAM superfamily that has hundreds of thousands of individual *** of these proteins are involved in the biosynthesis of pharmaceutically important natural products to catalyze chemically demanding *** the biosynthetic pathway of chuangxinmycin(CXM),a unique indole alkaloid antibiotic with potent anti-infective activity,functionalization of the characteristic thiopyrano[4,3,2-cd]indole scaffold by regio-and stereoselective C3-methylation is believed to rely on a Cbl-dependent radical process,which,however,remained to be reconstituted *** here report the dissection of this enzymatic process,which requires the incorporation of Cxm8,a Cbl-dependent radical SAM protein,with Cxm9,a DUF5825family protein that shares no homology to any proteins of known ***8 and Cxm9 function together by forming an unexpected heterodimeric complex that selectively catalyzes C3-methylation of the tricyclic indole-S-hetero ring system in a successive manner,achieving CXM and a recently identified,C3-dimethylated *** biochemical characterization,isotope labeling,structural simulation and bioinformatics analysis rationalized the catalysis of the Cxm8/Cxm9 complex and particularly the necessity of the DUF5825 protein for C3-methylase *** is the first example that a Cbl-dependent protein acts with a partner to exhibit radical SAM activity.

关键词： cbl-dependent radical SAM protein biosynthesis chuangxinmycin stereoselective methylation

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Intestinal Flatulence in Pampus argenteus:Changes in Gut Microbiota

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Journal of Ocean University of China 2025年第1期24卷 182-194页

作者： NIE Wenhao ZHANG Man ZHANG Youyi LI Yuanbo XU Shanliang HU Jiabao WANG Yajun YAN Xiaojun key laboratory of Applied Marine biotechnology Ministry of EducationNingbo UniversityNingbo 315832China key laboratory of Marine biotechnology of Zhejiang Province Ningbo UniversityNingbo 315832China College of Marine Sciences Ningbo UniversityNingbo 315832China

Pampus argenteus is a commercially valuable species in many *** artificial cultivation has been impacted by intestinal flatulence,leading to increased ***,the role of gut microbiota in this process remains ***,this study utilized high-throughput sequencing of 16S rRNA genes to investigate the gut microbiota in both flatulent and healthy ***.A total of 227571 high-quality and classifiable reads,representing 312 Amplicon Sequence Variants(ASVs),were *** emerged as the predominant phylum in all samples,with the flatulent group displaying the highest relative abundance(85.3%).microbial diversity was significantly greater in samples from water than those from *** analysis using Bray-Curtis distance via CPCoA revealed distinct gut microbiota compositions between the samples with flatulence and the healthy ***-occurrence network analysis demonstrated that the bacterial community in the flatulent group exhibited disorder due to the high abundance of *** predictive analysis(PICRUSt2)indicated that flatulence in *** was associated with impaired methane and lipid metabolism,potentially resulting in excessive methane synthesis utilizing hydrogen and acetic acid as substrates produced by Clostridium sensu stricto 1,Cetobacterium,and *** study holds significant implications for early diagnosis and prevention of intestinal flatulence through the regulation of gut microbiota.

关键词： Pampus argenteus gut microbiota 16S rRNA intestinal flatulence PICRUSt2

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Reconstruction characteristics of gut microbiota from patients with type 1 diabetes affect the phenotypic reproducibility of glucose metabolism in mice

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Science China(Life Sciences) 2025年第1期68卷 176-188页

作者： Zhiyi Wang Mengxue Gong Yuanyuan Fang Huijuan Yuan Chenhong Zhang State key laboratory of microbial Metabolism School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Department of Endocrinology Henan Provincial People’s HospitalPeople’s Hospital of Zhengzhou UniversityZhengzhou 450003China

The human microbiota-associated(HMA)mice model,especially the germ-free(GF)-humanized mice,has been widely used to probe the causal relationships between gut microbiota and human diseases such as type 1 diabetes(T1D).However,most studies have not clarified the extent to which the reconstruction of the human donor microbiota in recipient mice correlates with corresponding phenotypic *** this study,we transplanted fecal microbiota from five patients with T1D and four healthy people into GF mice,and microbiota from each donor were transplanted into 10 *** with similar microbiota structure to the donor exhibited better phenotypic *** characteristics of the microbial community assembly of donors also influenced the phenotypic reproducibility in mice,and individuals with a higher proportion of stochastic processes showed more severe *** enriched in patients with T1D had a stronger colonization potential in mice with impaired glucose metabolism,and microbiota functional features related to T1D were better reproduced in these *** indicates that assembly traits and colonization efficacy of microbiota influence phenotypic reproducibility in GF-humanized *** findings provide important insights for using HMA mice models to explore links between gut microbiota and human diseases.

关键词： gut microbiome human microbiota-associated animal model type 1 diabetes

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Deciphering fungal metabolon coupling tandem inverse-electrondemand Diels-Alder reaction and semipinacol rearrangement for the biosynthesis of spiro polycyclic alkaloids

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Science China Chemistry 2025年第1期68卷 288-296页

作者： Shuai Liu Wen-Qiang Xu Ying-Tong Di Man-Cheng Tang Ding-Kang Chen Ming-Ming Cao Yao-Wen Chang Hong-Yu Tang Chun-Mao Yuan Jun-Bo Yang Zhi-Li Zuo Han Guo Zi-Fei Xu Ying Zeng Yun-Dong Wu Xiao-Jiang Hao key laboratory of Phytochemistry and Natural Medicines(Chinese Academy of Sciences) Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Lab of Computational Chemistry and Drug Design State Key Laboratory of Chemical OncogenomicsPeking University Shenzhen Graduate SchoolShenzhen 518055China Shenzhen Bay laboratory Shenzhen 518055China University of Chinese Academy of Sciences Beijing 100049China State key laboratory of microbial Metabolism School of Life Sciences&BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China State key laboratory of Functions and Applications of Medicinal Plants Guizhou Medical UniversityGuiyang 550014China Molecular Biology Experimental Center Germplasm Bank of Wild Species in Southwest ChinaKunming Institute of BotanyChinese Academy of SciencesKunming 650201China Yunnan key laboratory for Wild Plant Resources Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Research Unit of Chemical Biology of Natural Anti-Virus Products Chinese Academy of Medical SciencesBeijing 100730China

In the intricate process of natural product biosynthesis,a metabolon can enhance metabolic flux by associating sequential enzymes.A fungal metabolon,comprising of flavin-dependent monooxygenase Spe F and P450 monooxygenase Spe G,is identified in the biosynthesis of spiro polycyclic alkaloids(+)-notoamide B and its diastereomer(+)-versicolamide *** notoamide E as a substance,Spe F/Spe G metabolon can control the stereoselectivity of its 2,3-epoxidation,followed by hydrogen atom ion at C-17 to generate reactive epoxide tau-m A with dienyl iminium ***,(+)-notoamide B and(+)-versicolamide B are produced via tandem nonenzymatic inverse-electron-demand Diels-Alder reaction and semipinacol *** provides the first example of metabolon in the biosynthesis of spiro-prenylated indole alkaloids.

关键词： metabolon Diels-Alder reaction semipinacol rearrangement biosynthesis notoamides spiro polycyclic alkaloids

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Predicting Lactobacillus delbrueckii ***-Streptococcus thermophilus interactions based on a highly accurate semi-supervised learning method

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Science China(Life Sciences) 2025年第2期68卷 558-574页

作者： Shujuan Yang Mei Bai Weichi Liu Weicheng Li Zhi Zhong Lai-Yu Kwok Gaifang Dong Zhihong Sun key laboratory of Dairy biotechnology and Engineering Ministry of EducationInner Mongolia Agricultural UniversityHohhot 010018China key laboratory of Dairy Products Processing Ministry of Agriculture and Rural AffairsInner Mongolia Agricultural UniversityHohhot 010018China Inner Mongolia key laboratory of Dairy biotechnology and Engineering Inner Mongolia Agricultural UniversityHohhot 010018China Collaborative Innovative Center for Lactic Acid Bacteria and Fermented Dairy Products Ministry of EducationInner Mongolia Agricultural UniversityHohhot 010018China College of Computer and Information Engineering Inner Mongolia Agricultural UniversityHohhot 010018China Inner Mongolia Autonomous Region key laboratory of Big Data Research and Application of Agriculture and Animal Husbandry Hohhot 010018China

Lactobacillus delbrueckii ***(***)and Streptococcus thermophilus(***)are commonly used starters in milk *** experiments revealed that *** interactions(Lb St I)substantially impact dairy product quality and *** biological humidity experiments are time-consuming and labor-intensive in screening interaction combinations,an artificial intelligence-based method for screening interactive starter combinations is ***,in the current research on artificial intelligence based interaction prediction in the field of bioinformatics,most successful models adopt supervised learning methods,and there is a lack of research on interaction prediction with only a small number of labeled ***,this study aimed to develop a semi-supervised learning framework for predicting Lb St I using genomic data from 362 isolates(181per species).The framework consisted of a two-part model:a co-clustering prediction model(based on the Kyoto Encyclopedia of Genes and Genomes(KEGG)dataset)and a Laplacian regularized least squares prediction model(based on K-mer analysis and gene composition of all isolates datasets).To enhance accuracy,we integrated the separate outcomes produced by each component of the two-part model to generate the ultimate Lb St I prediction results,which were verified through milk fermentation *** through milk fermentation experiments confirmed a high precision rate of 85%(17/20;validated with 20 randomly selected combinations of expected interacting isolates).Our data suggest that the biosynthetic pathways of cysteine,riboflavin,teichoic acid,and exopolysaccharides,as well as the ATP-binding cassette transport systems,contribute to the mutualistic relationship between these starter bacteria during milk ***,this finding requires further experimental *** presented model and data are valuable resources for academics an

关键词： Lactobacillus delbrueckii subsp.bulgaricus and Streptococcus thermophilus interaction prediction semi-supervised learning dairy starter artificial intelligence milk fermentation

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Impact of residual antibiotics on microbial decomposition of livestock manures in Eutric Regosol:Implications for sustainable nutrient recycling and soil carbon sequestration

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Journal of Environmental Sciences 2025年第1期147卷 498-511页

作者： Linfa Fang Prakash Lakshmanan Xiaoxuan Su Yujia Shi Zheng Chen Yu Zhang Wei Sun Junxi Wu Ran Xiao Xinping Chen Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin College of Resources and EnvironmentSouthwest UniversityChongqing 400715China key laboratory of Sugarcane biotechnology and Genetic Improvement(Guangxi) Ministry of Agriculture and Rural AffairsGuangxi Key Laboratory of Sugarcane Genetic ImprovementSugarcane Research InstituteGuangxi Academy of Agricultural SciencesNanning 530007China Queensland Alliance for Agriculture and Food Innovation University of QueenslandSt Lucia 4067QLDAustralia key laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and National Resources ResearchChinese Academy of SciencesBeijing 100101China

The land application of livestock manure has been widely acknowledged as a beneficial approach for nutrient recycling and environmental ***,the impact of residual antibiotics,a common contaminant of manure,on the degradation of organic compounds and nutrient release in Eutric Regosol is not well ***,we studied,how oxytetracycline(OTC)and ciprofloxacin(CIP)affect the decomposition,microbial community structure,extracellular enzyme activities and nutrient release from cattle and pig manure using litterbag incubation *** showed that OTC and CIP greatly inhibited livestock manure decomposition,causing a decreased rate of carbon(28%-87%),nitrogen(15%-44%)and phosphorus(26%-43%)*** relative abundance of gramnegative(G-)bacteria was reduced by 4.0%-13%while fungi increased by 7.0%-71%during a 28-day incubation ***-occurrence network analysis showed that antibiotic exposure disrupted microbial interactions,particularly among G-bacteria,G+bacteria,and *** changes in microbial community structure and function resulted in decreased activity of urease,β-1,4-N-acetyl-glucosaminidase,alkaline protease,chitinase,and catalase,causing reduced decomposition and nutrient release in cattle and pig *** findings advance our understanding of decomposition and nutrient recycling from manure-contaminated antibiotics,which will help facilitate sustainable agricultural production and soil carbon sequestration.

关键词： Residual antibiotics Livestock manure decomposition microbial community Co-occurrence network Enzyme activities

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Mixture of Bacillus Amyloliquefaciens and Bacillus Pumilus Modulates Community Structures of Rice Rhizosphere Soil to Suppress Rice Seedling Blight

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Rice science 2025年第1期32卷 118-130,I0067-I0070页

作者： JIANG Nan QIU Jiehua TIAN Dagang SHI Huanbin LIU Zhiquan WEN Hui XIE Shuwei CHEN Huizhe WU Meng KOU Yanjun State key laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 311400China biotechnology Research Institute Fujian Academy of Agricultural SciencesFuzhou 350003China State key laboratory of Soil and Sustainable Agriculture the Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China

Rice seedling blight,caused by various fungi,including Fusarium oxysporum,poses a severe threat to rice *** awareness grows regarding the environmental and safety hazards associated with the application of fungicides for managing rice seedling blight,there has been a shift in focus towards biological control *** this study,we isolated biocontrol bacteria from paddy fields that significantly inhibited the growth of *** in vitro and identified the strains as Bacillus amyloliquefaciens T40 and Bacillus pumilus ***,our findings indicated that the combined application of these Bacillus strains in soil was more effective in reducing the incidence of rice seedling blight than their individual *** of 16S and internal transcribed spacer rRNA gene sequencing data revealed that the mixture of the T40 and T208 strains exhibited the lowest average clustering coefficients,which were negatively correlated with the biomass of ***-inoculated rice ***,this mixture led to higher stochastic assembly(average|βNTI|microbial community structures,enhances microbial network stability,and boosts the resistance against rice seedling *** study supports the development and utilization of biological resources for crop protection.

关键词： application strategy disease control disease resistance microbial community structure microbial community assembly process Oryza sativa

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Photo-controllable multiple and orthogonal regulation of gene expression by chemically modified oligonucleotides

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Science China Chemistry 2025年第2期68卷 694-704页

作者： Yang Wang Qiu-Long Zhang Yan Liu Liang-Liang Wang Chao-Qun Wu Ming Shao Xiwen Xing Juan Du Liang Xu key laboratory of Tropical Biological Resources of Ministry of Education and One Health Institute School of Pharmaceutical SciencesHainan UniversityHaikou 570228China Central laboratory Department of The Second Affiliated Hospital School of MedicineThe Chinese University of Hong KongShenzhen&Longgang District People’s Hospital of ShenzhenShenzhen 518172China MOE key laboratory of Bioinorganic and Synthetic Chemistry School of ChemistrySun Yat-sen UniversityGuangzhou 510275China Department of biotechnology College of Life Science and TechnologyJinan University InstitutionGuangzhou 510632China School of Pharmacy and Medical Technology Putian UniversityPutian 351100China

Gene expression must be precisely regulated in cells and functional nucleic acids are the most widely utilized tools for gene *** of how these nucleic acid tools work in the cellular environment can precisely manipulate gene expression through a non-invasive *** we report a methodology on multiplex photocontrol of functional nucleic acids to achieve totally temporal and orthogonal regulation of gene expression in living *** select two functional nucleic acid systems as examples,DNAzyme and CRISPR/Cas9,and demonstrate the power of light control for precise gene manipulation by rational design of chemically modified oligonucleotides through introduction of two photocleavable *** the previous modulation of functional nucleic acids by simply activating or deactivating,we successfully achieve versatile controlling patterns using light as the governing *** design represents a generalized pathway towards the photo-controllable functional nucleic acids,which greatly enriches the toolbox for optogenetic studies.

关键词： functional nucleic acids optogenetics modified oligonucleotides gene technology

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Dietary supplementation with citrus peel extract in transition period improves rumen microbial composition and ameliorates energy metabolism and lactation performance of dairy cows

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Journal of Animal Science and biotechnology 2025年第1期16卷 441-454页

作者： Lingxue Ju Qi Shao Zhiyuan Fang Erminio Trevisi Meng Chen Yuxiang Song Wenwen Gao Lin Lei Xinwei Li Guowen Liu Xiliang Du State key laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Key Laboratory for Zoonosis Research of the Ministry of EducationInstitute of ZoonosisCollege of Veterinary MedicineJilin UniversityChangchun 130062China Department of Animal Sciences Food and NutritionFaculty of AgricultureFood and Environmental ScienceUniversitàCattolica del Sacro CuorePiacenza 29122Italy

Background During the transition period,excessive negative energy balance(NEB)lead to metabolic disorders and reduced milk *** microbes are responsible for resolving plant material and producing volatile fatty acids(VFA),which are the primary energy source for *** this study,we aimed to investigate the effect of citrus peel extract(CPE)supplementation on rumen microbiota composition,energy metabolism and milk performance of peri-partum dairy *** Dairy cows were fed either a basal diet(CON group)or the same basal diet supplemented with CPE via intragastric administration(4 g/d,CPE group)for 6 weeks(3 weeks before and 3 weeks after calving;n=15 per group).Samples of serum,milk,rumen fluid,adipose tissue,and liver were collected to assess the effects of CPE on rumen microbiota composition,rumen fermentation parameters,milk performance,and energy metabolic status of dairy *** CPE supplementation led to an increase in milk yield,milk protein and lactose contents,and serum glucose levels,while reduced serum concentrations of non-esterified fatty acid,β-hydroxybutyric acid,insulin,aspartate aminotransferase,alanine aminotransferase,and haptoglobin during the first month of *** supplemen-tation also increased the content of ruminal *** to the CON group,the abundance of Prevotellaceae,Methanobacteriaceae,Bacteroidales_RF16_group,and Selenomonadaceae was found increased,while the abun-dance of Oscillospiraceae,F082,Ruminococcaceae,Christensenellaceae,Muribaculaceae UCG-011,Saccharimona-daceae,Hungateiclostridiaceae,and Spirochaetaceae in the CPE group was found *** adipose tissue,CPE supplementation decreased lipolysis,and inflammatory response,while increased insulin *** the liver,CPE supplementation decreased lipid accumulation,increased insulin sensitivity,and upregulated expression of genes involved in *** Our findings suggest that CPE supplementation during the peripartum period

关键词： Adipose tissue Citrus peel extract Energy metabolism Liver Rumen microbiota

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Disentangling microbial coupled fillers mechanisms for the permeable layer optimization process in multi-soil-layering systems

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Journal of Environmental Sciences 2025年第1期147卷 538-549页

作者： Daxin Sun Chuanping Feng Yongheng Zhan Bingbing Deng Duoduo Mei Nan Chen Weiwu Hu School of Water Resources and Environment MOE Key Laboratory of Groundwater Circulation and Environmental EvolutionChina University of Geosciences(Beijing)Beijing 100083China Journal Center China University of Geosciences(Beijing)Beijing 100083China

Themulti-soil-layering(MSL)systems is an emerging solution for environmentally-friendly and cost-effective treatment of decentralized rural domestic ***,the role of the seemingly simple permeable layer has been overlooked,potentially holding the breakthroughs or directions to addressing suboptimal nitrogen removal performance in MSL *** this paper,the mechanism among diverse substrates(zeolite,green zeolite and biological ceramsite)coupled microorganisms in different systems(activated bacterial powder and activated sludge)for rural domestic wastewater purification was *** removal efficiencies performed by zeolite coupled with microorganisms within 3 days were 93.8%for COD,97.1%for TP,and 98.8%for NH_(4)^(+)-***,activated sludge showed better nitrification and comprehensive performance than specialized nitrifying bacteria *** attained an impressive 89.4%NH4+-N desorption efficiency,with a substantive fraction of NH_(4)^(+)-N manifesting as exchanged ***-throughput 16S rRNA gene sequencing revealed that aerobic and parthenogenetic anaerobic bacteria dominated the reactor,with anaerobic bacteria conspicuously *** the heterotrophic nitrificationaerobic denitrification(HN-AD)process was significant,with the presence of denitrifying phosphorus-accumulating organisms(DPAOs)for simultaneous nitrogen and phosphorus *** study not only raises awareness about the importance of the permeable layer and enhances comprehension of the HN-AD mechanism in MSL systems,but also provides valuable insights for optimizing MSL system construction,operation,and rural domestic wastewater treatment.

关键词： Rural domestic wastewater Multi-soil-layering(MSL)system Heterotrophic nitrification-aerobic denitrification(HN-AD) Nitrogen and phosphorus removal microbial evolution

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