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Eugenol targeting CrtM inhibits the biosynthesis of staphyloxanthin in Staphylococcus aureus

Food Science and Human Wellness 2024年第3期13卷 1368-1377页

作者： Jiang Chang Bo Chen Zeqian Du Bowen Zhao Jiahui Li Ziyi Li Kannappan Arunachalam Ting Shi Dongqing Wei Chunlei Shi MOST-USDA Joint Research Center for Food Safety School of Agriculture and BiologyState Key Laboratory of Microbial MetabolismShanghai Jiao Tong UniversityShanghai 200240China School of Life Sciences and biotechnology Shanghai Jiao Tong UniversityShanghai 200240China

Staphylococcus aureus is a serious foodborne pathogen threatening food safety and public *** the emergence of methicillin-resistant Staphylococcus aureus(MRSA)increased the difficulty of *** *** is a crucial virulence factor of *** staphyloxanthin production could help the host immune system counteract the invading *** *** this study,we first screened for staphyloxanthin inhibitors using a virtual screening *** outcome of the virtual screening method resulted in the identification of eugenol(300μg/mL),which significantly inhibits the staphyloxanthin production in *** ATCC 29213,*** Newman,MRSA ATCC 43300 and MRSA ATCC BAA1717by 84.2%,63.5%,68.1%,and 79.5%,*** outcome of the growth curve assay,field-emission scanning electron,and confocal laser scanning microscopy analyses confirmed that eugenol at the test concentration did not affect the morphology and growth of ***,the survival rate of *** ATCC 29213 and MRSA ATCC 43300 under H_(2)O_(2) pressure decreased to 51.9%and 45.5%in the presence of eugenol,*** quantitative RT-PCR and molecular simulation studies revealed that eugenol targets staphyloxanthin biosynthesis by downregulating the transcription of the crtM gene and inhibiting the activity of the CrtM *** together,we first determined that eugenol was a prominent compound for staphyloxanthin inhibitor to combat *** especially MRSA infections.

关键词： Staphylococcus aureus Staphyloxanthin Eugenol Virtual screening 4 4’-Diapophytoene synthase(CrtM)

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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 2024年

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 Sciences State Key Laboratory of microbial Technology Shandong University National Health Commission (NHC) Key Laboratory of biotechnology for microbial Drugs Institute of Medicinal BiotechnologyChinese Academy of Medical Science&Peking Union Medical College

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.

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Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39

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Marine Life Science & Technology 2024年第3期6卷 198-211页

作者： Wanyue Jiang Tongtong Lin Jiao Pan Caitlyn ERivera Clayton Tincher Yaohai Wang Yu Zhang Xiang Gao Yan Wang Ho‑Ching T.Tsui Malcolm E.Winkler Michael Lynch Hongan Long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Laboratory for Marine Biology and biotechnology Laoshan LaboratoryQingdao 266237China Department of Biology Indiana UniversityBloomingtonIN 47405USA School of Mathematics Science Ocean University of ChinaQingdao 266000China State Key Laboratory of microbial Technology Microbial Technology InstituteSchool of Life ScienceShandong UniversityQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA

Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic ***,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)*** rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T *** high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in *** line with this,*** D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among *** with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and *** lacks a stress response *** findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.

关键词： Neutral evolution Mutation spectrum Antibiotics DNA mismatch repair Oxidative damage repair

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Classical taxonomy,molecular phylogeny and genetic analysis of the genus Exitianus Ball,1929(Hemiptera:Cicadellidae:Deltocephalinae)from Egypt

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Zoological Systematics 2024年第2期49卷 143-157页

作者： Rabab M.El-Hady Ahmed F.El-Sayed Survey&Taxonomy Department Plant Protection Research InstituteAgriculture Research CentreGizaEgypt microbial Genetics Department Biotechnology Research InstituteNational Research CentreGizaEgypt Egypt Center for Research and Regenerative Medicine(ECRRM) CairoEgypt

Egyptian species of the leafhopper genus Exitianus Ball,1929,***(St?l,1855),***(Distant,1908),and *** Ross,1968 are ***,morphological descriptions,and a key for their identification are *** this study,we used molecular techniques to confirm morphological identification and detect phylogeny among the three Exitianus *** partial nucleotide sequences of the amplified products obtained were determined by Macrogen *** nucleotide sequences of 28S rDNA and COX genes of the EGY-ARC-9,EGY-ARC-4,and EGY-ARC-5 were determined by Macrogen Korea,blasted into BLAST at the National Center for biotechnology Information website(NCBI)and compared with those deposited in the GenBank DNA *** results represented the homology percentage between the partial sequences of the 28S rRNA and COX genes from each species and related species obtained from GenBank DNA *** morphological identifications of the three Exitianus species were confirmed by molecular characterization and sequencing of 28S rDNA and COX genes and identified as ***,***,and ***,their sequences of 28srDNA and COX genes were deposited in GenBank with an accession number(LC670610,LC670607,and OQ196105)for 28srDNA gene and(LC775357,LC775358,and LC775359)for the COX gene.

关键词： Auchenorrhyncha Chaismini taxonomic 28S rDNA phylogenetic

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Effects of dietary supplementation with tropical microfungi Mucor circinelloides and Trichoderma harzianum powder on growth performance,bacterial communities,and the biomass nutritional profile of white shrimp grow-out culture(Litopenaeus vannamei)

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Aquaculture and Fisheries 2024年第2期9卷 245-255页

作者： Robi Binur Salsabila Mutiara Kanti Muharam Tia Fahara Magdalena Lenny Situmorang I Nyoman Pugeg Aryantha Gede Suantika Department of Biology Faculty of Mathematics and Natural SciencesUniversitas PapuaJl.Gunung Salju AmbanManokwari98314Indonesia microbial biotechnology Research Group School of Life Sciences and TechnologyInstitut Teknologi BandungJl.Ganesha 10Bandung40132Indonesia Biosciences and biotechnology Research Center Institut Teknologi BandungJl.Ganesha 10Bandung40132Indonesia

Microfungi have been explored further as supplement constituents in shrimp culture due to their rich protein,lipid,essential amino acids,fatty acids,and various bioactive *** researchers have evaluated the effects of two microfungi powders(Mucor circinelloides and Trichoderma harzianum)as feed supplements on growth performance,bacterial communities,and the biomass nutritional profile of white shrimp(Litopenaeus vannamei).The results showed that commercial/artificial feed(Feng-Li)with supplementation microfungi powder had a different effect on white shrimp growth performance than control after 62 days of the grow-out *** with 1.5%*** powder(M-2)could improve the growth performance of white shrimp,especially the survival rate(81.33%),final body weight(5.21 g),and shrimp biomass(211.35 g).In contrast,supplementation with 1.5%*** powder(T-2)did not improve the growth performance of white shrimp compared to control(p>0.05).Furthermore,it also affected the profile of the bacterial community in culture water as well as in shrimp *** with both microfungi could reduce the total number of bacteria in culture water at the end of the experiment,where the lowest number was obtained in treatment T-2(3.9×10^(5)CFU/mL),followed by M-2(9.9×10^(5)CFU/mL)and control(4.4×10^(6)CFU/mL).In the culture water,20 isolates of culturable bacteria were found during the trial,with the dominant bacteria in M-2:Bacillus cereus,Bacillus velezensis,Gordonia polyisoprenivorans,T-2:Acinetobacter sp.,Gordonia polyisoprenivorans,Micrococcus *** on average well colour development(AWCD),the highest bacterial activity was in the M-2(0.297-0.707),followed by T-2(0.226-0.717)and control(0.094-0.694).The highest substrate group utilised in M-2 and T-2 were polymers(0.896 and 1.348)and control:amines(0.100).The highest Shannon diversity index was obtained in the M-2(2.508),followed by control(2.286)and the T-2(2.157).As many as

关键词： Microfungi Nutrition White shrimp Litopenaeus vannamei Grow-out Bacterial activity Probiotic bacteria

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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 2024年

作者： Zhiyi Wang Mengxue Gong Yuanyuan Fang Huijuan Yuan Chenhong Zhang State Key Laboratory of microbial Metabolism School of Life Sciences and Biotechnology Shanghai Jiao Tong University Department of Endocrinology Henan Provincial People's Hospital People's Hospital of Zhengzhou University

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 reproducibility. In 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 mice. Mice with similar microbiota structure to the donor exhibited better phenotypic reproducibility. The 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 disorders. Microbes 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 mice. This indicates that assembly traits and colonization efficacy of microbiota influence phenotypic reproducibility in GF-humanized mice. Our findings provide important insights for using HMA mice models to explore links between gut microbiota and human diseases.

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Rational Engineering of Secondary Metabolic Pathways in a Heterologous Host to Enable the Biosynthesis of Hibarimicin Derivatives with Enhanced Anti-Melanomic Activity

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Engineering 2024年第7期38卷 113-123页

作者： Xiangyang Liu Fei-Peng Zhao Tian Tian Wei-Chen Wang Zaizhou Liu Qiang Zhou Xian-Feng Hou Jing Wang Wenli Guo Shuangjun Lin Yasuhiro Igarashi Gong-Li Tang State Key Laboratory of Chemical Biology Shanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200032China School of Chemistry and Materials Science Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China State Key Laboratory of microbial Metabolism&Joint International Research Laboratory on Metabolic and Developmental Sciences School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China biotechnology Research Center Toyama Prefectural UniversityImizu 939-0398Japan

A 61-kb biosynthetic gene cluster(BGC),which is accountable for the biosynthesis of hibarimicin(HBM)B from Microbispora rosea *** TP-A0121,was heterologously expressed in Streptomyces coelicolor M1154,which generated a trace of the target products but accumulated a large amount of shunt *** on rational analysis of the relevant secondary metabolism,directed engineering of the biosynthetic pathways resulted in the high production of HBM B,as well as new HBM derivates with improved antitumor *** results not only establish a biosynthetic system to effectively synthesize HBMs-a class of the largest and most complex Type-Ⅱpolyketides,with a unique pseudo-dimeric structure-but also set the stage for further engineering and deep investigation of this complex biosynthetic pathway toward potent anticancer drugs.

关键词： Hibarimicin Biosynthesis Heterologous expression Biosynthetic gene cluster Rational engineering Type-II polyketide

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DeepSecE:A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria

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Research 2024年第3期2023卷 243-257页

作者： Yumeng Zhang Jiahao Guan Chen Li Zhikang Wang Zixin Deng Robin BGasser Jiangning Song Hong-Yu Ou state Key Laboratory of microbial Metabolism Joint International Laboratory on Metabolic&Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Key Laboratory of Veterinary biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash UniversityMelbourneViC 3800Australia Monash Data Futures Institute Monash UniversityMelbourneViC 3800Australia Melbourne Veterinary School Faculty of ScienceThe University of MelbourneParkvilleVIC 3010Australia.

Proteins secreted by Gram-negative bacteria are tightly linked to the virulence and adaptability of these microbes to environmental *** identification of such secreted proteins can facilitate the investigations of infections and diseases caused by these bacterial ***,current bioinformatic methods for predicting bacterial secreted substrate proteins have limited computational efficiency and application scope on a genome-wide ***,we propose a novel deep-learning-based framework—DeepSecE—for the simultaneous inference of multiple distinct groups of secreted proteins produced by Gram-negative *** remarkably improves their classification from nonsecreted proteins using a pretrained protein language model and transformer,achieving a macro-average accuracy of 0.883 on 5-fold *** benchmarking suggests that DeepSecE achieves competitive performance with the state-of-the-art binary predictors specialized for individual types of secreted *** attention mechanism corroborates salient patterns and motifs at the N or C termini of the protein *** this pipeline,we further investigate the genome-wide prediction of novel secreted proteins and their taxonomic distribution across~1,000 Gram-negative bacterial *** present analysis demonstrates that DeepSecE has major potential for the discovery of disease-associated secreted proteins in a diverse range of Gram-negative *** online web server of DeepSecE is also publicly available to predict and explore various secreted substrate proteins via the input of bacterial genome sequences.

关键词： Deep server competitive

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Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

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Marine Life Science & Technology 2024年第2期6卷 331-348页

作者： Hao Ling Yongxin Lv Yu Zhang Ning‑Yi Zhou Ying Xu State Key Laboratory of microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China State Key of Laboratory of Ocean Engineering Shanghai Jiao Tong UniversityShanghai 200240China

Phenolic compounds,as well as other aromatic compounds,have been reported to be abundant in hadal *** high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds,direct microbiological,genetic and biochemical evidence under in situ pressures remain ***,a microbial consortium and a pure culture of Pseudomonas,newly isolated from Mariana Trench sediments,efficiently degraded phenol under pressures up to 70 and 60 MPa,respectively,with concomitant increase in *** analyzing a high-pressure(70 MPa)culture metatranscriptome,not only was the entire range of metabolic processes under high pressure generated,but also genes encod-ing complete phenol degradation via ortho-and meta-cleavage pathways were *** isolate of Pseudomonas also contained genes encoding the complete degradation *** transcribed genes(dmpKLMNOP_(sed))were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous *** addition,key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial *** microbiological,genetic,bioinformatics,and biochemical levels,this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic *** information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

关键词： Hadal trench High hydrostatic pressure Phenolic compounds degradation Piezotolerant microorganisms Widespread distribution

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Identification of an immune-related gene signature for predicting prognosis and immunotherapy efficacy in liver cancer via cell-cell communication

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World Journal of Gastroenterology 2024年第11期30卷 1609-1620页

作者： Jun-Tao Li Hong-Mei Zhang Wei Wang Dong-Qing Wei College of Mathematics and Information Science Henan Normal UniversityXinxiang 453007Henan ProvinceChina College of Computer and Information Engineering Henan Normal UniversityXinxiang 453007Henan ProvinceChina State Key Laboratory of microbial Metabolism and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China

BACKGROUND Liver cancer is one of the deadliest malignant tumors *** has provided hope to patients with advanced liver cancer,but only a small fraction of patients benefit from this treatment due to individual *** immune-related gene signatures in liver cancer patients not only aids physicians in cancer diagnosis but also offers personalized treatment strategies,thereby improving patient survival *** several methods have been developed to predict the prognosis and immunotherapeutic efficacy in patients with liver cancer,the impact of cell-cell interactions in the tumor microenvir-onment has not been adequately *** To identify immune-related gene signals for predicting liver cancer prognosis and immunotherapy *** Cell grouping and cell-cell communication analysis were performed on single-cell RNA-sequencing data to identify highly active cell groups in immune-related *** active immune cells were identified by intersecting the highly active cell groups with B cells and T *** significantly differentially expressed genes between highly active immune cells and other cells were subsequently selected as features,and a least absolute shrinkage and selection operator(LASSO)regression model was constructed to screen for diagnostic-related *** genes that were selected more than 5 times in 10 LASSO regression experiments were included in a multivariable Cox regression ***,3 genes(stathmin 1,cofilin 1,and C-C chemokine ligand 5)significantly associated with survival were identified and used to construct an immune-related gene *** The immune-related gene signature composed of stathmin 1,cofilin 1,and C-C chemokine ligand 5 was identified through cell-cell *** effectiveness of the identified gene signature was validated based on experi-mental results of predictive immunotherapy response,tumor mutation burden analysis,immune cell infiltrat

关键词： Liver cancer Cell-cell communication Gene signature Prognosis Immunotherapy Single-cell RNA sequencing

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