FEMS microbiology reviews最新文献_第6页

Exploring the multilayered response of TB bacterium Mycobacterial tuberculosis to lysosomal injury. 探讨结核分枝杆菌对溶酶体损伤的多层反应。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf040

Mohd Shariq, Javaid Ahmad Sheikh, Asrar Ahmad Malik, Anwar Alam, Peter N Monk, Seyed E Hasnain, Nasreen Z Ehtesham

{"title":"Exploring the multilayered response of TB bacterium Mycobacterial tuberculosis to lysosomal injury.","authors":"Mohd Shariq, Javaid Ahmad Sheikh, Asrar Ahmad Malik, Anwar Alam, Peter N Monk, Seyed E Hasnain, Nasreen Z Ehtesham","doi":"10.1093/femsre/fuaf040","DOIUrl":"10.1093/femsre/fuaf040","url":null,"abstract":"Mtb subverts host immune surveillance by damaging phagolysosomal membranes, exploiting them as replication niches. In response, host cells initiate a coordinated LDR, integrating membrane repair, selective autophagy, and de novo biogenesis. This review delineates a systems-level model of lysosomal quality control governed by three critical regulatory axes: LGALS3/8/9, TRIM E3 ubiquitin ligases, and the AMPK-TFEB signaling pathway. LGALSs detect exposed glycans on ruptured membranes, triggering ESCRT-mediated repair and recruiting ARs. TRIM proteins mediate context-specific ubiquitination, enhancing cargo selection and facilitating transcriptional reprogramming via TFEB. Simultaneously, AMPK-TFEB signaling links metabolic stress to lysosomal regeneration, reinforcing immune defense and cellular adaptation. We highlight emerging mechanisms, including ATG8ylation, CASM, Ca2 + leakage, and SG formation, that refine this multilayered response. Mtb virulence factors selectively disrupt these pathways, revealing their relevance to pathogen persistence. Beyond infection, this triadic network maintains lysosomal integrity in neurodegeneration, inflammation, and lysosomal storage disorders. Understanding its modular design reveals novel therapeutic targets and HDTs for combatting drug-resistant TB. This review integrates recent advances into a coherent framework that redefines lysosomal function as a dynamic, immune-regulatory hub essential for cellular resilience under infectious and metabolic stress.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144948039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Standardizing experimental approaches to investigate interactions between bacteria and ectomycorrhizal fungi. 规范研究细菌与外生菌根真菌相互作用的实验方法。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae035

Louis Berrios, T Bertie Ansell, Peter D Dahlberg, Kabir G Peay

引用次数: 0

Microbial engineering for monocyclic aromatic compounds production. 单环芳香族化合物生产的微生物工程。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf003

Guipeng Hu, Cong Gao, Xiaomin Li, Wei Song, Jing Wu

引用次数: 0

Exploring antiviral strategies to combat African swine fever. 探索对抗非洲猪瘟的抗病毒策略。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf044

Ana Catarina Urbano, Beatriz Melo, Fernando Ferreira

{"title":"Exploring antiviral strategies to combat African swine fever.","authors":"Ana Catarina Urbano, Beatriz Melo, Fernando Ferreira","doi":"10.1093/femsre/fuaf044","DOIUrl":"10.1093/femsre/fuaf044","url":null,"abstract":"African swine fever (ASF), caused by the highly contagious African swine fever virus (ASFV), poses a significant threat to domestic and wild pigs worldwide. Despite its limited host range and lack of zoonotic potential, ASF has severe socio-economic and environmental consequences. Current control strategies primarily rely on early detection and culling of infected animals, but these measures are insufficient given the rapid spread of the disease. Developing effective therapeutics against ASFV is crucial to prevent further spread and mitigate economic losses. Although vaccination remains critical, recent vaccine approvals in Vietnam have raised safety and efficacy concerns. Moreover, as challenges persist in vaccine development and deployment, particularly in complex field conditions, antiviral agents have emerged as a critical complementary approach. These agents have the potential to mitigate side effects and control viral spread when vaccines alone are insufficient or when animals face simultaneous exposure to vaccine strains and wild-type viruses. However, advancing them from proof-of-concept to widespread practical application entails a significant interdisciplinary effort, given the logistical and economic constraints of in vivo testing. In this review, we examine emerging antiviral approaches and highlight key ASFV replication mechanisms and therapeutic targets to guide rational drug design amidst an evolving viral landscape.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145014216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions. 在计算机相遇：利用代谢模型来理解植物与微生物的相互作用。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf030

Martina Feierabend, Nadine Töpfer

{"title":"In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.","authors":"Martina Feierabend, Nadine Töpfer","doi":"10.1093/femsre/fuaf030","DOIUrl":"10.1093/femsre/fuaf030","url":null,"abstract":"Understanding plant-microbe interactions is vital for developing sustainable agricultural practices and mitigating the consequences of climate change on food security. Plant-microbe interactions can improve nutrient acquisition, reduce dependency on chemical fertilizers, affect plant health, growth, and yield, and impact plants' resistance to biotic and abiotic stresses. These interactions are largely driven by metabolic exchanges and can thus be understood through metabolic network modelling. Recent developments in genomics, metagenomics, phenotyping, and synthetic biology now enable researchers to harness the potential of metabolic modelling at the genome scale. Here, we review studies that utilize genome-scale metabolic modelling to study plant-microbe interactions in symbiotic, pathogenic, and microbial community systems. This review catalogues how metabolic modelling has advanced our understanding of the plant host and its associated microorganisms as a holobiont. We showcase how these models can contextualize heterogeneous datasets and serve as valuable tools to dissect and quantify underlying mechanisms. Finally, we consider studies that employ metabolic models as a testbed for in silico design of synthetic microbial communities with predefined traits. We conclude by discussing broader implications of the presented studies, future perspectives, and outstanding challenges.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer? 具有自然能力的细菌和它们的遗传寄生虫——一场控制水平基因转移的战斗？

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf035

Nina Vesel, Eva Stare, Polonca Štefanič, Valentina A Floccari, Ines Mandic-Mulec, Anna Dragoš

{"title":"Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer?","authors":"Nina Vesel, Eva Stare, Polonca Štefanič, Valentina A Floccari, Ines Mandic-Mulec, Anna Dragoš","doi":"10.1093/femsre/fuaf035","DOIUrl":"10.1093/femsre/fuaf035","url":null,"abstract":"Host-mediated natural competence for transformation of DNA and mobile genetic element (MGE)-driven conjugation and transduction are key modes of horizontal gene transfer. While these mechanisms are traditionally believed to shape bacterial evolution by enabling the acquisition of new genetic traits, numerous studies have elucidated an antagonistic relationship between natural transformation and MGEs. A new role of natural transformation as a chromosome-curing mechanism has now been proposed. Experimental data, along with mathematical models, suggest that transformation can eliminate deleterious MGEs. Supporting this hypothesis, MGEs have been shown to use various mechanisms to decrease or block transformability, such as disrupting competence genes, regulating the development of competence, hindering DNA uptake machinery, producing DNases that target the exogenous (transforming) DNA, and causing lysis of competent cells. A few examples of synergistic relationships between natural transformation and MGEs have also been reported, with natural transformation facilitating MGE transfer and phages enhancing transformation by supplying extracellular DNA through lysis and promoting competence via kin discrimination. Given the complexity of the relationships between natural transformation and MGEs, the balance between antagonism and synergy likely depends on specific selection pressures in a given context. The evidence collected here indicates a continuous conflict over horizontal gene transfer in bacteria, with semiautonomous MGEs attempting to disrupt host-controlled DNA acquisition, while host competence mechanisms work to resist MGE interference.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12378983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144845064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hierarchical metabolic engineering for rewiring cellular metabolism. 重组细胞代谢的分层代谢工程。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf047

Tiantian Chai, Yuxuan Tao, Chunlei Zhao, Xiulai Chen

引用次数: 0

Charting the microbial frontier: a comprehensive guidebook for advancing microbiome research. 绘制微生物前沿：推进微生物组研究的综合指南。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae033

Hui Wu

引用次数: 0

Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms. 揭示假单胞菌群的基因组多样性：探索分类、核心庞基因组和抗生素耐药性机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae025

Zulema Udaondo, Juan Luis Ramos, Kaleb Abram

{"title":"Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.","authors":"Zulema Udaondo, Juan Luis Ramos, Kaleb Abram","doi":"10.1093/femsre/fuae025","DOIUrl":"10.1093/femsre/fuae025","url":null,"abstract":"The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier \"Pseudomonas putida\" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as \"Pseudomonas putida\" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assembly of functional microbial ecosystems: from molecular circuits to communities. 功能微生物生态系统的组装：从分子电路到群落。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae026

Shengbo Wu, Yongsheng Zhou, Lei Dai, Aidong Yang, Jianjun Qiao

{"title":"Assembly of functional microbial ecosystems: from molecular circuits to communities.","authors":"Shengbo Wu, Yongsheng Zhou, Lei Dai, Aidong Yang, Jianjun Qiao","doi":"10.1093/femsre/fuae026","DOIUrl":"10.1093/femsre/fuae026","url":null,"abstract":"Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. First, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn procedure including function specification, chassis selection, interaction design, system build, performance test, modeling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11585282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0