FEMS microbiology reviews最新文献_第2页

Key roles of two-component systems in intestinal signal sensing and virulence regulation in enterohemorrhagic Escherichia coli. 双组分系统在肠出血性大肠杆菌肠道信号传感和毒力调节中的关键作用。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae028

Hongmin Sun, Di Huang, Yu Pang, Jingnan Chen, Chenbo Kang, Mengjie Zhao, Bin Yang

{"title":"Key roles of two-component systems in intestinal signal sensing and virulence regulation in enterohemorrhagic Escherichia coli.","authors":"Hongmin Sun, Di Huang, Yu Pang, Jingnan Chen, Chenbo Kang, Mengjie Zhao, Bin Yang","doi":"10.1093/femsre/fuae028","DOIUrl":"10.1093/femsre/fuae028","url":null,"abstract":"Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that infects humans by colonizing the large intestine. Upon reaching the large intestine, EHEC mediates local signal recognition and the transcriptional regulation of virulence genes to promote adherence and colonization in a highly site-specific manner. Two-component systems (TCSs) represent an important strategy used by EHEC to couple external stimuli with the regulation of gene expression, thereby allowing EHEC to rapidly adapt to changing environmental conditions. An increasing number of studies published in recent years have shown that EHEC senses a variety of host- and microbiota-derived signals present in the human intestinal tract and coordinates the expression of virulence genes via multiple TCS-mediated signal transduction pathways to initiate the disease-causing process. Here, we summarize how EHEC detects a wide range of intestinal signals and precisely regulates virulence gene expression through multiple signal transduction pathways during the initial stages of infection, with a particular emphasis on the key roles of TCSs. This review provides valuable insights into the importance of TCSs in EHEC pathogenesis, which has relevant implications for the development of antibacterial therapies against EHEC infection.","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/PMC11644481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142617004","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

The biochemical mechanisms of plastic biodegradation. 塑料生物降解的生化机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-11-23 DOI: 10.1093/femsre/fuae027

Ethan G Gates, Nathan Crook

引用次数: 0

The emerging role of SARS-CoV-2 nonstructural protein 1 (nsp1) in epigenetic regulation of host gene expression. SARS-CoV-2 非结构蛋白 1 (nsp1) 在宿主基因表达的表观遗传调控中的新作用。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae023

Konstantin I Ivanov, Haibin Yang, Ruixue Sun, Chunmei Li, Deyin Guo

{"title":"The emerging role of SARS-CoV-2 nonstructural protein 1 (nsp1) in epigenetic regulation of host gene expression.","authors":"Konstantin I Ivanov, Haibin Yang, Ruixue Sun, Chunmei Li, Deyin Guo","doi":"10.1093/femsre/fuae023","DOIUrl":"10.1093/femsre/fuae023","url":null,"abstract":"Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes widespread changes in epigenetic modifications and chromatin architecture in the host cell. Recent evidence suggests that SARS-CoV-2 nonstructural protein 1 (nsp1) plays an important role in driving these changes. Previously thought to be primarily involved in host translation shutoff and cellular mRNA degradation, nsp1 has now been shown to be a truly multifunctional protein that affects host gene expression at multiple levels. The functions of nsp1 are surprisingly diverse and include not only the downregulation of cellular mRNA translation and stability, but also the inhibition of mRNA export from the nucleus, the suppression of host immune signaling, and, most recently, the epigenetic regulation of host gene expression. In this review, we first summarize the current knowledge on SARS-CoV-2-induced changes in epigenetic modifications and chromatin structure. We then focus on the role of nsp1 in epigenetic reprogramming, with a particular emphasis on the silencing of immune-related genes. Finally, we discuss potential molecular mechanisms underlying the epigenetic functions of nsp1 based on evidence from SARS-CoV-2 interactome studies.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132261","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

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes. 波罗的海微生物的生物多样性：鉴定海洋微生物新方法的力量。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae024

Hanna Mazur-Marzec, Anders F Andersson, Agata Błaszczyk, Przemysław Dąbek, Ewa Górecka, Michał Grabski, Katarzyna Jankowska, Agata Jurczak-Kurek, Anna K Kaczorowska, Tadeusz Kaczorowski, Bengt Karlson, Marija Kataržytė, Justyna Kobos, Ewa Kotlarska, Beata Krawczyk, Aneta Łuczkiewicz, Kasia Piwosz, Bartosz Rybak, Krzysztof Rychert, Conny Sjöqvist, Waldemar Surosz, Beata Szymczycha, Anna Toruńska-Sitarz, Grzegorz Węgrzyn, Andrzej Witkowski, Alicja Węgrzyn

{"title":"Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.","authors":"Hanna Mazur-Marzec, Anders F Andersson, Agata Błaszczyk, Przemysław Dąbek, Ewa Górecka, Michał Grabski, Katarzyna Jankowska, Agata Jurczak-Kurek, Anna K Kaczorowska, Tadeusz Kaczorowski, Bengt Karlson, Marija Kataržytė, Justyna Kobos, Ewa Kotlarska, Beata Krawczyk, Aneta Łuczkiewicz, Kasia Piwosz, Bartosz Rybak, Krzysztof Rychert, Conny Sjöqvist, Waldemar Surosz, Beata Szymczycha, Anna Toruńska-Sitarz, Grzegorz Węgrzyn, Andrzej Witkowski, Alicja Węgrzyn","doi":"10.1093/femsre/fuae024","DOIUrl":"10.1093/femsre/fuae024","url":null,"abstract":"Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375361","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

The rise and future of CRISPR-based approaches for high-throughput genomics. 基于 CRISPR 的高通量基因组学方法的兴起与未来。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae020

Silke Vercauteren, Simon Fiesack, Laetitia Maroc, Natalie Verstraeten, Liselot Dewachter, Jan Michiels, Sibylle C Vonesch

{"title":"The rise and future of CRISPR-based approaches for high-throughput genomics.","authors":"Silke Vercauteren, Simon Fiesack, Laetitia Maroc, Natalie Verstraeten, Liselot Dewachter, Jan Michiels, Sibylle C Vonesch","doi":"10.1093/femsre/fuae020","DOIUrl":"10.1093/femsre/fuae020","url":null,"abstract":"Clustered regularly interspaced short palindromic repeats (CRISPR) has revolutionized the field of genome editing. To circumvent the permanent modifications made by traditional CRISPR techniques and facilitate the study of both essential and nonessential genes, CRISPR interference (CRISPRi) was developed. This gene-silencing technique employs a deactivated Cas effector protein and a guide RNA to block transcription initiation or elongation. Continuous improvements and a better understanding of the mechanism of CRISPRi have expanded its scope, facilitating genome-wide high-throughput screens to investigate the genetic basis of phenotypes. Additionally, emerging CRISPR-based alternatives have further expanded the possibilities for genetic screening. This review delves into the mechanism of CRISPRi, compares it with other high-throughput gene-perturbation techniques, and highlights its superior capacities for studying complex microbial traits. We also explore the evolution of CRISPRi, emphasizing enhancements that have increased its capabilities, including multiplexing, inducibility, titratability, predictable knockdown efficacy, and adaptability to nonmodel microorganisms. Beyond CRISPRi, we discuss CRISPR activation, RNA-targeting CRISPR systems, and single-nucleotide resolution perturbation techniques for their potential in genome-wide high-throughput screens in microorganisms. Collectively, this review gives a comprehensive overview of the general workflow of a genome-wide CRISPRi screen, with an extensive discussion of strengths and weaknesses, future directions, and potential alternatives.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11409895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859471","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

Fungal primary and opportunistic pathogens: an ecological perspective. 真菌原生病原体和机会病原体：生态学视角。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae022

Sybren de Hoog, Chao Tang, Xin Zhou, Bruna Jacomel, Bruno Lustosa, Yinggai Song, Hazal Kandemir, Sarah A Ahmed, Shaoqin Zhou, Ricardo Belmonte-Lopes, Yu Quan, Peiying Feng, Vania A Vicente, Yingqian Kang

{"title":"Fungal primary and opportunistic pathogens: an ecological perspective.","authors":"Sybren de Hoog, Chao Tang, Xin Zhou, Bruna Jacomel, Bruno Lustosa, Yinggai Song, Hazal Kandemir, Sarah A Ahmed, Shaoqin Zhou, Ricardo Belmonte-Lopes, Yu Quan, Peiying Feng, Vania A Vicente, Yingqian Kang","doi":"10.1093/femsre/fuae022","DOIUrl":"10.1093/femsre/fuae022","url":null,"abstract":"Fungal primary pathogenicity on vertebrates is here described as a deliberate strategy where the host plays a role in increasing the species' fitness. Opportunism is defined as the coincidental survival of an individual strain in host tissue using properties that are designed for life in an entirely different habitat. In that case, the host's infection control is largely based on innate immunity, and the etiologic agent is not transmitted after infection, and thus fungal evolution is not possible. Primary pathogens encompass two types, depending on their mode of transmission. Environmental pathogens have a double life cycle, and tend to become enzootic, adapted to a preferred host in a particular habitat. In contrast, pathogens that have a host-to-host transmission pattern are prone to shift to a neighboring, immunologically naive host, potentially leading to epidemics. Beyond these prototypical life cycles, some environmental fungi are able to make large leaps between dissimilar hosts/habitats, probably due to the similarity of key factors enabling survival in an entirely different niche, and thus allowing a change from opportunistic to primary pathogenicity. Mostly, such factors seem to be associated with extremotolerance.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11409879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906370","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

Methods for studying microbial acid stress responses: from molecules to populations. 研究微生物酸应激反应的方法：从分子到群体。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-09-18 DOI: 10.1093/femsre/fuae015

Merve Atasoy, Simona Bartkova, Zeynep Çetecioğlu-Gürol, Nuno P Mira, Conor O'Byrne, Fernando Pérez-Rodríguez, Aricia Possas, Ott Scheler, Jana Sedláková-Kaduková, Mirka Sinčák, Matthias Steiger, Carmit Ziv, Peter A Lund

{"title":"Methods for studying microbial acid stress responses: from molecules to populations.","authors":"Merve Atasoy, Simona Bartkova, Zeynep Çetecioğlu-Gürol, Nuno P Mira, Conor O'Byrne, Fernando Pérez-Rodríguez, Aricia Possas, Ott Scheler, Jana Sedláková-Kaduková, Mirka Sinčák, Matthias Steiger, Carmit Ziv, Peter A Lund","doi":"10.1093/femsre/fuae015","DOIUrl":"10.1093/femsre/fuae015","url":null,"abstract":"The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140956970","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

Mechanisms of host adaptation by bacterial pathogens. 细菌病原体适应宿主的机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae019

Matthew F Barber, J Ross Fitzgerald

引用次数: 0

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. 揭示环境细菌中抗生素和重金属抗药性共同选择的机制。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae017

Brodie F Gillieatt, Nicholas V Coleman

{"title":"Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria.","authors":"Brodie F Gillieatt, Nicholas V Coleman","doi":"10.1093/femsre/fuae017","DOIUrl":"10.1093/femsre/fuae017","url":null,"abstract":"The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11253441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426620","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

Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts. 宿主与细菌之间的相互作用：从古老的专业内共生菌中获得的生态学和进化论启示。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae021

Zélia Bontemps, Kiran Paranjape, Lionel Guy

{"title":"Host-bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts.","authors":"Zélia Bontemps, Kiran Paranjape, Lionel Guy","doi":"10.1093/femsre/fuae021","DOIUrl":"10.1093/femsre/fuae021","url":null,"abstract":"Interactions between eukaryotic hosts and their bacterial symbionts drive key ecological and evolutionary processes, from regulating ecosystems to the evolution of complex molecular machines and processes. Over time, endosymbionts generally evolve reduced genomes, and their relationship with their host tends to stabilize. However, host-bacteria relationships may be heavily influenced by environmental changes. Here, we review these effects on one of the most ancient and diverse endosymbiotic groups, formed by-among others-Legionellales, Francisellaceae, and Piscirickettsiaceae. This group is referred to as Deep-branching Intracellular Gammaproteobacteria (DIG), whose last common ancestor presumably emerged about 2 Ga ago. We show that DIGs are globally distributed, but generally at very low abundance, and are mainly identified in aquatic biomes. Most DIGs harbour a type IVB secretion system, critical for host-adaptation, but its structure and composition vary. Finally, we review the different types of microbial interactions that can occur in diverse environments, with direct or indirect effects on DIG populations. The increased use of omics technologies on environmental samples will allow a better understanding of host-bacterial interactions and help unravel the definition of DIGs as a group from an ecological, molecular, and evolutionary perspective.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11338181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141855341","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