FEMS microbiology reviews最新文献

The emerging role of SARS-CoV-2 non-structural 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 : 2024-09-04 DOI: 10.1093/femsre/fuae023

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

{"title":"The emerging role of SARS-CoV-2 non-structural 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":"https://doi.org/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 non-structural 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":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 : 2024-08-08 DOI: 10.1093/femsre/fuae022

Sybren de Hoog, Chao Tang, Xin Zhou, Bruna Jacomel, Bruno Lustosa, Yinggai Song, Hazal Kandemir, Sarah Ahmed, Shaoqin Zhou, Ricardo Belmonte, Yu Quan, Peiying Feng, Vania 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 Ahmed, Shaoqin Zhou, Ricardo Belmonte, Yu Quan, Peiying Feng, Vania Vicente, Yingqian Kang","doi":"10.1093/femsre/fuae022","DOIUrl":"https://doi.org/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 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 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":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 : 2024-07-31 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":"https://doi.org/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 non-essential 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 non-model 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":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":null,"pages":null},"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":null,"pages":null},"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

The vast landscape of carbohydrate fermentation in prokaryotes. 原核生物碳水化合物发酵的广阔前景

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae016

Timothy J Hackmann

{"title":"The vast landscape of carbohydrate fermentation in prokaryotes.","authors":"Timothy J Hackmann","doi":"10.1093/femsre/fuae016","DOIUrl":"10.1093/femsre/fuae016","url":null,"abstract":"Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11187502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183896","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

Escherichia coli DNA replication: the old model organism still holds many surprises. 大肠杆菌的 DNA 复制：这一古老的模式生物仍有许多惊喜。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2024-06-20 DOI: 10.1093/femsre/fuae018

Krystian Łazowski, Roger Woodgate, Iwona J Fijalkowska

{"title":"Escherichia coli DNA replication: the old model organism still holds many surprises.","authors":"Krystian Łazowski, Roger Woodgate, Iwona J Fijalkowska","doi":"10.1093/femsre/fuae018","DOIUrl":"10.1093/femsre/fuae018","url":null,"abstract":"Research on Escherichia coli DNA replication paved the groundwork for many breakthrough discoveries with important implications for our understanding of human molecular biology, due to the high level of conservation of key molecular processes involved. To this day, it attracts a lot of attention, partially by virtue of being an important model organism, but also because the understanding of factors influencing replication fidelity might be important for studies on the emergence of antibiotic resistance. Importantly, the wide access to high-resolution single-molecule and live-cell imaging, whole genome sequencing, and cryo-electron microscopy techniques, which were greatly popularized in the last decade, allows us to revisit certain assumptions about the replisomes and offers very detailed insight into how they work. For many parts of the replisome, step-by-step mechanisms have been reconstituted, and some new players identified. This review summarizes the latest developments in the area, focusing on (a) the structure of the replisome and mechanisms of action of its components, (b) organization of replisome transactions and repair, (c) replisome dynamics, and (d) factors influencing the base and sugar fidelity of DNA synthesis.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":null,"pages":null},"PeriodicalIF":10.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11253446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141563083","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 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2024-05-17 DOI: 10.1093/femsre/fuae015

M Atasoy, S Bartkova, Z Çetecioğlu-Gürol, N Mira, C O'Byrne, F Pérez-Rodríguez, A Possas, O Scheler, J Sedláková-Kaduková, M Sinčák, M Steiger, C Ziv, P A Lund

{"title":"Methods for studying microbial acid stress responses: from molecules to populations.","authors":"M Atasoy, S Bartkova, Z Çetecioğlu-Gürol, N Mira, C O'Byrne, F Pérez-Rodríguez, A Possas, O Scheler, J Sedláková-Kaduková, M Sinčák, M Steiger, C Ziv, P A Lund","doi":"10.1093/femsre/fuae015","DOIUrl":"https://doi.org/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":null,"pages":null},"PeriodicalIF":11.3,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Determinants of bacterial survival and proliferation in blood. 细菌在血液中存活和增殖的决定因素。

IF 11.3 2区生物学

FEMS microbiology reviews Pub Date : 2024-05-08 DOI: 10.1093/femsre/fuae013

Pierre Lê-Bury, Hebert Echenique-Rivera, Javier Pizarro-Cerdá, Olivier Dussurget

引用次数: 0