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Understanding the Diversity, Evolution, Ecology, and Applications of Mycoviruses. 了解霉菌病毒的多样性、进化、生态和应用。
IF 8.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-30 DOI: 10.1146/annurev-micro-041522-105358
Jiatao Xie, Daohong Jiang

Mycoviruses are widely distributed among various kinds of fungi. Over the past 10 years, more novel mycoviruses have been discovered with the use of high-throughput sequencing techniques, and research on mycoviruses has made fantastic progress, promoting our understanding of the diversity, classification, evolution, and ecology of the entire virosphere. Mycoviruses affect the biological and ecological functions of their hosts, for example, by suppressing or improving hosts' virulence and reproduction ability, and subsequently affect the microbiological community where their hosts live; hence, we may develop mycoviruses to regulate the health of environments, plants, animals, and human beings. In this review, we introduce recently discovered mycoviruses from fungi of humans, animals, plants, and environments, and their diversity, evolution, and ecological characteristics. We also present the potential application of mycoviruses by describing the latest progress on using mycoviruses to control plant diseases. Finally, we discuss the main issues facing mycovirus research in the future.

真菌病毒广泛分布于各种真菌中。近 10 年来,随着高通量测序技术的应用,更多新型霉菌病毒被发现,霉菌病毒研究取得了巨大进展,促进了我们对整个病毒界的多样性、分类、进化和生态学的了解。霉菌病毒会影响宿主的生物学和生态学功能,如抑制或提高宿主的毒力和繁殖能力,进而影响宿主所在的微生物群落;因此,我们可以开发霉菌病毒来调控环境、植物、动物和人类的健康。在这篇综述中,我们将介绍最近从人类、动物、植物和环境中的真菌中发现的真菌病毒,以及它们的多样性、进化和生态学特征。我们还介绍了利用真菌病毒控制植物病害的最新进展,从而展示了真菌病毒的潜在应用前景。最后,我们讨论了未来霉菌病毒研究面临的主要问题。
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引用次数: 0
Mechanisms Underlying Ophiocordyceps Infection and Behavioral Manipulation of Ants: Unique or Ubiquitous? 虫草蛇毒素感染和蚂蚁行为操纵的机制:独特还是普遍?
IF 10.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-13 DOI: 10.1146/annurev-micro-041522-092522
Emmeline van Roosmalen, Charissa de Bekker
Parasite manipulation of host behavior, as an effective strategy to establish transmission, has evolved multiple times across taxa, including fungi. Major strides have been made to propose molecular mechanisms that underlie manipulative parasite-host interactions including the manipulation of carpenter ant behavior by Ophiocordyceps. This research suggests that the secretion of parasite proteins and light-driven biological rhythms are likely involved in the infection and manipulation biology of Ophiocordyceps and other manipulating parasites. Here, we discuss research on Ophiocordyceps considering findings from other (fungal) parasites that either are relatively closely related (e.g., other insect- and plant-infecting Hypocreales) or also manipulate insect behavior (e.g., Entomophthorales). As such, this review aims to put forward this question: Are the mechanisms behind Ophiocordyceps manipulation and infection unique, or did they convergently evolve? From this discussion, we pose functional hypotheses about the infection biology of Ophiocordyceps that will need to be addressed in future studies.
寄生虫操纵宿主行为作为一种建立传播的有效策略,已经在包括真菌在内的不同类群中进化了多次。在提出操纵寄生虫-宿主相互作用的分子机制方面取得了重大进展,其中包括虫草蛇对木匠蚁行为的操纵。这些研究表明,寄生虫蛋白质的分泌和光驱动的生物节律很可能参与了蛇尾蝇蛆和其他操纵性寄生虫的感染和操纵生物学。在此,我们讨论了关于蛇尾蝇蛆的研究,同时考虑了其他(真菌)寄生虫的研究结果,这些寄生虫要么与蛇尾蝇蛆有相对密切的关系(如其他昆虫和植物感染下孢子虫科),要么也操纵昆虫的行为(如昆虫口器虫科)。因此,本综述旨在提出这一问题:线虫操纵和感染背后的机制是独特的,还是趋同进化的?通过讨论,我们提出了关于蛇尾藻感染生物学的功能性假设,这些假设需要在未来的研究中加以解决。
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引用次数: 0
Cyclic Diguanylate in the Wild: Roles During Plant and Animal Colonization 野生环境中的环状二官能团:植物和动物定殖过程中的作用
IF 10.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-13 DOI: 10.1146/annurev-micro-041522-101729
Ruth Y. Isenberg, Mark J. Mandel
Cyclic diguanylate (c-di-GMP) is a near-ubiquitous signaling molecule that regulates the motility-to-sessility transition in many bacterial species. Among the phenotypes influenced by c-di-GMP are biofilm formation, motility, cell cycle, and virulence. The hallmark phenotypes regulated by c-di-GMP—biofilm formation and motility—are key determinants of host–bacterial interactions. A large body of research has identified the roles of c-di-GMP in regulating phenotypes in culture. While numerous studies have investigated roles for c-di-GMP during the establishment and maintenance of pathogenic host–bacterial associations, considerably less attention has been devoted to defining the roles of c-di-GMP during beneficial and commensal associations. This review describes the known roles of c-di-GMP in regulating phenotypes that contribute to host colonization, with a focus on knowledge gaps and future prospects for examining c-di-GMP during beneficial colonization.
环状二胍酸盐(c-di-GMP)是一种几乎无处不在的信号分子,可调节许多细菌从运动到无活力的转变。受 c-di-GMP 影响的表型包括生物膜形成、运动性、细胞周期和毒力。受 c-di-GMP 调节的标志性表型--生物膜的形成和运动能力--是宿主与细菌相互作用的关键决定因素。大量研究已经确定了 c-di-GMP 在调节培养物表型中的作用。尽管许多研究都调查了 c-di-GMP 在致病宿主-细菌结合的建立和维持过程中的作用,但对 c-di-GMP 在有益和共生结合过程中的作用的研究却少得多。本综述介绍了 c-di-GMP 在调节有助于宿主定殖的表型方面的已知作用,重点是研究 c-di-GMP 在有益定殖过程中的知识差距和未来前景。
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引用次数: 0
How Bacteria Establish and Maintain Outer Membrane Lipid Asymmetry 细菌如何建立和维持外膜脂质的不对称性
IF 10.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-13 DOI: 10.1146/annurev-micro-032521-014507
Wee Boon Tan, Shu-Sin Chng
Gram-negative bacteria build an asymmetric outer membrane (OM), with lipopolysaccharides (LPS) and phospholipids (PLs) occupying the outer and inner leaflets, respectively. This distinct lipid arrangement is widely conserved within the Bacteria domain and confers strong protection against physical and chemical insults. The OM is physically separated from the inner membrane and the cytoplasm, where most cellular resources are located; therefore, the cell faces unique challenges in the assembly and maintenance of this asymmetric bilayer. Here, we present a framework for how gram-negative bacteria initially establish and continuously maintain OM lipid asymmetry, discussing the state-of-the-art knowledge of specialized lipid transport machines that place LPS and PLs directly into their corresponding leaflets in the OM, prevent excess PL accumulation and mislocalization, and correct any lipid asymmetry defects. We critically assess current studies, or the lack thereof, and highlight important future directions for research on OM lipid transport, homeostasis, and asymmetry.
革兰氏阴性细菌具有不对称的外膜(OM),脂多糖(LPS)和磷脂(PL)分别占据外叶和内叶。这种独特的脂质排列方式在细菌领域内广泛保留,可有效抵御物理和化学损伤。外膜与内膜和细胞质在物理上是分离的,而大多数细胞资源都位于细胞质中;因此,细胞在组装和维护这种不对称双分子层时面临着独特的挑战。在此,我们提出了革兰氏阴性细菌如何最初建立并持续维持OM脂质不对称的框架,讨论了有关专门脂质运输机器的最新知识,这些机器可将LPS和PL直接放入OM中相应的小叶,防止PL过度积累和错位,并纠正任何脂质不对称缺陷。我们对目前的研究或缺乏研究的情况进行了批判性评估,并强调了有关 OM 脂质转运、平衡和不对称性的重要未来研究方向。
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引用次数: 0
Dimethylsulfoniopropionate (DMSP): From Biochemistry to Global Ecological Significance. 二甲基硫代丙酸酯(DMSP):从生物化学到全球生态意义。
IF 8.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-04 DOI: 10.1146/annurev-micro-041222-024055
Chun-Yang Li, Hai-Yan Cao, Rocky D Payet, Jonathan D Todd, Yu-Zhong Zhang

Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur compounds with important roles in stress tolerance, chemotaxis, global carbon and sulfur cycling, and climate-active gas production. Diverse marine prokaryotes and eukaryotes produce DMSP via three known pathways (methylation, transamination, and decarboxylation) and metabolize DMSP via three further pathways (demethylation, cleavage, and oxidation). Over 20 key enzymes from these pathways have been identified to inform on the biodiversity and importance of DMSP cycling. The last dozen years have seen significant changes in our understanding of the enzymology and molecular mechanisms of these DMSP cycling enzymes through the application of biochemistry and structural biology. This has yielded more than 10 crystal structures and, in many cases, detailed explanations as to how and why organisms synthesis and metabolize DMSP. In this review, we describe recent progress in biochemical and mechanistic understandings of DMSP synthesis and metabolism, highlighting the important knowledge gleaned and current challenges that warrant further exploration.

二甲基硫代丙酸酯(DMSP)是地球上最丰富的有机硫化合物之一,在应激耐受性、趋化性、全球碳和硫循环以及气候活性气体产生方面具有重要作用。多种海洋原核生物和真核生物通过三种已知途径(甲基化、转胺和脱羧)产生 DMSP,并通过另外三种途径(脱甲基化、裂解和氧化)代谢 DMSP。这些途径中的 20 多种关键酶已被确定,为 DMSP 循环的生物多样性和重要性提供了信息。在过去的十几年中,通过生物化学和结构生物学的应用,我们对这些 DMSP 循环酶的酶学和分子机制的理解发生了重大变化。这已经产生了 10 多个晶体结构,并在许多情况下详细解释了生物如何以及为何合成和代谢 DMSP。在这篇综述中,我们将介绍对 DMSP 合成和新陈代谢的生化和机理认识的最新进展,重点介绍已获得的重要知识以及当前需要进一步探索的挑战。
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引用次数: 0
Roadmap to Success: How Oomycete Plant Pathogens Invade Tissues and Deliver Effectors. 成功路线图:植物卵菌病原体如何侵入组织并释放效应物?
IF 8.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-03 DOI: 10.1146/annurev-micro-032421-121423
Edouard Evangelisti, Francine Govers

Filamentous plant pathogens threaten global food security and ecosystem resilience. In recent decades, significant strides have been made in deciphering the molecular basis of plant-pathogen interactions, especially the interplay between pathogens' molecular weaponry and hosts' defense machinery. Stemming from interdisciplinary investigations into the infection cell biology of filamentous plant pathogens, recent breakthrough discoveries have provided a new impetus to the field. These advances include the biophysical characterization of a novel invasion mechanism (i.e., naifu invasion) and the unraveling of novel effector secretion routes. On the plant side, progress includes the identification of components of cellular networks involved in the uptake of intracellular effectors. This exciting body of research underscores the pivotal role of logistics management by the pathogen throughout the infection cycle, encompassing the precolonization stages up to tissue invasion. More insight into these logistics opens new avenues for developing environmentally friendly crop protection strategies in an era marked by an imperative to reduce the use of agrochemicals.

丝状植物病原体威胁着全球粮食安全和生态系统的恢复能力。近几十年来,在破译植物与病原体相互作用的分子基础,特别是病原体的分子武器与宿主防御机制之间的相互作用方面取得了重大进展。最近的突破性发现源于对丝状植物病原体感染细胞生物学的跨学科研究,为这一领域提供了新的动力。这些进展包括对一种新型入侵机制(即naifu入侵)进行生物物理鉴定,以及揭示新型效应物分泌途径。在植物方面,研究进展包括确定了参与吸收细胞内效应物的细胞网络的组成部分。这些令人兴奋的研究强调了病原体在整个感染周期中的后勤管理所起的关键作用,包括殖化前阶段直至组织入侵。在必须减少农用化学品使用的时代,对这些后勤管理的更多了解为开发环境友好型作物保护战略开辟了新的途径。
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引用次数: 0
Reconstructing Early Microbial Life. 重建早期微生物生命
IF 8.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-08-20 DOI: 10.1146/annurev-micro-041522-103400
Betül Kaçar

For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to overoxygenated atmospheres and cycling between hothouse conditions and global glaciations. Meanwhile, an ecological revolution took place. Earth evolved from one dominated by microbial life to one containing the plants and animals that are most familiar today. Many key cellular features evolved early in the history of life, collectively defining the nature of our biosphere and underpinning human survival. Recent advances in molecular and evolutionary biology have profoundly deepened our understanding of the origin and evolution of microbes across deep time. However, the incorporation of molecular genetics, population biology, and evolutionary biology approaches into the study of Precambrian biota remains a significant challenge. This review synthesizes our current knowledge of early microbial life with an emphasis on ancient metabolisms. It also outlines the foundations of an emerging interdisciplinary area that integrates microbiology, paleobiology, and evolutionary synthetic biology to reconstruct ancient biological innovations.

35 亿多年来,地球上的生命经历了剧烈的极端环境变化。其中包括从无氧大气到过氧大气的转变,以及温室条件和全球冰川之间的循环。与此同时,一场生态革命发生了。地球从一个以微生物生命为主的地方进化成了一个拥有今天人们最熟悉的植物和动物的地方。许多关键的细胞特征在生命史的早期就已经进化,共同决定了我们生物圈的性质,并支撑着人类的生存。分子生物学和进化生物学的最新进展大大加深了我们对微生物起源和进化的理解。然而,将分子遗传学、种群生物学和进化生物学方法纳入前寒武纪生物群的研究仍是一项重大挑战。这篇综述综述了我们目前对早期微生物生命的了解,重点是古代谢。它还概述了一个新兴跨学科领域的基础,该领域整合了微生物学、古生物学和进化合成生物学,以重建古代生物创新。
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引用次数: 0
Novel Antibody-Based Protection/Therapeutics in Staphylococcus aureus. 基于抗体的金黄色葡萄球菌新型保护/治疗方法。
IF 8.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-08-15 DOI: 10.1146/annurev-micro-041222-024605
Xinhai Chen, Dominique Missiakas

Staphylococcus aureus is a commensal of the skin and nares of humans as well as the causative agent of infections associated with significant mortality. The acquisition of antibiotic resistance traits complicates the treatment of such infections and has prompted the development of monoclonal antibodies. The selection of protective antigens is typically guided by studying the natural antibody responses to a pathogen. What happens when the pathogen masks these antigens and subverts adaptive responses, or when the pathogen inhibits or alters the effector functions of antibodies? S. aureus is constantly exposed to its human host and has evolved all these strategies. Here, we review how anti-S. aureus targets have been selected and how antibodies have been engineered to overcome the formidable immune evasive activities of this pathogen. We discuss the prospects of antibody-based therapeutics in the context of disease severity, immune competence, and history of past infections.

金黄色葡萄球菌是人类皮肤和鼻腔中的一种寄生菌,也是导致大量死亡的感染病原体。抗生素耐药性的产生使此类感染的治疗变得更加复杂,也促使了单克隆抗体的开发。保护性抗原的选择通常以研究病原体的天然抗体反应为指导。如果病原体掩盖了这些抗原并破坏了适应性反应,或者病原体抑制或改变了抗体的效应功能,会发生什么情况呢?金黄色葡萄球菌不断暴露于人类宿主,并进化出了所有这些策略。在这里,我们回顾了如何选择抗金黄色葡萄球菌的靶点,以及如何设计抗体来克服这种病原体可怕的免疫逃避活动。我们将根据疾病的严重程度、免疫能力和既往感染史讨论抗体疗法的前景。
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引用次数: 0
Biogenesis and Functionality of Sortase-Assembled Pili in Gram-Positive Bacteria. 革兰氏阳性细菌中分选酶组装的纤毛虫的生物生成和功能。
IF 8.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 DOI: 10.1146/annurev-micro-112123-100908
Chungyu Chang, Nicholas A Ramirez, Aadil H Bhat, Minh T Nguyen, Poonam Kumari, HyLam Ton-That, Asis Das, Hung Ton-That

A unique class of multimeric proteins made of covalently linked subunits known as pili, or fimbriae, are assembled and displayed on the gram-positive bacterial cell surface by a conserved transpeptidase enzyme named pilus-specific sortase. Sortase-assembled pili are produced by a wide range of gram-positive commensal and pathogenic bacteria inhabiting diverse niches such as the human oral cavity, gut, urogenital tract, and skin. These surface appendages serve many functions, such as molecular adhesins, immunomodulators, and virulence determinants, that significantly contribute to both the commensal and pathogenic attributes of producer microbes. Intensive genetic, biochemical, physiological, and structural studies have been devoted to unveiling the assembly mechanism and functions, as well as the utility of these proteins in vaccine development and other biotechnological applications. We provide a comprehensive review of these topics and discuss the current status and future prospects of the field.

由共价连接的亚基组成的一类独特的多聚体蛋白质被称为纤毛,由一种名为纤毛特异性分选酶的保守的转肽酶组装并显示在革兰氏阳性细菌的细胞表面。分选酶组装的纤毛由栖息在人类口腔、肠道、泌尿生殖道和皮肤等不同环境中的多种革兰氏阳性共生菌和致病菌产生。这些表面附属物具有多种功能,如分子粘合剂、免疫调节剂和毒力决定因子,对生产微生物的共生和致病属性都有重要作用。为了揭示这些蛋白质的组装机制和功能,以及它们在疫苗开发和其他生物技术应用中的效用,人们进行了大量的遗传学、生物化学、生理学和结构学研究。我们对这些主题进行了全面回顾,并讨论了该领域的现状和未来前景。
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引用次数: 0
From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance. 从培养皿到病人再到群体:驱动抗生素耐药性的规模和进化机制。
IF 8.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-08-14 DOI: 10.1146/annurev-micro-041522-102707
Célia Souque, Indra González Ojeda, Michael Baym

Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.

要应对抗生素耐药性带来的挑战,就必须了解其进化背后的机制。与任何进化过程一样,抗菌药耐药性(AMR)的进化也是由细菌种群的潜在变异和作用于细菌种群的选择压力所驱动的。重要的是,选择和变异都取决于考虑耐药性进化的规模(从单个病人体内的进化到宿主群体水平)。虽然实验室实验已经让我们对抗生素耐药性进化的机制有了基本的了解,但现在全基因组测序技术的进步让我们能够超越实验室,直接记录单个患者和宿主群体的抗生素耐药性进化。在此,我们回顾了在这些尺度上驱动抗生素耐药性的进化力量,强调了我们目前对 AMR 进化认识的差距,并讨论了未来以进化为指导的干预措施。
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引用次数: 0
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Annual review of microbiology
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