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Exploiting predatory bacteria as biocontrol agents across ecosystems. 利用掠食性细菌作为跨生态系统的生物防治剂。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2023-11-09 DOI: 10.1016/j.tim.2023.10.005
Lu Zhang, Lingyun Guo, Zhongli Cui, Feng Ju

Predatory bacteria have been increasingly known for their ubiquity in environments and great functional potentials in controlling unwanted microorganisms. Fundamental understanding of the predation mechanisms, population dynamics, and interaction patterns underlying bacterial predation is required for wise exploitation of predatory bacteria for enhancing ecoenvironmental, animal, and human health. Here, we review the recent achievements on applying predatory bacteria in different systems as biocontrol agents and living antibiotics as well as new findings in their phylogenetic diversity and predation mechanisms. We finally propose critical issues that deserve priority research and highlight the necessity to combine classic culture-based and advanced culture-independent approaches to push research frontiers of bacterial predation across ecosystems for promising biocontrol and therapy strategies towards a sustainable ecoenvironment and health.

掠食性细菌因其在环境中的普遍存在和在控制有害微生物方面的巨大功能潜力而日益为人所知。对细菌捕食机制、种群动态和相互作用模式的基本理解是明智地利用掠食性细菌以促进生态环境、动物和人类健康的必要条件。本文综述了近年来在不同系统中应用捕食性细菌作为生物防治剂和活抗生素的研究进展,以及在其系统发育多样性和捕食机制方面的新发现。最后,我们提出了值得优先研究的关键问题,并强调了将经典的基于培养和先进的非培养方法结合起来的必要性,以推动跨生态系统细菌捕食的研究前沿,为实现可持续的生态环境和健康提供有前途的生物防治和治疗策略。
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引用次数: 0
Gonococcal PorB: a multifaceted modulator of host immune responses. 淋球菌B:宿主免疫反应的多方面调节剂。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2023-10-25 DOI: 10.1016/j.tim.2023.10.002
Rebekah A Jones, Ann E Jerse, Christoph M Tang

Neisseria gonorrhoeae is a human-specific pathogen responsible for the sexually transmitted infection, gonorrhoea. N. gonorrhoeae promotes its survival by manipulating both innate and adaptive immune responses. The most abundant gonococcal outer-membrane protein is PorB, an essential porin that facilitates ion exchange. Importantly, gonococcal PorB has several immunomodulatory properties. To subvert the innate immune response, PorB suppresses killing mechanisms of macrophages and neutrophils, and recruits negative regulators of complement to the gonococcal cell surface. For manipulation of adaptive immune responses, gonococcal PorB suppresses the capability of dendritic cells to stimulate proliferation of T cells. As gonococcal PorB is highly abundant in outer-membrane vesicles, consideration of the immunomodulatory properties of this porin is critical when designing gonococcal vaccines.

淋病奈瑟菌是一种人类特有的病原体,是性传播感染淋病的罪魁祸首。淋病奈瑟菌通过操纵先天免疫反应和适应性免疫反应来促进其生存。最丰富的淋球菌外膜蛋白是PorB,一种促进离子交换的重要通道蛋白。重要的是,淋球菌PorB具有多种免疫调节特性。为了破坏先天免疫反应,PorB抑制巨噬细胞和中性粒细胞的杀伤机制,并将补体的负调节因子募集到淋球菌细胞表面。为了操纵适应性免疫反应,淋球菌PorB抑制树突细胞刺激T细胞增殖的能力。由于淋球菌PorB在外膜囊泡中高度丰富,在设计淋球菌疫苗时,考虑这种孔蛋白的免疫调节特性至关重要。
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引用次数: 0
Antimicrobial susceptibility prediction from genomes: a dream come true? 从基因组预测抗菌药敏感性:梦想成真?
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2024-03-03 DOI: 10.1016/j.tim.2024.02.012
Guido Werner, Hege Vangstein Aamot, Natacha Couto

Genome-based diagnostics provides relevant information to guide patient treatment and support pathogen and resistance surveillance. Recently, Coll et al. introduced a curated database for predicting antimicrobial resistance (AMR) from Enterococcus faecium genomics data, offering excellent predictive values for susceptibility to important antimicrobials. Challenges to predict resistance to last-resort antimicrobials remain.

基于基因组的诊断为指导患者治疗和支持病原体及耐药性监测提供了相关信息。最近,Coll 等人从粪肠球菌基因组学数据中引入了一个用于预测抗菌药耐药性(AMR)的编辑数据库,为重要抗菌药的敏感性提供了极好的预测值。预测对最后一种抗菌药物的耐药性仍面临挑战。
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引用次数: 0
Structure and molecular mechanism of bacterial transcription activation. 细菌转录激活的结构和分子机制。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2023-10-28 DOI: 10.1016/j.tim.2023.10.001
Dmytro Kompaniiets, Dong Wang, Yang Yang, Yangbo Hu, Bin Liu

Transcription activation is an important checkpoint of regulation of gene expression which occurs in response to different intracellular and extracellular signals. The key elements in this signal transduction process are transcription activators, which determine when and how gene expression is activated. Recent structural studies on a considerable number of new transcription activation complexes (TACs) revealed the remarkable mechanistic diversity of transcription activation mediated by different factors, necessitating a review and re-evaluation of the transcription activation mechanisms. In this review, we present a comprehensive summary of transcription activation mechanisms and propose a new, elaborate, and systematic classification of transcription activation mechanisms, primarily based on the structural features of diverse TAC components.

转录激活是基因表达调控的一个重要检查点,它发生在对不同细胞内和细胞外信号的反应中。这个信号转导过程中的关键元件是转录激活剂,它决定基因表达何时以及如何被激活。最近对大量新的转录激活复合物(TACs)的结构研究揭示了由不同因素介导的转录激活的显著机制多样性,因此有必要对转录激活机制进行回顾和重新评估。在这篇综述中,我们对转录激活机制进行了全面的总结,并主要基于不同TAC成分的结构特征,提出了一种新的、精细的、系统的转录激活机制分类。
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引用次数: 0
Endogenous retroviruses in development and health. 发育和健康中的内源性逆转录病毒。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2023-10-04 DOI: 10.1016/j.tim.2023.09.006
Jichang Wang, Xinyi Lu, Weiqi Zhang, Guang-Hui Liu

Endogenous retroviruses (ERVs) are evolutionary remnants of retroviral infections in which the viral genome became embedded as a dormant regulatory element within the host germline. When ERVs become activated, they comprehensively rewire genomic regulatory networks of the host and facilitate critical developmental events, such as preimplantation development and placentation, in a manner specific to species, developmental stage, and tissues. However, accumulating evidence suggests that aberrant ERV transcription compromises genome stability and has been implicated in cellular senescence and various pathogenic processes, underscoring the significance of host genomic surveillance mechanisms. Here, we revisit the prominent functions of ERVs in early development and highlight their emerging roles in mammalian post-implantation development and organogenesis. We also discuss their implications for aging and pathological processes such as microbial infection, immune response. Furthermore, we discuss recent advances in stem-cell-based models, single-cell omics, and genome editing technologies, which serve as beacons illuminating the versatile nature of ERVs in mammalian development and health.

内源性逆转录病毒(ERV)是逆转录病毒感染的进化残余,其中病毒基因组作为休眠的调节元件嵌入宿主种系中。当ERV被激活时,它们会全面重新连接宿主的基因组调控网络,并以物种、发育阶段和组织特有的方式促进关键的发育事件,如植入前发育和胎盘植入。然而,越来越多的证据表明,ERV的异常转录损害了基因组的稳定性,并与细胞衰老和各种致病过程有关,这突出了宿主基因组监测机制的重要性。在这里,我们回顾了ERV在早期发育中的突出功能,并强调了它们在哺乳动物植入后发育和器官发生中的新兴作用。我们还讨论了它们对衰老和病理过程的影响,如微生物感染、免疫反应。此外,我们讨论了基于干细胞的模型、单细胞组学和基因组编辑技术的最新进展,这些技术是阐明ERV在哺乳动物发育和健康中的多功能性的灯塔。
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引用次数: 0
Traits-based approach: leveraging genome size in plant-microbe interactions. 基于性状的方法:在植物-微生物相互作用中利用基因组大小。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2023-11-02 DOI: 10.1016/j.tim.2023.10.004
Haiyang Zhang, Hongwei Liu, Xingguo Han

Trait-based approaches have gained growing interest in studying plant-microbe interactions. However, current traits normally considered (e.g., morphological, physiological, or chemical traits) are biased towards those showing large intraspecific variations, necessitating the identification of fewer plastic traits that differ between species. Here, we propose using genome size (the amount of DNA in the nucleus of a cell) as a suitable trait for studying plant-microbiome interactions due to its relatively stable nature, minimally affected by external environmental variations. Emerging evidence suggests that plant genome size affects the plant-associated microbial community, and tissue-specific environments select microbes based on their genome size. These findings pinpoint environmental selection in genome size as an emerging driver of plant-microbiome interactions, potentially impacting ecosystem functions and productivity.

基于性状的方法在研究植物与微生物的相互作用方面越来越引起人们的兴趣。然而,目前通常考虑的性状(如形态、生理或化学性状)偏向于那些表现出较大种内变异的性状,因此需要识别出较少的不同物种的可塑性性状。在这里,我们建议使用基因组大小(细胞核中DNA的数量)作为研究植物-微生物组相互作用的合适特征,因为它的性质相对稳定,受外部环境变化的影响最小。新出现的证据表明,植物基因组大小会影响与植物相关的微生物群落,组织特异性环境会根据基因组大小选择微生物。这些发现将基因组大小的环境选择确定为植物-微生物组相互作用的新兴驱动因素,可能影响生态系统功能和生产力。
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引用次数: 0
Plasmid-mediated colistin-resistance genes: mcr. 质粒介导的粘菌素耐药基因。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2023-11-25 DOI: 10.1016/j.tim.2023.10.006
Jian-Hua Liu, Yi-Yun Liu, Ying-Bo Shen, Jun Yang, Timothy R Walsh, Yang Wang, Jianzhong Shen

Colistin is regarded as a last-line drug against serious infections caused by multidrug-resistant Gram-negative bacterial pathogens. Therefore, the emergence of mobile colistin resistance (mcr) genes has attracted global concern and led to policy changes for the use of colistin in food animals across many countries. Currently, the distribution, function, mechanism of action, transmission vehicles, origin of mcr, and new treatment strategies against MCR-producing pathogens have been extensively studied. Here we review the prevalence, structure and function of mcr, the fitness cost and persistence of mcr-carrying plasmids, the impact of MCR on host immune response, as well as the control strategies to combat mcr-mediated colistin resistance.

粘菌素被认为是对抗多重耐药革兰氏阴性细菌病原体引起的严重感染的最后一线药物。因此,移动粘菌素耐药性(mcr)基因的出现引起了全球的关注,并导致许多国家对粘菌素在食用动物中使用的政策发生了变化。目前,人们对mcr的分布、功能、作用机制、传播载体、起源以及针对mcr产生病原体的新治疗策略等进行了广泛的研究。本文综述了mcr的流行、结构和功能、携带mcr的质粒的适应性成本和持久性、mcr对宿主免疫反应的影响以及mcr介导的粘菌素耐药性的控制策略。
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引用次数: 0
Host cell environments and antibiotic efficacy in tuberculosis. 结核病的宿主细胞环境和抗生素疗效。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-03-01 Epub Date: 2023-09-12 DOI: 10.1016/j.tim.2023.08.009
Nathan J Day, Pierre Santucci, Maximiliano G Gutierrez

The aetiologic agent of tuberculosis (TB), Mycobacterium tuberculosis (Mtb), can survive, persist, and proliferate in a variety of heterogeneous subcellular compartments. Therefore, TB chemotherapy requires antibiotics crossing multiple biological membranes to reach distinct subcellular compartments and target these bacterial populations. These compartments are also dynamic, and our understanding of intracellular pharmacokinetics (PK) often represents a challenge for antitubercular drug development. In recent years, the development of high-resolution imaging approaches in the context of host-pathogen interactions has revealed the intracellular distribution of antibiotics at a new level, yielding discoveries with important clinical implications. In this review, we describe the current knowledge regarding cellular PK of antibiotics and the complexity of drug distribution within the context of TB. We also discuss the recent advances in quantitative imaging and highlight their applications for drug development in the context of how intracellular environments and microbial localisation affect TB treatment efficacy.

结核病(TB)的病原体--结核分枝杆菌(Mtb),可以在各种不同的亚细胞间质中生存、存活和增殖。因此,结核病化疗需要抗生素穿过多层生物膜,才能到达不同的亚细胞区室,针对这些细菌种群进行治疗。这些区室也是动态的,我们对细胞内药代动力学(PK)的了解往往是抗结核药物开发的一个挑战。近年来,在宿主与病原体相互作用的背景下,高分辨率成像方法的发展在新的层面上揭示了抗生素在细胞内的分布,并产生了具有重要临床意义的发现。在这篇综述中,我们将介绍目前有关抗生素细胞 PK 的知识以及结核病药物分布的复杂性。我们还讨论了定量成像技术的最新进展,并重点介绍了这些技术在药物开发中的应用,以及细胞内环境和微生物定位如何影响结核病的治疗效果。
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引用次数: 0
Starvation helps transition to abundance - a ferrosome story. 饥饿有助于向富裕过渡--一个铁一般的故事。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-03-01 Epub Date: 2024-01-28 DOI: 10.1016/j.tim.2024.01.006
Subham Mridha, Michael C Abt

Iron is an essential nutrient for bacterial pathogenesis. In their study, Skaar and colleagues (Pi et al.) discovered and determined the detailed structure of ferrosomes within Clostridioides difficile, the iron-storage organelles that form under iron-limited conditions in anticipation of future iron overload.

铁是细菌致病过程中必不可少的营养物质。在他们的研究中,Skaar 及其同事(Pi 等人)发现并确定了艰难梭菌体内铁储存体的详细结构,这种铁储存体是在铁有限的条件下形成的细胞器,以应对未来的铁超载。
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引用次数: 0
Biological interactions with Prochlorococcus: implications for the marine carbon cycle. 与 Prochlorococcus 的生物相互作用:对海洋碳循环的影响。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-03-01 Epub Date: 2023-09-17 DOI: 10.1016/j.tim.2023.08.011
Lanlan Cai, Haofu Li, Junwei Deng, Ruiqian Zhou, Qinglu Zeng

The unicellular picocyanobacterium Prochlorococcus is the most abundant photoautotroph and contributes substantially to global CO2 fixation. In the vast euphotic zones of the open ocean, Prochlorococcus converts CO2 into organic compounds and supports diverse organisms, forming an intricate network of interactions that regulate the magnitude of carbon cycling and storage in the ocean. An understanding of the biological interactions with Prochlorococcus is critical for accurately estimating the contributions of Prochlorococcus and interacting organisms to the marine carbon cycle. This review synthesizes the primary production contributed by Prochlorococcus in the global ocean. We outline recent progress on the interactions of Prochlorococcus with heterotrophic bacteria, phages, and grazers that multifacetedly determine Prochlorococcus carbon production and fate. We discuss that climate change might affect the biological interactions with Prochlorococcus and thus the marine carbon cycle.

单细胞微囊藻原绿球菌是最丰富的光自养菌,对全球二氧化碳固定做出了重大贡献。在广阔的开阔洋的极光带,原绿球菌将二氧化碳转化为有机化合物,并支持多种生物,形成了一个错综复杂的相互作用网络,调节着海洋中碳循环和碳储存的规模。了解原绿球藻与生物的相互作用对于准确估算原绿球藻和相互作用生物对海洋碳循环的贡献至关重要。本综述综述了原绿球藻对全球海洋初级生产的贡献。我们概述了原绿球藻与异养细菌、噬菌体和食草动物相互作用的最新进展,这些相互作用从多方面决定了原绿球藻的碳生产和归宿。我们讨论了气候变化可能会影响原绿球藻的生物相互作用,进而影响海洋碳循环。
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引用次数: 0
期刊
Trends in Microbiology
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