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Exposing the small protein load of bacterial life. 暴露细菌生命的小蛋白质负荷。
IF 11.3 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-11-01 DOI: 10.1093/femsre/fuad063
Laure Simoens, Igor Fijalkowski, Petra Van Damme

The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs). In recent years, continuous efforts led to great improvements in the annotation and characterization of such proteins, yet many challenges remain to fully comprehend the pervasive nature of small proteins and their impact on bacterial biology. In this work, we review the recent developments in the dynamic field of bacterial genome reannotation, catalog the important biological roles carried out by small proteins and identify challenges obstructing the way to full understanding of these elusive proteins.

不断增长的基因组技术继续扩大我们对原核生物基因组的真正多样性和丰富性的理解。核糖蛋白质基因组学为以前被忽视的基因组元件的动态研究奠定了基础。最引人注目的是,细菌基因组被揭示出具有强大的小开放阅读框(sorf)库,该库编码多种广泛表达的小蛋白或sorf编码的多肽(sep)。近年来,不断的努力使这些蛋白质的注释和表征取得了很大的进步,但要充分理解小蛋白质的普遍性质及其对细菌生物学的影响,仍然存在许多挑战。在这项工作中,我们回顾了细菌基因组重新注释动态领域的最新进展,编目了小蛋白质进行的重要生物学作用,并确定了阻碍充分理解这些难以捉摸的蛋白质的挑战。
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引用次数: 0
Chromosome structure and DNA replication dynamics during the life cycle of the predatory bacterium Bdellovibrio bacteriovorus. 捕食性细菌食杆菌生命周期中的染色体结构和DNA复制动力学。
IF 10.1 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-11-01 DOI: 10.1093/femsre/fuad057
Karolina Pląskowska, Jolanta Zakrzewska-Czerwińska

Bdellovibrio bacteriovorus, an obligate predatory Gram-negative bacterium that proliferates inside and kills other Gram-negative bacteria, was discovered more than 60 years ago. However, we have only recently begun to understand the detailed cell biology of this proficient bacterial killer. Bdellovibrio bacteriovorus exhibits a peculiar life cycle and bimodal proliferation, and thus represents an attractive model for studying novel aspects of bacterial cell biology. The life cycle of B. bacteriovorus consists of two phases: a free-living nonreplicative attack phase and an intracellular reproductive phase. During the reproductive phase, B. bacteriovorus grows as an elongated cell and undergoes binary or nonbinary fission, depending on the prey size. In this review, we discuss: (1) how the chromosome structure of B. bacteriovorus is remodeled during its life cycle; (2) how its chromosome replication dynamics depends on the proliferation mode; (3) how the initiation of chromosome replication is controlled during the life cycle, and (4) how chromosome replication is spatiotemporally coordinated with the proliferation program.

噬菌弧菌是一种专性捕食性革兰氏阴性细菌,在体内繁殖并杀死其他革兰氏阴性细菌。它是60多年前被发现的。然而,我们最近才开始了解这种熟练的细菌杀手的详细细胞生物学。B.bacteriovorus表现出独特的生命周期和双峰增殖,因此为研究细菌细胞生物学的新方面提供了一个有吸引力的模型。嗜杆菌的生命周期由两个阶段组成:自由生活的非复制攻击阶段和细胞内繁殖阶段。在繁殖阶段,嗜杆菌生长为细长细胞,并根据猎物的大小进行二元或非二元分裂。在这篇综述中,我们讨论了:(1)嗜杆菌的染色体结构在其生命周期中是如何重塑的;(2) 其染色体复制动力学如何取决于增殖模式;(3) 在生命周期中如何控制染色体复制的启动,以及(4)染色体复制如何与增殖程序在时空上协调。
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引用次数: 0
Role of the extracellular matrix in Candida biofilm antifungal resistance. 细胞外基质在念珠菌生物膜抗真菌耐药性中的作用。
IF 11.3 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-11-01 DOI: 10.1093/femsre/fuad059
Justin Massey, Robert Zarnowski, David Andes

Clinical infection due to Candida species frequently involve growth in biofilm communities. Recalcitrance despite antifungal therapy leads to disease persistence associated with high morbidity and mortality. Candida possesses several tools allowing evasion of antifungal effects. Among these, protection of biofilm cells via encasement by the extracellular matrix is responsible for a majority drug resistance phenotype. The Candida matrix composition is complex and includes a mannan-glucan complex linked to antifungal drug sequestration. This mechanism of resistance is conserved across the Candida genus and impacts each of the available antifungal drug classes. The exosome pathway is responsible for delivery and assembly of much of the Candida extracellular matrix as functional vesicle protein and polysaccharide cargo. Investigations demonstrate the vesicle matrix delivery pathway is a useful fungal biofilm drug target. Further elucidation of the vesicle pathway, as well as understanding the roles of biofilm driven cargo may provide additional targets to aid the diagnosis, prevention, and treatment of Candida biofilms.

念珠菌引起的临床感染经常涉及生物膜群落的生长。尽管进行了抗真菌治疗,但顽固性仍会导致与高发病率和死亡率相关的疾病持续存在。念珠菌有几种可以逃避抗真菌作用的工具。其中,通过细胞外基质包裹来保护生物膜细胞是大多数耐药表型的原因。念珠菌基质成分是复杂的,包括与抗真菌药物螯合有关的甘露聚糖-葡聚糖复合物。这种耐药性机制在念珠菌属中是保守的,并影响到每一种可用的抗真菌药物类别。外泌体途径负责念珠菌细胞外基质的递送和组装,作为功能性囊泡蛋白和多糖货物。研究表明,囊泡基质递送途径是一种有用的真菌生物膜药物靶点。进一步阐明囊泡途径,以及了解生物膜驱动货物的作用,可能会为念珠菌生物膜的诊断、预防和治疗提供额外的靶点。
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引用次数: 0
The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. 核团相关蛋白和拓扑异构酶在染色体结构、链分离和细菌表型异质性产生中的作用。
IF 11.3 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-11-01 DOI: 10.1093/femsre/fuac049
Vic Norris, Clara Kayser, Georgi Muskhelishvili, Yoan Konto-Ghiorghi

How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organize their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the nucleoid-associated proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs, and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU, and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes, and hence in the phenotypes of daughter cells.

如何适应不断变化的环境是细胞经常面临的一个基本问题。一种解决方案是,细胞将其成分组织成数量有限的空间延伸、功能相关的大分子集合体或超结构,然后将这些超结构不对称地分离到子细胞中。当某些超结构的分离仅与亲本 DNA 链中的一条有关,并且这种分离模式会持续到连续几代时,这种非对称分离就成为产生连贯表型多样性的一种特别有效的方法。原核生物中这种不对称分离的候选超结构包括那些含有核仁相关蛋白(NAP)和拓扑异构酶的超结构。另一种解决产生连贯表型多样性问题的方法是,沿着细菌染色体的复制原点至末端轴线,形成一种依赖于生长环境的超卷曲梯度。这种梯度受转录、NAPs 和拓扑异构酶的调节。在这里,我们主要关注大肠杆菌中的两种拓扑异构酶(TopoIV 和 DNA gyrase)、三种 NAP(H-NS、HU 和 IHF)以及单链结合蛋白 SSB。我们认为,依赖超螺旋梯度的拓扑异构酶活性和依赖链分离的拓扑异构酶活性的结合导致了子染色体超螺旋的显著差异,进而导致子细胞表型的显著差异。
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引用次数: 0
Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals. 共生的起源:动植物微生物致病、共生和互生的共同机制。
IF 11.3 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-11-01 DOI: 10.1093/femsre/fuac048
Christina L Wiesmann, Nicole R Wang, Yue Zhang, Zhexian Liu, Cara H Haney

Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.

无论共生的结果如何,是致病、互生还是共生,细菌都必须首先定殖宿主。耐人寻味的是,定殖于不同宿主并产生不同共生结果的近缘细菌具有一致的宿主关联和毒力因子。本综述描述了具有不同生活方式的细菌在与宿主发生关联过程中的共性。无论是病原体、共生菌还是互生菌,细菌都必须感知宿主的存在并向宿主迁移,与其他微生物争夺空间和养分,躲避宿主的免疫系统,并改变自身的生理机能以实现长期的宿主关联。我们的研究主要集中在假单胞菌等已被充分研究的类群,它们与不同的植物和动物模型宿主结合,产生了广泛的共生结果。鉴于机会性病原体和慢性感染在人类健康和农业中的重要性,了解促进细菌与其宿主之间共生关系的机制将有助于为人类和我们食用的植物开发疾病治疗方法提供信息。
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引用次数: 0
What's in a name? Characteristics of clinical biofilms. 名字里有什么?临床生物膜的特征。
IF 11.3 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad050
Mads Lichtenberg, Tom Coenye, Matthew R Parsek, Thomas Bjarnsholt, Tim Holm Jakobsen

In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial species. Various mechanisms enable biofilm-associated bacteria to withstand antibiotics, including physical barriers, physiological adaptations, and changes in gene expression. Gene expression profiles in biofilms differ from individual cells but, there is little consensus among studies and so far, a 'biofilm signature transcriptome' has not been recognized. Additionally, the spatial and temporal variability within biofilms varies greatly depending on the system or environment. Despite all these variable conditions, which produce very diverse structures, they are all noted as biofilms. We discuss that clinical biofilms may differ from those grown in laboratories and found in the environment and discuss whether the characteristics that are commonly used to define and characterize biofilms have been shown in infectious biofilms. We emphasize that there is a need for a comprehensive understanding of the specific traits that are used to define bacteria in infections as clinical biofilms.

体外生物膜是微生物群落,与单个细胞相比具有独特的特征。生物膜通常具有大小、粘附性和由细胞外物质构成的基质等物理特征。它们显示出独特的表型特征,如代谢活性和抗生素耐受性。不过,这些特征的相对重要性取决于环境和细菌种类。生物膜相关细菌耐受抗生素的机制多种多样,包括物理屏障、生理适应和基因表达变化。生物膜中的基因表达谱与单个细胞不同,但各研究之间几乎没有共识,迄今为止,"生物膜特征转录组 "尚未得到认可。此外,生物膜内的空间和时间可变性也因系统或环境的不同而有很大差异。尽管所有这些多变的条件会产生多种多样的结构,但它们都被称为生物膜。我们讨论了临床生物膜可能不同于实验室中生长的生物膜和环境中发现的生物膜,并讨论了通常用于定义和描述生物膜的特征是否已在感染性生物膜中显示出来。我们强调有必要全面了解用于将感染细菌定义为临床生物膜的具体特征。
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引用次数: 0
Correction to: Exploring probiotic effector molecules and their mode of action in gut-immune interactions. 更正:探索益生菌效应分子及其在肠道免疫相互作用中的作用模式。
IF 11.3 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad055
This review explores the functional importance and underlying mechanisms of probiotic components, their impact on gut–immune homeostasis, and their potential applications in promoting human health.
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引用次数: 0
Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. 具有异化硫酸盐/亚硫酸盐还原潜力的微生物的全球多样性和推断生态生理学。
IF 11.3 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad058
Muhe Diao, Stefan Dyksma, Elif Koeksoy, David Kamanda Ngugi, Karthik Anantharaman, Alexander Loy, Michael Pester

Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.

硫酸盐/亚硫酸盐还原微生物(SRM)在自然界中无处不在,推动着全球硫循环。SRM的一个标志是dsrAB基因编码的异化亚硫酸还原酶。基于对950个主要由宏基因组衍生的携带dsrAB的基因组的分析,我们重新定义了具有异化硫酸盐/亚硫酸盐还原潜力的微生物的全球多样性,并揭示了挑战早期对其能量代谢模式的概括的遗传库。我们发现:(i)23个细菌门中的19个和4个古菌门中的2个含有未鉴定的SRM,(ii)包括脱硫菌门在内的4个门含有具有在硫酸盐/亚硫酸盐还原和硫氧化之间切换的遗传潜力的微生物,以及(iii)不同dsrAB类型的组合以及存在/不存在,dsrL类型和dsrD为推断异化硫代谢的方向提供了指导。我们进一步提供了一个更新的dsrAB数据库,包括>60%的分类解析的、未培养的家族级谱系,并为环境调查提供了关于现有dsrAB靶向引物的建议。我们的工作总结了对新发现的SRM推断的生态生理学的见解,将SRM多样性纳入细菌和古菌分类学最近的重大变化的背景中,并为在全球范围内研究SRM提供了最新的框架。
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引用次数: 0
Type II bacterial toxin-antitoxins: hypotheses, facts, and the newfound plethora of the PezAT system. II型细菌毒素抗毒素:假说、事实和新发现的过量PezAT系统。
IF 10.1 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad052
Wai Ting Chan, Maria Pilar Garcillán-Barcia, Chew Chieng Yeo, Manuel Espinosa

Toxin-antitoxin (TA) systems are entities found in the prokaryotic genomes, with eight reported types. Type II, the best characterized, is comprised of two genes organized as an operon. Whereas toxins impair growth, the cognate antitoxin neutralizes its activity. TAs appeared to be involved in plasmid maintenance, persistence, virulence, and defence against bacteriophages. Most Type II toxins target the bacterial translational machinery. They seem to be antecessors of Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) RNases, minimal nucleotidyltransferase domains, or CRISPR-Cas systems. A total of four TAs encoded by Streptococcus pneumoniae, RelBE, YefMYoeB, Phd-Doc, and HicAB, belong to HEPN-RNases. The fifth is represented by PezAT/Epsilon-Zeta. PezT/Zeta toxins phosphorylate the peptidoglycan precursors, thereby blocking cell wall synthesis. We explore the body of knowledge (facts) and hypotheses procured for Type II TAs and analyse the data accumulated on the PezAT family. Bioinformatics analyses showed that homologues of PezT/Zeta toxin are abundantly distributed among 14 bacterial phyla mostly in Proteobacteria (48%), Firmicutes (27%), and Actinobacteria (18%), showing the widespread distribution of this TA. The pezAT locus was found to be mainly chromosomally encoded whereas its homologue, the tripartite omega-epsilon-zeta locus, was found mostly on plasmids. We found several orphan pezT/zeta toxins, unaccompanied by a cognate antitoxin.

毒素-抗毒素(TA)系统是在原核基因组中发现的实体,有八种报告类型。II型是最具特征的,由两个组织为操纵子的基因组成。尽管毒素会损害生长,但同源抗毒素会中和其活性。TAs似乎参与质粒的维持、持久性、毒力和对噬菌体的防御。大多数II型毒素以细菌转化机制为目标。它们似乎是高等真核生物和原核生物核苷酸结合(HEPN)核糖核酸酶、最小核苷酸转移酶结构域或CRISPR-Cas系统的前身。由肺炎链球菌RelBE、YefMYoeB、Phd-Doc和HicAB编码的总共四种TA属于HEPN RNA酶。第五个代表是PezAT/Epsilon Zeta。PezT/Zeta毒素磷酸化肽聚糖前体,从而阻断细胞壁合成。我们探索了为II型TA获得的知识(事实)和假设,并分析了PezAT家族积累的数据。生物信息学分析表明,PezT/Zeta毒素的同源物在14个细菌门中大量分布,主要分布在变形菌门(48%)、厚壁菌门(27%)和放线菌门(18%),表明该TA的广泛分布。pezAT基因座主要由染色体编码,而其同源物,三重ω-ε-ζ基因座,主要在质粒上发现。我们发现了几种孤儿pezT/zeta毒素,没有一种同源抗毒素。
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引用次数: 0
Methodologies for bacterial ribonuclease characterization using RNA-seq. 使用RNA-seq鉴定细菌核糖核酸酶的方法。
IF 10.1 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-09-05 DOI: 10.1093/femsre/fuad049
Laura Broglia, Anaïs Le Rhun, Emmanuelle Charpentier

Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target recognition. Recent advances in high-throughput RNA sequencing (RNA-seq) approaches have provided a better understanding of the roles and modes of action of bacterial RNases. Global studies aiming to identify direct targets of RNases have highlighted the diversity of RNase activity and RNA-based mechanisms of gene expression regulation. Here, we review recent RNA-seq approaches used to study bacterial RNases, with a focus on the methods for identifying direct RNase targets.

细菌通过小型调节RNA和RNA结合蛋白(包括核糖核酸酶)的复杂网络在转录后水平上调节基因表达。RNA酶在RNA代谢中起着重要作用,调节RNA的稳定性、衰变和活化。这些酶对基因表达、细菌生理学和不同的靶标识别策略表现出物种特异性的影响。高通量RNA测序(RNA-seq)方法的最新进展使人们更好地了解了细菌RNA酶的作用和作用模式。旨在确定RNase直接靶点的全球研究强调了RNase活性的多样性和基于RNA的基因表达调控机制。在这里,我们回顾了最近用于研究细菌核糖核酸酶的RNA-seq方法,重点是鉴定直接核糖核酶靶标的方法。
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引用次数: 0
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FEMS microbiology reviews
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