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Methyl-Based Methanogenesis: an Ecological and Genomic Review. 基于甲基的甲烷生成:生态学和基因组学回顾。
IF 8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2023-03-21 Epub Date: 2023-01-24 DOI: 10.1128/mmbr.00024-22
Clifton P Bueno de Mesquita, Dongying Wu, Susannah G Tringe

Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.

基于甲基的甲烷生成是古细菌厌氧甲烷生成的三大类之一,包括甲基歧化(甲养)途径和甲基还原(又称氢依赖性甲养)途径。基于甲基的甲烷生成越来越被认为是各种环境中甲烷的重要来源。在此,我们将概述基于甲基的甲烷生成研究,包括甲基甲烷生成成为甲烷排放主要来源的条件、区分不同甲烷生成途径的实验方法、所涉及的生化途径的分子细节以及参与这些过程的基因和生物体。我们还确定了目前的知识空白,并介绍了甲基甲烷生成基因的基因组和元基因组调查,强调了甲基甲烷生成菌在多个分类水平上的多样性,以及已知甲基甲烷生成基因和家族在不同环境中的广泛分布。
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引用次数: 0
The Fission Yeast Mating-Type Switching Motto: "One-for-Two" and "Two-for-One". 裂变酵母的交配类型转换格言:"一换二 "和 "二换一"。
IF 12.9 1区 生物学 Q1 Medicine Pub Date : 2023-03-21 Epub Date: 2023-01-11 DOI: 10.1128/mmbr.00008-21
Benoît Arcangioli, Serge Gangloff

Schizosaccharomyces pombe is an ascomycete fungus that divides by medial fission; it is thus commonly referred to as fission yeast, as opposed to the distantly related budding yeast Saccharomyces cerevisiae. The reproductive lifestyle of S. pombe relies on an efficient genetic sex determination system generating a 1:1 sex ratio and using alternating haploid/diploid phases in response to environmental conditions. In this review, we address how one haploid cell manages to generate two sister cells with opposite mating types, a prerequisite to conjugation and meiosis. This mating-type switching process depends on two highly efficient consecutive asymmetric cell divisions that rely on DNA replication, repair, and recombination as well as the structure and components of heterochromatin. We pay special attention to the intimate interplay between the genetic and epigenetic partners involved in this process to underscore the importance of basic research and its profound implication for a better understanding of chromatin biology.

酿酒酵母(Schizosaccharomyces pombe)是一种通过内侧裂殖进行分裂的子囊菌,因此通常被称为裂殖酵母,而不是与之关系密切的出芽酵母(Saccharomyces cerevisiae)。假丝酵母的生殖生活方式依赖于一个高效的遗传性别决定系统,该系统能产生 1:1 的性别比例,并能根据环境条件交替使用单倍体/二倍体阶段。在这篇综述中,我们将讨论一个单倍体细胞如何生成两个交配类型相反的姐妹细胞,这是结合和减数分裂的先决条件。这一交配类型转换过程依赖于两次高效率的连续不对称细胞分裂,而这依赖于DNA复制、修复和重组以及异染色质的结构和成分。我们特别关注参与这一过程的遗传和表观遗传伙伴之间的密切相互作用,以强调基础研究的重要性及其对更好地理解染色质生物学的深远影响。
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引用次数: 3
2022 Acknowledgment of MMBR Reviewers. 2022感谢MMBR审稿人。
IF 12.9 1区 生物学 Q1 Medicine Pub Date : 2022-12-21 DOI: 10.1128/mmbr.00162-22
Corrella S Detweiler
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引用次数: 0
How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts. 一切是如何开始的:有益共生体介导无脊椎动物宿主定殖的细菌因素。
IF 12.9 1区 生物学 Q1 Medicine Pub Date : 2022-12-21 Epub Date: 2022-10-27 DOI: 10.1128/mmbr.00126-21
Ramya Ganesan, Jürgen C Wierz, Martin Kaltenpoth, Laura V Flórez

Beneficial associations with bacteria are widespread across animals, spanning a range of symbiont localizations, transmission routes, and functions. While some of these associations have evolved into obligate relationships with permanent symbiont localization within the host, the majority require colonization of every host generation from the environment or via maternal provisions. Across the broad diversity of host species and tissue types that beneficial bacteria can colonize, there are some highly specialized strategies for establishment yet also some common patterns in the molecular basis of colonization. This review focuses on the mechanisms underlying the early stage of beneficial bacterium-invertebrate associations, from initial contact to the establishment of the symbionts in a specific location of the host's body. We first reflect on general selective pressures that can drive the transition from a free-living to a host-associated lifestyle in bacteria. We then cover bacterial molecular factors for colonization in symbioses from both model and nonmodel invertebrate systems where these have been studied, including terrestrial and aquatic host taxa. Finally, we discuss how interactions between multiple colonizing bacteria and priority effects can influence colonization. Taking the bacterial perspective, we emphasize the importance of developing new experimentally tractable systems to derive general insights into the ecological factors and molecular adaptations underlying the origin and establishment of beneficial symbioses in animals.

与细菌的有益联系在动物中广泛存在,涵盖了一系列共生体的定位、传播途径和功能。虽然其中一些关联已经演变成与宿主内永久共生体定位的义务关系,但大多数需要从环境中或通过母体供应对每一代宿主进行定殖。在有益细菌可以定植的宿主物种和组织类型的广泛多样性中,有一些高度专业化的建立策略,但在定植的分子基础上也有一些常见的模式。这篇综述的重点是有益细菌-无脊椎动物结合的早期机制,从最初接触到在宿主身体的特定位置建立共生体。我们首先反思了细菌从自由生活向宿主相关生活方式转变的一般选择性压力。然后,我们涵盖了在模型和非模型无脊椎动物系统共生体中定殖的细菌分子因素,包括陆地和水生宿主分类群。最后,我们讨论了多种定植细菌之间的相互作用和优先效应如何影响定植。从细菌的角度来看,我们强调开发新的实验可处理系统的重要性,以获得对动物有益共生体起源和建立背后的生态因素和分子适应的一般见解。
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引用次数: 9
Outer Membrane Vesicles: Biogenesis, Functions, and Issues. 外膜囊泡:生物学发生、功能和问题。
IF 12.9 1区 生物学 Q1 Medicine Pub Date : 2022-12-21 Epub Date: 2022-09-26 DOI: 10.1128/mmbr.00032-22
Rokas Juodeikis, Simon R Carding

This review focuses on nonlytic outer membrane vesicles (OMVs), a subtype of bacterial extracellular vesicles (BEVs) produced by Gram-negative organisms focusing on the mechanisms of their biogenesis, cargo, and function. Throughout, we highlight issues concerning the characterization of OMVs and distinguishing them from other types of BEVs. We also highlight the shortcomings of commonly used methodologies for the study of BEVs that impact the interpretation of their functionality and suggest solutions to standardize protocols for OMV studies.

这篇综述的重点是非溶解性外膜囊泡(OMVs),这是一种由革兰氏阴性菌产生的细菌细胞外囊泡(BEVs)的亚型,重点关注其生物发生、携带和功能的机制。在整个过程中,我们强调了与OMV的特性相关的问题,并将其与其他类型的纯电动汽车区分开来。我们还强调了影响其功能解释的纯电动汽车研究常用方法的缺点,并提出了标准化OMV研究协议的解决方案。
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引用次数: 13
Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation. 厌氧真菌(neocallimastigomyetes)中酶的发现促进了木质纤维素生物炼制的创新。
IF 12.9 1区 生物学 Q1 Medicine Pub Date : 2022-12-21 DOI: 10.1128/mmbr.00041-22
Thomas S Lankiewicz, Stephen P Lillington, Michelle A O'Malley
Lignocellulosic biorefineries require innovative solutions to realize their full potential, and the discovery of novel lignocellulose-active enzymes could improve biorefinery deconstruction processes. Enzymatic deconstruction of plant cell walls is challenging, as noncarbohydrate linkages in hemicellulosic sidechains and lignin protect labile carbohydrates from hydrolysis. SUMMARY Lignocellulosic biorefineries require innovative solutions to realize their full potential, and the discovery of novel lignocellulose-active enzymes could improve biorefinery deconstruction processes. Enzymatic deconstruction of plant cell walls is challenging, as noncarbohydrate linkages in hemicellulosic sidechains and lignin protect labile carbohydrates from hydrolysis. Highly specialized microbes that degrade plant biomass are attractive sources of enzymes for improving lignocellulose deconstruction, and the anaerobic gut fungi (Neocallimastigomycetes) stand out as having great potential for harboring novel lignocellulose-active enzymes. We discuss the known aspects of Neocallimastigomycetes lignocellulose deconstruction, including their extensive carbohydrate-active enzyme content, proficiency at deconstructing complex lignocellulose, unique physiology, synergistic enzyme complexes, and sizeable uncharacterized gene content. Progress describing Neocallimastigomycetes and their enzymes has been rapid in recent years, and it will only continue to expand. In particular, direct manipulation of anaerobic fungal genomes, effective heterologous expression of anaerobic fungal enzymes, and the ability to directly relate chemical changes in lignocellulose to fungal gene regulation will accelerate the discovery and subsequent deployment of Neocallimastigomycetes lignocellulose-active enzymes.
木质纤维素生物炼制需要创新的解决方案来实现其全部潜力,而新型木质纤维素活性酶的发现可以改善生物炼制的解构过程。酶解植物细胞壁是具有挑战性的,因为半纤维素侧链和木质素中的非碳水化合物键保护不稳定的碳水化合物不被水解。高度特化的降解植物生物量的微生物是改善木质纤维素分解的酶的有吸引力的来源,而厌氧肠道真菌(neocallimastigomyetes)因具有容纳新型木质纤维素活性酶的巨大潜力而脱颖而出。我们讨论了neocallimastigomyetes木质纤维素解构的已知方面,包括它们广泛的碳水化合物活性酶含量,解构复杂木质纤维素的熟练程度,独特的生理学,协同酶复合物和相当大的未表征基因含量。近年来,对新卡马菌及其酶的研究进展迅速,而且只会继续扩大。特别是,厌氧真菌基因组的直接操作,厌氧真菌酶的有效异源表达,以及将木质纤维素的化学变化与真菌基因调控直接联系起来的能力,将加速neocallimastigomyetes木质纤维素活性酶的发现和后续部署。
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引用次数: 3
Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. 利用模式生物的力量解开珊瑚Holobiont中的微生物功能。
IF 12.9 1区 生物学 Q1 Medicine Pub Date : 2022-12-21 Epub Date: 2022-10-26 DOI: 10.1128/mmbr.00053-22
Giulia Puntin, Michael Sweet, Sebastian Fraune, Mónica Medina, Koty Sharp, Virginia M Weis, Maren Ziegler

Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.

石珊瑚构成了珊瑚礁的框架,这些生态系统具有巨大的生态和经济重要性。这些生态系统的存在受到气候变化和其他人为压力的威胁,这些压力表现为珊瑚白化和疾病等微生物生态失调,通常导致珊瑚死亡。尽管进行了大量研究,但这些破坏性现象的最终机制,以及如何预防或减轻这些现象,仍有待解决。这主要是由于珊瑚实验中的实际挑战,以及珊瑚全生物的高度复杂性质,其中还包括细菌、古菌、原生生物和病毒。虽然这些伙伴的总体重要性得到了充分的认可,但它们对全生物功能及其种间动态的具体贡献在很大程度上仍未被探索。在这里,我们回顾了采用模式生物作为更易处理的系统来解决这些知识差距的潜力。我们借鉴更广泛的生物和生物医学领域的相似之处,指导新的和新兴的模式生物的建立、实施和整合,以满足珊瑚研究的具体需求。我们评估了珊瑚虫模型Hydra、Aiptasia、仙后座和Astrangia poculata;回顾珊瑚组织和细胞培养快速发展的领域;并提出了建立“真正的”热带珊瑚礁建造珊瑚模型的框架。基于这一评估,我们还建议未来的研究解决限制我们理解能力的关键方面,从而改善造礁珊瑚对未来海洋条件的反应。
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引用次数: 9
The Role of Chromatin and Transcriptional Control in the Formation of Sexual Fruiting Bodies in Fungi. 染色质和转录调控在真菌有性子实体形成中的作用。
IF 8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2022-12-21 Epub Date: 2022-11-21 DOI: 10.1128/mmbr.00104-22
Minou Nowrousian

Fungal fruiting bodies are complex, three-dimensional structures that arise from a less complex vegetative mycelium. Their formation requires the coordinated action of many genes and their gene products, and fruiting body formation is accompanied by major changes in the transcriptome. In recent years, numerous transcription factor genes as well as chromatin modifier genes that play a role in fruiting body morphogenesis were identified, and through research on several model organisms, the underlying regulatory networks that integrate chromatin structure, gene expression, and cell differentiation are becoming clearer. This review gives a summary of the current state of research on the role of transcriptional control and chromatin structure in fruiting body development. In the first part, insights from transcriptomics analyses are described, with a focus on comparative transcriptomics. In the second part, examples of more detailed functional characterizations of the role of chromatin modifiers and/or transcription factors in several model organisms (Neurospora crassa, Aspergillus nidulans, Sordaria macrospora, Coprinopsis cinerea, and Schizophyllum commune) that have led to a better understanding of regulatory networks at the level of chromatin structure and transcription are discussed.

真菌子实体是复杂的三维结构,由较不复杂的营养菌丝体产生。它们的形成需要许多基因及其基因产物的协同作用,子实体的形成伴随着转录组的重大变化。近年来,人们发现了许多参与子实体形态发生的转录因子基因和染色质修饰基因,通过对几种模式生物的研究,染色质结构、基因表达和细胞分化的潜在调控网络越来越清晰。本文综述了转录调控和染色质结构在子实体发育中的作用的研究现状。在第一部分中,描述了转录组学分析的见解,重点是比较转录组学。在第二部分中,我们讨论了染色质修饰剂和/或转录因子在几种模式生物(粗神经孢子菌、细粒曲霉、大孢子索达菌、铜opsis cinerea和Schizophyllum commune)中更详细的功能特征,这些特征有助于更好地理解染色质结构和转录水平上的调控网络。
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引用次数: 0
Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom. 真菌界合子后物种边界的强制执行。
IF 12.9 1区 生物学 Q1 Medicine Pub Date : 2022-12-21 DOI: 10.1128/mmbr.00098-22
Jui-Yu Chou, Po-Chen Hsu, Jun-Yi Leu

Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.

了解物种形成的分子基础是进化生物学的首要目标。合子后生殖隔离的形成导致杂交功能障碍,从而减少不同种群之间的基因流动,这对物种形成至关重要。利用各种先进的方法,包括染色体替换、杂交渗入和转录组学、群体基因组学和实验进化,科学家们揭示了真菌王国中涉及合子后屏障的多种机制。这些结果阐明了真菌物种形成的独特和一般特征。本文综述了真菌中Dobzhansky-Muller不相容、杀手减数分裂驱动、染色体重排和抗重组对合子后生殖分离的影响。我们还讨论了不同生殖隔离机制背后可能的进化力量,以及在红皇后假说和物种形成的表观遗传分化下进化军备竞赛的潜在作用。
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引用次数: 2
Roles of the Microbiota of the Female Reproductive Tract in Gynecological and Reproductive Health. 女性生殖道微生物群在妇科和生殖健康中的作用。
IF 8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2022-12-21 Epub Date: 2022-10-12 DOI: 10.1128/mmbr.00181-21
Bin Zhu, Zhi Tao, Laahirie Edupuganti, Myrna G Serrano, Gregory A Buck

The microbiome of the female reproductive tract defies the convention that high biodiversity is a hallmark of an optimal ecosystem. Although not universally true, a homogeneous vaginal microbiome composed of species of Lactobacillus is generally associated with health, whereas vaginal microbiomes consisting of other taxa are generally associated with dysbiosis and a higher risk of disease. The past decade has seen a rapid advancement in our understanding of these unique biosystems. Of particular interest, substantial effort has been devoted to deciphering how members of the microbiome of the female reproductive tract impact pregnancy, with a focus on adverse outcomes, including but not limited to preterm birth. Herein, we review recent research efforts that are revealing the mechanisms by which these microorganisms of the female reproductive tract influence gynecologic and reproductive health of the female reproductive tract.

女性生殖道的微生物组违背了高度生物多样性是最佳生态系统标志的惯例。尽管并非普遍正确,但由乳杆菌组成的同质阴道微生物组通常与健康有关,而由其他分类群组成的阴道微生物组一般与微生态失调和更高的疾病风险有关。在过去的十年里,我们对这些独特的生物系统的理解取得了迅速的进步。特别令人感兴趣的是,人们致力于解读女性生殖道微生物组成员如何影响妊娠,重点关注不良后果,包括但不限于早产。在此,我们回顾了最近的研究工作,这些研究工作揭示了女性生殖道中的这些微生物影响女性生殖道妇科和生殖健康的机制。
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引用次数: 0
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Microbiology and Molecular Biology Reviews
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