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Tradeoffs and constraints on the evolution of tailocins 尾蛋白进化过程中的权衡与制约因素
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-18 DOI: 10.1016/j.tim.2024.04.001
Talia Backman, Hernán A. Burbano, Talia L. Karasov

Phage tail-like bacteriocins (tailocins) are protein complexes produced by bacteria with the potential to kill their neighbors. Widespread throughout Gram-negative bacteria, tailocins exhibit extreme specificity in their targets, largely killing closely related strains. Despite their presence in diverse bacteria, the impact of these competitive weapons on the surrounding microbiota is largely unknown. Recent studies revealed the rapid evolution and genetic diversity of tailocins in microbial communities and suggest that there are constraints on the evolution of specificity and resistance. Given the precision of their targeted killing and the ease of engineering new specificities, understanding the evolution and ecological impact of tailocins may enable the design of promising candidates for novel targeted antibiotics.

噬菌体尾部类细菌素(tailocins)是细菌产生的蛋白质复合物,具有杀死邻近细菌的潜能。噬菌体尾蛋白广泛存在于革兰氏阴性细菌中,对目标具有极强的特异性,主要杀死近缘菌株。尽管它们存在于各种细菌中,但这些竞争性武器对周围微生物区系的影响在很大程度上还不为人所知。最近的研究揭示了尾蛋白在微生物群落中的快速进化和遗传多样性,并表明特异性和抗药性的进化受到了限制。由于尾蛋白具有精确的靶向杀伤力,而且很容易设计出新的特异性,因此了解尾蛋白的进化和对生态的影响可能有助于设计出有前途的新型靶向抗生素候选物。
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引用次数: 0
The use of experimentally evolved coral photosymbionts for reef restoration. 利用实验进化的珊瑚光合共生体恢复珊瑚礁。
IF 14 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-12 DOI: 10.1016/j.tim.2024.05.008
Matthew R Nitschke, David Abrego, Corinne E Allen, Carlos Alvarez-Roa, Nadine M Boulotte, Patrick Buerger, Wing Yan Chan, Wladimir A Fae Neto, Elizabeth Ivory, Bede Johnston, Luka Meyers, Catalina Parra V, Lesa Peplow, Tahirih Perez, Hugo J Scharfenstein, Madeleine J H van Oppen

The heat tolerance of corals is largely determined by their microbial photosymbionts (Symbiodiniaceae, colloquially known as zooxanthellae). Therefore, manipulating symbiont communities may enhance the ability of corals to survive summer heatwaves. Although heat-tolerant and -sensitive symbiont species occur in nature, even corals that harbour naturally tolerant symbionts have been observed to bleach during summer heatwaves. Experimental evolution (i.e., laboratory selection) of Symbiodiniaceae cultures under elevated temperatures has been successfully used to enhance their upper thermal tolerance, both in vitro and, in some instances, following their reintroduction into corals. In this review, we present the state of this intervention and its potential role within coral reef restoration, and discuss the next critical steps required to bridge the gap to implementation.

珊瑚的耐热性在很大程度上取决于其微生物光合共生体(Symbiodiniaceae,俗称zooxanthellae)。因此,操纵共生体群落可以提高珊瑚在夏季热浪中的生存能力。虽然自然界中存在耐热和不耐热的共生物种,但即使是天然耐热共生物种的珊瑚也会在夏季热浪中出现白化现象。在高温条件下对共生藻培养物进行实验性进化(即实验室选择)已被成功地用于提高它们在体外以及在某些情况下重新引入珊瑚后的上层耐热性。在这篇综述中,我们介绍了这种干预措施的现状及其在珊瑚礁恢复中的潜在作用,并讨论了弥合实施差距所需的下一个关键步骤。
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引用次数: 0
KAP1/TRIM28 - antiviral and proviral protagonist of herpesvirus biology. KAP1/TRIM28--疱疹病毒生物学中的抗病毒和激病毒主角。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-12 DOI: 10.1016/j.tim.2024.05.007
Sumita Bhaduri-McIntosh, Beth A Rousseau

Dysregulation of the constitutive heterochromatin machinery (HCM) that silences pericentromeric regions and endogenous retroviral elements in the human genome has consequences for aging and cancer. By recruiting epigenetic regulators, Krüppel-associated box (KRAB)-associated protein 1 (KAP1/TRIM28/TIF1β) is integral to the function of the HCM. Epigenetically silencing DNA genomes of incoming herpesviruses to enforce latency, KAP1 and HCM also serve in an antiviral capacity. In addition to gene silencing, newer reports highlight KAP1's ability to directly activate cellular gene transcription. Here, we discuss the many facets of KAP1, including recent findings that unexpectedly connect KAP1 to the inflammasome, reveal KAP1 cleavage as a novel mode of regulation, and argue for a pro-herpesviral KAP1 function that ensures transition from transcription to replication of the herpesvirus genome.

组成型异染色质机制(HCM)沉默了人类基因组中的围中心染色质区域和内源性逆转录病毒元件,这种机制的失调会对衰老和癌症产生影响。通过招募表观遗传调节因子,Krüppel相关盒(KRAB)相关蛋白1(KAP1/TRIM28/TIF1β)对HCM的功能起着不可或缺的作用。KAP1 和 HCM 还能在表观遗传学上沉默传入疱疹病毒的 DNA 基因组,以加强潜伏性。除了基因沉默之外,最新的报告还强调了 KAP1 直接激活细胞基因转录的能力。在此,我们将讨论 KAP1 的方方面面,包括最近的研究结果,这些结果出人意料地将 KAP1 与炎症小体联系在一起,揭示了 KAP1 裂解是一种新的调控模式,并论证了 KAP1 的促疱疹病毒功能,该功能可确保疱疹病毒基因组从转录过渡到复制。
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引用次数: 0
The growing repertoire of phage anti-defence systems. 噬菌体抗防御系统的种类越来越多。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-05 DOI: 10.1016/j.tim.2024.05.005
Khalimat Murtazalieva, Andre Mu, Aleksandra Petrovskaya, Robert D Finn

The biological interplay between phages and bacteria has driven the evolution of phage anti-defence systems (ADSs), which evade bacterial defence mechanisms. These ADSs bind and inhibit host defence proteins, add covalent modifications and deactivate defence proteins, degrade or sequester signalling molecules utilised by host defence systems, synthesise and restore essential molecules depleted by bacterial defences, or add covalent modifications to phage molecules to avoid recognition. Overall, 145 phage ADSs have been characterised to date. These ADSs counteract 27 of the 152 different bacterial defence families, and we hypothesise that many more ADSs are yet to be discovered. We discuss high-throughput approaches (computational and experimental) which are indispensable for discovering new ADSs and the limitations of these approaches. A comprehensive characterisation of phage ADSs is critical for understanding phage-host interplay and developing clinical applications, such as treatment for multidrug-resistant bacterial infections.

噬菌体与细菌之间的生物相互作用推动了噬菌体抗防御系统(ADS)的进化,这种系统可以躲避细菌的防御机制。这些 ADS 可结合并抑制宿主防御蛋白,添加共价修饰并使防御蛋白失活,降解或封存宿主防御系统使用的信号分子,合成并恢复被细菌防御系统耗尽的必需分子,或对噬菌体分子添加共价修饰以避免被识别。迄今为止,已对 145 种噬菌体 ADS 进行了鉴定。这些 ADS 抵消了 152 种不同细菌防御家族中的 27 种,我们假设还有更多的 ADS 尚待发现。我们讨论了发现新 ADS 必不可少的高通量方法(计算和实验)以及这些方法的局限性。全面描述噬菌体 ADS 对于理解噬菌体与宿主的相互作用以及开发临床应用(如治疗耐多药细菌感染)至关重要。
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引用次数: 0
Subscription and Copyright Information 订阅和版权信息
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-04 DOI: 10.1016/s0966-842x(24)00121-5
No Abstract
无摘要
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引用次数: 0
Unraveling host regulation of gut microbiota through the epigenome-microbiome axis. 通过表观基因组-微生物组轴揭示宿主对肠道微生物群的调控。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-04 DOI: 10.1016/j.tim.2024.05.006
Michael L Pepke, Søren B Hansen, Morten T Limborg

Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.

最近对宿主生物的表观遗传修饰与其相关肠道微生物群的组成或活性之间的动态相互作用的研究表明,宿主有机会通过表观遗传改变来塑造其微生物群,从而导致基因表达和非编码 RNA 活性的变化。我们利用从微生物诱导的表观遗传变化中获得的洞察力来审视宿主对其肠道微生物组进行表观遗传调控的潜力,由此产生了一个双向的 "表观遗传组-微生物组轴"。该轴包含环境诱导的变异,可能会影响宿主-微生物相互作用的适应性进化。此外,我们还介绍了如何在整体原子框架内理解和研究表观基因组-微生物组轴,并将其应用于应用健康和食品科学领域。
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引用次数: 0
Advisory Board and Contents 咨询委员会和内容
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-04 DOI: 10.1016/s0966-842x(24)00118-5
No Abstract
无摘要
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引用次数: 0
Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition. 加强农业生态系统氮管理:改善硝化抑制的微生物见解。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-01 Epub Date: 2023-11-15 DOI: 10.1016/j.tim.2023.10.009
Fabian Beeckman, Laure Annetta, Mario Corrochano-Monsalve, Tom Beeckman, Hans Motte

Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.

硝化作用是氮(N)循环中将氨转化为硝酸盐的关键微生物过程。过度硝化作用通常发生在农业生态系统中,具有负面的环境影响,包括富营养化和温室气体排放。硝化抑制剂通过降低硝化速率和提高氮素利用效率,在农业系统中广泛应用于氮素管理。然而,NIs的有效性可能因土壤条件而异,而土壤条件反过来又影响微生物群落和硝化微生物不同功能群之间的平衡。了解土壤微生物群落或非生物因素对氮肥有效性的影响机制,对促进可持续施肥至关重要。因此,本文综述了不同类型的NIs以及非生物参数如何影响硝化群落,从而影响NIs的功效。通过讨论该领域的最新研究,我们提供了一些见解,可以促进更有针对性、更高效或互补的NIs的发展,从而提高NIs在农业生态系统可持续管理实践中的应用。
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引用次数: 0
Projecting global biological N2 fixation under climate warming across land and ocean. 预测气候变暖条件下陆地和海洋的全球生物 N2 固定量。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-01 Epub Date: 2024-01-22 DOI: 10.1016/j.tim.2023.12.007
Curtis Deutsch, Keisuke Inomura, Ya-Wei Luo, Ying-Ping Wang

Biological N2 fixation sustains the global inventory of nitrogenous nutrients essential for the productivity of terrestrial and marine ecosystems. Like most metabolic processes, rates of biological N2 fixation vary strongly with temperature, making it sensitive to climate change, but a global projection across land and ocean is lacking. Here we use compilations of field and laboratory measurements to reveal a relationship between N2 fixation rates and temperature that is similar in both domains despite large taxonomic and environmental differences. Rates of N2 fixation increase gradually to a thermal optimum around ~25°C, and decline more rapidly toward a thermal maximum, which is lower in the ocean than on land. In both realms, the observed temperature sensitivities imply that climate warming this century could decrease N2 fixation rates by ~50% in the tropics while increasing rates by ~50% in higher latitudes. We propose a conceptual framework for understanding the physiological and ecological mechanisms that underpin and modulate the observed temperature dependence of global N2 fixation rates, facilitating cross-fertilization of marine and terrestrial research to assess its response to climate change.

生物固氮维持着陆地和海洋生态系统生产力所必需的全球氮营养物质库存。与大多数新陈代谢过程一样,生物固氮的速率随温度的变化而变化,因此对气候变化非常敏感,但目前还缺乏对陆地和海洋的全球预测。在这里,我们通过对野外和实验室测量数据的汇编,揭示了氮固定率与温度之间的关系,尽管在分类学和环境方面存在巨大差异,但这两个领域的氮固定率与温度之间的关系是相似的。N2固定率在约25°C时逐渐升高到最佳温度,在达到最高温度时则迅速下降,海洋中的最高温度低于陆地。在这两个领域中,观测到的温度敏感性意味着,本世纪气候变暖可能会使热带地区的氮固定率下降约 50%,而使高纬度地区的氮固定率上升约 50%。我们提出了一个概念框架,用于理解支撑和调节所观测到的全球 N2 固定率的温度依赖性的生理和生态机制,促进海洋和陆地研究的交叉融合,以评估其对气候变化的响应。
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引用次数: 0
Revisiting methane-dependent denitrification. 重新审视甲烷依赖性反硝化作用。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-01 Epub Date: 2024-03-22 DOI: 10.1016/j.tim.2024.03.007
Mengxiong Wu, Tao Liu, Jianhua Guo

Methane-dependent denitrification links the global nitrogen and methane cycles. Since its initial discovery in 2006, this process has been understood to involve a division of labor between an archaeal group and a bacterial group, which sequentially perform nitrate and nitrite reduction, respectively. Yao et al. have now revised this paradigm by identifying a Methylomirabilis bacterium capable of performing methane-dependent complete denitrification on its own.

依赖甲烷的反硝化作用将全球氮和甲烷循环联系在一起。自 2006 年首次发现以来,人们一直认为这一过程涉及古菌群和细菌群之间的分工,它们依次分别进行硝酸盐和亚硝酸盐还原。现在,Yao 等人修正了这一模式,发现了一种 Methylomirabilis 细菌,它能够独立完成依赖甲烷的完全反硝化作用。
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引用次数: 0
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Trends in Microbiology
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