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Cas9 degradation in human cells using phage anti-CRISPR proteins 利用噬菌体抗 CRISPR 蛋白在人体细胞中降解 Cas9
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-08 DOI: 10.1371/journal.pbio.3002431
Zuriah Meacham, Luisa Arake de Tacca, Joseph Bondy-Denomy, David Rabuka, Michael Schelle
Bacteriophages encode anti-CRISPR (Acr) proteins that inactivate CRISPR-Cas bacterial immune systems, allowing successful invasion, replication, and prophage integration. Acr proteins inhibit CRISPR-Cas systems using a wide variety of mechanisms. AcrIIA1 is encoded by numerous phages and plasmids, binds specifically to the Cas9 HNH domain, and was the first Acr discovered to inhibit SpyCas9. Here, we report the observation of AcrIIA1-induced degradation of SpyCas9 and SauCas9 in human cell culture, the first example of Acr-induced degradation of CRISPR-Cas nucleases in human cells. AcrIIA1-induced degradation of SpyCas9 is abolished by mutations in AcrIIA1 that break a direct physical interaction between the 2 proteins. Targeted Cas9 protein degradation by AcrIIA1 could modulate Cas9 nuclease activity in human therapies. The small size and specificity of AcrIIA1 could be used in a CRISPR-Cas proteolysis-targeting chimera (PROTAC), providing a tool for developing safe and precise gene editing applications.
噬菌体编码抗crispr (Acr)蛋白,使CRISPR-Cas细菌免疫系统失活,从而成功入侵、复制和整合噬菌体。Acr蛋白通过多种机制抑制CRISPR-Cas系统。AcrIIA1被许多噬菌体和质粒编码,特异结合Cas9 HNH结构域,是第一个被发现抑制SpyCas9的Acr。在这里,我们报道了在人细胞培养中观察到的acria1诱导的SpyCas9和SauCas9的降解,这是acr诱导的CRISPR-Cas核酸酶在人细胞中降解的第一个例子。由于AcrIIA1突变破坏了这两种蛋白之间的直接物理相互作用,从而消除了AcrIIA1诱导的SpyCas9降解。在人类治疗中,靶向性降解Cas9蛋白可调节Cas9核酸酶活性。AcrIIA1的小尺寸和特异性可用于CRISPR-Cas蛋白水解靶向嵌合体(PROTAC),为开发安全和精确的基因编辑应用提供了工具。
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引用次数: 0
Sensory processing in humans and mice fluctuates between external and internal modes 人类和小鼠的感官处理在外部和内部模式之间波动
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-08 DOI: 10.1371/journal.pbio.3002410
V. Weilnhammer, Heiner Stuke, K. Standvoss, Philipp Sterzer
Perception is known to cycle through periods of enhanced and reduced sensitivity to external information. Here, we asked whether such slow fluctuations arise as a noise-related epiphenomenon of limited processing capacity or, alternatively, represent a structured mechanism of perceptual inference. Using 2 large-scale datasets, we found that humans and mice alternate between externally and internally oriented modes of sensory analysis. During external mode, perception aligns more closely with the external sensory information, whereas internal mode is characterized by enhanced biases toward perceptual history. Computational modeling indicated that dynamic changes in mode are enabled by 2 interlinked factors: (i) the integration of subsequent inputs over time and (ii) slow antiphase oscillations in the perceptual impact of external sensory information versus internal predictions that are provided by perceptual history. We propose that between-mode fluctuations generate unambiguous error signals that enable optimal inference in volatile environments.
我们知道,感知是在对外部信息的敏感度增强和降低的周期中循环的。在这里,我们询问这种缓慢的波动是作为有限处理能力的噪声相关的附带现象出现的,还是代表了感知推理的结构化机制。使用2个大规模的数据集,我们发现人类和小鼠在外部和内部导向的感官分析模式之间交替。在外部模式下,感知与外部感官信息更紧密地联系在一起,而内部模式的特点是对感知历史的偏见增强。计算模型表明,模式的动态变化是由两个相互关联的因素实现的:(i)随着时间的推移整合后续输入;(ii)外部感官信息对感知影响的缓慢反相位振荡,而不是由感知历史提供的内部预测。我们提出,模间波动产生明确的误差信号,使最优推理在多变的环境。
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引用次数: 0
Eukaryotic CD-NTase, STING, and viperin proteins evolved via domain shuffling, horizontal transfer, and ancient inheritance from prokaryotes 真核生物的 CD-NTase、STING 和蝰蛇蛋白是通过结构域洗牌、水平转移和原核生物的古老遗传进化而来的
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-08 DOI: 10.1371/journal.pbio.3002436
Edward M. Culbertson, T. C. Levin
Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to antiphage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for 3 innate immune families (CD-NTases [including cGAS], STINGs, and viperins) by deeply sampling protein diversity across eukaryotes. We find that viperins and OAS family CD-NTases are ancient immune proteins, likely inherited since the earliest eukaryotes first arose. In contrast, we find other immune proteins that were acquired via at least 4 independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while 2 more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the cGLR superfamily (containing cGAS) that has diversified via a series of animal-specific duplications and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STING protein domains undergoing convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial antiphage genes.
动物使用多种细胞自主的先天免疫蛋白来检测病毒感染并防止复制。最近的研究发现,哺乳动物抗病毒蛋白的一个子集与细菌中的噬菌体防御蛋白具有同源性,这意味着在生命之树中存在先天免疫的某些方面。虽然这些研究大多集中在描述细菌蛋白质的多样性和生化功能上,但动物和细菌蛋白质之间的进化关系却不太清楚。这种不确定性部分是由于动物和细菌蛋白质之间的进化距离较远,这模糊了它们之间的关系。在这里,我们通过深入采样真核生物的蛋白质多样性来解决3个先天免疫家族(cd - nases[包括cGAS], STINGs和viperins)的这个问题。我们发现蝰蛇和OAS家族cd - nase是古老的免疫蛋白,可能从最早的真核生物出现以来就遗传了。相比之下,我们发现其他免疫蛋白是通过至少4个独立的细菌水平基因转移(HGT)事件获得的。其中两个事件允许藻类获得新的细菌蝰蛇,而另外两个HGT事件产生了真核生物cd - nase的不同超家族:cGLR超家族(包含cGAS)通过一系列动物特异性复制而多样化,以及以前未定义的eSMODS超家族,它更类似于细菌cd - nase。最后,我们发现cGAS和STING蛋白具有本质上不同的历史,STING蛋白结构域在细菌和真核生物中经历了收敛的结构域改组。总的来说,我们的研究结果描绘了真核生物先天免疫的高度动态图景,真核生物通过重复使用蛋白质结构域和反复采样丰富的细菌噬菌体基因库,建立了它们古老的抗病毒能力。
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引用次数: 0
Collective production of hydrogen sulfide gas enables budding yeast lacking MET17 to overcome their metabolic defect 集体产生硫化氢气体可使缺乏 MET17 的芽殖酵母克服代谢缺陷
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-07 DOI: 10.1371/journal.pbio.3002439
Sonal, Alex E. Yuan, Xueqin Yang, Wenying Shou
Assimilation of sulfur is vital to all organisms. In S. cerevisiae, inorganic sulfate is first reduced to sulfide, which is then affixed to an organic carbon backbone by the Met17 enzyme. The resulting homocysteine can then be converted to all other essential organosulfurs such as methionine, cysteine, and glutathione. This pathway has been known for nearly half a century, and met17 mutants have long been classified as organosulfur auxotrophs, which are unable to grow on sulfate as their sole sulfur source. Surprisingly, we found that met17Δ could grow on sulfate, albeit only at sufficiently high cell densities. We show that the accumulation of hydrogen sulfide gas underpins this density-dependent growth of met17Δ on sulfate and that the locus YLL058W (HSU1) enables met17Δ cells to assimilate hydrogen sulfide. Hsu1 protein is induced during sulfur starvation and under exposure to high sulfide concentrations in wild-type cells, and the gene has a pleiotropic role in sulfur assimilation. In a mathematical model, the low efficiency of sulfide assimilation in met17Δ can explain the observed density-dependent growth of met17Δ on sulfate. Thus, having uncovered and explained the paradoxical growth of a commonly used “auxotroph,” our findings may impact the design of future studies in yeast genetics, metabolism, and volatile-mediated microbial interactions.
硫的同化对所有生物都是至关重要的。在酿酒酵母中,无机硫酸盐首先被还原成硫化物,然后由Met17酶附着在有机碳主链上。由此产生的同型半胱氨酸可以转化为所有其他必需的有机硫,如蛋氨酸、半胱氨酸和谷胱甘肽。这一途径已经被发现了近半个世纪,而met17突变体长期以来一直被归类为有机硫营养不良体,它们不能以硫酸盐作为唯一的硫源生长。令人惊讶的是,我们发现met17Δ可以在硫酸盐上生长,尽管只有在足够高的细胞密度下。我们发现,硫化氢气体的积累支撑了met17Δ在硫酸盐上的这种密度依赖性生长,并且YLL058W (HSU1)位点使met17Δ细胞能够吸收硫化氢。在野生型细胞中,Hsu1蛋白在硫饥饿和高浓度硫环境下被诱导,该基因在硫同化中具有多向性作用。在数学模型中,met17Δ中硫化物同化的低效率可以解释met17Δ对硫酸盐的密度依赖性生长。因此,发现并解释了一种常用的“营养不良菌”的矛盾生长,我们的发现可能会影响酵母遗传学、代谢和挥发物介导的微生物相互作用的未来研究设计。
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引用次数: 0
Changes in sea floor productivity are crucial to understanding the impact of climate change in temperate coastal ecosystems according to a new size-based model 根据一种基于尺寸的新模型,海底生产力的变化对于了解气候变化对温带沿海生态系统的影响至关重要
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-01 DOI: 10.1371/journal.pbio.3002392
A. Audzijonyte, Gustav W. Delius, R. Stuart‐Smith, C. Novaglio, G. Edgar, Neville S. Barrett, Julia L. Blanchard
The multifaceted effects of climate change on physical and biogeochemical processes are rapidly altering marine ecosystems but often are considered in isolation, leaving our understanding of interactions between these drivers of ecosystem change relatively poor. This is particularly true for shallow coastal ecosystems, which are fuelled by a combination of distinct pelagic and benthic energy pathways that may respond to climate change in fundamentally distinct ways. The fish production supported by these systems is likely to be impacted by climate change differently to those of offshore and shelf ecosystems, which have relatively simpler food webs and mostly lack benthic primary production sources. We developed a novel, multispecies size spectrum model for shallow coastal reefs, specifically designed to simulate potential interactive outcomes of changing benthic and pelagic energy inputs and temperatures and calculate the relative importance of these variables for the fish community. Our model, calibrated using field data from an extensive temperate reef monitoring program, predicts that changes in resource levels will have much stronger impacts on fish biomass and yields than changes driven by physiological responses to temperature. Under increased plankton abundance, species in all fish trophic groups were predicted to increase in biomass, average size, and yields. By contrast, changes in benthic resources produced variable responses across fish trophic groups. Increased benthic resources led to increasing benthivorous and piscivorous fish biomasses, yields, and mean body sizes, but biomass decreases among herbivore and planktivore species. When resource changes were combined with warming seas, physiological responses generally decreased species’ biomass and yields. Our results suggest that understanding changes in benthic production and its implications for coastal fisheries should be a priority research area. Our modified size spectrum model provides a framework for further study of benthic and pelagic energy pathways that can be easily adapted to other ecosystems.
气候变化对物理和生物地球化学过程的多方面影响正在迅速改变海洋生态系统,但往往被孤立地考虑,使我们对这些生态系统变化驱动因素之间的相互作用的理解相对较差。对于浅海生态系统来说尤其如此,这些生态系统是由不同的上层和底栖能量途径组合而成的,它们可能以根本不同的方式对气候变化作出反应。这些系统支持的鱼类生产可能受到气候变化的影响,这与近海和大陆架生态系统的影响不同,后者的食物网相对简单,而且大多缺乏底栖生物的初级生产来源。我们开发了一种新的、多物种大小的浅海珊瑚礁光谱模型,专门用于模拟底栖生物和远洋生物能量输入和温度变化的潜在交互结果,并计算这些变量对鱼类群落的相对重要性。我们的模型使用广泛的温带珊瑚礁监测项目的现场数据进行校准,预测资源水平的变化将对鱼类生物量和产量产生更大的影响,而不是由温度生理反应驱动的变化。在浮游生物丰度增加的情况下,预计所有鱼类营养类群的生物量、平均大小和产量都会增加。相比之下,底栖生物资源的变化在鱼类营养群体中产生了不同的反应。底栖生物资源的增加导致了食性和食性鱼类的生物量、产量和平均体型的增加,但草食和浮游生物的生物量减少。当资源变化与海洋变暖相结合时,生理反应通常会降低物种的生物量和产量。我们的研究结果表明,了解底栖生物产量的变化及其对沿海渔业的影响应该是一个优先研究领域。我们改进的尺寸谱模型为进一步研究底栖生物和远洋生物的能量途径提供了一个框架,可以很容易地适应其他生态系统。
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引用次数: 1
It is time to authenticate the Microbiome Sciences with accredited educational programs and departments 现在是时候通过经认可的教育计划和部门对微生物组科学进行认证了
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-01 DOI: 10.1371/journal.pbio.3002420
Nichole Ginnan, Seth R. Bordenstein
The Microbiome Sciences are at a crucial maturation stage. Scientists and educators should now view the Microbiome Sciences as a flourishing and autonomous discipline, creating degree programs and departments that are conducive to cohesive growth.
微生物组学正处于关键的成熟阶段。科学家和教育工作者现在应该将微生物组科学视为一个蓬勃发展的自主学科,创建有利于凝聚力增长的学位课程和部门。
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引用次数: 0
Towards detailed predictions of coastal ecosystem function under climate change 努力详细预测气候变化下的沿岸生态系统功能
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-01 DOI: 10.1371/journal.pbio.3002430
Diego R. Barneche, Renato A. Morais
The complex ways in which ongoing warming will restructure ecosystems remains poorly understood. A new simulation study in PLOS Biology suggests that expected changes in food resources for marine consumers will outpace the direct, pervasive effects of predicted +2.5°C warming.
持续变暖将以何种复杂的方式重构生态系统,人们仍知之甚少。PLOS Biology上的一项新的模拟研究表明,海洋消费者食物资源的预期变化将超过预测的+2.5°C变暖的直接、普遍影响。
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引用次数: 0
Editorial Note: The Communication Factor EDF and the Toxin-Antitoxin Module mazEF Determine the Mode of Action of Antibiotics. 编者按:通讯因子EDF和毒素抗毒素模块mazEF决定了抗生素的作用模式。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-18 eCollection Date: 2023-09-01 DOI: 10.1371/journal.pbio.3002325
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引用次数: 0
SEC14-like condensate phase transitions at plasma membranes regulate root growth in Arabidopsis. 质膜上类似SEC14的缩合物相变调节拟南芥根系的生长。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-18 eCollection Date: 2023-09-01 DOI: 10.1371/journal.pbio.3002305
Chen Liu, Andriani Mentzelopoulou, Fotini Papagavriil, Prashanth Ramachandran, Artemis Perraki, Lucas Claus, Sebastian Barg, Peter Dörmann, Yvon Jaillais, Philipp Johnen, Eugenia Russinova, Electra Gizeli, Gabriel Schaaf, Panagiotis Nikolaou Moschou

Protein function can be modulated by phase transitions in their material properties, which can range from liquid- to solid-like; yet, the mechanisms that drive these transitions and whether they are important for physiology are still unknown. In the model plant Arabidopsis, we show that developmental robustness is reinforced by phase transitions of the plasma membrane-bound lipid-binding protein SEC14-like. Using imaging, genetics, and in vitro reconstitution experiments, we show that SEC14-like undergoes liquid-like phase separation in the root stem cells. Outside the stem cell niche, SEC14-like associates with the caspase-like protease separase and conserved microtubule motors at unique polar plasma membrane interfaces. In these interfaces, SEC14-like undergoes processing by separase, which promotes its liquid-to-solid transition. This transition is important for root development, as lines expressing an uncleavable SEC14-like variant or mutants of separase and associated microtubule motors show similar developmental phenotypes. Furthermore, the processed and solidified but not the liquid form of SEC14-like interacts with and regulates the polarity of the auxin efflux carrier PINFORMED2. This work demonstrates that robust development can involve liquid-to-solid transitions mediated by proteolysis at unique plasma membrane interfaces.

蛋白质的功能可以通过其材料性质的相变来调节,材料性质可以从液态到固态;然而,驱动这些转变的机制以及它们对生理学是否重要仍然未知。在模式植物拟南芥中,我们发现质膜结合的脂质结合蛋白SEC14-like的相变增强了发育的稳健性。利用成像、遗传学和体外重建实验,我们发现SEC14-like在根干细胞中经历液相分离。在干细胞生态位之外,SEC14样与胱天蛋白酶样蛋白酶分离酶结合,并在独特的极性质膜界面上保守微管马达。在这些界面中,SEC14-like通过分离酶进行处理,从而促进其从液体到固体的转变。这种转变对根系发育很重要,因为表达分离酶和相关微管马达的不可清除的SEC14样变体或突变体的系表现出相似的发育表型。此外,加工和固化但不是液体形式的SEC14-like与生长素流出载体PINFORMED2相互作用并调节其极性。这项工作表明,稳健的发展可能涉及在独特的质膜界面上通过蛋白水解介导的液体到固体的转变。
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引用次数: 0
Selective retention of dysfunctional mitochondria during asymmetric cell division in yeast. 酵母不对称细胞分裂过程中功能失调线粒体的选择性保留。
IF 9.8 1区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-18 eCollection Date: 2023-09-01 DOI: 10.1371/journal.pbio.3002310
Xenia Chelius, Veronika Bartosch, Nathalie Rausch, Magdalena Haubner, Jana Schramm, Ralf J Braun, Till Klecker, Benedikt Westermann

Decline of mitochondrial function is a hallmark of cellular aging. To counteract this process, some cells inherit mitochondria asymmetrically to rejuvenate daughter cells. The molecular mechanisms that control this process are poorly understood. Here, we made use of matrix-targeted D-amino acid oxidase (Su9-DAO) to selectively trigger oxidative damage in yeast mitochondria. We observed that dysfunctional mitochondria become fusion-incompetent and immotile. Lack of bud-directed movements is caused by defective recruitment of the myosin motor, Myo2. Intriguingly, intact mitochondria that are present in the same cell continue to move into the bud, establishing that quality control occurs directly at the level of the organelle in the mother. The selection of healthy organelles for inheritance no longer works in the absence of the mitochondrial Myo2 adapter protein Mmr1. Together, our data suggest a mechanism in which the combination of blocked fusion and loss of motor protein ensures that damaged mitochondria are retained in the mother cell to ensure rejuvenation of the bud.

线粒体功能下降是细胞衰老的标志。为了抵消这一过程,一些细胞不对称地继承线粒体,使子细胞恢复活力。控制这一过程的分子机制尚不清楚。在这里,我们利用基质靶向D-氨基酸氧化酶(Su9-DAO)选择性触发酵母线粒体的氧化损伤。我们观察到功能失调的线粒体变得融合无能和不稳定。缺乏芽定向运动是由肌球蛋白运动Myo2的募集缺陷引起的。有趣的是,存在于同一细胞中的完整线粒体继续进入芽中,从而确定质量控制直接发生在母亲细胞器的水平上。在缺乏线粒体Myo2衔接蛋白Mmr1的情况下,选择健康细胞器进行遗传不再有效。总之,我们的数据表明了一种机制,在这种机制中,融合受阻和运动蛋白损失的结合确保了受损的线粒体保留在母细胞中,以确保芽的再生。
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引用次数: 0
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