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The Prokaryotic Roots of Eukaryotic Immune Systems 真核生物免疫系统的原核根源
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-12 DOI: 10.1146/annurev-genet-111523-102448
L. Aravind, Gianlucca G. Nicastro, Lakshminarayan M. Iyer, A. Maxwell Burroughs
Over the past two decades, studies have revealed profound evolutionary connections between prokaryotic and eukaryotic immune systems, challenging the notion of their unrelatedness. Immune systems across the tree of life share an operational framework, shaping their biochemical logic and evolutionary trajectories. The diversification of immune genes in the prokaryotic superkingdoms, followed by lateral transfer to eukaryotes, was central to the emergence of innate immunity in the latter. These include protein domains related to nucleotide second messenger–dependent systems, NAD+/nucleotide degradation, and P-loop NTPase domains of the STAND and GTPase clades playing pivotal roles in eukaryotic immunity and inflammation. Moreover, several domains orchestrating programmed cell death, ultimately of prokaryotic provenance, suggest an intimate link between immunity and the emergence of multicellularity in eukaryotes such as animals. While eukaryotes directly adopted some proteins from bacterial immune systems, they repurposed others for new immune functions from bacterial interorganismal conflict systems. These emerging immune components hold substantial biotechnological potential.
在过去二十年里,研究揭示了原核生物和真核生物免疫系统之间深刻的进化联系,挑战了它们互不相关的观念。生命树上的免疫系统共享一个运作框架,塑造了它们的生化逻辑和进化轨迹。原核生物超级王国中免疫基因的多样化,以及随后向真核生物的横向转移,是真核生物出现先天性免疫的关键。这些基因包括与核苷酸第二信使依赖系统、NAD+/核苷酸降解有关的蛋白质结构域,以及在真核生物免疫和炎症中发挥关键作用的 STAND 和 GTPase 家族的 P 环 NTPase 结构域。此外,一些协调细胞程序性死亡的结构域最终来源于原核生物,这表明免疫与真核生物(如动物)多细胞性的出现之间存在密切联系。真核生物直接从细菌免疫系统中采用了一些蛋白质,同时还从细菌的机体间冲突系统中重新利用了其他蛋白质来实现新的免疫功能。这些新出现的免疫成分蕴含着巨大的生物技术潜力。
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引用次数: 0
The Nature and Nurture of Extracellular Vesicle-Mediated Signaling. 细胞外囊泡介导的信号传导的性质和发展。
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-04 DOI: 10.1146/annurev-genet-111523-102725
Amy H Buck, Esther N M Nolte-'t Hoen

In the last decade, it has become clear that extracellular vesicles (EVs) are a ubiquitous component of living systems. These small membrane-enclosed particles can confer diverse functions to the cells that release, capture, or coexist with them in an environment. We use examples across living systems to produce a conceptual framework that classifies three modes by which EVs exert their functions: (a) EV release that serves a function for producing cells, (b) EV modification of the extracellular environment, and (c) EV interactions with, and alteration of, receiving cells. We provide an overview of the inherent properties of EVs (i.e., their nature) as well as factors in the environment and receiving cell (i.e., nurture) that determine whether transmission of EV cargo leads to functional cellular responses. This review broadens the context for ruminating on EV functions and highlights the emergent properties of EVs that define their role in biology and will shape their applications in medicine.

近十年来,人们已经清楚地认识到,细胞外囊泡(EVs)是生命系统中无处不在的组成部分。这些被膜包裹的小颗粒可以为释放、捕获它们或与它们共存于环境中的细胞赋予各种功能。我们利用生命系统中的实例建立了一个概念框架,将 EVs 发挥其功能的三种模式进行了分类:(a)EV 释放,为产生细胞提供功能;(b)EV 改变细胞外环境;以及(c)EV 与接收细胞相互作用并改变接收细胞。我们概述了 EVs 的固有特性(即其本质)以及环境和接收细胞中决定 EV 货物运输是否会导致功能性细胞反应的因素(即养育)。这篇综述拓宽了研究EV功能的背景,突出了EV的新特性,这些特性决定了EV在生物学中的作用,并将影响其在医学中的应用。
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引用次数: 0
Integrating the Study of Polyploidy Across Organisms, Tissues, and Disease. 整合跨生物体、组织和疾病的多倍体研究。
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-03 DOI: 10.1146/annurev-genet-111523-102124
John P Morris, Timour Baslan, Douglas E Soltis, Pamela S Soltis, Donald T Fox

Polyploidy is a cellular state containing more than two complete chromosome sets. It has largely been studied as a discrete phenomenon in either organismal, tissue, or disease contexts. Increasingly, however, investigation of polyploidy across disciplines is coalescing around common principles. For example, the recent Polyploidy Across the Tree of Life meeting considered the contribution of polyploidy both in organismal evolution over millions of years and in tumorigenesis across much shorter timescales. Here, we build on this newfound integration with a unified discussion of polyploidy in organisms, cells, and disease. We highlight how common polyploidy is at multiple biological scales, thus eliminating the outdated mindset of its specialization. Additionally, we discuss rules that are likely common to all instances of polyploidy. With increasing appreciation that polyploidy is pervasive in nature and displays fascinating commonalities across diverse contexts, inquiry related to this important topic is rapidly becoming unified.

多倍体是一种含有两个以上完整染色体组的细胞状态。在生物体、组织或疾病背景下,多倍体在很大程度上是作为一种离散现象进行研究的。不过,各学科对多倍体的研究正越来越多地围绕共同的原则展开。例如,最近召开的 "生命树上的多倍体"(Polyploidy Across the Tree of Life)会议审议了多倍体在数百万年的生物进化过程中以及在更短时间内的肿瘤发生过程中的贡献。在此,我们在这一新发现的整合基础上,对生物体、细胞和疾病中的多倍体进行了统一讨论。我们强调了多倍体在多种生物尺度上的普遍性,从而消除了其特殊性的过时观念。此外,我们还讨论了所有多倍体情况下可能存在的共同规则。随着越来越多的人认识到多倍体在自然界中普遍存在,并在不同的环境中显示出迷人的共性,与这一重要课题相关的研究正迅速走向统一。
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引用次数: 0
Placental Evolution: Innovating how to Feed Babies. 胎盘进化:创新婴儿喂养方式
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-03 DOI: 10.1146/annurev-genet-111523-102135
Julie C Baker

The evolution of the placenta was transformative. It changed how offspring are fed during gestation from depositing all the resources into an egg to continually supplying resources throughout gestation. Placental evolution is infinitely complex, with many moving parts, but at the core it is driven by a conflict over resources between the mother and the baby, which sets up a Red Queen race, fueling rapid diversification of morphological, cellular, and genetic forms. Placentas from even closely related species are highly divergent in form and function, and many cellular processes are distinct. If we could extract the entirety of genomic information for placentas across all species, including the many hundreds that have evolved in fish and reptiles, we could find their shared commonality, and that would tell us which of the many pieces really matter. We do not have this information, but we do have clues. Convergent evolution mechanisms were repeatedly used in the placenta, including the intense selective pressure to co-opt an envelope protein to build a multinucleated syncytium, the use of the same hormones and structural proteins in placentas derived from separate embryonic origins that arose hundreds of millions of years apart, and the co-option of endogenous retroviruses to form capsids as a way of transport and as mutagens to form new enhancers. As a result, the placental genome is the Wild West of biology, set up to rapidly change, adapt, and innovate. This ability to adapt facilitated the evolution of big babies with big brains and will continue to support offspring and their mothers in our ever-changing global environment.

胎盘的进化是一场变革。它改变了妊娠期喂养后代的方式,从将所有资源存入卵中,到在整个妊娠期不断提供资源。胎盘的进化是无限复杂的,有许多活动的部分,但其核心是由母体和胎儿之间的资源冲突驱动的,这种冲突引发了一场红皇后竞赛,推动了形态、细胞和遗传形式的快速多样化。即使是近亲物种的胎盘在形态和功能上也有很大差异,许多细胞过程也各不相同。如果我们能提取所有物种胎盘的全部基因组信息,包括在鱼类和爬行动物中进化出的数百种胎盘,我们就能找到它们的共同点,从而告诉我们在众多信息中哪些是真正重要的。我们没有这些信息,但我们有线索。聚合进化机制在胎盘中被反复使用,包括在强烈的选择压力下共同采用一种包膜蛋白来构建多核合胞体;在来自不同胚胎起源的胎盘中使用相同的激素和结构蛋白,这些胚胎起源相差数亿年;共同采用内源性逆转录病毒来形成囊壳,作为一种运输方式,并作为突变剂来形成新的增强子。因此,胎盘基因组是生物学中的狂野西部,可以快速变化、适应和创新。这种适应能力促进了大脑袋婴儿的进化,并将继续在不断变化的全球环境中支持后代和他们的母亲。
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引用次数: 0
Population Genomic Scans for Natural Selection and Demography. 用于自然选择和人口统计的种群基因组扫描。
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-03 DOI: 10.1146/annurev-genet-111523-102651
Xiaoheng Cheng, Matthias Steinrücken

Uncovering the fundamental processes that shape genomic variation in natural populations is a primary objective of population genetics. These processes include demographic effects such as past changes in effective population size or gene flow between structured populations. Furthermore, genomic variation is affected by selection on nonneutral genetic variants, for example, through the adaptation of beneficial alleles or balancing selection that maintains genetic variation. In this article, we discuss the characterization of these processes using population genetic models, and we review methods developed on the basis of these models to unravel the underlying processes from modern population genomic data sets. We briefly discuss the conditions in which these approaches can be used to infer demography or identify specific nonneutral genetic variants and cases in which caution is warranted. Moreover, we summarize the challenges of jointly inferring demography and selective processes that affect neutral variation genome-wide.

揭示形成自然种群基因组变异的基本过程是群体遗传学的首要目标。这些过程包括人口效应,如有效种群规模的过去变化或结构化种群之间的基因流动。此外,基因组变异还受到非中性遗传变异选择的影响,例如,通过有益等位基因的适应或维持遗传变异的平衡选择。在本文中,我们将讨论利用种群遗传模型描述这些过程的特征,并回顾在这些模型基础上开发的从现代种群基因组数据集中揭示潜在过程的方法。我们简要讨论了这些方法可用于推断人口统计学或识别特定非中性遗传变异的条件,以及需要谨慎对待的情况。此外,我们还总结了联合推断人口结构和影响全基因组中性变异的选择过程所面临的挑战。
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引用次数: 0
Cellular, Molecular, and Genetic Mechanisms of Avian Beak Development and Evolution. 鸟喙发育和进化的细胞、分子和遗传机制。
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-09-03 DOI: 10.1146/annurev-genet-111523-101929
Richard A Schneider

Diverse research programs employing complementary strategies have been uncovering cellular, molecular, and genetic mechanisms essential to avian beak development and evolution. In reviewing these discoveries, I offer an interdisciplinary perspective on bird beaks that spans their derivation from jaws of dinosaurian reptiles, their anatomical and ecological diversification across major taxonomic groups, their common embryonic origins, their intrinsic patterning processes, and their structural integration. I describe how descriptive and experimental approaches, including gene expression and cell lineage analyses, tissue recombinations, surgical transplants, gain- and loss-of-function methods, geometric morphometrics, comparative genomics, and genome-wide association studies, have identified key constituent parts and putative genes regulating beak morphogenesis and evolution. I focus throughout on neural crest mesenchyme, which generates the beak skeleton and other components, and describe how these embryonic progenitor cells mediate species-specific pattern and link form and function as revealed by 20 years of research using chimeras between quail and duck embryos.

采用互补策略的各种研究计划一直在揭示对鸟类喙的发育和进化至关重要的细胞、分子和遗传机制。在回顾这些发现的过程中,我从跨学科的角度探讨了鸟类喙的起源,包括鸟类喙从恐龙爬行动物的下颌衍生而来、鸟类喙在主要分类群中的解剖学和生态学多样性、鸟类喙的共同胚胎起源、鸟类喙的固有模式化过程以及鸟类喙的结构整合。我将介绍描述性和实验性方法,包括基因表达和细胞系分析、组织重组、外科移植、功能增益和功能缺失方法、几何形态计量学、比较基因组学和全基因组关联研究,是如何确定调控喙形态发生和进化的关键组成部分和假定基因的。我将重点放在神经嵴间充质上,它生成了喙的骨骼和其他组成部分,并描述了这些胚胎祖细胞如何介导物种特异性模式,以及利用鹌鹑和鸭胚胎嵌合体进行的 20 年研究揭示的形态和功能之间的联系。
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引用次数: 0
The Molecular Substrates of Insect Eusociality. 昆虫群居性的分子基础
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-08-15 DOI: 10.1146/annurev-genet-111523-102510
Sarah Kocher, Callum Kingwell

The evolution of eusociality in Hymenoptera-encompassing bees, ants, and wasps-is characterized by multiple gains and losses of social living, making this group a prime model to understand the mechanisms that underlie social behavior and social complexity. Our review synthesizes insights into the evolutionary history and molecular basis of eusociality. We examine new evidence for key evolutionary hypotheses and molecular pathways that regulate social behaviors, highlighting convergent evolution on a shared molecular toolkit that includes the insulin/insulin-like growth factor signaling (IIS) and target of rapamycin (TOR) pathways, juvenile hormone and ecdysteroid signaling, and epigenetic regulation. We emphasize how the crosstalk among these nutrient-sensing and endocrine signaling pathways enables social insects to integrate external environmental stimuli, including social cues, with internal physiology and behavior. We argue that examining these pathways as an integrated regulatory circuit and exploring how the regulatory architecture of this circuit evolves alongside eusociality can open the door to understanding the origin of the complex life histories and behaviors of this group.

膜翅目昆虫--包括蜜蜂、蚂蚁和黄蜂--的 "雌雄同体 "进化的特点是社会生活的多次得失,这使该类群成为了解社会行为和社会复杂性的基本机制的主要模型。我们的综述综合了对电子社会性的进化历史和分子基础的见解。我们研究了调控社会行为的关键进化假说和分子途径的新证据,强调了共享分子工具包的趋同进化,其中包括胰岛素/胰岛素样生长因子信号传导(IIS)和雷帕霉素靶标(TOR)途径、幼年激素和蜕皮激素信号传导以及表观遗传调控。我们强调这些营养传感和内分泌信号通路之间的相互影响如何使社会性昆虫将外部环境刺激(包括社会线索)与内部生理和行为结合起来。我们认为,将这些通路作为一个整合的调控回路进行研究,并探索这一回路的调控结构如何随着社会性的发展而演变,可以为理解这一群体复杂的生活史和行为的起源打开一扇大门。
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引用次数: 0
Neural Stem Cell Regulation in Zebrafish. 斑马鱼的神经干细胞调控
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-08-09 DOI: 10.1146/annurev-genet-111523-101949
Tanya Foley, Melina Thetiot, Laure Bally-Cuif

Neural stem cells (NSCs) are progenitor cell populations generating glial cells and neurons and endowed with long-lasting self-renewal and differentiation potential. While some neural progenitors (NPs) in the embryonic nervous system are also long-lived and match this definition, the term NSC classically refers to such progenitor types in the adult. With the discovery of extensive NSC populations in the adult brain of Danio rerio (zebrafish) and of their high neurogenic activity, including for neuronal regeneration, this model organism has become a powerful tool to characterize and mechanistically dissect NSC properties. On these bases, this article will consider NSCs in the adult zebrafish brain, with a focus on its most extensively characterized domain, the telencephalon (notably its dorsal part, the pallium). Whenever necessary, we will also refer to other brain subdivisions, embryonic processes, and the mouse adult brain, whether for comparative purposes or because more information is available in these other systems.

神经干细胞(NSC)是产生神经胶质细胞和神经元的祖细胞群,具有持久的自我更新和分化潜能。虽然胚胎神经系统中的一些神经祖细胞(NPs)也具有长寿命并符合这一定义,但NSC一词通常是指成体中的此类祖细胞类型。随着在斑马鱼(Danio rerio)成体大脑中发现广泛的 NSC 群体及其高神经源活性(包括神经元再生),这种模式生物已成为表征和从机理上剖析 NSC 特性的有力工具。在此基础上,本文将研究成年斑马鱼大脑中的间充质干细胞,重点关注其特征最丰富的区域--端脑(尤其是其背侧部分--胼胝体)。必要时,我们也会参考其他脑分支、胚胎过程和小鼠成体大脑,无论是出于比较目的,还是因为在这些其他系统中可以获得更多信息。
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引用次数: 0
Biological Roles of Local Protein Synthesis in Axons: A Journey of Discovery. 轴突中局部蛋白质合成的生物学作用:发现之旅
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-08-09 DOI: 10.1146/annurev-genet-072220-030822
Christine E Holt

The remit of this review is to give an autobiographical account of our discovery of the role of local protein synthesis in axon guidance. The paper reporting our initial findings was published in 2001 (10). Here, I describe some of the work that led to this publication, the skepticism our findings initially received, and the subsequent exciting years of follow-up work that helped gradually to convince the neuroscience community of the existence and functional importance of local protein synthesis in multiple aspects of axon biology-guidance, branching, synaptogenesis, and maintenance. The journey has been an exhilarating one, taking me into a new field of RNA biology, with many unexpected twists and turns. In retelling it here, I have tried to recall the major influences on my thinking at the time rather than give a comprehensive review, and I apologize for any omissions due to my own ignorance during that era.

这篇综述的目的是自述我们发现局部蛋白质合成在轴突导向中的作用。报告我们最初发现的论文发表于2001年(10)。在这里,我将描述发表这篇论文之前的一些工作、我们的发现最初受到的质疑,以及随后几年令人振奋的后续工作,这些工作帮助神经科学界逐渐相信局部蛋白合成在轴突生物学的多个方面--引导、分支、突触发生和维持--的存在和功能重要性。这段旅程令人振奋,带我进入了一个全新的 RNA 生物学领域,经历了许多意想不到的曲折。在这里,我试图回顾一下当时对我的思想产生影响的主要因素,而不是进行全面的回顾,如果由于我在那个时代的无知而有任何遗漏,我深表歉意。
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引用次数: 0
De Novo Genes. 新基因
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-08-01 DOI: 10.1146/annurev-genet-111523-102413
Li Zhao, Nicolas Svetec, David J Begun

Although the majority of annotated new genes in a given genome appear to have arisen from duplication-related mechanisms, recent studies have shown that genes can also originate de novo from ancestrally nongenic sequences. Investigating de novo-originated genes offers rich opportunities to understand the origin and functions of new genes, their regulatory mechanisms, and the associated evolutionary processes. Such studies have uncovered unexpected and intriguing facets of gene origination, offering novel perspectives on the complexity of the genome and gene evolution. In this review, we provide an overview of the research progress in this field, highlight recent advancements, identify key technical and conceptual challenges, and underscore critical questions that remain to be addressed.

尽管特定基因组中大多数已注释的新基因似乎都是通过与复制相关的机制产生的,但最近的研究表明,基因也可能从祖先的非基因序列中重新起源。对新起源基因的研究为了解新基因的起源和功能、其调控机制以及相关的进化过程提供了丰富的机会。这些研究揭示了基因起源的意想不到和引人入胜的方面,为了解基因组和基因进化的复杂性提供了新的视角。在这篇综述中,我们概述了这一领域的研究进展,重点介绍了最新进展,指出了关键技术和概念上的挑战,并强调了有待解决的关键问题。
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引用次数: 0
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Annual review of genetics
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