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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
Annual review of genetics Pub Date : 2024-09-12 DOI: 10.1146/annurev-genet-111523-102448
L. Aravind, Gianlucca G. Nicastro, Lakshminarayan M. Iyer, A. Maxwell Burroughs
{"title":"The Prokaryotic Roots of Eukaryotic Immune Systems","authors":"L. Aravind, Gianlucca G. Nicastro, Lakshminarayan M. Iyer, A. Maxwell Burroughs","doi":"10.1146/annurev-genet-111523-102448","DOIUrl":"https://doi.org/10.1146/annurev-genet-111523-102448","url":null,"abstract":"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.","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":11.1,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics Pub Date : 2024-09-04 DOI: 10.1146/annurev-genet-111523-102725
Amy H Buck, Esther N M Nolte-'t Hoen
{"title":"The Nature and Nurture of Extracellular Vesicle-Mediated Signaling.","authors":"Amy H Buck, Esther N M Nolte-'t Hoen","doi":"10.1146/annurev-genet-111523-102725","DOIUrl":"https://doi.org/10.1146/annurev-genet-111523-102725","url":null,"abstract":"<p><p>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: (<i>a</i>) EV release that serves a function for producing cells, (<i>b</i>) EV modification of the extracellular environment, and (<i>c</i>) 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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics 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
{"title":"Integrating the Study of Polyploidy Across Organisms, Tissues, and Disease.","authors":"John P Morris, Timour Baslan, Douglas E Soltis, Pamela S Soltis, Donald T Fox","doi":"10.1146/annurev-genet-111523-102124","DOIUrl":"10.1146/annurev-genet-111523-102124","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics Pub Date : 2024-09-03 DOI: 10.1146/annurev-genet-111523-102135
Julie C Baker
{"title":"Placental Evolution: Innovating how to Feed Babies.","authors":"Julie C Baker","doi":"10.1146/annurev-genet-111523-102135","DOIUrl":"https://doi.org/10.1146/annurev-genet-111523-102135","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics Pub Date : 2024-09-03 DOI: 10.1146/annurev-genet-111523-102651
Xiaoheng Cheng, Matthias Steinrücken
{"title":"Population Genomic Scans for Natural Selection and Demography.","authors":"Xiaoheng Cheng, Matthias Steinrücken","doi":"10.1146/annurev-genet-111523-102651","DOIUrl":"https://doi.org/10.1146/annurev-genet-111523-102651","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics Pub Date : 2024-09-03 DOI: 10.1146/annurev-genet-111523-101929
Richard A Schneider
{"title":"Cellular, Molecular, and Genetic Mechanisms of Avian Beak Development and Evolution.","authors":"Richard A Schneider","doi":"10.1146/annurev-genet-111523-101929","DOIUrl":"10.1146/annurev-genet-111523-101929","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics Pub Date : 2024-08-15 DOI: 10.1146/annurev-genet-111523-102510
Sarah Kocher, Callum Kingwell
{"title":"The Molecular Substrates of Insect Eusociality.","authors":"Sarah Kocher, Callum Kingwell","doi":"10.1146/annurev-genet-111523-102510","DOIUrl":"10.1146/annurev-genet-111523-102510","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics Pub Date : 2024-08-09 DOI: 10.1146/annurev-genet-111523-101949
Tanya Foley, Melina Thetiot, Laure Bally-Cuif
{"title":"Neural Stem Cell Regulation in Zebrafish.","authors":"Tanya Foley, Melina Thetiot, Laure Bally-Cuif","doi":"10.1146/annurev-genet-111523-101949","DOIUrl":"https://doi.org/10.1146/annurev-genet-111523-101949","url":null,"abstract":"<p><p>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 <i>Danio rerio</i> (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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141911499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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
Annual review of genetics Pub Date : 2024-08-09 DOI: 10.1146/annurev-genet-072220-030822
Christine E Holt
{"title":"Biological Roles of Local Protein Synthesis in Axons: A Journey of Discovery.","authors":"Christine E Holt","doi":"10.1146/annurev-genet-072220-030822","DOIUrl":"https://doi.org/10.1146/annurev-genet-072220-030822","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141911498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
De Novo Genes. 新基因
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2024-08-01 DOI: 10.1146/annurev-genet-111523-102413
Li Zhao, Nicolas Svetec, David J Begun
{"title":"De Novo Genes.","authors":"Li Zhao, Nicolas Svetec, David J Begun","doi":"10.1146/annurev-genet-111523-102413","DOIUrl":"10.1146/annurev-genet-111523-102413","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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