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Annual review of genetics最新文献

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Genetic Approaches for Identifying and Characterizing Effectors in Bacterial Pathogens. 识别和描述细菌病原体效应器的基因方法。
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2024-11-01 DOI: 10.1146/annurev-genet-111523-102030
Nicole A Ellis, Matthias P Machner
{"title":"Genetic Approaches for Identifying and Characterizing Effectors in Bacterial Pathogens.","authors":"Nicole A Ellis, Matthias P Machner","doi":"10.1146/annurev-genet-111523-102030","DOIUrl":"10.1146/annurev-genet-111523-102030","url":null,"abstract":"<p><p>Microbial pathogens have coevolved with their hosts, often for millions of years, and in the process have developed a variety of virulence mechanisms to ensure their survival, typically at the host's expense. At the center of this host-pathogen warfare are proteins called effectors that are delivered by bacteria into their host where they alter the intracellular environment to promote bacterial proliferation. Many effectors are believed to have been acquired by the bacteria from their host during evolution, explaining why researchers are keen to understand their function, as this information may provide insight into both microbial virulence strategies and biological processes that happen within our own cells. Help for accomplishing this goal has come from the recent development of increasingly powerful genetic approaches, which are the focus of this review.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"58 1","pages":"233-247"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715099","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
Regulatory Networks Underlying Plant Responses and Adaptation to Cold Stress. 植物应对和适应寒冷胁迫的调控网络。
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2024-11-01 Epub Date: 2024-11-14 DOI: 10.1146/annurev-genet-111523-102226
Yanglin Ding, Yiting Shi, Shuhua Yang
{"title":"Regulatory Networks Underlying Plant Responses and Adaptation to Cold Stress.","authors":"Yanglin Ding, Yiting Shi, Shuhua Yang","doi":"10.1146/annurev-genet-111523-102226","DOIUrl":"10.1146/annurev-genet-111523-102226","url":null,"abstract":"<p><p>Cold is an important environmental factor limiting plant growth and development. Recent studies have revealed the complex regulatory networks associated with plant responses to cold and identified their interconnections with signaling pathways related to light, the circadian clock, plant hormones, and pathogen defense. In this article, we review recent advances in understanding the molecular basis of cold perception and signal transduction pathways. We also summarize recent developments in the study of cold-responsive growth and flowering. Finally, we propose future directions for the study of long-term cold sensing, RNA secondary structures in response to cold, and the development of cold-tolerant and high-yield crops.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"43-65"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632487","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 : 2024-11-01 Epub Date: 2024-11-14 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":"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":" ","pages":"319-339"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","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
De Novo Genes. 新基因
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2024-11-01 Epub Date: 2024-11-14 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":" ","pages":"211-232"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12051474/pdf/","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":"OA","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 : 2024-11-01 Epub Date: 2024-11-14 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":"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":" ","pages":"391-408"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","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
Müller Glial Cell-Dependent Regeneration of the Retina in Zebrafish and Mice. 斑马鱼和小鼠视网膜的缪勒神经胶质细胞再生
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2024-11-01 Epub Date: 2024-11-14 DOI: 10.1146/annurev-genet-111523-102000
Jonathan Jui, Daniel Goldman
{"title":"Müller Glial Cell-Dependent Regeneration of the Retina in Zebrafish and Mice.","authors":"Jonathan Jui, Daniel Goldman","doi":"10.1146/annurev-genet-111523-102000","DOIUrl":"10.1146/annurev-genet-111523-102000","url":null,"abstract":"<p><p>Sight is one of our most precious senses. People fear losing their sight more than any other disability. Thus, restoring sight to the blind is an important goal of vision scientists. Proregenerative species, such as zebrafish, provide a system for studying endogenous mechanisms underlying retina regeneration. Nonregenerative species, such as mice, provide a system for testing strategies for stimulating retina regeneration. Key to retina regeneration in zebrafish and mice is the Müller glial cell, a malleable cell type that is amenable to a variety of regenerative strategies. Here, we review cellular and molecular mechanisms used by zebrafish to regenerate a retina, as well as the application of these mechanisms, and other strategies to stimulate retina regeneration in mice. Although our focus is on Müller glia (MG), niche components and their impact on MG reprogramming are also discussed.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"67-90"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141320368","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 : 2024-11-01 Epub Date: 2024-11-14 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":" ","pages":"273-295"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11588544/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phenotypic Heterogeneity in Pathogens. 病原体的表型异质性
IF 8.6 1区 生物学
Annual review of genetics Pub Date : 2024-11-01 Epub Date: 2024-11-14 DOI: 10.1146/annurev-genet-111523-102459
Jessica Sherry, E Hesper Rego
{"title":"Phenotypic Heterogeneity in Pathogens.","authors":"Jessica Sherry, E Hesper Rego","doi":"10.1146/annurev-genet-111523-102459","DOIUrl":"10.1146/annurev-genet-111523-102459","url":null,"abstract":"<p><p>Pathogen diversity within an infected organism has traditionally been explored through the lens of genetic heterogeneity. Hallmark studies have characterized how genetic diversity within pathogen subpopulations contributes to treatment escape and infectious disease progression. However, recent studies have begun to reveal the mechanisms by which phenotypic heterogeneity is established within genetically identical populations of invading pathogens. Furthermore, exciting new work highlights how these phenotypically heterogeneous subpopulations contribute to a pathogen population better equipped to handle the complex and fluctuating environment of a host organism. In this review, we focus on how bacterial pathogens, including <i>Staphylococcus aureus</i>, <i>Salmonella typhimurium</i>, <i>Pseudomonas aeruginosa</i>, and <i>Mycobacterium tuberculosis</i>, establish and maintain phenotypic heterogeneity, and we explore recent work demonstrating causative links between this heterogeneity and infection outcome.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"183-209"},"PeriodicalIF":8.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141858886","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
A Genetic Bridge Between Medicine and Neurodiversity for Autism. 自闭症医学与神经多样性之间的基因桥梁。
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2024-11-01 DOI: 10.1146/annurev-genet-111523-102614
Claire S Leblond, Thomas Rolland, Eli Barthome, Zakaria Mougin, Mathis Fleury, Christine Ecker, Stéf Bonnot-Briey, Freddy Cliquet, Anne-Claude Tabet, Anna Maruani, Boris Chaumette, Jonathan Green, Richard Delorme, Thomas Bourgeron
{"title":"A Genetic Bridge Between Medicine and Neurodiversity for Autism.","authors":"Claire S Leblond, Thomas Rolland, Eli Barthome, Zakaria Mougin, Mathis Fleury, Christine Ecker, Stéf Bonnot-Briey, Freddy Cliquet, Anne-Claude Tabet, Anna Maruani, Boris Chaumette, Jonathan Green, Richard Delorme, Thomas Bourgeron","doi":"10.1146/annurev-genet-111523-102614","DOIUrl":"10.1146/annurev-genet-111523-102614","url":null,"abstract":"<p><p>Autism represents a large spectrum of diverse individuals with varying underlying genetic architectures and needs. For some individuals, a single de novo or ultrarare genetic variant has a large effect on the intensity of specific dimensions of the phenotype, while, for others, a combination of thousands of variants commonly found in the general population are involved. The variants with large impact are found in up to 30% of autistic individuals presenting with intellectual disability, significant speech delay, motor delay, and/or seizures. The common variants are shared with those found in individuals with attention-deficit/hyperactivity disorder, major depressive disorders, greater educational attainment, and higher cognitive performance, suggesting overlapping genetic architectures. The genetic variants modulate the function of chromatin remodeling and synaptic proteins that influence the connectivity of neuronal circuits and, in interaction with the environment of each individual, the subsequent cognitive and personal trajectory of the child. Overall, this genetic heterogeneity mirrors the phenotypic diversity of autistic individuals and provides a helpful bridge between biomedical and neurodiversity perspectives. We propose that participative and multidisciplinary research should use this information to understand better the assessment, treatments, and accommodations that individuals with autism and families need.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"58 1","pages":"487-512"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715088","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 : 2024-11-01 Epub Date: 2024-11-14 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":"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. 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":" ","pages":"1-18"},"PeriodicalIF":8.7,"publicationDate":"2024-11-01","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
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