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Current Opinion in Systems Biology最新文献

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New faces of prokaryotic mobile genetic elements: Guide RNAs link transposition with host defense mechanisms 原核可移动遗传元件的新面孔：引导RNA与宿主防御机制的连接
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-29 DOI: 10.1016/j.coisb.2023.100473
Eugene V. Koonin , Mart Krupovic
{"title":"New faces of prokaryotic mobile genetic elements: Guide RNAs link transposition with host defense mechanisms","authors":"Eugene V. Koonin ,&nbsp;Mart Krupovic","doi":"10.1016/j.coisb.2023.100473","DOIUrl":"10.1016/j.coisb.2023.100473","url":null,"abstract":"<div><p><span><span><span>Most life forms harbor multiple, diverse mobile genetic elements (MGE) that widely differ in their rates and mechanisms of mobility. Recent findings on two classes of MGE in </span>prokaryotes revealed a novel mechanism, RNA-guided transposition, where a transposon-encoded guide </span>RNA<span><span><span> directs the transposase to a unique site in the host genome. Tn7-like transposons, on multiple occasions, recruited </span>CRISPR systems that lost the capacity to cleave target </span>DNA<span> and instead mediate RNA-guided transposition via CRISPR RNA. Conversely, the abundant transposon-associated, RNA-guided nucleases IscB and TnpB that appear to promote proliferation of IS</span></span></span><em>200</em>/IS<em>605</em> and IS<em>607</em><span> transposons were the likely evolutionary ancestors of type II and type V CRISPR systems, respectively. Thus, RNA-guided target recognition is a major biological phenomenon that connects MGE with host defense mechanisms. More RNA-guided defensive and MGE-associated functionalities are likely to be discovered.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100473"},"PeriodicalIF":3.7,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41166361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolution of new metabolic pathways and microbial communities 新代谢途径和微生物群落的进化
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-25 DOI: 10.1016/j.coisb.2023.100472
Dan Kehila, Kimberly Tsz Ching Wong, Nobuhiko Tokuriki
{"title":"Evolution of new metabolic pathways and microbial communities","authors":"Dan Kehila,&nbsp;Kimberly Tsz Ching Wong,&nbsp;Nobuhiko Tokuriki","doi":"10.1016/j.coisb.2023.100472","DOIUrl":"10.1016/j.coisb.2023.100472","url":null,"abstract":"<div><p>The evolution of metabolic pathways in microbes is traditionally envisioned to take place within a single organism. The diverse repertoire of enzymes in the microbial community points to another exciting possibility: namely, that new metabolic pathways may evolve in a community setting, where pathway steps are distributed across several strains. The readiness with which microbes form stable relationships to collectively degrade manmade ‘xenobiotic’ pollutants, as evidenced from natural and laboratory-enriched consortia, provides valuable insights into the evolution of enzymes and pathways. Nonetheless, many open questions remain to be addressed. In this review, we consider the key determinants of pathway evolution in microbial communities, drawing from principles of social evolutionary theory in microbes, and also exploring the role of diffusion and horizontal gene transfer.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100472"},"PeriodicalIF":3.7,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45099772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent advances in non-model bacterial chassis construction 非模型细菌底盘结构研究进展
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-19 DOI: 10.1016/j.coisb.2023.100471
Soonkyu Hwang , Chanyoung Joung , Woori Kim , Bernhard Palsson , Byung-Kwan Cho
{"title":"Recent advances in non-model bacterial chassis construction","authors":"Soonkyu Hwang ,&nbsp;Chanyoung Joung ,&nbsp;Woori Kim ,&nbsp;Bernhard Palsson ,&nbsp;Byung-Kwan Cho","doi":"10.1016/j.coisb.2023.100471","DOIUrl":"10.1016/j.coisb.2023.100471","url":null,"abstract":"<div><p>The development of bacterial chassis to increase productivity and reduce industrial costs in value-added biochemical production has gained significant attention. Current efforts have focused on model bacteria, thus limiting their suitability to produce specialized products. Therefore, there is a growing emphasis on developing specialized non-model bacterial chassis to expand the repertoire of bioproducts. However, the lack of genetic information and tools for non-model bacteria remains challenging. In this review, we categorize and introduce non-model chassis based on their characteristics in relation to the target products. We also provide an overview of the trends in the development of genome-reduced chassis to enhance productivity. Furthermore, we propose synthetic biology technologies that can be applied to a broad range of non-model bacteria.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100471"},"PeriodicalIF":3.7,"publicationDate":"2023-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43537194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution 微生物在自然界中是如何生长的?种群动态在微生物生态学和进化中的作用
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-08-09 DOI: 10.1016/j.coisb.2023.100470
Justus Wilhelm Fink , Michael Manhart
{"title":"How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution","authors":"Justus Wilhelm Fink ,&nbsp;Michael Manhart","doi":"10.1016/j.coisb.2023.100470","DOIUrl":"10.1016/j.coisb.2023.100470","url":null,"abstract":"<div><p>The growth of microbial populations in nature is dynamic, as the cellular physiology and environment of these populations change. Population dynamics have wide-ranging consequences for ecology and evolution, determining how species interact and which mutations fix. Understanding these dynamics is also critical for clinical and environmental applications in which we need to promote or inhibit microbial growth<span>. We first address the latest efforts and outstanding challenges in measuring microbial population dynamics in natural environments. We next summarize fundamental concepts and empirical data on how population dynamics both shape and are shaped by evolutionary processes. Finally, we discuss the role of tradeoffs in microbial population dynamics, which may reveal physiological constraints and help to maintain ecological diversity. We find that current evidence for tradeoffs in population dynamics is limited, but that consideration of the evolutionary context of these tradeoffs is necessary for designing future experiments that can better address this problem.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"36 ","pages":"Article 100470"},"PeriodicalIF":3.7,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42046217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
How prebiotic complexity increases through Darwinian evolution 达尔文进化如何增加益生元的复杂性
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-06-01 DOI: 10.1016/j.coisb.2023.100456
Kohtoh Yukawa , Ryo Mizuuchi , Norikazu Ichihashi
{"title":"How prebiotic complexity increases through Darwinian evolution","authors":"Kohtoh Yukawa ,&nbsp;Ryo Mizuuchi ,&nbsp;Norikazu Ichihashi","doi":"10.1016/j.coisb.2023.100456","DOIUrl":"10.1016/j.coisb.2023.100456","url":null,"abstract":"<div><p>Present-day life is amazingly diverse and complex owing to Darwinian evolution. Despite the simplicity of the principle of Darwinian evolution, the process and its outcomes are largely unpredictable. Evolutionary simulation and experiments are useful methods for gaining insights into the process and outcomes of Darwinian evolution. In this short review, we discuss recent progress in theoretical and experimental approaches to understanding the possible evolutionary processes of prebiotic self-replicators. We especially focus on research addressing how a prebiotic self-replicator increases complexity through evolution, including our recent experiments, in which a complex replication network consisting of multiple self-replicating molecules spontaneously evolved from a single replicating RNA.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"34 ","pages":"Article 100456"},"PeriodicalIF":3.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49417919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial Board Page 编辑委员会页面
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-06-01 DOI: 10.1016/S2452-3100(23)00021-5
{"title":"Editorial Board Page","authors":"","doi":"10.1016/S2452-3100(23)00021-5","DOIUrl":"https://doi.org/10.1016/S2452-3100(23)00021-5","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"34 ","pages":"Article 100464"},"PeriodicalIF":3.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50172800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulation of the microtubule network; the shaft matters! 微管网络的调控;轴很重要!
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-06-01 DOI: 10.1016/j.coisb.2023.100457
Amine Mehidi , Charlotte Aumeier
{"title":"Regulation of the microtubule network; the shaft matters!","authors":"Amine Mehidi ,&nbsp;Charlotte Aumeier","doi":"10.1016/j.coisb.2023.100457","DOIUrl":"10.1016/j.coisb.2023.100457","url":null,"abstract":"<div><p>In cells, the microtubule network continually assembles and disassembles. The regulation of microtubule growth or shortening has almost exclusively been studied at their dynamic ends. However, microtubules are dynamic all along their entire shaft. A dynamic shaft increases the lifetime and length of a microtubule by reducing the shortening phases and promoting its regrowth. Here, we discuss how shaft dynamics can regulate microtubule network organization, intracellular transport, and polarization of the network.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"34 ","pages":"Article 100457"},"PeriodicalIF":3.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44457140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolutionary implications of host genetic control for engineering beneficial microbiomes 宿主基因控制对工程有益微生物群的进化意义
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-06-01 DOI: 10.1016/j.coisb.2023.100455
Lucas P. Henry, Joy Bergelson
{"title":"Evolutionary implications of host genetic control for engineering beneficial microbiomes","authors":"Lucas P. Henry,&nbsp;Joy Bergelson","doi":"10.1016/j.coisb.2023.100455","DOIUrl":"10.1016/j.coisb.2023.100455","url":null,"abstract":"<div><p>Engineering new functions in the microbiome requires understanding how host genetic control and microbe–microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe–microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"34 ","pages":"Article 100455"},"PeriodicalIF":3.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10242548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9600074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Order from chaos: How mechanics shape epithelia and promote self-organization 混乱中的秩序:力学如何塑造上皮并促进自组织
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-03-01 DOI: 10.1016/j.coisb.2023.100446
Filipe Nunes Vicente, Alba Diz-Muñoz
{"title":"Order from chaos: How mechanics shape epithelia and promote self-organization","authors":"Filipe Nunes Vicente,&nbsp;Alba Diz-Muñoz","doi":"10.1016/j.coisb.2023.100446","DOIUrl":"10.1016/j.coisb.2023.100446","url":null,"abstract":"<div><p>Collective cell behaviors are essential for the shape and function of tissues. The last decades have provided unequivocal experimental evidence that tissue mechanics are key drivers of morphogenesis. In particular, the spatiotemporal coordination of cellular contractility, adhesion and volume regulation can drive morphogenetic events in various epithelia. At the same time, the epithelial sheets themselves have remarkable mechanical properties, being able to distribute mechanical stress throughout the whole material to resist the physical deformations necessary for their function. In this review, we address recent findings on epithelia morphogenesis and mechanical resistance and highlight the importance of quantitative new approaches for achieving novel understanding.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"32 ","pages":"Article 100446"},"PeriodicalIF":3.7,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47110194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Mechanisms of enhancer function in neuronal systems in health and disease 健康和疾病中神经元系统增强子功能的机制
IF 3.7
Current Opinion in Systems Biology Pub Date : 2023-03-01 DOI: 10.1016/j.coisb.2022.100443
Luna Zea-Redondo , Ana Pombo
{"title":"Mechanisms of enhancer function in neuronal systems in health and disease","authors":"Luna Zea-Redondo ,&nbsp;Ana Pombo","doi":"10.1016/j.coisb.2022.100443","DOIUrl":"10.1016/j.coisb.2022.100443","url":null,"abstract":"<div><p><span>Enhancers are genomic elements that regulate gene expression through a variety of mechanisms. In neuronal systems, enhancer-promoter interactions regulate cell- and tissue-specific transcriptional programs, during neuronal specification and upon terminal differentiation, and play major roles in the tight regulation of activity-dependent mechanisms, such as in memory formation. Enhancers are also hotspots for non-coding genetic variants associated with neurological disorders, such as schizophrenia and </span>Parkinson's disease (PD). Understanding how enhancer grammar informs gene expression programs in neuronal systems in development and disease remains a major challenge, and is a growing avenue to discover the molecular mechanisms directly altered by non-coding genetic variants. In this review, we discuss the diverse mechanisms by which enhancers integrate internal and external stimuli to regulate the gene expression programs that guide neuronal specification and sustain neuronal-specific and activity-dependent processes.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"32 ","pages":"Article 100443"},"PeriodicalIF":3.7,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48337920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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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