Current Opinion in Systems Biology最新文献_第8页

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-09-01 DOI: 10.1016/S2452-3100(22)00025-7

引用次数: 0

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-06-01 DOI: 10.1016/S2452-3100(22)00014-2

引用次数: 0

Enhanced underground metabolism challenges life at high temperature–metabolic thermoadaptation in hyperthermophilic Archaea 增强的地下代谢挑战了超嗜热古菌高温代谢热适应的生命

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-06-01 DOI: 10.1016/j.coisb.2022.100423

Christian Schmerling , Theresa Kouril , Jacky Snoep , Christopher Bräsen , Bettina Siebers

{"title":"Enhanced underground metabolism challenges life at high temperature–metabolic thermoadaptation in hyperthermophilic Archaea","authors":"Christian Schmerling , Theresa Kouril , Jacky Snoep , Christopher Bräsen , Bettina Siebers","doi":"10.1016/j.coisb.2022.100423","DOIUrl":"10.1016/j.coisb.2022.100423","url":null,"abstract":"<div><p><span><span>The text-book picture of a perfect, well organised metabolism with highly specific enzymes<span>, is challenged by non-enzymatic reactions and promiscuous enzymes. This, so-called ‘underground metabolism’, is a special challenge for hyperthermophilic Archaea that thrive at temperatures above 80 °C and possess modified central metabolic pathways often with promiscuous enzymes. Hence, the question arises how extremely </span></span>thermophilic Archaea can operate their unusual metabolism at temperatures where many pathway intermediates are unstable? We herein discuss current insights in the underground metabolism and metabolic </span>thermoadaptation<span><span> of (hyper)thermophilic Archaea. So far, only a few repair enzymes and salvaging pathways have been investigated in Archaea. Studies of the central </span>carbohydrate metabolism indicate that a number of different strategies have evolved: 1) reduction of the concentration of unstable metabolites, 2) different pathway topologies are used with newly induced enzymes, and 3) damaged metabolites are removed via new metabolic pathways.</span></p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"30 ","pages":"Article 100423"},"PeriodicalIF":3.7,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46353795","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

Synthetic metabolism approaches: A valuable resource for systems biology 合成代谢方法:系统生物学的宝贵资源

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-06-01 DOI: 10.1016/j.coisb.2022.100417

Sebastian Wenk , Nico J. Claassens , Steffen N. Lindner

{"title":"Synthetic metabolism approaches: A valuable resource for systems biology","authors":"Sebastian Wenk , Nico J. Claassens , Steffen N. Lindner","doi":"10.1016/j.coisb.2022.100417","DOIUrl":"10.1016/j.coisb.2022.100417","url":null,"abstract":"<div><p>Synthetic biology modifies biological systems with the aim of creating new biological parts, devices, and even organisms. Systems biology deciphers the design principles of biological systems trying to derive the mathematical logic behind biological processes. Although different in their respective research approaches and questions, both disciplines are clearly interconnected. Without sufficient understanding of the biological system, synthetic biology studies cannot be properly designed and conducted. On the other hand, systems biology can profit from new biological systems generated by synthetic biology approaches, which can reveal important insights into cellular processes and allow a better understanding of the principles of life. In this article, we present state-of-the-art synthetic biology approaches that focus on the engineering of synthetic metabolism in microbial hosts and show how their implementation has led to new fundamental discoveries on enzyme reversibility, promiscuity, and “underground metabolism”. We further discuss how the combination of rational engineering and adaptive laboratory evolution has enabled the generation of microbes with a synthetic central metabolism, leading to completely new metabolic phenotypes. These organisms provide a great resource for future studies to deepen our systems-level understanding on the principles that govern metabolic networks and evolution.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"30 ","pages":"Article 100417"},"PeriodicalIF":3.7,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310022000038/pdfft?md5=c9f96786811b96040d981e16ebdbfe34&pid=1-s2.0-S2452310022000038-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46772608","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: 1

Metabolic dynamics during the cell cycle 细胞周期中的代谢动力学

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-06-01 DOI: 10.1016/j.coisb.2022.100415

Andre Zylstra, Matthias Heinemann

{"title":"Metabolic dynamics during the cell cycle","authors":"Andre Zylstra, Matthias Heinemann","doi":"10.1016/j.coisb.2022.100415","DOIUrl":"10.1016/j.coisb.2022.100415","url":null,"abstract":"<div><p>While we have a solid understanding of the cell biological and biochemical control aspects of the eukaryotic cell growth and division process, much less is known about the metabolic and biosynthetic dynamics during the cell cycle. Here, we review recent discoveries made at the single-cell and population level that show that budding yeast (<em>Saccharomyces cerevisiae</em>) metabolism oscillates in synchrony with the cell cycle in actively dividing cells, as well as independently when the cell cycle is halted. In fact, emerging evidence suggests that the cell cycle-independent metabolic oscillations interact with elements of the cell cycle machinery via several possible mechanisms. Furthermore, recent reports indicate that different biosynthetic processes exhibit temporally changing activity patterns during the cell cycle. Thus, resources are drawn from primary metabolism in a dynamic manner, potentially giving rise to metabolic oscillations. Finally, we highlight work with mammalian cells indicating that similar metabolic dynamics might also exist in higher eukaryotes.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"30 ","pages":"Article 100415"},"PeriodicalIF":3.7,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310022000014/pdfft?md5=0ceeea28044602a21abcb5841856610a&pid=1-s2.0-S2452310022000014-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41405427","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: 4

Organelle dysfunction and its contribution to metabolic impairments in aging and age-related diseases 细胞器功能障碍及其对衰老和年龄相关疾病代谢损伤的贡献

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-06-01 DOI: 10.1016/j.coisb.2022.100416

Julia C. Heiby, Alessandro Ori

引用次数: 1

Editorial overview: Control engineering in synthetic biology: Foundations and applications 编辑概述:合成生物学中的控制工程:基础和应用

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-03-01 DOI: 10.1016/j.coisb.2021.100406

Ron Weiss, Velia Siciliano

引用次数: 0

Metabolomics in diagnostics of inborn metabolic disorders 代谢组学在先天性代谢紊乱诊断中的应用

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-03-01 DOI: 10.1016/j.coisb.2021.100409

Judith JM. Jans , Melissa H. Broeks , Nanda M. Verhoeven-Duif

{"title":"Metabolomics in diagnostics of inborn metabolic disorders","authors":"Judith JM. Jans , Melissa H. Broeks , Nanda M. Verhoeven-Duif","doi":"10.1016/j.coisb.2021.100409","DOIUrl":"10.1016/j.coisb.2021.100409","url":null,"abstract":"<div><p>Finding a diagnosis for patients with a rare inborn metabolic disorder can be a long and difficult path. Whereas next generation sequencing is now a commonly used modality, which has significantly impacted the diagnostic yield and speed, next generation metabolic screening through untargeted metabolomics is next in line to prove its value in the diagnostic trajectory.</p><p>Untargeted metabolomics, often based on mass spectrometry platforms, is a well-established technology for the identification of novel disease markers. However, untargeted metabolomics as first line diagnostics for rare disease is now only gradually making its way into clinical practice. Most retrospective studies show that the majority of inborn metabolic disorder can be detected through untargeted metabolomics. Some diseases will still go undetected, which diagnoses are missed depends on the specific metabolomics method chosen; there is no single all-encompassing platform. Therefore, careful assessments of the opportunities and limitations are currently undertaken in prospective studies, combining untargeted metabolomics in the diagnostics setting with the current gold standard genetic and biochemical diagnostic modalities. These studies show an increased diagnostic yield when implementing untargeted metabolomics. Given the continuing technological advances, defining the optimal timing, place, and order of the various diagnostic modalities will keep on evolving in the foreseen future.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"29 ","pages":"Article 100409"},"PeriodicalIF":3.7,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310021001049/pdfft?md5=967143ed4644a1e92c1cb82efc3ba605&pid=1-s2.0-S2452310021001049-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42607685","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: 7

Editorial Board Page 编委会页面

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-03-01 DOI: 10.1016/S2452-3100(22)00004-X

引用次数: 0

Compartmentalization of metabolism between cell types in multicellular organisms: A computational perspective 多细胞生物中细胞类型间代谢的区隔化:计算视角

IF 3.7

Current Opinion in Systems Biology Pub Date : 2022-03-01 DOI: 10.1016/j.coisb.2021.100407

Xuhang Li, L. Safak Yilmaz, Albertha J.M. Walhout

{"title":"Compartmentalization of metabolism between cell types in multicellular organisms: A computational perspective","authors":"Xuhang Li, L. Safak Yilmaz, Albertha J.M. Walhout","doi":"10.1016/j.coisb.2021.100407","DOIUrl":"10.1016/j.coisb.2021.100407","url":null,"abstract":"<div><p><span>In multicellular organisms, metabolism is compartmentalized at many levels, including tissues and organs, different cell types, and subcellular compartments. Compartmentalization<span> creates a coordinated homeostatic system where each compartment contributes to the production of energy and biomolecules that the organism needs to carry out specific metabolic tasks. Experimentally studying metabolic compartmentalization and metabolic interactions between cells and tissues in multicellular organisms is challenging at a systems level. However, recent progress in computational modeling<span> provides an alternative approach to this problem. Here, we discuss how integrating metabolic network modeling<span> with omics data offers an opportunity to reveal metabolic states at the level of organs, tissues and, ultimately, individual cells. We review the current status of genome-scale metabolic network models in multicellular organisms, methods to study metabolic compartmentalization </span></span></span></span><em>in silico</em>, and insights gained from computational analyses. We also discuss outstanding challenges and provide perspectives for the future directions of the field.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"29 ","pages":"Article 100407"},"PeriodicalIF":3.7,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10800315","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: 2