{"title":"Navigating the microalgal maze: a comprehensive review of recent advances and future perspectives in biological networks.","authors":"Bahman Panahi, Robab Khalilpour Shadbad","doi":"10.1007/s00425-024-04543-7","DOIUrl":null,"url":null,"abstract":"<p><strong>Main conclusion: </strong>PPI analysis deepens our knowledge in critical processes like carbon fixation and nutrient sensing. Moreover, signaling networks, including pathways like MAPK/ERK and TOR, provide valuable information in how microalgae respond to environmental changes and stress. Additionally, species-species interaction networks for microalgae provide a comprehensive understanding of how different species interact within their environments. This review examines recent advancements in the study of biological networks within microalgae, with a focus on the intricate interactions that define these organisms. It emphasizes how network biology, an interdisciplinary field, offers valuable insights into microalgae functions through various methodologies. Crucial approaches, such as protein-protein interaction (PPI) mapping utilizing yeast two-hybrid screening and mass spectrometry, are essential for comprehending cellular processes and optimizing functions, such as photosynthesis and fatty acid biosynthesis. The application of advanced computational methods and information mining has significantly improved PPI analysis, revealing networks involved in critical processes like carbon fixation and nutrient sensing. The review also encompasses transcriptional networks, which play a role in gene regulation and stress responses, as well as metabolic networks represented by genome-scale metabolic models (GEMs), which aid in strain optimization and the prediction of metabolic outcomes. Furthermore, signaling networks, including pathways like MAPK/ERK and TOR, are crucial for understanding how microalgae respond to environmental changes and stress. Additionally, species-species interaction networks for microalgae provide a comprehensive understanding of how different species interact within their environments. The integration of these network biology approaches has deepened our understanding of microalgal interactions, paving the way for more efficient cultivation and new industrial applications.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":null,"pages":null},"PeriodicalIF":3.6000,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Planta","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s00425-024-04543-7","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0
Abstract
Main conclusion: PPI analysis deepens our knowledge in critical processes like carbon fixation and nutrient sensing. Moreover, signaling networks, including pathways like MAPK/ERK and TOR, provide valuable information in how microalgae respond to environmental changes and stress. Additionally, species-species interaction networks for microalgae provide a comprehensive understanding of how different species interact within their environments. This review examines recent advancements in the study of biological networks within microalgae, with a focus on the intricate interactions that define these organisms. It emphasizes how network biology, an interdisciplinary field, offers valuable insights into microalgae functions through various methodologies. Crucial approaches, such as protein-protein interaction (PPI) mapping utilizing yeast two-hybrid screening and mass spectrometry, are essential for comprehending cellular processes and optimizing functions, such as photosynthesis and fatty acid biosynthesis. The application of advanced computational methods and information mining has significantly improved PPI analysis, revealing networks involved in critical processes like carbon fixation and nutrient sensing. The review also encompasses transcriptional networks, which play a role in gene regulation and stress responses, as well as metabolic networks represented by genome-scale metabolic models (GEMs), which aid in strain optimization and the prediction of metabolic outcomes. Furthermore, signaling networks, including pathways like MAPK/ERK and TOR, are crucial for understanding how microalgae respond to environmental changes and stress. Additionally, species-species interaction networks for microalgae provide a comprehensive understanding of how different species interact within their environments. The integration of these network biology approaches has deepened our understanding of microalgal interactions, paving the way for more efficient cultivation and new industrial applications.
主要结论PPI 分析加深了我们对碳固定和营养传感等关键过程的了解。此外,信号网络(包括 MAPK/ERK 和 TOR 等通路)为微藻如何应对环境变化和压力提供了有价值的信息。此外,微藻类的物种-物种相互作用网络提供了对不同物种如何在其环境中相互作用的全面了解。本综述探讨了微藻类生物网络研究的最新进展,重点是决定这些生物的错综复杂的相互作用。它强调了网络生物学这一跨学科领域如何通过各种方法为了解微藻的功能提供有价值的见解。利用酵母双杂交筛选和质谱法绘制蛋白质-蛋白质相互作用(PPI)图谱等关键方法,对于理解细胞过程和优化光合作用和脂肪酸生物合成等功能至关重要。先进计算方法和信息挖掘的应用极大地改进了 PPI 分析,揭示了参与碳固定和营养传感等关键过程的网络。综述还包括在基因调控和应激反应中发挥作用的转录网络,以及以基因组尺度代谢模型(GEM)为代表的代谢网络,后者有助于菌株优化和代谢结果预测。此外,信号网络(包括 MAPK/ERK 和 TOR 等通路)对于了解微藻如何应对环境变化和压力至关重要。此外,微藻类的物种-物种相互作用网络让人们全面了解不同物种如何在其环境中相互作用。这些网络生物学方法的整合加深了我们对微藻类相互作用的理解,为更高效的培养和新的工业应用铺平了道路。
期刊介绍:
Planta publishes timely and substantial articles on all aspects of plant biology.
We welcome original research papers on any plant species. Areas of interest include biochemistry, bioenergy, biotechnology, cell biology, development, ecological and environmental physiology, growth, metabolism, morphogenesis, molecular biology, new methods, physiology, plant-microbe interactions, structural biology, and systems biology.