Vandereyken Katy, Van Leene Jelle, De Coninck Barbara, Cammue Bruno P A
Centre of Microbial and Plant Genetics, KU Leuven, Heverlee, Belgium.
VIB Center for Plant Systems Biology, Ghent, Belgium.
Front Plant Sci. 2018 Jun 5;9:694. doi: 10.3389/fpls.2018.00694. eCollection 2018.
Plant stress responses involve numerous changes at the molecular and cellular level and are regulated by highly complex signaling pathways. Studying protein-protein interactions (PPIs) and the resulting networks is therefore becoming increasingly important in understanding these responses. Crucial in PPI networks are the so-called hubs or hub proteins, commonly defined as the most highly connected central proteins in scale-free PPI networks. However, despite their importance, a growing amount of confusion and controversy seems to exist regarding hub protein identification, characterization and classification. In order to highlight these inconsistencies and stimulate further clarification, this review critically analyses the current knowledge on hub proteins in the plant interactome field. We focus on current hub protein definitions, including the properties generally seen as hub-defining, and the challenges and approaches associated with hub protein identification. Furthermore, we give an overview of the most important large-scale plant PPI studies of the last decade that identified hub proteins, pointing out the lack of overlap between different studies. As such, it appears that although major advances are being made in the plant interactome field, defining hub proteins is still heavily dependent on the quality, origin and interpretation of the acquired PPI data. Nevertheless, many hub proteins seem to have a reported role in the plant stress response, including transcription factors, protein kinases and phosphatases, ubiquitin proteasome system related proteins, (co-)chaperones and redox signaling proteins. A significant number of identified plant stress hubs are however still functionally uncharacterized, making them interesting targets for future research. This review clearly shows the ongoing improvements in the plant interactome field but also calls attention to the need for a more comprehensive and precise identification of hub proteins, allowing a more efficient systems biology driven unraveling of complex processes, including those involved in stress responses.
植物应激反应涉及分子和细胞水平的众多变化，并由高度复杂的信号通路调控。因此，研究蛋白质-蛋白质相互作用（PPI）及其产生的网络对于理解这些反应变得越来越重要。PPI网络中的关键是所谓的枢纽或枢纽蛋白，通常定义为无标度PPI网络中连接最紧密的中心蛋白。然而，尽管它们很重要，但关于枢纽蛋白的鉴定、表征和分类似乎存在越来越多的混淆和争议。为了突出这些不一致之处并促进进一步的澄清，本综述批判性地分析了植物相互作用组领域中关于枢纽蛋白的现有知识。我们关注当前枢纽蛋白的定义，包括通常被视为枢纽定义的特性，以及与枢纽蛋白鉴定相关的挑战和方法。此外，我们概述了过去十年中鉴定出枢纽蛋白的最重要的大规模植物PPI研究，指出不同研究之间缺乏重叠。因此，尽管植物相互作用组领域正在取得重大进展，但枢纽蛋白的定义仍然严重依赖于所获得的PPI数据的质量、来源和解释。尽管如此，许多枢纽蛋白似乎在植物应激反应中发挥了作用，包括转录因子、蛋白激酶和磷酸酶、泛素蛋白酶体系统相关蛋白、（共）伴侣蛋白和氧化还原信号蛋白。然而，大量已鉴定的植物应激枢纽在功能上仍未得到表征，这使它们成为未来研究的有趣靶点。本综述清楚地展示了植物相互作用组领域正在进行的改进，但也提请注意需要更全面、精确地鉴定枢纽蛋白，以便更有效地通过系统生物学揭示复杂过程，包括那些参与应激反应的过程。
