{"title":"古塑菌VPS13蛋白的系统发育和结构分析揭示了其在植物中复杂的进化历史。","authors":"Sébastien Leterme, Olivier Bastien, Riccardo Aiese Cigliano, Alberto Amato, Morgane Michaud","doi":"10.1177/25152564231211976","DOIUrl":null,"url":null,"abstract":"<p><p>VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. VPS13 folds into a long hydrophobic tunnel, allowing lipid transport, decorated by distinct domains involved in protein localization and regulation. Whereas VPS13 organization and function have been extensively studied in yeast and mammals, information in organisms originating from primary endosymbiosis is scarce. In the higher plant <i>Arabidopsis thaliana</i>, four paralogs, AtVPS13S, X, M1, and M2, were identified, AtVPS13S playing a role in the regulation of root growth, cell patterning, and reproduction. In this work, we performed phylogenetic, as well as domain and structural modeling of VPS13 proteins in Archaeplastida in order to understand their general organization and evolutionary history. We confirmed the presence of human VPS13B orthologues in some phyla and described two new VPS13 families presenting a particular domain arrangement: VPS13R in Rhodophytes and VPS13Y in Chlorophytes and Streptophytes. By focusing on Viridiplantae, we were able to draw the evolutionary history of these proteins made by multiple gene gains and duplications as well as domain rearrangements. We showed that some Chlorophytes have only three (AtVPS13M, S, Y) whereas some Charophytes have up to six VPS13 paralogs (AtVPS13M1, M2, S, Y, X, B). We also highlighted specific structural features of VPS13M and X paralogs. This study reveals the complex evolution of VPS13 family and opens important perspectives for their functional characterization in photosynthetic organisms.</p>","PeriodicalId":101304,"journal":{"name":"Contact (Thousand Oaks (Ventura County, Calif.))","volume":"6 ","pages":"25152564231211976"},"PeriodicalIF":0.0000,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10683392/pdf/","citationCount":"0","resultStr":"{\"title\":\"Phylogenetic and Structural Analyses of VPS13 Proteins in Archaeplastida Reveal Their Complex Evolutionary History in Viridiplantae.\",\"authors\":\"Sébastien Leterme, Olivier Bastien, Riccardo Aiese Cigliano, Alberto Amato, Morgane Michaud\",\"doi\":\"10.1177/25152564231211976\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. 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By focusing on Viridiplantae, we were able to draw the evolutionary history of these proteins made by multiple gene gains and duplications as well as domain rearrangements. We showed that some Chlorophytes have only three (AtVPS13M, S, Y) whereas some Charophytes have up to six VPS13 paralogs (AtVPS13M1, M2, S, Y, X, B). We also highlighted specific structural features of VPS13M and X paralogs. 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引用次数: 0
摘要
VPS13是一个在真核生物中保守的脂质转移蛋白家族,在包括自噬和细胞器生物发生在内的囊泡运输和膜扩张的基本过程中发挥作用。VPS13折叠成一个长长的疏水通道,允许脂质运输,由不同的区域装饰,涉及蛋白质定位和调节。虽然VPS13的组织和功能已经在酵母和哺乳动物中得到了广泛的研究,但关于起源于初级内共生的生物的信息却很少。在高等植物拟南芥(Arabidopsis thaliana)中,AtVPS13S、X、M1和M2 4个同源基因被鉴定出来,AtVPS13S在根生长、细胞模式和繁殖的调控中发挥作用。在这项工作中,我们进行了系统发育,以及VPS13蛋白的结构域和结构建模,以了解它们的一般组织和进化历史。我们证实了人类VPS13B同源基因在一些门中存在,并描述了两个新的VPS13家族,它们具有特定的结构域排列:红藻中的VPS13R和绿藻和链藻中的VPS13Y。通过对植物Viridiplantae的研究,我们能够绘制出这些蛋白质的进化史,这些蛋白质是由多个基因获得和复制以及结构域重排形成的。结果表明,一些绿藻中只有3个VPS13M, S, Y,而一些绿藻中有多达6个VPS13类似物(AtVPS13M1, M2, S, Y, X, B)。我们还强调了VPS13M和X类似物的具体结构特征。该研究揭示了VPS13家族的复杂进化过程,为其在光合生物中的功能表征开辟了重要的视角。
Phylogenetic and Structural Analyses of VPS13 Proteins in Archaeplastida Reveal Their Complex Evolutionary History in Viridiplantae.
VPS13 is a lipid transfer protein family conserved among Eukaryotes and playing roles in fundamental processes involving vesicular transport and membrane expansion including autophagy and organelle biogenesis. VPS13 folds into a long hydrophobic tunnel, allowing lipid transport, decorated by distinct domains involved in protein localization and regulation. Whereas VPS13 organization and function have been extensively studied in yeast and mammals, information in organisms originating from primary endosymbiosis is scarce. In the higher plant Arabidopsis thaliana, four paralogs, AtVPS13S, X, M1, and M2, were identified, AtVPS13S playing a role in the regulation of root growth, cell patterning, and reproduction. In this work, we performed phylogenetic, as well as domain and structural modeling of VPS13 proteins in Archaeplastida in order to understand their general organization and evolutionary history. We confirmed the presence of human VPS13B orthologues in some phyla and described two new VPS13 families presenting a particular domain arrangement: VPS13R in Rhodophytes and VPS13Y in Chlorophytes and Streptophytes. By focusing on Viridiplantae, we were able to draw the evolutionary history of these proteins made by multiple gene gains and duplications as well as domain rearrangements. We showed that some Chlorophytes have only three (AtVPS13M, S, Y) whereas some Charophytes have up to six VPS13 paralogs (AtVPS13M1, M2, S, Y, X, B). We also highlighted specific structural features of VPS13M and X paralogs. This study reveals the complex evolution of VPS13 family and opens important perspectives for their functional characterization in photosynthetic organisms.