Mueller Stefanie J, Lang Daniel, Hoernstein Sebastian N W, Lang Erika G E, Schuessele Christian, Schmidt Anton, Fluck Melanie, Leisibach Desirée, Niegl Christina, Zimmer Andreas D, Schlosser Andreas, Reski Ralf
Plant Biotechnology, Faculty of Biology , University of Freiburg, 79104 Freiburg, Germany;
Plant Physiol. 2014 Apr;164(4):2081-95. doi: 10.1104/pp.114.235754. Epub 2014 Feb 10.
Extant eukaryotes are highly compartmentalized and have integrated endosymbionts as organelles, namely mitochondria and plastids in plants. During evolution, organellar proteomes are modified by gene gain and loss, by gene subfunctionalization and neofunctionalization, and by changes in protein targeting. To date, proteomics data for plastids and mitochondria are available for only a few plant model species, and evolutionary analyses of high-throughput data are scarce. We combined quantitative proteomics, cross-species comparative analysis of metabolic pathways, and localizations by fluorescent proteins in the model plant Physcomitrella patens in order to assess evolutionary changes in mitochondrial and plastid proteomes. This study implements data-mining methodology to classify and reliably reconstruct subcellular proteomes, to map metabolic pathways, and to study the effects of postendosymbiotic evolution on organellar pathway partitioning. Our results indicate that, although plant morphologies changed substantially during plant evolution, metabolic integration of organelles is largely conserved, with exceptions in amino acid and carbon metabolism. Retargeting or regulatory subfunctionalization are common in the studied nucleus-encoded gene families of organelle-targeted proteins. Moreover, complementing the proteomic analysis, fluorescent protein fusions revealed novel proteins at organelle interfaces such as plastid stromules (stroma-filled tubules) and highlight microcompartments as well as intercellular and intracellular heterogeneity of mitochondria and plastids. Thus, we establish a comprehensive data set for mitochondrial and plastid proteomes in moss, present a novel multilevel approach to organelle biology in plants, and place our findings into an evolutionary context.
现存的真核生物具有高度的区室化结构，并且已将内共生体整合为细胞器，即植物中的线粒体和质体。在进化过程中，细胞器蛋白质组通过基因的获得和丢失、基因的亚功能化和新功能化以及蛋白质靶向的变化而发生改变。到目前为止，仅少数植物模式物种有质体和线粒体的蛋白质组学数据，高通量数据的进化分析也很匮乏。我们结合了定量蛋白质组学、代谢途径的跨物种比较分析以及在模式植物小立碗藓中通过荧光蛋白进行的定位，以评估线粒体和质体蛋白质组的进化变化。本研究采用数据挖掘方法来分类和可靠地重建亚细胞蛋白质组、绘制代谢途径图谱，并研究内共生后进化对细胞器途径分配的影响。我们的结果表明，尽管植物形态在植物进化过程中发生了显著变化，但细胞器的代谢整合在很大程度上是保守的，氨基酸和碳代谢方面存在例外情况。在研究的靶向细胞器的蛋白质的核编码基因家族中，重新靶向或调节性亚功能化很常见。此外，作为蛋白质组学分析的补充，荧光蛋白融合揭示了细胞器界面处的新蛋白质，如质体小管（充满基质的小管），并突出了微区室以及线粒体和质体的细胞间和细胞内异质性。因此，我们建立了苔藓线粒体和质体蛋白质组的综合数据集，提出了一种新的植物细胞器生物学多层次方法，并将我们的发现置于进化背景中。
