Martinez-Seidel Federico, Beine-Golovchuk Olga, Hsieh Yin-Chen, Kopka Joachim
Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany.
School of BioSciences, University of Melbourne, Parkville, VIC, Australia.
Front Plant Sci. 2020 Jun 25;11:948. doi: 10.3389/fpls.2020.00948. eCollection 2020.
Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, , which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
植物将大量的能量和资源用于核糖体的生产。从历史上看，这些多蛋白核糖体复合物一直被视为静态的蛋白质合成机器，不受广泛调控，只是读取mRNA并相应地产生多肽。越来越多来自各种模式生物的新证据表明核糖体具有异质性。这种异质性可以构成专门调节mRNA翻译和控制蛋白质合成的核糖体。核糖体异质性的一个突出例子见于模式植物拟南芥，由于基因组加倍，每个核糖体蛋白（RP）基因都有多个旁系同源基因。我们支持这样一种观点，即植物进化促使高RP旁系同源基因向功能异质性方向分化，部分原因是大量的核糖体突变体资源表明这种特化超出了单个结构RP或RP旁系同源基因的多效性影响。因此，拟南芥是研究这一现象的非常合适的模式生物。拟南芥能够采用反向遗传学方法，这些方法可以提供核糖体特化的证据。在这篇综述中，我们批判性地评估了植物核糖体特化的证据，并强调了核糖体生物发生过程中可能出现异质性的步骤，通过提供来自人类或酵母领域的先进见解来填补植物科学中的知识空白。我们提出了一种数据分析流程，用于推断核糖体复合物的异质性以及与应激事件相关的与标准结构组成的偏差。通过与其他高通量方法（如蛋白质组学）相结合，可以推断和增强这个分析流程。诸如动力学质谱和核糖体分析等技术对于解析翻译调控的时间和空间方面将是必要的，而核糖体亚群的功能特征将通过反向遗传学和系统生物学方法的结合而变得清晰。
