Table_5_Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root Meristems.XLSX

Due to their sessile nature, plants rely on root systems to mediate many biotic and abiotic cues. To overcome these challenges, the root proteome is shaped to specific responses. Proteome-wide reprogramming events are magnified in meristems due to their active protein production. Using meristems as a test system, here, we study the major rewiring that plants undergo during cold acclimation. We performed tandem mass tag-based bottom-up quantitative proteomics of two consecutive segments of barley seminal root apexes subjected to suboptimal temperatures. After comparing changes in total and ribosomal protein (RP) fraction-enriched contents with shifts in individual protein abundances, we report ribosome accumulation accompanied by an intricate translational reprogramming in the distal apex zone. Reprogramming ranges from increases in ribosome biogenesis to protein folding factors and suggests roles for cold-specific RP paralogs. Ribosome biogenesis is the largest cellular investment; thus, the vast accumulation of ribosomes and specific translation-related proteins during cold acclimation could imply a divergent ribosomal population that would lead to a proteome shift across the root. Consequently, beyond the translational reprogramming, we report a proteome rewiring. First, triggered protein accumulation includes spliceosome activity in the root tip and a ubiquitous upregulation of glutathione production and S-glutathionylation (S-GSH) assemblage machineries in both root zones. Second, triggered protein depletion includes intrinsically enriched proteins in the tip-adjacent zone, which comprise the plant immune system. In summary, ribosome and translation-related protein accumulation happens concomitantly to a proteome reprogramming in barley root meristems during cold acclimation. The cold-accumulated proteome is functionally implicated in feedbacking transcript to protein translation at both ends and could guide cold acclimation.

鉴于植物具有固着生长的特性，其依靠根系介导各类生物与非生物信号的感知与传递。为克服此类环境挑战，根系蛋白质组会形成特异性应答模式。由于分生组织的蛋白质合成活动极为活跃，其蛋白质组范围的重编程事件会被显著放大。本研究以分生组织为实验体系，探究植物在冷驯化过程中所经历的主要全局调控重编程。我们对处于亚适宜温度环境下的大麦初生根根尖的两个连续区段，开展了基于串联质量标签（tandem mass tag, TMT）的自下而上定量蛋白质组学分析。在对比总蛋白质组分与核糖体蛋白（ribosomal protein, RP）富集组分的含量变化，以及单个蛋白质的丰度偏移后，我们发现远端根尖区出现了核糖体积累现象，并伴随复杂的翻译重编程过程。该重编程过程涵盖核糖体生物发生（ribosome biogenesis）的增强与蛋白质折叠因子的调控变化，同时暗示了冷胁迫特异性RP旁系同源物的功能作用。核糖体生物发生是细胞内规模最大的能量与物质投入过程；因此，冷驯化过程中核糖体与特定翻译相关蛋白质的大量积累，可能意味着核糖体群体发生了分化，进而引发整个根系的蛋白质组改变。因此，除翻译重编程之外，我们还观测到了蛋白质组的全局重编程。其一，被诱导积累的蛋白质包括根尖中的剪接体（spliceosome）活性相关蛋白，以及两个根尖区段中普遍上调的谷胱甘肽生成与S-谷胱甘肽化（S-GSH）组装机制相关蛋白。其二，被诱导消耗的蛋白质包括根尖邻近区段中固有富集的、参与植物免疫系统的蛋白质。综上，在冷驯化过程中，大麦根系分生组织内的核糖体与翻译相关蛋白质积累，与蛋白质组重编程同步发生。冷胁迫下积累的蛋白质组，在功能上参与了两端组织中转录本到蛋白质翻译的反馈调控，并可能对冷驯化过程起到指导作用。