Bhattacharya Oindrila, Ortiz Irma, Hendricks Nathan, Walling Linda L
Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States.
Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States.
Front Plant Sci. 2023 Aug 28;14:1020275. doi: 10.3389/fpls.2023.1020275. eCollection 2023.
Tomato () is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato's world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,278 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 545 and 92 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 91 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.
番茄（）是研究果实发育、创伤、食草动物侵害和病原体攻击的模式物种。尽管番茄具有全球经济重要性，且叶绿体作为代谢中心和环境信号整合者发挥着作用，但对番茄的基质蛋白质组却知之甚少。我们采用一种高产的叶绿体和基质蛋白分离方案、多维蛋白质鉴定技术（MudPIT）纳升级液相色谱-串联质谱分析、一个用于预测番茄蛋白质体定位的强大内部蛋白质数据库（图谱）以及基质蛋白质组纳入/排除的严格选择标准，鉴定出了1278种番茄基质蛋白质组蛋白。我们提供了迄今为止最可靠的基质蛋白质组之一，分别为545种和92种此前未在番茄质体和拟南芥基质中描述过的蛋白质提供了实验证据。使用指数修正蛋白质丰度指数（emPAI）测定了番茄基质蛋白的相对丰度。番茄和拟南芥基质蛋白质组丰度的比较为基质蛋白稳态的物种特异性性质提供了证据。对番茄基质蛋白质组的人工整理将蛋白质分为十个功能类别，形成了一个便于使用的番茄叶绿体蛋白汇编。整理后，只有91种蛋白质仍为未知、未表征或功能未知的酶。对番茄基质蛋白的整理还表明，番茄有一些拟南芥中不存在的旁系同源蛋白，它们在叶绿体中积累到不同水平。由于其中一些蛋白质在关键代谢途径中发挥作用，或在感知或传递对植物适应生物和非生物胁迫至关重要的信号方面发挥作用，这些数据表明番茄可能以一种新的方式调节叶绿体与细胞核之间的双向通讯。基质蛋白质组为番茄叶绿体-核信号领域未来的机制研究提供了丰富的研究基础，并且是我们阐明由番茄茄科特异性、基质和伤口诱导型亮氨酸氨肽酶A控制的基质蛋白质组动态这一目标的基础。
