Proteome remodeling is a fundamental adaptive response, and proteins in complexes and functionally related proteins are often co-expressed. Using a deep sampling strategy we define core proteomes of Arabidopsis thaliana tissues with around 10 000 proteins per tissue, and absolutely quantify (copy numbers per cell) nearly 16 000 proteins throughout the plant lifecycle. A proteome-wide survey of global post-translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue- and age-specific roles of entire signaling modules regulating transcription in photosynthesis, seed development, and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of cysteine-rich receptor-like kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were found to be co-expressed in a tissue- and age-specific manner, indicating functional promiscuity in the assembly of these less-studied protein complexes in Arabidopsis.Furthermore, we characterized detailed proteome remodeling in basal immunity by treating Arabidopsis seeldings with flg22. Through simultaneously monitoring phytohormone and transcript changes upon flg22 treatment, we obtained strong evidence of suppression of jasmonate (JA) and JA-isoleucine (JA-Ile) levels by deconjugation and hydroxylation by IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2), respectively, under the control of JASMONATE INSENSITIVE 1 (MYC2), suggesting an unrecognized role of a new JA regulatory switch in pattern-triggered immunity. Taken together, the datasets generated in this study present extensive coverage of the Arabidopsis proteome in various biological scenarios, providing a rich resource available to the whole plant science community.

蛋白质组重塑是一种基本的适应性反应，复合物中的蛋白质和功能相关的蛋白质通常共同表达。使用深度采样策略，我们确定拟南芥的核心蛋白质组每个组织中含有约10,000种蛋白质的组织，并且在整个植物生命周期中绝对定量（每个细胞的拷贝数）近1.6万种蛋白质。一项针对全球翻译后修饰的蛋白质组研究表明，氨基酸交换表明真核生物可能存在翻译不忠。蛋白质丰度的相关分析揭示了在光合作用，种子发育以及衰老和脱落中调节转录的整个信号传导模块的潜在新的组织和年龄特异性作用。除其他外，数据表明RD26和其他NAC转录因子在种子发育中具有与脱水耐性相关的潜在功能，以及富含半胱氨酸的受体样激酶（CRK）作为衰老中ROS传感器的可能功能。拟南芥此外，我们通过用flg22处理拟南芥的种质来表征蛋白质组在基础免疫中的重塑。通过同时监测flg22处理后的植物激素和转录物变化，我们获得了强有力的证据，证明IAA-ALA RESISTANT3（IAR3）和茉莉酸诱导的氧合酶2的解偶联和羟基化作用抑制了茉莉酸（JA）和JA-异亮氨酸（JA-Ile）的水平。 （JOX2）分别在JASMONATE INSENSITIVE 1（MYC2）的控制下，提示了新的JA调控开关在模式触发的免疫中的作用尚未得到认识。综上所述，本研究产生的数据集广泛涵盖了拟南芥 各种生物学场景中的蛋白质组，为整个植物科学界提供了丰富的资源。