The ubiquitin system is crucial for the development and fitness of higher plants. De-etiolation, during which green plants initiate photomorphogenesis and establish autotrophy, is a dramatic and complicated process that is tightly regulated by a massive number of ubiquitylation/de-ubiquitylation events. Here we present site-specific quantitative proteomic data for the ubiquitylomes of de-etiolating seedling leaves of Zea mays L. (exposed to light for 1, 6, or 12?h) achieved through immunoprecipitation-based high-resolution mass spectrometry (MS). Through the integrated analysis of multiple ubiquitylomes, we identified and quantified 1926 unique ubiquitylation sites corresponding to 1053 proteins. We analyzed these sites and found five potential ubiquitylation motifs, KA, AXK, KXG, AK, and TK. Time-course studies revealed that the ubiquitylation levels of 214 sites corresponding to 173 proteins were highly correlated across two replicate MS experiments, and significant alterations in the ubiquitylation levels of 78 sites (fold change >1.5) were detected after de-etiolation for 12?h. The majority of the ubiquitylated sites we identified corresponded to substrates involved in protein and DNA metabolism, such as ribosomes and histones. Meanwhile, multiple ubiquitylation sites were detected in proteins whose functions reflect the major physiological changes that occur during plant de-etiolation, such as hormone synthesis/signaling proteins, key C4 photosynthetic enzymes, and light signaling proteins. This study on the ubiquitylome of the maize seedling leaf is the first attempt ever to study the ubiquitylome of a C4 plant and provides the proteomic basis for elucidating the role of ubiquitylation during plant de-etiolation.
蛋白质的泛素化翻译后修饰在植物发育及其健康成长过程中发挥着极为重要的作用。去黄化，亦称为转绿过程，是绿色高等植物开启光形态建成和自养生活的过程。这是一个被大量蛋白质泛素化与去泛素化修饰事件紧密调控的复杂而又剧烈变化的生物学过程。本研究中，我们展示了利用基于免疫共沉淀-高通量蛋白质质谱分析技术获得的玉米幼苗转绿过程中叶片（光照1、6、12小时）的位点特异性泛素化定量蛋白质组学数据。通过整合分析多个泛素化修饰蛋白质组，我们鉴定并定量了位于 1041个蛋白质之上的1926位点的泛素化修饰。通过对这些泛素化修饰位点氨基酸序列分析，我们发现了五个潜在泛素化修饰基序：KA、AXK、KXG、AK和TK。时间进程分析表明，对应于173个蛋白质上的214个氨基酸位点上的泛素化修饰水平在两次生物学重复实验中高度吻合，其中78个修饰位点上的泛素化修饰水平在玉米幼苗被光照12小时后发生了显著性变化（基于定量结果变化倍数大于1.5倍的标准）。本研究所鉴定的被泛素化修饰的蛋白质主要参与了蛋白质和DNA代谢过程，像核糖体蛋白和组蛋白。同时发现参与植物转绿过程主要生理变化的蛋白质上存在多个泛素化修饰位点的情况。例如，植物激素合成和信号转导途径的蛋白质、C4光合作用关键酶和光信号转导途径关键蛋白等。此项基于玉米幼苗泛素化修饰蛋白质组学研究工作，为进一步解析C4植物幼苗转绿过程中蛋白质泛素化修饰的作用提供了依据。





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