Lu Yao, Ma Liqun, Cheng Ke, Li Jinyan, Tang Hui, Zhu Guoning, Wen Hongyi, Zhu Benzhong, Fu Daqi, Qu Guiqin, Luo Yunbo, Zhu Hongliang
College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
Plant J. 2025 May;122(3):e70215. doi: 10.1111/tpj.70215.
RNA-binding proteins (RBPs) have emerged as key players in posttranscriptional gene regulation, yet their full scale role in fruit ripening remains to be fully elucidated. However, due to the complex structure and composition of fruit tissue, exploring RBPs in fruits still faces many challenges. Here, we optimized the plant phase extraction method and successfully applied it to tomato fruits for the unbiased excavation of RBPs in fruits, this method were named as "plant phase extraction in tomato fruit" (termed tfPPE). We yielded a comprehensive candidate RNA-binding proteome (RBPome) composed of 230 proteins and disclosed that approximately 66% of them were unconventional RBPs. Validation of the RNA-binding activities of six candidate RBPs unveiled that metabolic enzymes function as moonlighting RBPs. Furthermore, combined with transcriptome analysis, we identified 41 candidate RBPs associated with fruit ripening. Remarkably, we proposed that SlER21 and SlFER1 play significant roles in fruit coloring and ripening process. Taken together, these results demonstrate that tfPPE was an impactful approach for unbiased excavation RBPs in fruits and pave the way for investigating RBP functions in fruit-ripening regulatory network.
RNA结合蛋白（RBPs）已成为转录后基因调控的关键因子，但其在果实成熟过程中的全面作用仍有待充分阐明。然而，由于果实组织结构和成分复杂，在果实中探索RBPs仍面临诸多挑战。在此，我们优化了植物相提取方法，并成功将其应用于番茄果实，以无偏差地挖掘果实中的RBPs，该方法被命名为“番茄果实植物相提取”（简称tfPPE）。我们获得了一个由230种蛋白质组成的全面的候选RNA结合蛋白质组（RBPome），并发现其中约66%为非常规RBPs。对6种候选RBPs的RNA结合活性进行验证后发现，代谢酶具有兼职RBPs的功能。此外，结合转录组分析，我们鉴定出41种与果实成熟相关的候选RBPs。值得注意的是，我们提出SlER21和SlFER1在果实着色和成熟过程中发挥重要作用。综上所述，这些结果表明tfPPE是一种在果实中无偏差挖掘RBPs的有效方法，为研究RBPs在果实成熟调控网络中的功能铺平了道路。
