辅因子抗坏血酸对RNA去甲基化酶活性和选择性的差异调控
Differential control of RNA demethylase activity and selectivity by cofactor ascorbate.
作者信息
Calzini Lucas O, Warminski Marcin, Kowalska Joanna, Jemielity Jacek, Mugridge Jeffrey S
机构信息
Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716, United States.
Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland.
出版信息
bioRxiv. 2025 May 8:2025.05.06.652568. doi: 10.1101/2025.05.06.652568.
The Fe(II)- and 2-oxoglutarate(2-OG)-dependent dioxygenase (FOGDD) enzyme superfamily catalyzes the oxidation of RNA, DNA, and peptide substrates to install chemical modifications that regulate the diverse functions of these biomolecules. For decades, it has been appreciated that many FOGDDs require ascorbate (Vitamin C) as a cofactor for efficient catalysis, but ascorbate requirements across different FOGDD enzymes, its effects on the catalysis of different substrates, and how it engages the FOGDD active site, remain poorly understood. Here, we use RNA demethylases FTO and AlkBH5 as model FOGDD enzymes and show that their ascorbate requirements for efficient demethylation reactions are dramatically different. Furthermore, FTO was found to have strikingly different ascorbate requirements for its own demethylation reactions with different methylated RNA substrates. Our enzymology experiments suggest FTO and AlkBH5, and likely FOGDDs generally, can have widely different ascorbate dependencies based on the balance between an enzyme's intrinsic ability to decarboxylate co-substrate 2-oxoglutarate and the kinetics of its substrate oxidation reaction. Finally, we determined a crystal structure of FTO in complex with ascorbate, which for the first time shows how ascorbate selectively engages the FOGDD active site. Together, our biochemical and structural data show that ascorbate can selectively tune the RNA demethylation reactions of FTO and AlkBH5, and that more globally, differences in ascorbate concentrations in different environments or diseases may regulate the activity and specificity of diverse FOGDD-catalyzed oxidation reactions in the cell.
依赖Fe(II)和2-酮戊二酸(2-OG)的双加氧酶(FOGDD)酶超家族催化RNA、DNA和肽底物的氧化,以进行化学修饰,从而调节这些生物分子的多种功能。几十年来,人们已经认识到许多FOGDD需要抗坏血酸(维生素C)作为辅助因子来实现高效催化,但不同FOGDD酶对抗坏血酸的需求、其对不同底物催化作用的影响以及它如何与FOGDD活性位点结合,仍然知之甚少。在这里,我们使用RNA去甲基化酶FTO和AlkBH5作为模型FOGDD酶,并表明它们对高效去甲基化反应的抗坏血酸需求存在显著差异。此外,发现FTO对不同甲基化RNA底物自身去甲基化反应的抗坏血酸需求也有显著不同。我们的酶学实验表明,基于酶对共底物2-酮戊二酸脱羧的内在能力与其底物氧化反应动力学之间的平衡,FTO和AlkBH5以及一般的FOGDD可能具有广泛不同的抗坏血酸依赖性。最后,我们确定了FTO与抗坏血酸复合物的晶体结构,这首次展示了抗坏血酸如何选择性地与FOGDD活性位点结合。总之,我们的生化和结构数据表明,抗坏血酸可以选择性地调节FTO和AlkBH5的RNA去甲基化反应,更广泛地说,不同环境或疾病中抗坏血酸浓度的差异可能调节细胞中多种FOGDD催化的氧化反应的活性和特异性。