Tandem repeat proteins (TRPs) are widely distributed and bind to a wide variety of ligands. DNA-binding TRPs such as zinc finger (ZNF) and transcription activator-like effector (TALE) play important roles in biology and biotechnology. In this study, we first conducted an extensive analysis of TRPs in public databases, and found that the enormous diversity of TRPs is largely unexplored. We then focused our efforts on identifying novel TRPs possessing DNA-binding capabilities. We established a protein language model for DNA-binding protein prediction (PLM-DBPPred), and predicted a large number of DNA-binding TRPs. A subset was then selected for experimental screening, leading to the identification of 11 novel DNA-binding TRPs, with six showing sequence specificity. Notably, members of the STAR (Short TALE-like Repeat proteins) family can be programmed to target specific 9 bp DNA sequences with high affinity. Leveraging this property, we generated artificial transcription factors using reprogrammed STAR proteins and achieved targeted activation of endogenous gene sets. Furthermore, the members of novel families such as MOON (Marine Organism-Originated DNA binding protein) and pTERF (prokaryotic mTERF-like protein) exhibit unique features and distinct DNA-binding characteristics, revealing interesting biological clues. Our study expands the diversity of DNA-binding TRPs, and demonstrates that a systematic approach greatly enhances the discovery of new biological insights and tools.

中文翻译：

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系统发现 DNA 结合串联重复序列蛋白


串联重复蛋白 （TRP） 分布广泛，并与多种配体结合。锌指 （ZNF） 和转录激活因子样效应子 （TALE） 等 DNA 结合 TRP 在生物学和生物技术中发挥着重要作用。在这项研究中，我们首先对公共数据库中的 TRP 进行了广泛的分析，发现 TRP 的巨大多样性在很大程度上尚未得到探索。然后，我们专注于鉴定具有 DNA 结合能力的新型 TRP。我们建立了用于 DNA 结合蛋白预测的蛋白质语言模型 （PLM-DBPPred），并预测了大量 DNA 结合 TRP。然后选择一个子集进行实验筛选，鉴定出 11 个新型 DNA 结合 TRP，其中 6 个显示出序列特异性。值得注意的是，STAR（Short TALE-like Repeat proteins）家族的成员可以被编程为以高亲和力靶向特异性 9 bp DNA 序列。利用这一特性，我们使用重编程的 STAR 蛋白生成人工转录因子，并实现了内源性基因集的靶向激活。此外，MOON （海洋生物来源的 DNA 结合蛋白） 和 pTERF （原核 mTERF 样蛋白） 等新家族的成员表现出独特的特征和独特的 DNA 结合特性，揭示了有趣的生物学线索。我们的研究扩大了 DNA 结合 TRP 的多样性，并表明系统方法极大地增强了新的生物学见解和工具的发现。