Dong Puting, Yang Mengdi, Hu Jie, Cen Lujia, Zhou Peng, Xu Difei, Xiong Peng, Li Jiahe, He Xuesong
Department of Microbiology, The American Dental Association Forsyth Institute, Cambridge, MA, USA.
Department of Bioengineering, Northeastern University, Boston, MA, USA.
Int J Oral Sci. 2025 Jun 11;17(1):48. doi: 10.1038/s41368-025-00378-4.
Host-derived small RNAs are emerging as critical regulators in the dynamic interactions between host tissues and the microbiome, with implications for microbial pathogenesis and host defense. Among these, transfer RNA-derived small RNAs (tsRNAs) have garnered attention for their roles in modulating microbial behavior. However, the bacterial factors mediating tsRNA interaction and functionality remain poorly understood. In this study, using RNA affinity pull-down assay in combination with mass spectrometry, we identified a putative membrane-bound protein, annotated as P-type ATPase transporter (PtaT) in Fusobacterium nucleatum (Fn), which binds Fn-targeting tsRNAs in a sequence-specific manner. Through targeted mutagenesis and phenotypic characterization, we showed that in both the Fn type strain and a clinical tumor isolate, deletion of ptaT led to reduced tsRNA intake and enhanced resistance to tsRNA-induced growth inhibition. Global RNA sequencing and label-free Raman spectroscopy revealed the phenotypic differences between Fn wild type and PtaT-deficient mutant, highlighting the functional significance of PtaT in purine and pyrimidine metabolism. Furthermore, AlphaFold 3 prediction provides evidence supporting the specific binding between PtaT and Fn-targeting tsRNA. By uncovering the first RNA-binding protein in Fn implicated in growth modulation through interactions with host-derived small RNAs (sRNAs), our study offers new insights into sRNA-mediated host-pathogen interplay within the context of microbiome-host interactions.
宿主来源的小RNA正在成为宿主组织与微生物群动态相互作用中的关键调节因子，对微生物致病机制和宿主防御具有重要意义。其中，转运RNA衍生的小RNA（tsRNA）因其在调节微生物行为中的作用而受到关注。然而，介导tsRNA相互作用和功能的细菌因子仍知之甚少。在本研究中，我们结合RNA亲和拉下试验和质谱分析，在具核梭杆菌（Fn）中鉴定出一种假定的膜结合蛋白，注释为P型ATPase转运蛋白（PtaT），它以序列特异性方式结合靶向Fn的tsRNA。通过靶向诱变和表型特征分析，我们发现，在Fn标准菌株和临床肿瘤分离株中，ptaT的缺失均导致tsRNA摄取减少，并增强了对tsRNA诱导的生长抑制的抗性。全基因组RNA测序和无标记拉曼光谱揭示了Fn野生型和PtaT缺陷型突变体之间的表型差异，突出了PtaT在嘌呤和嘧啶代谢中的功能意义。此外，AlphaFold 3预测提供了支持PtaT与靶向Fn的tsRNA特异性结合的证据。通过揭示Fn中首个通过与宿主来源的小RNA（sRNA）相互作用参与生长调节的RNA结合蛋白，我们的研究为微生物群-宿主相互作用背景下sRNA介导的宿主-病原体相互作用提供了新的见解。
