Department of Biology, Massachusetts Institute of Technology; Cambridge, Massachusetts, United States of America.
Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
PLoS Genet. 2024 Sep 6;20(9):e1011100. doi: 10.1371/journal.pgen.1011100. eCollection 2024 Sep.
Pseudouridine (Ψ) is an ubiquitous RNA modification, present in the tRNAs and rRNAs of species across all domains of life. Conserved pseudouridine synthases modify the mRNAs of diverse eukaryotes, but the modification has yet to be identified in bacterial mRNAs. Here, we report the discovery of pseudouridines in mRNA from E. coli. By testing the mRNA modification capacity of all 11 known pseudouridine synthases, we identify RluA as the predominant mRNA-modifying enzyme. RluA, a known tRNA and 23S rRNA pseudouridine synthase, modifies at least 31 of the 44 high-confidence sites we identified in E. coli mRNAs. Using RNA structure probing data to inform secondary structures, we show that the target sites of RluA occur in a common sequence and structural motif comprised of a ΨURAA sequence located in the loop of a short hairpin. This recognition element is shared with previously identified target sites of RluA in tRNAs and rRNA. Overall, our work identifies pseudouridine in key mRNAs and suggests the capacity of Ψ to regulate the transcripts that contain it.
假尿嘧啶核苷（Ψ）是一种普遍存在的 RNA 修饰，存在于所有生命领域的物种的 tRNA 和 rRNA 中。保守的假尿嘧啶合酶修饰不同真核生物的 mRNA，但在细菌 mRNA 中尚未发现该修饰。在这里，我们报告了在大肠杆菌 mRNA 中发现假尿嘧啶核苷。通过测试所有 11 种已知假尿嘧啶合酶的 mRNA 修饰能力，我们确定 RluA 是主要的 mRNA 修饰酶。RluA 是一种已知的 tRNA 和 23S rRNA 假尿嘧啶合酶，修饰了我们在大肠杆菌 mRNA 中鉴定的至少 31 个 44 个高可信度位点中的 31 个。我们使用 RNA 结构探测数据来提供二级结构信息，表明 RluA 的靶位点位于一个由位于短发夹环中的 ΨURAA 序列组成的常见序列和结构基序中。该识别元件与之前在 tRNA 和 rRNA 中鉴定的 RluA 的靶位点共享。总的来说，我们的工作在关键的 mRNA 中鉴定了假尿嘧啶核苷，并表明 Ψ 能够调节包含它的转录物。
