Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France.
Nucleic Acids Res. 2009 Nov;37(21):7239-57. doi: 10.1093/nar/gkp668.
Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE-mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.
生物信息学分析预测金黄色葡萄球菌基因间区有多个调控区。通过这项分析，我们鉴定了 11 种新型非编码 RNA（RsaA-K），它们在不同实验条件下在多个金黄色葡萄球菌菌株中表达。其中许多在生长的指数晚期积累。所有的 ncRNA 都是稳定的，它们的表达不依赖于 Hfq。其中一些的转录受替代 sigma B 因子（RsaA、D 和 F）调节，而 RsaE 的表达依赖于 agrA。这 6 种 ncRNA 是金黄色葡萄球菌特有的，4 种在其他葡萄球菌中保守，RsaE 也存在于芽孢杆菌科中。转录组和蛋白质组分析表明，RsaE 调节参与各种代谢途径的蛋白质的合成。系统发育分析结合 RNA 结构探测、RsaE-mRNA 碱基配对搜索和 toe-printing 测定表明，RsaE 保守且未配对的 UCCC 序列基序结合靶 mRNA，阻止核糖体起始复合物的形成。这项研究出人意料地表明，大多数新型 ncRNA 都携带保守的 C 丰富基序，表明它们是一类通过共享机制靶向 mRNA 的 ncRNA 成员。
