University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany.
NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.
Sci Rep. 2019 Oct 4;9(1):14331. doi: 10.1038/s41598-019-49881-9.
The sRNA Yfr1 and members of the Yfr2 sRNA family are almost universally present within cyanobacteria. The conserved motifs of these sRNAs are nearly complementary to each other, suggesting their ability to participate in crosstalk. The conserved motif of Yfr1 is shared by members of the Yfr10 sRNA family, members of which are otherwise less conserved in sequence, structure, and synteny compared to Yfr1. The different structural properties enable the discrimination of unique targets of Yfr1 and Yfr10. Unlike most studied regulatory sRNAs, Yfr1 gene expression only slightly changes under the tested stress conditions and is present at high levels at all times. In contrast, cellular levels of Yfr10 increase during the course of acclimation to darkness, and levels of Yfr2 increase when cells are shifted to high light or nitrogen limitation conditions. In this study, we investigated the targetomes of Yfr2, Yfr1, and Yfr10 in Prochlorococcus MED4, establishing CRAFD-Seq as a new method for identifying direct targets of these sRNAs that is applicable to all bacteria, including those that are not amenable to genetic modification. The results suggest that these sRNAs are integrated within a regulatory network of unprecedented complexity in the adjustment of carbon and nitrogen-related primary metabolism.
sRNA Yfr1 和 Yfr2 sRNA 家族的成员几乎普遍存在于蓝细菌中。这些 sRNA 的保守基序彼此几乎互补，表明它们能够参与串扰。Yfr1 的保守基序与 Yfr10 sRNA 家族的成员共享，与 Yfr1 相比，该家族的成员在序列、结构和基因排列上的保守性较低。不同的结构特性使 Yfr1 和 Yfr10 能够区分独特的靶标。与大多数研究的调控 sRNA 不同，Yfr1 基因表达仅在测试的应激条件下略有变化，并且始终保持高水平。相比之下，在适应黑暗的过程中，Yfr10 的细胞水平增加，而当细胞转移到高光或氮限制条件时，Yfr2 的水平增加。在这项研究中，我们研究了 Prochlorococcus MED4 中 Yfr2、Yfr1 和 Yfr10 的靶标组，建立了 CRAFD-Seq 作为鉴定这些 sRNA 直接靶标的新方法，该方法适用于所有细菌，包括那些不易进行遗传修饰的细菌。结果表明，这些 sRNA 整合在一个前所未有的复杂的与碳和氮相关的初级代谢物调节的调控网络中。
