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UTR 衍生的 sRNAs 的成熟度在适应不同生长条件的过程中受到调节。

Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions.

机构信息

Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.

出版信息

Int J Mol Sci. 2021 Nov 12;22(22):12260. doi: 10.3390/ijms222212260.

DOI:10.3390/ijms222212260
PMID:34830143
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8625941/
Abstract

Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3' untranslated regions (UTRs). In this study, we investigated the maturation of 5' and 3' UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium . Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5 UTRs and 16 in 3' UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5'/3' end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.

摘要

小调控 RNA 通过与其靶 mRNA 结合在细菌基因调控中发挥主要作用，这主要影响靶标 mRNA 的稳定性或翻译。sRNA 的表达水平通常受其自身启动子的调节，但最近的报道强调了源自 mRNA 3'非翻译区（UTR）的 sRNA 的存在和重要性。在这项研究中，我们在兼性光养型 α-变形菌中全面研究了 5'和 3'UTR 衍生 sRNA 的成熟。包括一些已知的 UTR 衍生 sRNA，如 UpsM 或 CcsR1-4，预测有 14 个 sRNA 位于 5'UTR 中，16 个位于 3'UTR 中。基于相应缺失菌株的 RNA 下一代测序 (NGS) 数据的差异 RNA 5'/3'端分析预测了不同核糖核酸酶在成熟过程中的参与。结果在体内得到验证，并强调了多核苷酸磷酸化酶 (PNPase) 和核糖核酸酶 E (RNase E) 在加工和成熟过程中的重要性。当培养物暴露于外部应激条件（如氧化应激）和不同生长阶段时，一些 UTR 衍生 sRNA 的丰度会发生变化。启动子融合表明，这种影响不能仅仅归因于转录率的改变。此外，在早期稳定期和铁耗竭条件下，RNase E 依赖性切割几种 UTR 衍生 sRNA 的差异非常显著。我们得出结论，核糖核酸酶加工的改变会影响 UTR 衍生 sRNA 的水平，从而可能间接影响它们的 mRNA 靶标。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/e58a0b2bbfc3/ijms-22-12260-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/20b2ca7e54a2/ijms-22-12260-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/933de85f8070/ijms-22-12260-g002.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/ccfae3e95e8e/ijms-22-12260-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/6ec491d54605/ijms-22-12260-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/74e606b43fa4/ijms-22-12260-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/42235f161201/ijms-22-12260-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/5e54d0a8a3ee/ijms-22-12260-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/e58a0b2bbfc3/ijms-22-12260-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/20b2ca7e54a2/ijms-22-12260-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/933de85f8070/ijms-22-12260-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/69ad1f5a7012/ijms-22-12260-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/ccfae3e95e8e/ijms-22-12260-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/6ec491d54605/ijms-22-12260-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/74e606b43fa4/ijms-22-12260-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/42235f161201/ijms-22-12260-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/5e54d0a8a3ee/ijms-22-12260-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f1ef/8625941/e58a0b2bbfc3/ijms-22-12260-g009.jpg

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