Houserova Dominika, Dahmer Donovan J, Amin Shivam V, King Valeria M, Barnhill Emmaline C, Zambrano Mike E, Dean Meghan A, Crucello Aline, Aria Kevin M, Spector Michael P, Borchert Glen M
Department of Pharmacology, USA College of Medicine, Mobile, AL 36688-0002, USA.
Department of Biomedical Sciences, University of South Alabama, Mobile, AL 36688-0002, USA.
Antibiotics (Basel). 2021 Mar 16;10(3):305. doi: 10.3390/antibiotics10030305.
An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of stress survival. Generally thought to be 50-500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the C-starvation response (CSR), confirming its involvement in the CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in , experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the sRNAs described to date.
非编码RNA（ncRNAs）在环境应激期间协调基因表达的作用日益明显。越来越多的证据表明，小RNA（sRNAs）是应激存活的关键驱动因素。sRNAs通常被认为长度为50-500个核苷酸，存在于基因间区域，其通常通过与mRNA靶标碱基配对来调节蛋白质表达。在这项工作中，我们采用了一种更精确的sRNAs定义，该定义允许更短的序列以及sRNA基因座与注释的蛋白质编码基因座重叠，从而鉴定出475个先前未注释的sRNAs，它们在碳饥饿（C-饥饿）期间显著差异表达。Northern印迹法和定量RT-PCR证实了其中几种新型sRNAs的表达和身份，并且我们的计算分析发现大多数sRNAs与已知sRNAs高度保守且在结构上相关。重要的是，我们表明在C-饥饿期间动态表达的一种sRNA，即sRNA4130247的缺失，会显著损害C-饥饿反应（CSR），证实了其参与CSR。总之，本文所呈现的工作首次对[具体物种或研究对象未给出]中的基因内sRNAs进行了表征，通过实验证实了在CSR期间动态表达的sRNAs直接参与应激存活，并且使迄今所描述的sRNAs数量增加了一倍多。
