Origin, Evolution, and Loss of Bacterial Small RNAs.
Origin, Evolution, and Loss of Bacterial Small RNAs.
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DOI：
10.1128/microbiolspec.rwr-0004-2017
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发表时间：
2018-04
影响因子：
3.7
通讯作者：
Raghavan R
中科院分区：
文献类型：
--
作者：
Dutcher HA;Raghavan R
尽管细菌非编码小 RNA (sRNA) 在转录后调控中发挥着核心作用，但人们对其进化知之甚少。在这里，我们汇编了迄今为止的研究成果，并追踪了 sRNA 的生命周期——从它们的出现机制、变化过程和频繁的新功能化，到它们从细菌谱系中消失。由于它们具有相对不受限制的结构要求，我们发现 sRNA 起源多种多样，包括从头出现以及通过复制事件和水平基因转移从预先存在的遗传元件形成。仅需要与其 mRNA 靶标部分互补，就会促进明显的快速变化，这也为跨广泛进化距离追踪 sRNA 带来了重大挑战。我们记录了最近出现的 sRNA 特别快速进化，反映了在真核生物中的功能类似物 microRNA 中观察到的动态。 mRNA 结合区、转录调节因子或 sigma 因子结合位点以及蛋白质结合区的突变都可能是 sRNA 调节作用转变的来源。最后，我们使用现有的少数进化研究中的例子，研究了 sRNA 丢失的案例，并描述了这些可能是除了中性过程之外的适应性结果。我们强调需要对 sRNA 进化模式进行更全面的分析，以此作为改进新型 sRNA 检测、增强基因组注释并加深我们对细菌调控网络的理解的手段。
Despite the central role of bacterial non-coding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here, we compile what has been studied to date and trace a life cycle of sRNAs—from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from pre-existing genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently-emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss, and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.