Regulatory context drives conservation of glycine riboswitch aptamers
Regulatory context drives conservation of glycine riboswitch aptamers
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DOI：
10.1371/journal.pcbi.1007564
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发表时间：
2019-12-01
影响因子：
4.3
通讯作者：
Meyer, Michelle M.
中科院分区：
文献类型：
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作者：
Crum, Matt;Ram-Mohan, Nikhil;Meyer, Michelle M.
与蛋白质编码序列相比，突变和自然选择对非编码基因（ncRNA）序列和功能的影响尚不清楚。许多ncRNA基因只分布在少数生物体中，并且似乎正在迅速进化。与蛋白质编码序列相比，传统的系统发育方法无法很好地解决与ncrna评估相关的许多挑战，包括：序列长度短，缺乏一级序列保护，以及二级结构对生物功能的重要性。核糖开关是一种结构化的ncrna，它直接与小分子相互作用，调节细菌中的基因表达。它们通常由配体结合域（适体）组成，其折叠变化驱动基因表达的变化。由于串联适体排列（tandem）的广泛存在，甘氨酸核糖开关是研究得最充分的基因之一，其中两个同源适体与甘氨酸相互作用并相互调节基因表达。然而，很大一部分甘氨酸核糖开关是由单个适体组成的（单例）。在研究串联和单核苷酸适配体之间的关系时，我们使用图聚类来克服传统系统发育分析的局限性。图聚类允许使用更广泛的两两比较措施来评估适体相似性。使用这种方法，我们发现串联甘氨酸核糖开关对中的一个适体通常是高度保守的，而哪个适体是保守的取决于被调节的基因。此外，我们的分析还表明，单体适配体与第一或第二串联适配体更相似，这也是基于受调控基因。综上所述，我们的研究结果表明，串联甘氨酸核糖开关降解成功能单一的，受调节的基因决定了哪个甘氨酸结合适体是保守的。甘氨酸核糖开关是一种ncRNA，负责调节细菌中几种不同的基因集，这些基因集具有一个（单）或两个（串联）适体，每个适体都直接感知甘氨酸。哪个适体在基因调控中更重要，串联适体和单配体的功能差异是核糖开关领域长期存在的问题。像许多具有生物学功能的rna一样，甘氨酸适配体需要特定的3D折叠构象。因此，它们在远亲同源物之间的一级序列相似性较低，序列长度的巨大变化使得创建和分析准确的多序列比对具有挑战性。为了更好地理解串联和单体适配体之间的关系，我们使用了一种图聚类方法，该方法允许我们使用测量序列和结构相似性的度量来比较适配体的相似性。我们的研究表明，在串联甘氨酸核糖开关中，一个适体比另一个更高度保守，哪个适体保守取决于被调节的基因。此外，我们发现许多单核苷酸核糖开关可能源于串联核糖开关，其中非保守适配体的配体结合位点随着时间的推移而降解。
In comparison to protein coding sequences, the impact of mutation and natural selection on the sequence and function of non-coding (ncRNA) genes is not well understood. Many ncRNA genes are narrowly distributed to only a few organisms, and appear to be rapidly evolving. Compared to protein coding sequences, there are many challenges associated with assessment of ncRNAs that are not well addressed by conventional phylogenetic approaches, including: short sequence length, lack of primary sequence conservation, and the importance of secondary structure for biological function. Riboswitches are structured ncRNAs that directly interact with small molecules to regulate gene expression in bacteria. They typically consist of a ligand-binding domain (aptamer) whose folding changes drive changes in gene expression. The glycine riboswitch is among the most well-studied due to the widespread occurrence of a tandem aptamer arrangement (tandem), wherein two homologous aptamers interact with glycine and each other to regulate gene expression. However, a significant proportion of glycine riboswitches are comprised of single aptamers (singleton). Here we use graph clustering to circumvent the limitations of traditional phylogenetic analysis when studying the relationship between the tandem and singleton glycine aptamers. Graph clustering enables a broader range of pairwise comparison measures to be used to assess aptamer similarity. Using this approach, we show that one aptamer of the tandem glycine riboswitch pair is typically much more highly conserved, and that which aptamer is conserved depends on the regulated gene. Furthermore, our analysis also reveals that singleton aptamers are more similar to either the first or second tandem aptamer, again based on the regulated gene. Taken together, our findings suggest that tandem glycine riboswitches degrade into functional singletons, with the regulated gene(s) dictating which glycine-binding aptamer is conserved.Author summary The glycine riboswitch is a ncRNA responsible for the regulation of several distinct gene sets in bacteria that is found with either one (singleton) or two (tandem) aptamers, each of which directly senses glycine. Which aptamer is more important for gene-regulation, and the functional difference between tandem and singleton aptamers, are long-standing questions in the riboswitch field. Like many biologically functional RNAs, glycine aptamers require a specific 3D folded conformation. Thus, they have low primary sequence similarity across distantly related homologs, and large changes in sequence length that make creation and analysis of accurate multiple sequence alignments challenging. To better understand the relationship between tandem and singleton aptamers, we used a graph clustering approach that allows us to compare the similarity of aptamers using metrics that measure both sequence and structure similarity. Our investigation reveals that in tandem glycine riboswitches, one aptamer is more highly conserved than the other, and which aptamer is conserved depends on what gene(s) are regulated. Moreover, we find that many singleton glycine riboswitches likely originate from tandem riboswitches in which the ligand-binding site of the non-conserved aptamer has degraded over time.