The distributions, mechanisms, and structures of metabolite-binding riboswitches.
The distributions, mechanisms, and structures of metabolite-binding riboswitches.
复制标题
代谢物结合核糖开关的分布，机制和结构。
DOI：
10.1186/gb-2007-8-11-r239
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Breaker, Ronald R
中科院分区：
文献类型：
--
作者：
Barrick, Jeffrey E;Breaker, Ronald R
系统发育分析揭示了核糖开关类在不同微生物组中的分布，结构分析导致更新的适体结构模型和这些非编码RNA结构的机制的见解。核糖开关是一种非编码RNA结构，它可以根据细胞条件的变化适当调节基因。参与基本代谢过程的许多蛋白质的表达由感知相关小分子配体的核糖开关控制。已经报道了识别腺苷钴胺素（adenosylcobalamin，BCB 1）、焦磷酸硫胺素（thiamin pyrophosphate，TPP）、赖氨酸、甘氨酸、黄素单核苷酸肽（flavin monolithictide，FMN）、鸟嘌呤、腺嘌呤、葡糖胺-6-磷酸（glcN 6P）、7-氨乙基7-脱氮鸟嘌呤（preQ 1）和S-腺苷甲硫氨酸（S-adenosylmethionine，SAM）的代谢物结合核糖开关。我们已经使用协方差模型搜索，以确定10个广泛的核糖开关类的例子，在生物体的基因组中的所有三个领域的生活。该数据集严格定义了这些核糖开关类的系统发育分布，并揭示了它们的基因控制机制如何在不同的微生物群体中变化。通过检查这些搜索产生的扩展适体序列比对，我们也重新评估和完善了它们的共有二级结构。更新的核糖开关结构模型突出了额外的RNA结构基序，包括一个不寻常的双T-环的安排共同的RISKCbl和FMN核糖开关适体，并纳入新的，有时非经典的，碱基相互作用预测的互信息分析。核糖开关是许多基因组的重要组成部分。本文报道的其他核糖开关变体和更新的适体结构模型将改善未来在基因组序列中注释这些广泛的调控RNA的工作，并为正在进行的结构生物学工作提供信息。仍然有重要的问题是什么生理和进化力量影响核糖开关的分布和机制，以及什么形式的调节替代核糖开关，似乎是在某些谱系中丢失。
Phylogenetic analyses revealed insights into the distribution of riboswitch classes in different microbial groups, and structural analyses led to updated aptamer structure models and insights into the mechanism of these non-coding RNA structures. Riboswitches are noncoding RNA structures that appropriately regulate genes in response to changing cellular conditions. The expression of many proteins involved in fundamental metabolic processes is controlled by riboswitches that sense relevant small molecule ligands. Metabolite-binding riboswitches that recognize adenosylcobalamin (AdoCbl), thiamin pyrophosphate (TPP), lysine, glycine, flavin mononucleotide (FMN), guanine, adenine, glucosamine-6-phosphate (GlcN6P), 7-aminoethyl 7-deazaguanine (preQ1), and S-adenosylmethionine (SAM) have been reported. We have used covariance model searches to identify examples of ten widespread riboswitch classes in the genomes of organisms from all three domains of life. This data set rigorously defines the phylogenetic distributions of these riboswitch classes and reveals how their gene control mechanisms vary across different microbial groups. By examining the expanded aptamer sequence alignments resulting from these searches, we have also re-evaluated and refined their consensus secondary structures. Updated riboswitch structure models highlight additional RNA structure motifs, including an unusual double T-loop arrangement common to AdoCbl and FMN riboswitch aptamers, and incorporate new, sometimes noncanonical, base-base interactions predicted by a mutual information analysis. Riboswitches are vital components of many genomes. The additional riboswitch variants and updated aptamer structure models reported here will improve future efforts to annotate these widespread regulatory RNAs in genomic sequences and inform ongoing structural biology efforts. There remain significant questions about what physiological and evolutionary forces influence the distributions and mechanisms of riboswitches and about what forms of regulation substitute for riboswitches that appear to be missing in certain lineages.