A recent evolutionary origin of a bacterial small RNA that controls multicellular fruiting body development
A recent evolutionary origin of a bacterial small RNA that controls multicellular fruiting body development
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DOI：
10.1016/j.ympev.2014.01.001
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发表时间：
2014-04-01
影响因子：
4.1
通讯作者：
Velicer, Gregory J.
中科院分区：
文献类型：
--
作者：
Chen, I-Chen Kimberly;Griesenauer, Brad;Velicer, Gregory J.
在动物和植物中，非编码小RNA在转录后水平调节许多基因的表达。最近，人们还发现许多非编码小RNA（sRNA）可以调节细菌中的多种重要生物过程，包括社会性状，但人们对此类细菌sRNA的系统发育或机制起源知之甚少。在这里，我们提出了粘细菌 sRNA Pxr 的系统发育起源，它作为营养水平的函数，对黄色粘球菌子实体发育的起始进行负调控，并检查了其在粘球菌目中的多样化。 pxr 的同源物在整个 Cystobacterineae 亚目中被发现（有一些可能的损失），但在该分支之外没有发现，这表明 Pxr 调节系统在基础 Cystobacterineae 谱系中具有单一起源。囊杆菌亚科之间的 pxr 序列进化速率差异很大，其方式无法通过整体基因组差异来预测。在大多数物种中都发现了 pxr 的单个拷贝，其中 17% 的核苷酸位置是多态性的。然而，囊杆菌属内存在三个串联旁系同源物，并且这些等位基因一起表现出较高的分化率。似乎对维持预测的茎环结构进行了强有力的选择，因为多态性优先在环或凸出区域积累，或者作为预测茎内的互补取代。所有检测到的 pxr 同源物均位于 sigma(54) 依赖性反应调节因子 nla19 和预测的 NADH 脱氢酶基因之间的基因间区域，但其他邻近基因内容已多样化。 (C) 2014 年作者。由爱思唯尔公司出版。保留所有权利。
In animals and plants, non-coding small RNAs regulate the expression of many genes at the post-transcriptional level. Recently, many non-coding small RNAs (sRNAs) have also been found to regulate a variety of important biological processes in bacteria, including social traits, but little is known about the phylogenetic or mechanistic origins of such bacterial sRNAs. Here we propose a phylogenetic origin of the myxobacterial sRNA Pxr, which negatively regulates the initiation of fruiting body development in Myxococcus xanthus as a function of nutrient level, and also examine its diversification within the Myxococcocales order. Homologs of pxr were found throughout the Cystobacterineae suborder (with a few possible losses) but not outside this clade, suggesting a single origin of the Pxr regulatory system in the basal Cystobacterineae lineage. Rates of pxr sequence evolution varied greatly across Cystobacterineae sub-clades in a manner not predicted by overall genome divergence. A single copy of pxr was found in most species with 17% of nucleotide positions being polymorphic among them. However three tandem paralogs were present within the genus Cystobacter and these alleles together exhibited an elevated rate of divergence. There appears to have been strong selection for maintenance of a predicted stem-loop structure, as polymorphisms accumulated preferentially at loop or bulge regions or as complementary substitutions within predicted stems. All detected pxr homologs are located in the intergenic region between the sigma(54)-dependent response regulator nla19 and a predicted NADH dehydrogenase gene, but other neighboring gene content has diversified. (C) 2014 The Authors. Published by Elsevier Inc. All rights reserved.