Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis
Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis
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DOI：
10.4161/rna.9.1.18008
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发表时间：
2012-01-01
期刊：
影响因子：
4.1
通讯作者：
Evguenieva-Hackenberg, Elena
中科院分区：
文献类型：
--
作者：
Madhugiri, Ramakanth;Pessi, Gabriella;Evguenieva-Hackenberg, Elena
小RNA（small RNAs，sRNAs）在细菌基因调控中起着关键作用。然而，绝大多数具有测序基因组的细菌的sRNA仍然是未知的，因为sRNA基因通常难以识别，因此没有注释。在此，通过大豆共生体大豆慢生根瘤菌USDA 110的RNA的RNA凝胶印迹杂交、微阵列和深度测序分析，验证了通过慢生根瘤菌和红曲霉成员的基因组比较预测的七种sRNA（BjrC2a、BjrC2b、BjrC2c、BjrC68、BjrC80、BjrC174和BjrC1505）的表达。BjrC2a、BjrC2b和BjrC2c属于RNA家族RF00519，而其他sRNA是新的。对于一些sRNA，我们观察到根瘤中自由生活的细菌和类细菌之间的表达差异。BjrC1505在结核中的含量减少。相反，BjrC2a、BjrC68、BjrC80、BjrC174和先前描述的6S RNA的量在结节中增加，并且观察到这些sRNA的截短形式的积累。比较基因组学和深度测序表明，BjrC2a是一个反义RNA调节肌醇单磷酸酶的表达。所分析的sRNA显示出在根瘤菌目中不同程度的保守性，并且证实了BjrC2、BjrC68、BjrC1505和6S RNA的同源物在自由生活的紫色细菌Rhodopyruspalustris 5D中的表达。
Small RNAs (sRNAs) play a pivotal role in bacterial gene regulation. However, the sRNAs of the vast majority of bacteria with sequenced genomes still remain unknown since sRNA genes are usually difficult to recognize and thus not annotated. Here, expression of seven sRNAs (BjrC2a, BjrC2b, BjrC2c, BjrC68, BjrC80, BjrC174 and BjrC1505) predicted by genome comparison of Bradyrhizobium and Rhodopseudomonas members, was verified by RNA gel blot hybridization, microarray and deep sequencing analyses of RNA from the soybean symbiont Bradyrhizobium japonicum USDA 110. BjrC2a, BjrC2b and BjrC2c belong to the RNA family RF00519, while the other sRNAs are novel. For some of the sRNAs we observed expression differences between free-living bacteria and bacteroids in root nodules. The amount of BjrC1505 was decreased in nodules. By contrast, the amount of BjrC2a, BjrC68, BjrC80, BjrC174 and the previously described 6S RNA was increased in nodules, and accumulation of truncated forms of these sRNAs was observed. Comparative genomics and deep sequencing suggest that BjrC2a is an antisense RNA regulating the expression of inositol-monophosphatase. The analyzed sRNAs show a different degree of conservation in Rhizobiales, and expression of homologs of BjrC2, BjrC68, BjrC1505, and 6S RNA was confirmed in the free-living purple bacterium Rhodopseudomonas palustris 5D.