Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
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DOI：
10.1186/gb-2010-11-3-r31
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发表时间：
2010
期刊：
影响因子：
12.3
通讯作者：
Breaker RR
中科院分区：
文献类型：
--
作者：
Weinberg Z;Wang JX;Bogue J;Yang J;Corbino K;Moy RH;Breaker RR
在细菌、古细菌和宏基因组数据的比较基因组分析中鉴定的新基序揭示了超过100种候选结构RNA。结构化的非编码RNA执行许多对于蛋白质合成、RNA加工和基因调控至关重要的功能。结构化RNA可以通过比较基因组学来检测，其中同源序列被鉴定并检查保留RNA二级结构的突变。通过对细菌和古细菌的基因组和宏基因组序列应用基于比较基因组学的方法，我们鉴定了104种候选结构RNA，并推断了其中许多RNA的推定功能。鉴定了十二种候选代谢物结合RNA，其中三种被验证，包括本文报道的结合辅酶S-腺苷甲硫氨酸的一种。新发现的顺式调节RNA参与蓝藻的光合作用或氮调节、嘌呤和一碳代谢、螺杆菌的胃感染以及许多其他生理过程。一个被称为crcB的候选核糖开关在细菌和古细菌中都有代表。另一个RNA基序可能控制来自mRNA的3 '-非翻译区的基因表达，这在细菌中是不寻常的。许多可能反式作用的非编码RNA也被揭示出来，并且几种非编码RNA候选物主要或专门存在于宏基因组DNA序列中。这项工作极大地扩展了已知存在于细菌和古细菌中的高度结构化的非编码RNA的种类，并为验证其生物功能所需的生化和遗传研究提供了起点。考虑到RNA发现的持续速度超过了几个类似的项目，我们预计从细菌和古生物中仍然可以发现更多的结构化RNA。
Novel motifs identified in a comparative genomic analysis of bacterial, archaeal and metagenomic data reveals over 100 candidate structured RNAs. Structured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure. By applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured RNAs and inferred putative functions for many of these. Twelve candidate metabolite-binding RNAs were identified, three of which were validated, including one reported herein that binds the coenzyme S-adenosylmethionine. Newly identified cis-regulatory RNAs are implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection by Helicobacter, and many other physiological processes. A candidate riboswitch termed crcB is represented in both bacteria and archaea. Another RNA motif may control gene expression from 3'-untranslated regions of mRNAs, which is unusual for bacteria. Many noncoding RNAs that likely act in trans are also revealed, and several of the noncoding RNA candidates are found mostly or exclusively in metagenome DNA sequences. This work greatly expands the variety of highly structured noncoding RNAs known to exist in bacteria and archaea and provides a starting point for biochemical and genetic studies needed to validate their biologic functions. Given the sustained rate of RNA discovery over several similar projects, we expect that far more structured RNAs remain to be discovered from bacterial and archaeal organisms.
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通过比较基因组分析鉴定蓝细菌非编码RNA。
影响因子：
12.3
作者：
Axmann, Ilka M;Kensche, Philip;Vogel, Jorg;Kohl, Stefan;Herzel, Hanspeter;Hess, Wolfgang R
通讯作者：
Hess, Wolfgang R
影响因子：
14.9
作者：
ANTAO, VP;TINOCO, I
通讯作者：
TINOCO, I
影响因子：
4.4
作者：
Derzelle, S;Bolotin, A;Rul, F
通讯作者：
Rul, F
影响因子：
3.2
作者：
Chou, Han Ting;Kwon, Dong-Hyeon;Lu, Chung-Dar
通讯作者：
Lu, Chung-Dar
影响因子：
2.1
作者：
Duan, KM;Liu, CQ;Dunn, NW
通讯作者：
Dunn, NW