Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.
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DOI：
10.1186/1471-2164-10-268
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发表时间：
2009-06-16
期刊：
影响因子：
4.4
通讯作者：
Breaker RR
中科院分区：
文献类型：
--
作者：
Meyer MM;Ames TD;Smith DP;Weinberg Z;Schwalbach MS;Giovannoni SJ;Breaker RR
宏基因组序列数据被证明是发现生物组分的巨大资源。然而，对这些数据的分析，以确定功能RNA落后于努力表征蛋白质的多样性。“普适性长杆菌”HTCC 1062的基因组与大约20%的海洋宏基因组序列读段最接近。它也很小，几乎不含非编码DNA，GC含量极低。为了帮助发现海洋宏基因组中的RNA基序，我们利用了'Cand'的基因组特性。通过将我们的搜索目标定位于具有相对高GC含量的长基因间区域（IGR），来对P.ubique进行“定位”。已知RNA（rRNA、tRNA、核糖开关等）的分析显示结构化RNA显著富集于此类IGR中。为了鉴定另外的候选结构化RNA，我们检查了具有与“Cand”相似特征的其他IGR。使用比较基因组学方法结合海洋宏基因组数据。采用这种策略，我们发现了四个候选的结构RNA，包括一个新的核糖开关类以及三个额外的可能的顺式调控元件之前的基因编码核糖体蛋白S2和S12，和细胞质蛋白组分的信号识别颗粒。我们还描述了四个额外的潜在的RNA基序，很少或没有例子发生以外的宏基因组数据。这项工作开始了识别宏基因组数据中存在的功能性RNA基序的过程，并说明了如何使用现有的完整基因组来帮助完成这项任务。
Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content. To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of 'Cand. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from 'Cand. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data. This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.
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