Identification of cyanobacterial non-coding RNAs by comparative genome analysis.
Identification of cyanobacterial non-coding RNAs by comparative genome analysis.
复制标题
通过比较基因组分析鉴定蓝细菌非编码RNA。
DOI：
10.1186/gb-2005-6-9-r73
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发表时间：
2005
期刊：
影响因子：
12.3
通讯作者：
Hess, Wolfgang R
中科院分区：
文献类型：
--
作者：
Axmann, Ilka M;Kensche, Philip;Vogel, Jorg;Kohl, Stefan;Herzel, Hanspeter;Hess, Wolfgang R
首次对蓝藻中的非编码RNA(NcRNAs)进行全基因组和系统的筛选。通过计算预测了几个ncRNAs，并对它们的存在进行了生化验证。这些ncRNAs可能具有调节功能，并且每个ncRNAs都显示出不同的系统发育分布。海洋蓝藻的全基因组测序揭示了前所未有的基因组变异和精简程度。原氯球菌属，大小为1.66兆碱基对。MED4是这些基因组中最紧凑的，为数不多的已确定的调控蛋白是如何有效地维持生态上成功的海洋微生物的生活方式，这是一个谜。真核生物和细菌中的小分子非编码RNA(NcRNAs)控制着大量的过程；然而，对于肠道细菌以外的大多数真细菌门，系统地寻找ncRNAs仍然是缺乏的。基于计算预测，我们发现在原氯球菌-聚球藻的几种不同的蓝藻中存在几个ncRNAs(蓝藻功能RNA或Yfr)。一些ncRNA基因只存在于所研究的四个毒株中的两到三个，而RNAs Yfr2到Yfr5在结构上高度相关，由一个快速进化的基因家族编码，因为它们的基因存在于四个所研究的基因组中的不同拷贝数和不同的位置。一种名为Yfr7的ncRNA存在于至少其他七种蓝藻中。此外，还预测了几个核糖体操纵子的控制元件以及硫胺素焦磷酸和钴胺的核糖开关。这是第一次对蓝藻中的ncRNAs进行全基因组和系统的筛选。几个ncRNA都是通过计算预测的，它们的存在得到了生化验证。这些RNA可能具有调节功能，每个都显示出不同的系统发育分布。我们的方法可以应用于任何一组微生物，其中有一个以上的全基因组序列可用于比较分析。
The first genome-wide and systematic screen for non-coding RNAs (ncRNAs) in cyanobacteria. Several ncRNAs were computationally predicted and their presence was biochemically verified. These ncRNAs may have regulatory functions, and each shows a distinct phylogenetic distribution. Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria. Based on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin. This is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.