Axmann Ilka M, Kensche Philip, Vogel Jörg, Kohl Stefan, Herzel Hanspeter, Hess Wolfgang R
Humboldt-University, Department of Biology/Genetics, Chausseestrasse, D-Berlin, Germany.
Genome Biol. 2005;6(9):R73. doi: 10.1186/gb-2005-6-9-r73. Epub 2005 Aug 17.
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.
海洋蓝藻的全基因组测序揭示了前所未有的基因组变异程度和精简情况。聚球藻属MED4菌株的基因组大小为166万个碱基对，是这些基因组中最紧凑的，而目前还不清楚少数已鉴定的调控蛋白如何有效地维持这种在生态上成功的海洋微生物的生活方式。小非编码RNA（ncRNA）在真核生物和细菌中控制着大量过程；然而，除肠道细菌外，大多数真细菌门仍缺乏对ncRNA的系统性搜索。
基于计算预测，我们发现在聚球藻-集胞藻谱系的几种不同蓝藻中存在几种ncRNA（蓝藻功能性RNA或Yfr）。一些ncRNA基因仅存在于所研究的四个菌株中的两三个菌株中，而Yfr2至Yfr5的RNA在结构上高度相关，由一个快速进化的基因家族编码，因为它们的基因在四个所研究的基因组中存在不同的拷贝数和不同的位置。一种ncRNA，Yfr7，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焦磷酸和钴胺素的核糖开关。
这是首次对蓝藻进行全基因组范围的ncRNA系统性筛选。通过计算预测了几种ncRNA，并通过生化方法验证了它们的存在。这些RNA可能具有调控功能，且每种都显示出独特的系统发育分布。我们的方法可应用于任何有多个全基因组序列可用于比较分析的微生物群体。
