INSERM U1002, Paris, France.
BMC Genomics. 2010 Nov 10;11:625. doi: 10.1186/1471-2164-11-625.
Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the disease tularaemia in humans and animals. Relatively little is known about the regulatory networks existing in this organism that allows it to survive in a wide array of environments and no sRNA regulators have been identified so far.
We have used a combination of experimental assays and in silico prediction to identify sRNAs in F. tularensis strain LVS. Using a cDNA cloning and sequencing approach we have shown that F. tularensis expresses homologues of several sRNAs that are well-conserved among diverse bacteria. We have also discovered two abundant putative sRNAs that share no sequence similarity or conserved genomic context with any previously annotated regulatory transcripts. Deletion of either of these two loci led to significant changes in the expression of several mRNAs that likely include the cognate target(s) of these sRNAs. Deletion of these sRNAs did not, however, significantly alter F. tularensis growth under various stress conditions in vitro, its replication in murine cells, or its ability to induce disease in a mouse model of F. tularensis infection. We also conducted a genome-wide in silico search for intergenic loci that suggests F. tularensis encodes several other sRNAs in addition to the sRNAs found in our experimental screen.
Our findings suggest that F. tularensis encodes a significant number of non-coding regulatory RNAs, including members of well conserved families of structural and housekeeping RNAs and other poorly conserved transcripts that may have evolved more recently to help F. tularensis deal with the unique and diverse set of environments with which it must contend.
小 RNA（sRNA）对细菌基因表达的调控已被证明对许多生物学过程很重要。弗朗西斯氏菌是一种高度致病性的革兰氏阴性菌，可引起人类和动物的土拉热。目前，人们对该生物体中存在的调节网络知之甚少，这些网络使它能够在广泛的环境中生存，而且到目前为止还没有发现 sRNA 调节剂。
我们使用实验测定和计算机预测相结合的方法，鉴定了 LVS 株弗朗西斯氏菌中的 sRNA。我们通过 cDNA 克隆和测序方法表明，弗朗西斯氏菌表达了几种 sRNA 的同源物，这些 sRNA 在不同的细菌中高度保守。我们还发现了两个丰富的假定 sRNA，它们与任何以前注释的调控转录物都没有序列相似性或保守的基因组背景。这两个基因座中的任何一个缺失都会导致几个 mRNA 的表达发生显著变化，这些 mRNA 可能包括这些 sRNA 的同源靶标。然而，这些 sRNA 的缺失并没有显著改变弗朗西斯氏菌在体外各种应激条件下的生长、在鼠细胞中的复制能力，或在弗朗西斯氏菌感染的小鼠模型中引起疾病的能力。我们还进行了全基因组计算机搜索，发现弗朗西斯氏菌在基因间区域编码了几个其他 sRNA，除了我们实验筛选中发现的 sRNA 之外。
我们的研究结果表明，弗朗西斯氏菌编码了大量的非编码调节 RNA，包括结构和管家 RNA 的高度保守家族成员以及其他保守程度较低的转录本，这些转录本可能是为了帮助弗朗西斯氏菌应对其必须应对的独特而多样的环境而最近进化而来的。
