Target identification and functional analysis of regulatory small RNAs in Sinorhizobium meliloti and related alpha-proteobacteria

利用深度测序、微阵列、Affymetrics芯片和生物信息学分析，我们已经确定了S. meliloti中400多个小的非编码rna候选序列，在不同条件下转录。该项目的第二阶段将重点关注212个反式编码sRNA候选分子，并通过实验和生物信息学方法寻找这些候选分子的相互作用伙伴。它将详细研究涉及共生和群体感应的候选物种，并使用比较生物信息学工具将有关已确认的功能性ncrna的知识传递给α -变形菌群。在实验方面，这将包括转录物和蛋白质水平的表达谱分析，以及sRNA过表达和突变株的分析等技术。我们还将进一步研究选定的反式编码sRNA候选物的sRNA- mrna靶标相互作用的功能。这包括突变和结构分析。在生物信息学方面，将开发基于保守的二级结构（但可能缺乏序列保守性）的sRNAs比较分析的新方法。

We have identified more than 400 candidates for small, non-coding RNAs in S. meliloti, transcribed under varying conditions, using deep sequencing, microarrays, Affymetrics chips, and bioinformatics analysis. The second phase of the project will focus on 212 trans-encoded sRNA candidates and seek for interactions partners of these candidates with experimental and bioinformatics methods. It will study in detail candidates involved in symbiosis and quorum sensing, and use comparative bioinformatics tools to transfer knowledge about confirmed functional ncRNAs to the group of alpha-proteobacteria. On the experimental side this will include techniques such as expression profiling at transcript and protein level, as well as analysis of sRNA overexpression and mutant strains. We will also further functionally study sRNA-mRNA target interactions of selected trans-encoded sRNA candidates. This includes mutational and structural analyses. On the bioinformatics side, new methods for comparative analysis of sRNAs based on a conserved secondary structure, but possibly lacking sequence conservation, will be developed.