Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.
Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.
复制标题
通过比较基因组分析和功能测定，扩展了控制根源发育的分泌肽的曲目。
DOI：
10.1093/jxb/erv346
复制
发表时间：
2015-08
影响因子：
6.9
通讯作者：
Hilson P
中科院分区：
文献类型：
--
作者：
Ghorbani S;Lin YC;Parizot B;Fernandez A;Njo MF;Van de Peer Y;Beeckman T;Hilson P
比较基因组分析结合转录组挖掘确定分泌肽可能参与根的发展。当应用于拟南芥根时，选择的候选物以特定的方式影响生长或分枝。植物基因组编码大量的小分泌肽，其功能尚待研究。基于已知参与胚后发育的SSP家族的结构特征，这种比较基因组分析导致鉴定了编码可能参与细胞间通讯的寡肽的基因。由于基于短序列同源性的基因组注释是困难的，保守SSP序列的从头鉴定和聚集的标准首先在五个参考植物物种中进行基准测试。由此产生的基因家族随后扩展到32个基因组序列，包括主要作物。全球系统发育模式共同的功能特点SSP家庭表明，他们的出现和扩张与陆地植物相吻合。可以在线搜索SSP家族的成员、序列和共有序列（）。为了寻找可能的根发育调控因子，基于拟南芥SSP基因在侧根形成过程中特定时期和特定细胞类型的表达，通过转录组元分析进一步筛选出了SSP基因。作为一个额外的迹象表明，以前未表征的SSP可能控制发展，这项研究表明，根的生长和分支被改变的应用程序的合成肽匹配保守的SSP基序，有时在非常具体的方式。该研究中使用的策略结合了比较基因组学，转录组荟萃分析和植物中的肽功能测定，精确定位了可能参与非细胞自主调控机制的因素。类似的方法可以在不同的物种中实施，以研究广泛的发育计划。
Comparative genome analysis combined with transcriptome mining identified secreted peptides possibly involved in root development. When applied on Arabidopsis roots, selected candidates affected growth or branching in specific ways. Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.