Guía Marylens Hernández, Pérez Abel González, Angarica Vladimir Espinosa, Vasconcelos Ana T, Collado-Vides Julio
National Bioinformatics Center, Industria y San José, Capitolio Nacional, Habana, Cuba.
In Silico Biol. 2005;5(2):209-19.
Prokaryotic genomes annotation has focused on genes location and function. The lack of regulatory information has limited the knowledge on cellular transcriptional regulatory networks. However, as more phylogenetically close genomes are sequenced and annotated, the implementation of phylogenetic footprinting strategies for the recognition of regulators and their regulons becomes more important. In this paper we describe a comparative genomics approach to the prediction of new gamma-proteobacterial regulon members. We take advantage of the phylogenetic proximity of Escherichia coli and other 16 organisms of this subdivision and the intensive search of the space sequence provided by a pattern-matching strategy. Using this approach we complement predictions of regulatory sites made using statistical models currently stored in Tractor_DB, and increase the number of transcriptional regulators with predicted binding sites up to 86. All these computational predictions may be reached at Tractor_DB (www.bioinfo.cu/Tractor_DB, www.tractor.lncc.br, www.ccg.unam.mx/Computational_Genomics/tractorDB/). We also take a first step in this paper towards the assessment of the conservation of the architecture of the regulatory network in the gamma-proteobacteria through evaluating the conservation of the overall connectivity of the network.
原核生物基因组注释一直聚焦于基因的位置和功能。调控信息的缺失限制了我们对细胞转录调控网络的了解。然而，随着越来越多亲缘关系相近的基因组被测序和注释，利用系统发育足迹法策略识别调控因子及其调控子变得愈发重要。在本文中，我们描述了一种用于预测新型γ-变形菌调控子成员的比较基因组学方法。我们利用了大肠杆菌与该分类下其他16种生物的系统发育相近性，以及通过模式匹配策略对空间序列进行的深入搜索。使用这种方法，我们补充了利用目前存储在Tractor_DB中的统计模型所做出的调控位点预测，并将具有预测结合位点的转录调控因子数量增加到了86个。所有这些计算预测都可以在Tractor_DB（www.bioinfo.cu/Tractor_DB、www.tractor.lncc.br、www.ccg.unam.mx/Computational_Genomics/tractorDB/）上获取。在本文中，我们还通过评估网络整体连通性的保守性，朝着评估γ-变形菌调控网络结构的保守性迈出了第一步。
