Identification of Proteins Likely To Be Involved in Morphogenesis, Cell Division, and Signal Transduction in Planctomycetes by Comparative Genomics
Identification of Proteins Likely To Be Involved in Morphogenesis, Cell Division, and Signal Transduction in Planctomycetes by Comparative Genomics
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DOI：
10.1128/jb.01325-12
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发表时间：
2012-12-01
影响因子：
3.2
通讯作者：
Kolter, Roberto
中科院分区：
文献类型：
--
作者：
Jogler, Christian;Waldmann, Jost;Kolter, Roberto
浮霉菌分支的成员具有许多细菌不寻常的特征。它们的细胞质含有膜结合的区室，缺乏肽聚糖和 FtsZ，通过极芽分裂，并且能够进行内吞作用。浮霉菌基因组仍然是个谜，通常非常大（高达 9 Mb），并且平均 55% 的预测蛋白质具有未知功能。重要的是，与浮霉菌不寻常特征相关的蛋白质仍然很大程度上未知。因此，我们开始对这些基因组进行生物信息学分析，以预测可能参与区室化、细胞分裂和信号转导的蛋白质。我们使用了三种互补的策略。首先，我们定义了浮霉菌核心基因组并减去了经过充分研究的模式生物的基因。其次，我们分析了形态发生和细胞分裂基因的基因内容和同线性，并使用“关联罪”方法将两种方法结合起来。第三，我们确定了信号转导系统和西格玛因子。这些分析为未来的遗传学研究提供了一个可管理的候选基因列表，并为浮霉菌中复杂的信号传导提供了证据，类似于在具有复杂生活方式的细菌（例如黄色粘球菌）中观察到的信号传导。
Members of the Planctomycetes clade share many unusual features for bacteria. Their cytoplasm contains membrane-bound compartments, they lack peptidoglycan and FtsZ, they divide by polar budding, and they are capable of endocytosis. Planctomycete genomes have remained enigmatic, generally being quite large (up to 9 Mb), and on average, 55% of their predicted proteins are of unknown function. Importantly, proteins related to the unusual traits of Planctomycetes remain largely unknown. Thus, we embarked on bioinformatic analyses of these genomes in an effort to predict proteins that are likely to be involved in compartmentalization, cell division, and signal transduction. We used three complementary strategies. First, we defined the Planctomycetes core genome and subtracted genes of well-studied model organisms. Second, we analyzed the gene content and synteny of morphogenesis and cell division genes and combined both methods using a "guilt-by-association" approach. Third, we identified signal transduction systems as well as sigma factors. These analyses provide a manageable list of candidate genes for future genetic studies and provide evidence for complex signaling in the Planctomycetes akin to that observed for bacteria with complex life-styles, such as Myxococcus xanthus.