Bioinformatics and experimental analysis of proteins of two-component systems in Myxococcus xanthus
Bioinformatics and experimental analysis of proteins of two-component systems in Myxococcus xanthus
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DOI：
10.1128/jb.01502-07
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发表时间：
2008-01-01
影响因子：
3.2
通讯作者：
Sogaard-Andersen, Lotte
中科院分区：
文献类型：
--
作者：
Shi, Xingqi;Wegener-Feldbruegge, Sigrun;Sogaard-Andersen, Lotte
双组分系统（TCS）的蛋白质在细菌中感知外部和自身产生的信号以及产生适当的输出响应方面具有重要功能。因此，在黄色粘球菌中，TCS对于正常运动和子实体形成和孢子形成是重要的。我们分析了M。xanthus基因组中编码TCS的基因的存在和遗传组织。共鉴定出272个TCS基因，其中251个不属于基因簇。我们报告说，TCS基因是不寻常的组织，与55%的孤儿和16%的复杂基因簇，而只有29%的显示标准的配对基因组织。杂合组氨酸蛋白激酶和组氨酸蛋白激酶预测将被定位到细胞质中的孤儿基因编码的蛋白质或复杂的基因簇中的过度代表。类似地，没有输出结构域的反应调节子在由孤儿基因编码的蛋白质中或在复杂的基因簇中过度表达。在反应调节器中最常出现的输出结构域参与DNA结合和环状二GMP代谢。我们的分析表明，由孤儿基因和复杂基因簇编码的TCS在功能上不同于由配对基因编码的TCS，并且由孤儿基因和复杂基因簇编码的TCS构成的通路的连接性不同于涉及由配对基因编码的TCS的通路的连接性。在实验中，我们观察到孤儿TCS基因在子实体形成过程中显示转录改变的基因中比例过高。系统分析的25个孤儿基因编码组氨酸蛋白激酶的转录上调，在发展过程中表明，2个这样的基因可能是必不可少的生存能力，并确定了7个组氨酸蛋白激酶，包括4个以前没有的特点，有重要的功能，在子实体形成或孢子萌发。
Proteins of two-component systems (TCS) have essential functions in the sensing of external and self-generated signals in bacteria and in the generation of appropriate output responses. Accordingly, in Myxococcus xanthus, TCS are important for normal motility and fruiting body formation and sporulation. Here we analyzed the M. xanthus genome for the presence and genetic organization of genes encoding TCS. Two hundred seventy-two TCS genes were identified, 251 of which are not part of the gene clusters. We report that the TCS genes are unusually organized, with 55% being orphan and 16% in complex gene clusters whereas only 29% display the standard paired gene organization. Hybrid histidine protein kinases and histidine protein kinases predicted to be localized to the cytoplasm are overrepresented among proteins encoded by orphan genes or in complex gene clusters. Similarly, response regulators without output domains are overrepresented among proteins encoded by orphan genes or in complex gene clusters. The most frequently occurring output domains in response regulators are involved in DNA binding and cyclic-di-GMP metabolism. Our analyses suggest that TCS encoded by orphan genes and complex gene clusters are functionally distinct from TCS encoded by paired genes and that the connectivity of the pathways made up of TCS encoded by orphan genes and complex gene clusters is different from that of pathways involving TCS encoded by paired genes. Experimentally, we observed that orphan TCS genes are overrepresented among genes that display altered transcription during fruiting body formation. The systematic analysis of the 25 orphan genes encoding histidine protein kinases that are transcriptionally up-regulated during development showed that 2 such genes are likely essential for viability and identified 7 histidine protein kinases, including 4 not previously characterized that have important function in fruiting body formation or spore germination.