The σ54 regulon (sigmulon) of Pseudomonas putida
The σ54 regulon (sigmulon) of Pseudomonas putida
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DOI：
10.1111/j.1462-2920.2003.00528.x
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发表时间：
2003-12-01
影响因子：
5.1
通讯作者：
de Lorenzo, V
中科院分区：
文献类型：
--
作者：
Cases, I;Ussery, DW;de Lorenzo, V
Sigma（54）在细菌Sigma因子中是独一无二的。除了与其他因子在序列上不相关外，其转录启动机制也完全不同，需要转录激活子的参与。此外，尽管其他可选择的sigma因子通常参与某种程度上相关生物功能的转录，但对于sigma（54）来说并非如此，许多不同的和不相关的基因已被证明是从sigma（54）依赖的启动子转录的，范围从鞭笞，到利用几种不同的碳和氮源，或海藻酸盐生物合成。这些基因已经在许多不同的细菌物种中被表征，直到最近，随着完整基因组序列的到来，我们才能够从基因组的角度来看待sigma（54）的功能作用。在计算方法的辅助下，研究了大肠杆菌、鼠伤寒沙门氏菌和根瘤菌科几种细菌的sigma（54）调控子。在这里，我们分析了恶臭假单胞菌KT2440全基因组中的sigma（54）调控子（sigmulon）。我们开发了一种预测sigma（54）依赖性启动子的改进方法，该方法结合了sigma(54)-RNAP靶序列和激活子结合位点的分数。结合从染色体背景中获得的其他证据以及与密切相关的细菌的相似性，我们已经能够高度自信地预测出恶臭假单胞菌80%以上的sigma（54）依赖性启动子。我们的分析揭示了sigma的新功能（54），并且通过与先前研究的比较分析，我们得出了该调控系统进化的潜在机制。
sigma(54) is unique among the bacterial sigma factors. Besides not being related in sequence with the rest of such factors, its mechanism of transcription initiation is completely different and requires the participation of a transcription activator. In addition, whereas the rest of the alternative sigma factors use to be involved in transcription of somehow related biological functions, this is not the case for sigma(54) and many different and unrelated genes have been shown to be transcribed from sigma(54)-dependent promoters, ranging from flagellation, to utilization of several different carbon and nitrogen sources, or alginate biosynthesis. These genes have been characterized in many different bacterial species and, only until recently with the arrival of complete genome sequences, we have been able to look at the sigma(54) functional role from a genomic perspective. Aided by computational methods, the sigma(54) regulon has been studied both in Escherichia coli, Salmonella typhimurium and several species of the Rhizobiaceae. Here we present the analysis of the sigma(54) regulon (sigmulon) in the complete genome of Pseudomonas putida KT2440. We have developed an improved method for the prediction of sigma(54)-dependent promoters which combines the scores of sigma(54)-RNAP target sequences and those of activator binding sites. In combination with other evidence obtained from the chromosomal context and the similarity with closely related bacteria, we have been able to predict more than 80% of the sigma(54)-dependent promoters of P. putida with high confidence. Our analysis has revealed new functions for sigma(54) and, by means of comparative analysis with the previous studies, we have drawn a potential mechanism for the evolution of this regulatory system.