Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA.

Gene regulation and systems biology Pub Date : 2012-01-01 Epub Date: 2012-05-30 DOI:10.4137/GRSB.S9357
Michael R Leuze, Tatiana V Karpinets, Mustafa H Syed, Alexander S Beliaev, Edward C Uberbacher
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Abstract

Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of which are palindromic, are known as regulatory elements or transcription factor binding sites (TFBS). Some TFs are global regulators that can modulate the expression of hundreds of genes. In this study we examine global regulator half-sites, where a half-site, which we shall call a binding motif (BM), is one half of a palindromic TFBS. We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full TFBS quality or location.

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细菌基因启动子中的结合基团调节全局调控因子 CRP 和 ArcA 的转录效应
细菌基因调控涉及转录因子(TF),它们与操作子启动子中的 DNA 识别序列结合。这些识别序列被称为调控元件或转录因子结合位点(TFBS)。有些转录因子是全局调控因子,可以调节数百个基因的表达。在本研究中,我们研究了全局调控因子半位点,半位点(我们称之为结合基序(BM))是回文 TFBS 的一半。我们研究了 CRP 和 ArcA 调控子转录谱分析的经验数据,探讨了 BM 数量在转录调控中起重要作用的假设。我们比较了 BM 数量和完整 TFBS 特征预测诱导转录活性的能力。我们发现,CRP BM 数量对 CRP 依赖性转录活性有非线性影响,并且比完整 TFBS 的质量或位置更能预测这种活性。
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