Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
Biophys J. 2011 Sep 7;101(5):1123-9. doi: 10.1016/j.bpj.2011.07.041.
Many prokaryotic transcription factors home in on one or a few target sites in the presence of a huge number of nonspecific sites. Our analysis of λ-repressor in the Escherichia coli genome based on single basepair substitution experiments shows the presence of hundreds of sites having binding energy within 3 Kcal/mole of the O(R)1 binding energy, and thousands of sites with binding energy above the nonspecific binding energy. The effect of such sites on DNA-based processes has not been fully explored. The presence of such sites dramatically lowers the occupation probability of the specific site far more than if the genome were composed of nonspecific sites only. Our Brownian dynamics studies show that the presence of quasi-specific sites results in very significant kinetic effects as well. In contrast to λ-repressor, the E. coli genome has orders of magnitude lower quasi-specific sites for GalR, an integral transcription factor, thus causing little competition for the specific site. We propose that GalR and perhaps repressors of the same family have evolved binding modes that lead to much smaller numbers of quasi-specific sites to remove the untoward effects of genomic DNA.
许多原核转录因子在存在大量非特异性位点的情况下，能够特异地结合到一个或几个靶位点上。我们基于单碱基取代实验对大肠杆菌基因组中的 λ 阻遏物进行分析，结果表明存在数百个结合能在 O(R)1 结合能 3 Kcal/mol 范围内的位点，以及数千个结合能高于非特异性结合能的位点。这些位点对基于 DNA 的过程的影响尚未得到充分探索。这些位点的存在极大地降低了特定位点的占据概率，如果基因组仅由非特异性位点组成，那么这种降低的幅度会更大。我们的布朗动力学研究表明，准特异性位点的存在也会产生非常显著的动力学效应。与 λ 阻遏物不同，对于全转录因子 GalR 来说，大肠杆菌基因组中准特异性位点的数量要低几个数量级，因此对特异性位点的竞争很小。我们提出，GalR 或许与其同一家族的阻遏物已经进化出了结合模式，从而导致准特异性位点的数量大大减少，以消除基因组 DNA 的不利影响。
