The mechanistic origin of p53 selectivity and functionality

The ability of transcription factors to bind uniquely to their specific binding sites is the basis of gene expression. Recognition of specific sites is accomplished by direct contacts to DNA and by recognizing the shape and dynamics of the DNA double helix. Both types of recognition contribute to the interaction between p53 and its response elements (REs). The tumor suppressor protein p53 is part of a complex cellular network that is activated in response to various cellular stress signals. Currently, it is unknown how p53 coordinates its myriad genes, in accordance with the severity of the stress signal, and organizes its functional outcome in an orderly manner. We previously showed that DNA torsional flexibility distinguishes among p53 REs. We will show that the arrangement of p53 half-sites within its REs relative to transcription direction is not random, and is (at least partly) encoded in the structural properties of the REs. Furthermore, by connecting functional pathways to p53-dependent genes, we show that genes belonging to pathways activated rapidly upon stress contain REs having DNA flexibilities that are significantly higher relative to REs of genes involved in pathways that are activated later in the response to stress. We will show that flexible REs induce a reporter gene at lower p53 levels and with faster rates than rigid REs. Moreover, published endogenous mRNA levels of p53-dependent genes support our hypothesis. Thus, torsional flexibility of p53 RE has an important role in singling out the time-wise appropriate target sites among the numerous p53-dependent promoters.