defining the plasticity of transcription factor binding sites by deconstructing dna consensus sequences the phop-binding sites among gammaenterobacteria定义塑性解构dna转录因子结合位点的共识序列phop-binding gammaenterobacteria网站.pdfVIP

Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria 1,2 3 3 3,4 1,3,4 Oscar Harari , Sun-Yang Park , Henry Huang , Eduardo A. Groisman , Igor Zwir * 1 Department of Computer Science and Artificial Intelligence, University of Granada, Granada, Spain, 2 Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America, 3 Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America, 4 Howard Hughes Medical Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America Abstract Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. Here, we address this problem by investigating the target promoters controlled by the DNA-binding PhoP protein, which governs virulence and Mg2+ homeostasis in several bacterial species. PhoP is particularly interesting; it is highly conserved in different gamma/enterobacteria, regulating not only ancestral genes but also governing the expression of dozens of horizontally acquired genes that differ from species to species. Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of mot