reconstruction of the core and extended regulons of global transcription factors重建的核心和扩展全球转录因子的调节子.pdfVIP

Reconstruction of the Core and Extended Regulons of Global Transcription Factors 1,2 3 1 Yann S. Dufour , Patricia J. Kiley , Timothy J. Donohue * 1 Department of Bacteriology, University of Wisconsin – Madison, Madison, Wisconsin, United States of America, 2 BACTER Institute, University of Wisconsin – Madison, Madison, Wisconsin, United States of America, 3 Department of Biomolecular Chemistry, University of Wisconsin – Madison, Madison, Wisconsin, United States of America Abstract The processes underlying the evolution of regulatory networks are unclear. To address this question, we used a comparative genomics approach that takes advantage of the large number of sequenced bacterial genomes to predict conserved and variable members of transcriptional regulatory networks across phylogenetically related organisms. Specifically, we developed a computational method to predict the conserved regulons of transcription factors across a-proteobacteria. We focused on the CRP/FNR super-family of transcription factors because it contains several well-characterized members, such as FNR, FixK, and DNR. While FNR, FixK, and DNR are each proposed to regulate different aspects of anaerobic metabolism, they are predicted to recognize very similar DNA target sequences, and they occur in various combinations among individual a-proteobacterial species. In this study, the composition of the respective FNR, FixK, or DNR conserved regulons across 87 a-proteobacterial species was predicted by comparing the phylogenetic profiles of the regulators with the profiles of putative target genes. The utility of our predictions was evaluated by experimentally characterizing the FnrL regulon (a FNR-type regulator) in the a-proteobacterium Rhodobacter sphaeroides. Our