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The role of DNA-binding specificity in the evolution of bacterial regulatory networks

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dc.creator Lozada-Chávez, Irma
dc.creator Espinosa Angarica, Vladimir
dc.creator Collado-Vides, Julio
dc.creator Contreras-Moreira, Bruno
dc.creator Contreras-Moreira, Bruno
dc.date 2008-06-11T13:38:49Z
dc.date 2008-06-11T13:38:49Z
dc.date 2008-06-02
dc.date.accessioned 2017-01-31T01:39:33Z
dc.date.available 2017-01-31T01:39:33Z
dc.identifier Journal of Molecular Biology, 379(3): 627-643
dc.identifier 0022-2386
dc.identifier http://hdl.handle.net/10261/4998
dc.identifier 10.1016/j.jmb.2008.04.008
dc.identifier.uri http://dspace.mediu.edu.my:8181/xmlui/handle/10261/4998
dc.description The definitive version is available at: http://www.sciencedirect.com/science/journal/00222836
dc.description Understanding the mechanisms by which transcriptional regulatory networks (TRNs) change through evolution is a fundamental problem. Here we analyze this question using data from Escherichia coli and Bacillus subtilis, finding that paralogy relationships are insufficient to explain the global or local role observed for transcription factors (TFs) within regulatory networks. Our results provide a picture in which DNA-binding specificity, a molecular property that can be measured in different ways, is a predictor of the role of transcription factors. In particular, we observe that global regulators consistently display low binding specificities, while displaying comparatively higher expression values in microarray experiments. In addition, in this work we find a strong negative correlation between binding specificity and the number of co-regulators which help coordinate genetic expression at a genomic scale. A close look at several orthologous TFs, including FNR, a regulator found to be global in E. coli and local in B. subtilis, confirms the diagnostic value of specificity in order to understand their regulatory function, and also highlights the importance of evaluating the metabolic and ecological relevance of effectors as another variable in the evolutionary equation of regulatory networks. Finally, a general model is presented that integrates some evolutionary forces and molecular properties, aiming to explain how regulons grow and shrink, as bacteria tune their regulation to increase adaptation.
dc.description NIH grant RO1-GM071962 Fundación Aragón I+D
dc.description Peer reviewed
dc.format 197026 bytes
dc.format 613100 bytes
dc.format application/pdf
dc.format application/pdf
dc.language eng
dc.rights openAccess
dc.subject transcription
dc.subject regulatory network
dc.subject binding specificity
dc.subject global regulator
dc.subject paralogy
dc.title The role of DNA-binding specificity in the evolution of bacterial regulatory networks
dc.type Artículo


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