Chapter title |
Methods for Analyzing the Evolutionary Relationship of NF-κB Proteins Using Free, Web-Driven Bioinformatics and Phylogenetic Tools.
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Chapter number | 37 |
Book title |
NF-kappa B
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Published in |
Methods in molecular biology, February 2015
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DOI | 10.1007/978-1-4939-2422-6_37 |
Pubmed ID | |
Book ISBNs |
978-1-4939-2421-9, 978-1-4939-2422-6
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Authors |
John R Finnerty, Thomas D Gilmore, John R. Finnerty, Thomas D. Gilmore, Finnerty, John R., Gilmore, Thomas D. |
Editors |
Michael J. May |
Abstract |
Phylogenetic analysis enables one to reconstruct the functional evolution of proteins. Current understanding of NF-κB signaling derives primarily from studies of a relatively small number of laboratory models-mainly vertebrates and insects-that represent a tiny fraction of animal evolution. As such, NF-κB has been the subject of limited phylogenetic analysis. The recent discovery of NF-κB proteins in "basal" marine animals (e.g., sponges, sea anemones, corals) and NF-κB-like proteins in non-metazoan lineages extends the origin of NF-κB signaling by several hundred million years and provides the opportunity to investigate the early evolution of this pathway using phylogenetic approaches. Here, we describe a combination of bioinformatic and phylogenetic analyses based on menu-driven, open-source computer programs that are readily accessible to molecular biologists without formal training in phylogenetic methods. These phylogenetically based comparisons of NF-κB proteins are powerful in that they reveal deep conservation and repeated instances of parallel evolution in the sequence and structure of NF-κB in distant animal groups, which suggest that important functional constraints limit the evolution of this protein. |
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