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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Acknowledgments
Research in the authors’ laboratories on the evolution of NF-κB is supported by NSF grants MCB-0920461 and IOS-1354935.
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Finnerty, J.R., Gilmore, T.D. (2015). Methods for Analyzing the Evolutionary Relationship of NF-κB Proteins Using Free, Web-Driven Bioinformatics and Phylogenetic Tools. In: May, M. (eds) NF-kappa B. Methods in Molecular Biology, vol 1280. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2422-6_37
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DOI: https://doi.org/10.1007/978-1-4939-2422-6_37
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