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PLoS Comput Biol. 2011 Dec;7(12):e1002318. doi: 10.1371/journal.pcbi.1002318. Epub 2011 Dec 22.

The FGGY carbohydrate kinase family: insights into the evolution of functional specificities.

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1
Graduate School of Biomedical Sciences, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America.

Abstract

Function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS) of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB) evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose). Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.

PMID:
22215998
PMCID:
PMC3245297
DOI:
10.1371/journal.pcbi.1002318
[Indexed for MEDLINE]
Free PMC Article
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