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Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

ABSTRACT: The gap between the amount of genome information released by genome sequencing projects and our knowledge about the proteins' functions is rapidly increasing. To fill this gap, various 'genomic-context' methods have been proposed that exploit sequenced genomes to predict the functions of the encoded proteins. One class of methods, phylogenetic profiling, predicts protein function by correlating the phylogenetic distribution of genes with that of other genes or phenotypic characteristics. The functions of a number of proteins, including ones of medical relevance, have thus been predicted and subsequently confirmed experimentally. Additionally, various approaches to measure the similarity of phylogenetic profiles and to account for the phylogenetic bias in the data have been proposed. We review the successful applications of phylogenetic profiling and analyse the performance of various profile similarity measures with a set of one microsporidial and 25 fungal genomes. In the fungi, phylogenetic profiling yields high-confidence predictions for the highest and only the highest scoring gene pairs illustrating both the power and the limitations of the approach. Both practical examples and theoretical considerations suggest that in order to get a reliable and specific picture of a protein's function, results from phylogenetic profiling have to be combined with other sources of evidence.

SUBMITTER: Kensche PR

PROVIDER: S-EPMC2405902 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature

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Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

Kensche Philip R PR van Noort Vera V Dutilh Bas E BE Huynen Martijn A MA

Journal of the Royal Society, Interface 20080201 19

The gap between the amount of genome information released by genome sequencing projects and our knowledge about the proteins' functions is rapidly increasing. To fill this gap, various 'genomic-context' methods have been proposed that exploit sequenced genomes to predict the functions of the encoded proteins. One class of methods, phylogenetic profiling, predicts protein function by correlating the phylogenetic distribution of genes with that of other genes or phenotypic characteristics. The fun ...[more]

PMID: 17535793

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Project description:Background and aimsFerns are the second largest group of vascular plants and are distributed nearly worldwide. Although ferns have been integrated into some comparative ecological studies focusing on hydathodes, there is a considerable gap in our understanding of the functional anatomy of these secretory tissues that are found on the vein endings of many fern leaves. In this study, we aimed to investigate the phylogenetic distribution, structure and function of fern hydathodes.MethodsWe performed a global review on fern hydathodes and their phylogenetic distribution, carried out an ancestral character state reconstruction, and studied the structure, guttation and elemental composition of salt residues of eight species, and the diurnal patterns of xylem pressure of two species.Key resultsHydathodes are known from 1189 fern species, 92 genera and 19 families of 2 orders, Equisetales and Polypodiales. Stochastic character mapping indicated multiple gains and losses of hydathodes at the genus level, occurring especially during the last 50 million years of fern evolution. Hydathodes were located on the adaxial leaf surface and characterized by a cytoplasm-rich, pore-free epidermis, and became functional for several weeks after nearly complete leaf expansion. In two species, positive xylem pressure built up at night, potentially facilitating guttation. Guttation fluid was rich in Ca and often Si, but also contained P, Mg, Na and Al.ConclusionsStochastic character mapping and the structural and functional diversity of hydathodes indicate multiple origins, and their presence/absence in closely related taxa implies secondary losses during fern evolution. Positive xylem pressure and high air humidity play an important role as drivers of guttation. Hydathodes may contribute to the regulation of leaf nutrient stoichiometry by the release of excessive compounds and minerals other than waste products, but the presence of essential chemical elements in salt residues also indicates possible leakage.

Dataset Information

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

Publications

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.

Similar Datasets

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