Evolution of Protein Superfamilies and Bacterial Genome Size

We present the structural annotation of 56 different bacterial species based on the assignment of genes to 816 evolutionary superfamilies in the CATH domain structure database. These assignments have enabled us to analyse the recurrence of specific superfamilies within and across the genomes. We hav...

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Bibliographic Details
Published in:Journal of molecular biology 2004-02, Vol.336 (4), p.871-887
Main Authors: Ranea, Juan A.G., Buchan, Daniel W.A., Thornton, Janet M., Orengo, Christine A.
Format: Article
Language:English
Subjects:
bacteria
Databases, Protein
domain distribution
Evolution, Molecular
genome size
Genome, Bacterial
Open Reading Frames
Protein Conformation
protein family
Proteins - chemistry
Proteins - classification
Proteins - genetics
Statistics as Topic
three-dimensional structure
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Summary:We present the structural annotation of 56 different bacterial species based on the assignment of genes to 816 evolutionary superfamilies in the CATH domain structure database. These assignments have enabled us to analyse the recurrence of specific superfamilies within and across the genomes. We have selected the superfamilies that have a very broad representation and therefore appear to be universally distributed in a significant number of bacterial lineages. Occurrence profiles of these universally distributed superfamilies are compared with genome size in order to estimate the correlation between superfamily duplication and the increase in proteome size. This distinguishes between those size-dependent superfamilies where frequency of occurrence is highly correlated with increase in genome size, and size-independent superfamilies where no correlation is observed. Consideration of the size correlation and the ratio between the mean and the standard deviations for all the superfamily profiles allows more detailed subdivisions and classification of superfamilies. For example, within the size-independent superfamilies, we distinguished a group that are distributed evenly amongst all the genomes. Within the size-dependent superfamilies we differentiated two groups: linearly distributed and non-linearly distributed. Functional annotation using the COG database was performed for all superfamilies in each of these groups, and this revealed significant differences amongst the three sets of superfamilies. Evenly distributed, size-independent domains are shown to be involved primarily in protein translation and biosynthesis. For the size-dependent superfamilies, linearly distributed superfamilies are involved mainly in metabolism, and non-linearly distributed superfamily domains are involved principally in gene regulation.
ISSN:0022-2836
1089-8638
DOI:10.1016/j.jmb.2003.12.044