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Joint scaling laws in functional and evolutionary categories in prokaryotic genomes.

TitleJoint scaling laws in functional and evolutionary categories in prokaryotic genomes.
Publication TypeJournal Article
Year of Publication2012
AuthorsGrilli, J, Bassetti, B, Maslov, S, Cosentino Lagomarsino, M
JournalNucleic Acids Res
Volume40
Issue2
Pagination530-40
Date Published2012 Jan
ISSN1362-4962
KeywordsEvolution, Molecular, Genome Size, Genome, Bacterial, Genomics, Models, Genetic
Abstract

We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model, numbers of genes in different functional categories are coupled to each other. For example, an increase in the number of metabolic enzymes in a genome is usually accompanied by addition of new transcription factors regulating these enzymes. Such coupling can be thought of as a proportional 'recipe' for genome composition of the type 'a spoonful of sugar for each egg yolk'. The model jointly reproduces two known empirical laws: the distribution of family sizes and the non-linear scaling of the number of genes in certain functional categories (e.g. transcription factors) with genome size. In addition, it allows us to derive a novel relation between the exponents characterizing these two scaling laws, establishing a direct quantitative connection between evolutionary and functional categories. It predicts that functional categories that grow faster-than-linearly with genome size to be characterized by flatter-than-average family size distributions. This relation is confirmed by our bioinformatics analysis of prokaryotic genomes. This proves that the joint quantitative trends of functional and evolutionary classes can be understood in terms of evolutionary growth with proportional recipes.

DOI10.1093/nar/gkr711
Alternate JournalNucleic Acids Res.
PubMed ID21937509
PubMed Central IDPMC3258127