Joint scaling laws in functional and evolutionary categories in prokaryotic genomes

TL;DR

This paper introduces a model of prokaryotic genome evolution that links gene family distributions and functional category scaling, revealing a quantitative relationship between evolutionary and functional genome features.

Contribution

The study presents a novel coupled model explaining the joint scaling laws of gene families and functional categories in prokaryotic genomes, connecting evolutionary and functional aspects.

Findings

The model reproduces empirical distribution of gene family sizes.

It explains the nonlinear scaling of functional categories with genome size.

Bioinformatics analysis confirms the predicted relation between scaling exponents.

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 nonlinear 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 characterising 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 characterised 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.