Scaling Laws in the Functional Content of Genomes

By E. van Nimwegen. 2003

361 citations recorded by the source corpus.

With the number of sequenced genomes now totaling more than 100, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the statistics of gene content across genomes. In this article I show that, for many high-level functional categories, the number of genes in each category scales as a power-law of the total number of genes in the genome. The occurrence of such scaling laws can be explained using a simple theoretical model, and this model suggests that the exponents of the observed scaling laws correspond to universal constants of the evolutionary process. I discuss some consequences of these scaling laws for our understanding of organism design.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fbe3802ccbede622423e695df202f7e3350b5cca

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In Molecular Biology

Citations in the corpus

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics (2014, background): “This integrated biophysics-population dynamics model of fold evolution could potentially explain the dependence of the power law exponent on genome size [70,71].”
The many faces of the helix-turn-helix domain: transcription regulation and beyond. (2005, result): “This non-linear scaling of HTH domain numbers with gene number is consistent with recent studies that have suggested that the transcription factor counts follow a power equation with respect to gene number [171].”
Using graph theory to analyze biological networks (2011, background): “The number of regulators N reg grows faster than the number of genes N tot they regulate and it has been shown that N reg N tot ≈ N for prokaryotes and N reg N tot ≈ N 0.3 for eukaryotes, where N is the network size [161,162].”
Is prokaryotic complexity limited by accelerated growth inregulatory overhead? (2003, background): “In particular, a recent study analyzed the scaling of gene counts nc for each of 44 functional protein categories in relation to the total number of genes n, across 64 bacterial genomes [5].”
Non-coding RNA. (2006, background): “Regulatory proteins scale almost quadratically with genome size in prokaryotes (20,21), and extrapolation of this relationship suggests that prokaryotes have been limited in their complexity by their reliance on a protein-based regulatory architecture, probably for most of their evolutionary history”
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008, background): “(143) in the course of the genome analysis of the bacterium Pseudomonas aeruginosa, investigated in detail by Van Nimwegen (130) and subsequently independently confirmed and explored by several groups (117,131,132), genes in different functional categories show dramatic differences in their dependen”