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Theory Biosci. 2005 Apr;123(4):381-411. doi: 10.1016/j.thbio.2005.02.002.

Inherent size constraints on prokaryote gene networks due to "accelerating" growth.

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1
ARC Special Research Centre for Functional and Applied Genomics Institute for Molecular Bioscience, University of Queensland, 4072, Brisbane, Qld, Australia, m.gagen@imb.uq.edu.au.

Abstract

Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and either reach a limit or exhibit graduated transitions from nonstationary-to-stationary statistics and from random to scale-free to regular statistics as the network size grows. However, if for any reason the network cannot tolerate such gross structural changes then accelerating networks are constrained to have sizes below some critical value. This is of interest as the regulatory gene networks of single-celled prokaryotes are characterized by an accelerating quadratic growth and are size constrained to be less than about 10,000 genes encoded in DNA sequence of less than about 10 megabases. This paper presents a probabilistic accelerating network model for prokaryotic gene regulation which closely matches observed statistics by employing two classes of network nodes (regulatory and non-regulatory) and directed links whose inbound heads are exponentially distributed over all nodes and whose outbound tails are preferentially attached to regulatory nodes and described by a scale-free distribution. This model explains the observed quadratic growth in regulator number with gene number and predicts an upper prokaryote size limit closely approximating the observed value.

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