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De novo evolution of complex, global and hierarchical gene regulatory mechanisms
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Jenkins, Dafyd J. and Stekel, Dov (2010) De novo evolution of complex, global and hierarchical gene regulatory mechanisms. Journal of Molecular Evolution, Vol.71 (No.2). pp. 128-140. doi:10.1007/s00239-010-9369-4 ISSN 0022-2844.
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Official URL: http://dx.doi.org/10.1007/s00239-010-9369-4
Abstract
Gene regulatory networks exhibit complex, hierarchical features such as global regulation and network motifs. There is much debate about whether the evolutionary origins of such features are the results of adaptation, or the by-products of non-adaptive processes of DNA replication. The lack of availability of gene regulatory networks of ancestor species on evolutionary timescales makes this a particularly difficult problem to resolve. Digital organisms, however, can be used to provide a complete evolutionary record of lineages. We use a biologically realistic evolutionary model that includes gene expression, regulation, metabolism and biosynthesis, to investigate the evolution of complex function in gene regulatory networks. We discover that: (i) network architecture and complexity evolve in response to environmental complexity, (ii) global gene regulation is selected for in complex environments, (iii) complex, inter-connected, hierarchical structures evolve in stages, with energy regulation preceding stress responses, and stress responses preceding growth rate adaptations and (iv) robustness of evolved models to mutations depends on hierarchical level: energy regulation and stress responses tend not to be robust to mutations, whereas growth rate adaptations are more robust and non-lethal when mutated. These results highlight the adaptive and incremental evolution of complex biological networks, and the value and potential of studying realistic in silico evolutionary systems as a way of understanding living systems.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre | ||||
Library of Congress Subject Headings (LCSH): | Genetic regulation -- Computer simulation, Genes -- Evolution, Biological models | ||||
Journal or Publication Title: | Journal of Molecular Evolution | ||||
Publisher: | Springer | ||||
ISSN: | 0022-2844 | ||||
Official Date: | August 2010 | ||||
Dates: |
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Volume: | Vol.71 | ||||
Number: | No.2 | ||||
Number of Pages: | 13 | ||||
Page Range: | pp. 128-140 | ||||
DOI: | 10.1007/s00239-010-9369-4 | ||||
Status: | Peer Reviewed | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC) | ||||
Grant number: | BBF0037651 (BBSRC), BBS/S/S/2005/12006 (BBSRC), BB/D524624/1 (BBSRC) |
Data sourced from Thomson Reuters' Web of Knowledge
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