Investigating the evolution of diversity and complexity of Prokaryotic gene regulatory networks using in silico models

Jenkins, Dafyd James (2009). Investigating the evolution of diversity and complexity of Prokaryotic gene regulatory networks using in silico models. University of Birmingham. Ph.D.


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There is much debate about the evolutionary origins of diversity and many complex gene regulatory network features, such as global regulation. Using novel in silico models the evolutionary origins of complex features, heterogeneity and the role of stochastic molecular processes in gene regulatory network evolution are investigated. It is shown that: i) Repression is essential, even in constant environments, due to energetic constraints. ii) Stochastic basal gene expression forces shrinkage of genomes, whilst its absence leads to ‘bloating’. iii) Models evolved towards a biological goal have a very different network structure to nonadaptively evolved models. iv) Unstable mRNA, stable protein and rapid but robust replication times are strongly selected properties of evolved networks. v) Multiple network solutions within identical environmental conditions are observed with the presence of stochastic basal gene expression. vi) Two attractor states, one with high, and one with low stochastic basal gene expression, are observed in networks which can evolve their levels of basal expression. vii) Functional complexity of a gene regulatory network is dependent on environmental complexity. viii) Functional complexity evolves in hierarchical stages, requiring ‘core’ energy regulation mechanisms before environmental responses and adaptations for growth can be sustained and fixed. ix) Global gene regulation is strongly selected as an efficient energy regulation mechanism

Type of Work: Thesis (Doctorates > Ph.D.)
Award Type: Doctorates > Ph.D.
College/Faculty: Colleges (2008 onwards) > College of Life & Environmental Sciences
School or Department: School of Biosciences
Funders: Biotechnology and Biological Sciences Research Council
Subjects: Q Science > Q Science (General)


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