Our way of understanding evolution has changed completely with the era of genomics, particularly since the emergence of comparative genomics, a discipline allowing the analysis of complete genomes and biological processes over vast periods of time. In this volume, internationally recognized experts present and discuss an update of the evolutionary processes at the onset of organismal diversification and complexity, and review the mechanisms leading to the acquisition of new traits and functions. Different levels of evolution are considered, from internal modules in genes and proteins to interactomes and biological networks, with integration of the influence of both the genomic environment and the ecological context. Particular emphasis will be given to the origin of novel genes and gene functions as well as to the evolutionary impact of the duplication of genetic information, with several chapters devoted to transposable elements. Providing an excellent update on gene and protein evolution, this book will be appreciated by researchers in biology and medicine, biology teachers and anyone interested in evolution and genomics.
66 - 80: General Trends in the Evolution of Prokaryotic Transcriptional Regulatory Networks
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Published:2007
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Discontinued Book Series: Genome Dynamics
M. Madan Babu, S. Balaji, L. Aravind, 2007. "General Trends in the Evolution of Prokaryotic Transcriptional Regulatory Networks", Gene and Protein Evolution, J.-N. Volff
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Abstract
Gene expression in organisms is controlled by regulatory proteins termed transcriptionfactors, which recognize and bind to specific nucleotide sequences. Over the years, considerableinformation has accumulated on the regulatory interactions between transcription factorsand their target genes in various model prokaryotes, such as Escherichia coli andBacillus subtilis. This has allowed the representation of this information in the form of adirected graph, which is commonly referred to as the transcriptional regulatory network. Thenetwork representation provides us with an excellent conceptual framework to understandthe structure of the transcriptional regulation, both at local and global levels of organization.Several studies suggest that the transcriptional network inferred from model organisms maybe approximated by a scale-free topology, which in turn implies the presence of a relativelysmall group of highly connected regulators (hubs or global regulators). While the graph theoreticalprinciples have been applied to infer various properties of such networks, there havebeen few studies that have actually investigated the evolution of the transcriptional regulatorynetworks across diverse organisms. Using recently developed computational methods thatexploit various evolutionary principles, we have attempted to reconstruct and compare thesenetworks across a wide-range of prokaryotes. This has provided several insights on the modificationand diversification of network structures of various organisms in course of evolution.Firstly, we observed that target genes show a much higher level of conservation thantheir transcriptional regulators. This in turn suggested that the same set of functions could bedifferently controlled across diverse organisms, contributing significantly to their adaptiveradiations. In particular, at the local level of network structure, organism-specific optimizationof the transcription network has evolved primarily via tinkering of individual regulatoryinteractions rather than whole scale reuse or deletion of network motifs (local structure). Inturn, as phylogenetic diversification proceeds, this process appears to have favored repeatedconvergence to scale-free-like structures, albeit with different regulatory hubs.
