Structure and Evolution of Transcriptional Regulatory Networks
Guilhem Chalancon and M. Madan Babu
from: Bacterial Gene Regulation and Transcriptional Networks (Edited by: M. Madan Babu). Caister Academic Press, U.K. (2013)
Regulation of gene expression is primarily mediated by proteins called transcription factors (TFs), which recognize and bind specific nucleotide sequences and affect transcription of nearby genes. Over the last years, considerable information has been accumulated on regulatory interactions between the TFs and their regulated target genes (TGs) in various model prokaryotic systems such as Escherichia coli and Bacillus subtilis. This has permitted researchers to model the transcriptional regulatory system of an organism as a network, wherein TFs or TGs are represented as nodes and regulatory interactions are denoted as directed links. Representation of this information as a network has provided us with a robust conceptual framework to investigate this system, and work in the last decade has uncovered several fundamental general principles pertaining to its structure and evolution. In this chapter, we first introduce the concept of transcriptional regulatory networks. We then discuss our current understanding of the structure of transcriptional regulatory networks. Specifically, we discuss the local and global structure of such networks. We then discuss the various forces that influence network evolution such as gene duplication, horizontal gene transfer, and gene loss. In particular, we discuss how the transcriptional regulatory network evolves across organisms that live in different environments. Finally, we conclude by discussing major challenges for future research and highlighting how the new understanding can have implications for biotechnology and medicine and can be exploited in applications such as microbial engineering and synthetic biology read more ...