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Chapter 1 : Structure and Evolution of Transcriptional Regulatory Networks

Authors: Guilhem Chalancon1, M. Madan Babu2
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Affiliations: 1: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom; 2: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
Content Type: Monograph
Publication Year: 2011

Category: Microbial Genetics and Molecular Biology

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Abstract:

Regulation of transcription is mediated through proteins called transcription factors (TFs). TFs are DNA binding proteins that bind to specific regions, the -regulatory elements, in the promoter regions of certain genes and eventually influence gene expression. The binding of a TF to a promoter region can either result in an increased or decreased transcription of the regulated target gene (TG). The first part of this chapter discusses the main characteristics of the structure of prokaryotic transcriptional regulatory networks (TRNs). The second part discusses the various forces that influence their evolution, and finally the chapter discusses how the understanding gained is being exploited in biotechnology and medicine. Horizontal gene transfer (HGT) requires the physical incorporation of foreign DNA into the receiver organism, its integration into the host regulatory network, and eventually its selection through the bacterial population. The incorporation of DNA during HGT is driven by three distinct mechanisms referred to as conjugation, transduction, and transformation. Approaches used to address the problem of the inference of TRN from other prokaryotes can broadly be grouped into two categories, depending on whether one focuses on orthology or on sequence similarity of TF binding sites.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1

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Gene Expression and Regulation
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Structure and Evolution of Transcriptional Regulatory Networks
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Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
/content/10.1128/9781555816841.ch01.ch01fig01
Figure 1.
Structure of a TRN. (A) The basic unit consists of a TF, which recognizes specific regulatory sequence upstream of its TG. (B) At the local level, the basic units assemble to form network motifs (FFM, SIM, and MIM). (C) At the global level, TRNs display a scale-free topology, which is characterized by the presence of a few TFs (hubs or global regulators) that regulate many genes and many TFs that regulate a few genes.
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10.1128/9781555816841/f0006-01.gif
Image of Figure 1.
Figure 1.

Structure of a TRN. (A) The basic unit consists of a TF, which recognizes specific regulatory sequence upstream of its TG. (B) At the local level, the basic units assemble to form network motifs (FFM, SIM, and MIM). (C) At the global level, TRNs display a scale-free topology, which is characterized by the presence of a few TFs (hubs or global regulators) that regulate many genes and many TFs that regulate a few genes.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
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Figure 2.
The major evolutionary forces that drive TRN evolution.
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10.1128/9781555816841/f0009-01.gif
Image of Figure 2.
Figure 2.

The major evolutionary forces that drive TRN evolution.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
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Figure 3.
General principles of evolution at three distinct levels of network organization.
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10.1128/9781555816841/f0012-01.gif
Image of Figure 3.
Figure 3.

General principles of evolution at three distinct levels of network organization.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
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Tables

Structure and Evolution of Transcriptional Regulatory Networks
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Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
/content/10.1128/9781555816841.ch01.ch01table01
Table 1.
Databases and computer programs for investigating transcriptional regulatory networks
Generic image for table
Table 1.

Databases and computer programs for investigating transcriptional regulatory networks

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1

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