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EcoSal Plus

Domain 5:

Responding to the Environment

The SOS Regulatory Network

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • Authors: Lyle A. Simmons1, James J. Foti2, Susan E. Cohen3, and Graham C. Walker4
  • Editor: James M. Slauch5
    Affiliations: 1: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; 2: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; 3: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; 4: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; 5: The Schoold of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL
  • Received 05 February 2008 Accepted 17 April 2008 Published 25 July 2008
  • Address correspondence to Graham C. Walker [email protected]
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  • Abstract:

    All organisms possess a diverse set of genetic programs that are used to alter cellular physiology in response to environmental cues. The gram-negative bacterium induces a gene regulatory network known as the “SOS response” following exposure to DNA damage, replication fork arrest, and a myriad of other environmental stresses. For over 50 years, E. coli has served as the paradigm for our understanding of the transcriptional and physiological changes that occur after DNA damage. In this chapter, we summarize the current view of the SOS response and discuss how this genetic circuit is regulated. In addition to examining the SOS response, we include a discussion of the SOS regulatory networks found in other bacteria to provide a broad perspective on the mechanism and diverse physiological responses that ensueto protect cells and maintain genome integrity.

  • Citation: Simmons L, Foti J, Cohen S, Walker G. 2008. The SOS Regulatory Network, EcoSal Plus 2008; doi:10.1128/ecosalplus.5.4.3


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All organisms possess a diverse set of genetic programs that are used to alter cellular physiology in response to environmental cues. The gram-negative bacterium induces a gene regulatory network known as the “SOS response” following exposure to DNA damage, replication fork arrest, and a myriad of other environmental stresses. For over 50 years, E. coli has served as the paradigm for our understanding of the transcriptional and physiological changes that occur after DNA damage. In this chapter, we summarize the current view of the SOS response and discuss how this genetic circuit is regulated. In addition to examining the SOS response, we include a discussion of the SOS regulatory networks found in other bacteria to provide a broad perspective on the mechanism and diverse physiological responses that ensueto protect cells and maintain genome integrity.

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Image of Figure 1
Figure 1

(A) In the uninduced state, replication proceeds unperturbed and the limited amount of ssDNA present at the replication fork is not available for RecA binding. Transcription of (green), (purple), (orange), and other SOS-regulated genes is largely repressed. After DNA damage (red circle), RecA binds to the increasing amount of ssDNA in the cell creating the RecA/ssDNA nucleoprotein filament (purple and yellow). The RecA/ssDNA nucleoprotein filament acts as a coprotease to cleave LexA, resulting in the expression of the SOS regulon. As the gene products of the SOS regulon repair the DNA damage, the cell will return to the uninduced state as normal replication proceeds and the switch is reset. (B) Generation and stabilization of a RecA nucleoprotein filament is regulated by a number of cellular factors. RecBCD and RecFOR can act at a stalled replication fork (Left) to generate ssDNA for RecA binding. RecA binding and filamentation can be aided by RecFOR or prevented by RecX (Center). Once formed, the RecA filament can be stabilized by DinI binding (Right).

Adapted from an illustration by Patricia J. Wynne and ( 134 ) with permission (http://www.sciencedirect.com).

Citation: Simmons L, Foti J, Cohen S, Walker G. 2008. The SOS Regulatory Network, EcoSal Plus 2008; doi:10.1128/ecosalplus.5.4.3
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Image of Figure 2
Figure 2

By using electron microscopy, a model of the RecA filament was generated that positions ATP between RecA subunits. (A) The RecA filament is shown to display the DNA binding channel (Left) and then subsequently turned 90° (Right). (B) An ATP molecule (shown) binds at the interface of two RecA subunits, positioning it to explain the cooperative nature of ATP hydrolysis observed for RecA-DNA filaments. Conserved residues in bacterial RecA proteins (green) are positioned along the subunit interface near the ATP binding pocket. The figure was generated using PyMOL and PDB file 1N03.

Adapted from ( 254 ) with permission (http://www.sciencedirect.com).

Citation: Simmons L, Foti J, Cohen S, Walker G. 2008. The SOS Regulatory Network, EcoSal Plus 2008; doi:10.1128/ecosalplus.5.4.3
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Figure 3

LexA (A) and UmuD (B) proteins undergo a large rearrangement from a noncleavable conformation (NC) to a cleavable conformation (C). (A) LexA crystal structures indicate that the Ala-Gly residues (purple) can be positioned 20 Ã away from Lys (green) and Ser (orange) in the NC form (Left) to a position allowing for an autoproteolytic cleavage event in the cleavable form (Right) ( 162 ). (B) Full-length models of the noncleavable (Left) and cleavable (Center) UmuD dimer. The N-terminal arms of UmuD (purple) fold to present the cleavage site (C24 purple spheres) to Ser (orange) and Lys (green) (compare Left and Center). NMR data suggest that after the cleavage event forming UmuD′ (Right), the dimer undergoes a significant conformational change that consequently alters cellular activity.

Adapted from ( 323 ), ( 162 ), ( 324 ), and ( 325 ) with permission (http://www.sciencedirect.com).

Citation: Simmons L, Foti J, Cohen S, Walker G. 2008. The SOS Regulatory Network, EcoSal Plus 2008; doi:10.1128/ecosalplus.5.4.3
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Table 1

SOS-regulated genes

Citation: Simmons L, Foti J, Cohen S, Walker G. 2008. The SOS Regulatory Network, EcoSal Plus 2008; doi:10.1128/ecosalplus.5.4.3
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Table 2

Potential SOS-regulated genes

Citation: Simmons L, Foti J, Cohen S, Walker G. 2008. The SOS Regulatory Network, EcoSal Plus 2008; doi:10.1128/ecosalplus.5.4.3

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