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Chapter 17 : Structure and Function of MarA and Its Homologs

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Abstract:

Researchers have spent the last decade studying the molecular basis of transcriptional activation by MarA, the activator first identified by Stuart Levy and coworkers. Depending on the distance from the RNAP binding site, the MarA binding sites can be functional in two orientations. A second feature of the model that may be significant is that conformational changes at the MarA surface resulting from interaction with acarboxy-terminal domain (CTD) appear to be propagated internally through the molecule to amino acids of helix 3, causing small conformational changes at Q45 and W42. It is worth noting that the principal contacts between MarA and α-CTD are hydrophobic, and most involve backbone atoms of the peptide chains rather than the amino acid side groups. Several lines of reasoning suggest that MarA may not function via this recruitment model. As pointed out above, each chromosome contains ˜10,000 potential binding sites for MarA. It has been demonstrated that two members of the AraC family, RhaS and MelR, interact with domain 4 of the σ subunit of RNAP at class II promoters. It has been observed that σ is not needed to bind RNAP to MarA in the absence of DNA in vitro. Thus, if MarA also interacts with σ at class II promoters, perhaps it does so only after the scanning complex has bound to the DNA.

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17

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Figures

Image of Figure 1.
Figure 1.

Ribbon diagram of MarA interacting with its DNA binding site ( ). The DNA shows an overall bend of ∼35°.

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17
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Image of Figure 2.
Figure 2.

Consensus sequence for MarA/SoxS/Rob DNA binding site. R = A or G, W = A or T, Y = T or C, H = a, T, or C, and N = any nucleotide. Note that the binding site is usually indicated as being 20 bp long since any additional bp at either end strongly enhances binding ( ).

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17
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Image of Figure 3.
Figure 3.

Diagram showing functional configurations of the MarA binding sites relative to the RNAP binding site ( ). The MarA binding sites centered at −42 and −52 nt (relative to the transcription start site) are in the forward orientation while those centered at −62 and −72 (not shown) are in the backward orientation. The distances of the MarA binding sites from the −10 site indicate that MarA is essentially on the same surface of the DNA relative to RNAP in each configuration.

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17
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Image of Figure 4.
Figure 4.

Representations of RNAP interacting via α-CTD with MarA at two promoter configurations (not to scale). Theα, β,β′, and σ subunits of RNAP are shown. Each α-CTD is connected to the α-NTD by a flexible tether (curved lines). Significant MarA amino acids involved at the interface with α-CTD are indicated. The α-CTD domain that does not contact MarA is shown in contact with the DNA, but this is speculative. The model predicts that the spatial relationship between α-CTD and MarA will be similar at both class I* () and class I () promoters.

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17
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Image of Figure 5.
Figure 5.

Two different types of interaction of α-CTD with activators at class I promoters. RNAP is indicated as in Fig. 4 . In the CRP (or FIS) complex, one α-CTD contacts the AR1 site of CRP (black balls) via the 287-determinant (gray protrusion) and DNA via the 265-determinant (white ovals with dashed borders), whereas the other α-CTD makes contact only with DNA. In the MarA complex, the model envisions the 265-determinant of one α-CTD as making contact with the W19 site of MarA only.

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17
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Image of Figure 6.
Figure 6.

Effect of UP elements on the induction of the and promoters. Variants of the and promoters were constructed with or without the indicated UP element. The cells were treated with fructose, salicylate or paraquat to express CRP, MarA or SoxS, respectively. The effects on promoter activity were then assayed using a reporter gene fused to each construct (β-galactosidase specific activity expressed in Miller Units). Additive effects of the UP element were seen with MarA and SoxS, but a cooperative effect was seen with CRP.

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17
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Image of Figure 7.
Figure 7.

Double disk diffusion assays ( ) showing effects of several antibiotics on resistance to cephalexin. About 2 × 10 strain AG100 cells ( ) were plated on Luria agar, and a 12.8 mm paper disk containing either (A) 87.5 μg of ampicillin, (B) 25 μg of chloramphenicol, (C) 87.5 µg of tetracycline, or (D) 13.2 mg of sodium salicylate was placed on the center of the plate. Three 6.4 mm paper disks containing 50 µg of cephalexin were added to the periphery of the plates at different distances from the central disk, and the plates were incubated at 30°C overnight. A reduced zone of inhibition around the cephalexin disk facing the central disk indicates induction of resistance, as seen at the bottom of (D).

Citation: Martin R, Rosner J. 2005. Structure and Function of MarA and Its Homologs, p 235-246. In White D, Alekshun M, McDermott P (ed), Frontiers in Antimicrobial Resistance. ASM Press, Washington, DC. doi: 10.1128/9781555817572.ch17
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