The RNA Polymerase “Switch Region” Is a Target for Inhibitors

Howard Hughes Medical Institute, Rutgers University, Piscataway, NJ 08854, USA.
Cell (Impact Factor: 32.24). 11/2008; 135(2):295-307. DOI: 10.1016/j.cell.2008.09.033
Source: PubMed


The alpha-pyrone antibiotic myxopyronin (Myx) inhibits bacterial RNA polymerase (RNAP). Here, through a combination of genetic, biochemical, and structural approaches, we show that Myx interacts with the RNAP "switch region"--the hinge that mediates opening and closing of the RNAP active center cleft--to prevent interaction of RNAP with promoter DNA. We define the contacts between Myx and RNAP and the effects of Myx on RNAP conformation and propose that Myx functions by interfering with opening of the RNAP active-center cleft during transcription initiation. We further show that the structurally related alpha-pyrone antibiotic corallopyronin (Cor) and the structurally unrelated macrocyclic-lactone antibiotic ripostatin (Rip) function analogously to Myx. The RNAP switch region is distant from targets of previously characterized RNAP inhibitors, and, correspondingly, Myx, Cor, and Rip do not exhibit crossresistance with previously characterized RNAP inhibitors. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.

Download full-text


Available from: Kalyan Das,
  • Source
    • "Myxopyronin is one antibiotic that targets the switch regions [9] [11]. Structural analyses indicate that myxopyronin makes direct contacts with SW 1, 2, 4 and 5 [9]. Residues of SW 1–3 make direct contacts with the DNA template [8] [12] [13]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: In bacterial RNA polymerase, the bridge helix and switch regions form an intricate network with the catalytic active centre and the main channel. These interactions are important for catalysis, hydrolysis and clamp domain movement. By targeting conserved residues in Escherichia coli RNA polymerase, we are able to show that functions of these regions are differentially required during σ(70)- and the contrasting σ(54)-dependent transcription activation, and so potentially underlie the key mechanistic differences between the two transcription paradigms. We further demonstrate that the transcription factor DksA directly regulates σ(54)-dependent activation both positively and negatively. This finding is consistent with the observed impacts of DksA on σ(70)-dependent promoters. DksA does not seem to significantly affect RNAP binding to a pre-melted promoter DNA but affects extensively activity at the stage of initial RNA synthesis on σ(54)-regulated promoters. Strikingly, removal of the σ(54) Region I is sufficient to invert the action of DksA (from stimulation to inhibition or vice versa) at two test promoters. The RNA polymerase mutants we generated also show a strong propensity to backtrack. These mutants increase the rate of transcript-hydrolysis cleavage to a level comparable to that seen in the Thermus aquaticus RNAP even in the absence of a non-complementary nucleotide. These novel phenotypes imply an important function of the bridge helix and switch regions as an anti-backtracking ratchet and an RNA hydrolysis regulator.
    Journal of Molecular Biology 09/2015; DOI:10.1016/j.jmb.2015.09.005 · 4.33 Impact Factor
  • Source
    • "Several natural products targeting the switch region, namely corallopyronin, lipiarmycin, myxopyronin, and ripostatin have been discovered (Mukhopadhyay et al., 2008; Sergio et al., 1975). Common to all of these molecules is their potent activity against drug-sensitive and drug-resistant strains of Gram-positive bacteria. "

  • Source
    • "It acts as inhibiting or binding bacterial RNAP by changing the structure of the RNAP switch region of the β-subunit of the enzyme. That renders the reading and transmitting DNA code inactive, resulting in bacterial control (Irschik et al., 1983; Campbell et al., 2001; Mukhopadhyay et al., 2008; Belogurov et al., 2009; Ho et al., 2009; Srivastava et al., 2011). Rifampin, an RNAP inhibitor in clinical utilization is capable of binds to the β-subunit of RNAP within the DNA/RNA channel and blocks the RNA elongation when the transcript converts two to three nucleotides in length (Campbell et al., 2001). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Bacterial infections are raising serious concern across the globe. The effectiveness of conventional antibiotics is decreasing due to global emergence of multi-drug-resistant (MDR) bacterial pathogens. This process seems to be primarily caused by an indiscriminate and inappropriate use of antibiotics in non-infected patients and in the food industry. New classes of antibiotics with different actions against MDR pathogens need to be developed urgently. In this context, this review focuses on several ways and future directions to search for the next generation of safe and effective antibiotics compounds including antimicrobial peptides, phage therapy, phytochemicals, metalloantibiotics, lipopolysaccharide, and efflux pump inhibitors to control the infections caused by MDR pathogens.
    Frontiers in Pharmacology 05/2014; 5:105. DOI:10.3389/fphar.2014.00105 · 3.80 Impact Factor
Show more