Summary We report the target, biochemical basis, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the α-pyrone antibiotic myxopyronin (Myx). We show that Myx interacts with the RNAP “switch region,” the hinge that mediates opening and closing of the RNAP active-center cleft. We show that Myx prevents interaction of RNAP with promoter DNA. We present a crystal structure that defines contacts between Myx and RNAP and defines effects of Myx on RNAP conformation. We propose that Myx functions by preventing opening of the RNAP active-center cleft to permit entry of DNA during transcription initiation (“hinge jamming”). We establish further that the structurally related α-pyrone antibiotic corallopyronin and the structurally unrelated macrocyclic-lactone antibiotic ripostatin function through the same target and same mechanism. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.

Using single-molecule fluorescence resonance energy transfer, we have defined bacterial RNA polymerase (RNAP) clamp formation at each step in transcription initiation and elongation. We find that the clamp predominantly is open in free RNAP and early intermediates in transcription initiation, but closes upon formation of a catalytically competent transcription initiation complex and remains closed during initial transcription and transcription elongation. We show that four RNAP inhibitors interfere with clamp opening. We propose that clamp opening allows DNA to be loaded into and unwound in the RNAP active-center cleft, that DNA loading and unwinding trigger clamp closure, and that clamp closure accounts for the high stability of initiation complexes and the high stability and processivity of elongation complexes.

A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP b subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.

A new drug target-- the "switch region"--has been identified within bacterial RNA polymerase (RNAP), the enzyme that mediates bacterial RNA synthesis. The new target serves as the binding site for compounds that inhibit bacterial RNA synthesis and kill bacteria. Since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. Since the new target is different from targets of other antibacterial agents, compounds that bind to the new target are not cross-resistant with other antibacterial agents. Four antibiotocs that function through the new target have been identified: myxopyronin, corallopyronin, ripostatin, and lipiarmycin. This review summarizes the switch region, switch-region inhibitors, and implications for antibacterial drug discovery.

The effect of ten naturally occurring and two synthetic inhibitors of NADH :ubiquinone oxidoreductase (complex I) of bovine heart, Neurosporu crassa and Escherichia coli and g1ucose:ubiquinone oxidoreductase (glucose dehydrogenase) of Gluconobacter oxidans was investigated. These inhibitors could be divided into two classes with regard to their specifity and mode of action. Class I inhibitors, including the naturally occuring piericidin A, annonin VI, phenalamid A2, aurachins A and B, thiangazole and the synthetic fenpyroximate, inhibit complex I from all three species in a partially competitive manner and glucose dehydrogenase in a competitive manner, both with regard to ubiquinone. Class I1 inhibitors including the naturally occuring rotenone, phenoxan, aureothin and the synthetic benzimidazole inhibit complex I from all species in an non-competitive manner, but have no effect on the glucose dehydrogenase. Myxalamid PI could not be classified as above because it inhibits only the mitochondrial complex I and in a competitive manner. All inhibitors affect the electron-transfer step from the high-potential iron-sulphur cluster to ubiquinone. Class I inhibitors appear to act directly at the ubiquinone-catalytic site which is related in complex I and glucose dehydrogenase.NADH : ubiquinone oxidoreductase, also known as respiratory complex I of mitochondria, transfers electrons from NADH to ubiquinone and links this process with translocation of protons across the inner membrane.

A key regulated step of transcription in all cellular organisms is promoter melting by the RNA polymerase (RNAP) to form the open promoter complex1–3. To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12–14 base pairs (bps) of the DNA duplex, and load the template-strand (t-strand) DNA into the RNAP active site. Formation of the open complex is a multi-step process with transient intermediates of unknown structures4–6. Here, we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including the first structures of partially melted intermediates. The structures unequivocally show that late steps of promoter melting occur within the RNAP cleft, delineate key roles for fork-loop 2 (FL2) and switch 2 (Sw2), universal structural features of RNAP, in restricting access of DNA to the RNAP active site, and explain why clamp opening is required to allow entry of single-stranded template DNA into the active site. The key roles of the FL2 and Sw2 suggest a common mechanism for late steps in promoter DNA opening to enable gene expression in all domains of life.

Some bacterial clades are important sources of novel bioactive natural products. Estimating the magnitude of chemical diversity available from such a resource is complicated by issues including cultivability, isolation bias and limited analytical data sets. Here we perform a systematic metabolite survey of ~2300 bacterial strains of the order Myxococcales, a well-established source of natural products, using mass spectrometry. Our analysis encompasses both known and previously unidentified metabolites detected under laboratory cultivation conditions, thereby enabling large-scale comparison of production profiles in relation to myxobacterial taxonomy. We find a correlation between taxonomic distance and the production of distinct secondary metabolite families, further supporting the idea that the chances of discovering novel metabolites are greater by examining strains from new genera rather than additional representatives within the same genus. In addition, we report the discovery and structure elucidation of rowithocin, a myxobacterial secondary metabolite featuring an uncommon phosphorylated polyketide scaffold.

We report here the discovery, isolation, and chemical and preliminary biological characterization of a new antibiotic compound, 7-O-malonyl macrolactin A (MMA), produced by a Bacillus subtilis soil isolate. MMA is a bacteriostatic antibiotic that inhibits a number of multidrug-resistant gram-positive bacterial pathogens, including methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, and a small-colony variant of Burkholderia cepacia. MMA-treated staphylococci and enterococci were pseudomulticellular and exhibited multiple asymmetric initiation points of septum formation, indicating that MMA may inhibit a cell division function.The spread of resistance to antibiotics undermines the therapeutic utility of anti-infective drugs in current clinical use (1). For example, Staphylococcus aureus, a major cause of community-and hospital-acquired infections, has developed resistance to most classes of antibiotics. Methicillin-resistant S. aureus (MRSA) strains appeared in the hospital environment after introduction of the semisynthetic penicillin methicillin, leaving vancomycin as the last line of defense for MRSA treatment (7). S. aureus organisms intermediately susceptible to vancomycin were first isolated in 1997 in Japan (15) and later in other countries (8). With the recent appearance of vancomycin-resistant clinical isolates (32,36,38), no antibiotic class is effective against multiresistant S. aureus infections. The increase in vancomycin-resistant enterococci (VRE), important agents of nosocomial infections, is another cause of great concern (2,3,19,27). Therapy options for multiresistant gramnegative opportunistic bacterial pathogens are also diminishing. Such bacteria, like Pseudomonas aeruginosa and Burkholderia cepacia (6), are common environmental organisms and opportunistic pathogens having the capacity to infect essentially all tissues of patients with compromised host defenses (21).Compounding the problem of genetically determined transmissible antibiotic resistance is the development of phenotypically resistant, often slow-growing, forms in chronic bacterial infections. These may take the form of biofilm microbes or small-colony variants (SCV) (12; reviewed in reference 14), are known to include both gram-positive and gram-negative pathogens, and are usually associated with a worsening of the disease prognosis.Thus, new antibiotics and therapy options are urgently needed to improve the management of bacterial infections (29, 35), and a major challenge is to find drugs that act against SCV and/or bacteria growing in biofilms.In this study, we report the discovery and preliminary characterization of 7-O-malonyl macrolactin A (MMA), a new antibiotic having bacteriostatic activity against clinical strains of MRSA, VRE, and a SCV of Burkholderia cepacia. The parental wild-type (WT) and SCV pairs of P. aeruginosa and B. cepacia, as well as Stenotrophomonas maltophilia strain 1124, were isolated from cystic fibrosis patients in the Department of Medical Microbiology at the Medical School...