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Antibiotics with novel modes of action targetingGram-negative bacteria are needed to resolve the antimicrobial resistance crisis 1-3 . These pathogens are protected by an additional outer membrane, rendering proteins on the cell surface attractive drug targets 4,5 . The natural compound darobactin targets the insertase BamA 6 , the central unit of the essential BAM complex, which facilitates folding and insertion of outer membrane proteins 7-13 . BamA lacks a typical catalytic center, and it is not obvious how a small molecule such as darobactin might inhibit its function. Here, we resolve the darobactin mode of action at the atomic level by a combination of cryo-electron microscopy, X-ray crystallography, native mass spectrometry, in vivo experiments and molecular dynamics simulations. Two unique cyclizations pre-organize the darobactin peptide in a rigid βstrand conformation. This creates a mimic of the recognition signal of native substrates with a superior ability to bind to the lateral gate of BamA. Upon binding, darobactin replaces a lipid molecule from the lateral gate to use the membrane environment as an extended binding pocket. Because the interaction between darobactin and BamA is largely mediated by backbone contacts, it is particularly robust against potential resistance mutations. Our results identify the lateral gate as a functional hotspot in BamA and open the path for rational design of antibiotics targeting this bacterial Achilles heel.The BAM complex was purified from E. coli outer membranes (OMs), reconstituted in n-dodecyl maltoside (DDM) micelles and incubated with darobactin A (darobactin). The cryo-EM reconstruction at 3.0 Å resolution revealed the position of a bound darobactin molecule (Fig. 1a, Extended Data Fig. 1, Supplementary Table 1). BamA features a lateral gate facing the membrane, formed by strands β1 and β16 through a kink in strand β16 at residue Gly807.Previous work showed that substrate-free BamA exists in two interchanging conformations with the gate either being open or being closed by the β16-strand straightening to zip up against

e Antibiotics have either bactericidal or bacteriostatic activity. However, they also induce considerable gene expression in bacteria when used at subinhibitory concentrations (below the MIC). We found that lincomycin, which inhibits protein synthesis by binding to the ribosomes of Gram-positive bacteria, was effective for inducing the expression of genes involved in secondary metabolism in Streptomyces strains when added to medium at subinhibitory concentrations. In Streptomyces coelicolor A3(2), lincomycin at 1/10 of its MIC markedly increased the expression of the pathway-specific regulatory gene actII-ORF4 in the bluepigmented antibiotic actinorhodin (ACT) biosynthetic gene cluster, which resulted in ACT overproduction. Intriguingly, S. lividans 1326 grown in the presence of lincomycin at a subinhibitory concentration (1/12 or 1/3 of its MIC) produced abundant antibacterial compounds that were not detected in cells grown in lincomycin-free medium. Bioassay and mass spectrometry analysis revealed that some antibacterial compounds were novel congeners of calcium-dependent antibiotics. Our results indicate that lincomycin at subinhibitory concentrations potentiates the production of secondary metabolites in Streptomyces strains and suggest that activating these strains by utilizing the dose-response effects of lincomycin could be used to effectively induce the production of cryptic secondary metabolites. In addition to these findings, we also report that lincomycin used at concentrations for markedly increased ACT production resulted in alteration of the cytoplasmic protein (F o F 1 ATP synthase ␣ and ␤ subunits, etc.) profile and increased intracellular ATP levels. A fundamental mechanism for these unique phenomena is also discussed. Streptomyces is the largest genus of Gram-positive filamentous actinomycetes, and members of this genus produce abundant amounts of numerous bioactive metabolites, including antitumor agents, immunosuppressants, and antibiotics in particular (1, 2). Whole-genome sequencing studies of Streptomyces strains have shown that each species could produce many more secondary metabolites than were expected. For example, Streptomyces coelicolor A3(2), S. avermitilis MA-4680, and S. griseus IFO 13350 each produce several secondary metabolites, although they have more than 20 gene clusters that can encode a number of known or predicted biosynthetic pathways for secondary metabolites (3-5). This indicates that the vast majority of secondary metabolites remain unexpressed or barely expressed under standard laboratory conditions. Thus, there is considerable interest in exploring practical means to induce this genetic potential in streptomycetes, which could result in the isolation of novel bioactive secondary metabolites.Recent developments in new methodologies, including physiological and genetic engineering approaches, have opened the door for the discovery of novel secondary metabolites by activating cryptic biosynthetic pathways in streptomycetes (6-13). The improvements and modifications of ...

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Members of the genus Streptomyces are gram-positive filamentous bacteria that produce various secondary metabolites, which are exemplified by antibiotics. Because more than two-thirds of clinically useful antibiotics are produced from Streptomyces, 1 members of this genus are of high pharmacological and industrial interest. Additionally, recent genome-sequencing projects have revealed that many biosynthetic gene clusters, producing unknown secondary metabolites, exist in Streptomyces genomes. [2][3][4] The exploitation of the genomic potential of Streptomyces may lead to the isolation of new biologically active compounds. 5,6 Therefore, it is extremely important for antibiotic discovery research to investigate their unexploited abilities to produce secondary metabolites and to clarify their activation mechanism. We previously demonstrated a method for activating unexpressed or poorly expressed Streptomyces genes to synthesize secondary metabolites through a mutation that confers resistance to drugs targeting the RNA polymerase and/or ribosomes. [7][8][9] This led to the discovery of piperidamycin, a novel antibiotic produced by Streptomyces sp. 631689, which rarely produces antibiotics in any type of culture media. 10 Here, we describe a new technique for advanced utilization of the abovementioned method to take complete advantage of the ability of Streptomyces to produce secondary metabolites.Erythromycin is a macrolide antibiotic that inhibits protein synthesis by binding to the bacterial 50S ribosomal subunit. Previous studies have demonstrated that generating a mutation that confers resistance to a drug, such as rifampicin, streptomycin, gentamicin, paromomycin or thiostrepton, is an effective approach to increasing the production of the blue-pigmented antibiotic actinorhodin (ACT) in Streptomyces coelicolor A3(2) and Streptomyces lividans. 9,11-13 S. coelicolor A3(2) and S. lividans are well-characterized strains of Streptomyces from a physiological and genetic viewpoint; however, the effects of an erythromycin resistance mutation on antibiotic production in S. coelicolor A3(2) and S. lividans have not been assessed. Therefore, we examined whether the acquisition of erythromycin resistance enables S. coelicolor A3(2) and S. lividans to overproduce antibiotics.We isolated 259 and 300 spontaneous erythromycin-resistant (Ery r ) mutants of S. coelicolor A3(2) strain 1147 (SCP1 þ , SCP2 þ , prototroph) and S. lividans strain 1326 (S. lividans 66, SLP2 þ , SLP3 þ , prototroph), respectively, from colonies that grew within 4 weeks after the spores (approximately 10 11 spores) were spread on GYM agar plates containing 170 or 420 mg ml -1 of erythromycin, which corresponds to approximately 3-to 14-fold amount of minimum inhibitory concentration. These spontaneous Ery r mutants were first characterized for the production of ACT and levels of resistance to erythromycin. The mutants were cultured using GYM, R4, R4C or modified R5 (MR5) agar medium, which revealed that 22 and 20% of spontaneous Ery r mutants isolated...

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Lincomycin forms cross-links within the peptidyl transferase loop region of the 23S ribosomal RNA (rRNA) of the 50S subunit of the bacterial ribosome, which is the site of peptide bond formation, thereby inhibiting protein synthesis. We have previously reported that lincomycin at concentrations below the minimum inhibitory concentration potentiates the production of secondary metabolites in actinomycete strains, suggesting that activation of these strains by utilizing the dose-dependent response of lincomycin could be used to effectively induce the production of cryptic secondary metabolites. Here, we aimed to elucidate the fundamental mechanisms underlying lincomycin induction of secondary metabolism in actinomycetes. In the present study, the dose-dependent response of lincomycin on gene expression of the model actinomycete Streptomyces coelicolor A3(2) and possible relationships to secondary metabolism were investigated. RNA sequencing analysis indicated that lincomycin produced enormous changes in gene expression profiles. Moreover, reverse transcription PCR and/or comparative proteome analysis revealed that in S. coelicolor A3(2), lincomycin, which was used at concentrations for markedly increased blue-pigmented antibiotic actinorhodin production, rapidly enhanced expression of the gene encoding the lincomycin-efflux ABC transporter, the 23S rRNA methyltransferase, and the ribosome-splitting factor to boost the intrinsic lincomycin resistance mechanisms and to reconstruct the probably stalled 70S ribosomes with lincomycin; and in contrast temporarily but dramatically reduced mRNA levels of housekeeping genes, such as those encoding FF ATP synthase, RNA polymerase, ribosomal proteins, and transcription and translation factors, with an increase in intracellular NTPs. A possible mechanism for lincomycin induction of secondary metabolism in S. coelicolor A3(2) is discussed on the basis of these results.

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