Draft Genome Sequence of Streptomyces sp. Strain AM-2504, Identified by 16S rRNA Comparative Analysis as a Streptomyces kasugaensis Strain

Genomic and Biocontrol Potential of the Crude Lipopeptide by Streptomyces bikiniensis HD-087 Against Magnaporthe oryzae

Rice blast caused by Magnaporthe oryzae is one of the most destructive plant diseases. The secondary metabolites of Streptomyces have potential as biological control agents against M. oryzae. However, no commercial secondary antimicrobial products of Streptomyces have been found by gene prediction, and, particularly relevant for this study, a biocontrol agent obtained from Streptomyces bikiniensis has yet to be found. In this research, genomic analysis was used to predict the secondary metabolites of Streptomyces, and the ability to develop biocontrol pharmaceuticals rapidly was demonstrated. The complete genome of the S. bikiniensis HD-087 strain was sequenced and revealed a number of key functional gene clusters that contribute to the biosynthesis of active secondary metabolites. The crude extract of lipopeptides (CEL) predicted by NRPS gene clusters was extracted from the fermentation liquid of S. bikiniensis HD-087 by acid precipitation followed by methanol extraction, and surfactins, iturins, and fengycins were identified by liquid chromatography-mass spectrometry (LC–MS). In vitro, the CEL of this strain inhibited spore germination and appressorial formation of M. oryzae by destroying membrane integrity and through the leakage of cellular components. In vivo, this CEL reduced the disease index of rice blast by approximately 76.9% on detached leaves, whereas its control effect on leaf blast during pot experiments was approximately 60%. Thus, the S. bikiniensis CEL appears to be a highly suitable alternative to synthetic chemical fungicides for controlling M. oryzae.

Characterization of the Self-Resistance Mechanism to Dityromycin in the Streptomyces Producer Strain

Dityromycin is a peptide antibiotic isolated from the culture broth of the soil microorganism Streptomyces sp. strain AM-2504. Recent structural studies have shown that dityromycin targets the ribosomal protein S12 in the 30S ribosomal subunit, inhibiting translocation. Herein, by using in vitro protein synthesis assays, we identified the resistance mechanism of the producer strain to the secondary metabolite dityromycin. The results show that the self-resistance mechanism of the Streptomyces sp. strain AM-2504 is due to a specific modification of the ribosome. In particular, two amino acid substitutions, located in a highly conserved region of the S12 protein corresponding to the binding site of the antibiotic, were found. These mutations cause a substantial loss of affinity of the dityromycin for the 30S ribosomal subunit, protecting the producer strain from the toxic effect of the antibiotic. In addition to providing a detailed description of the first mechanism of self-resistance based on a mutated ribosomal protein, this work demonstrates that the molecular determinants of the dityromycin resistance identified in Streptomyces can be transferred to Escherichia coli ribosomes, where they can trigger the same antibiotic resistance mechanism found in the producer strain.IMPORTANCE The World Health Organization has identified antimicrobial resistance as a substantial threat to human health. Because of the emergence of pathogenic bacteria resistant to multiple antibiotics worldwide, there is a need to identify the mode of action of antibiotics and to unravel the basic mechanisms responsible for drug resistance. Antibiotic producers' microorganisms can protect themselves from the toxic effect of the drug using different strategies; one of the most common involves the modification of the antibiotic's target site. In this work, we report a detailed analysis of the molecular mechanism, based on protein modification, devised by the soil microorganism Streptomyces sp. strain AM-2504 to protect itself from the activity of the peptide antibiotic dityromycin. Furthermore, we demonstrate that this mechanism can be reproduced in E. coli, thereby eliciting antibiotic resistance in this human commensal bacterium.