Draft Genome Sequence of Streptomyces albidoflavus 09MW18-IS, Cultivated from the Atlantic Ocean off the Coast of Virginia

We report a draft genome sequence for Streptomyces albidoflavus strain 09MW18-IS, isolated from the Atlantic slope off the coast of Virginia. The whole-genome sequence will provide novel insights into biosynthetic gene clusters and ecological adaptation in an oligotrophic environment.

STRUCTURAL DETERMINATION OF L-ASPARAGINASE II OF STREPTOMYCES ALBIDOFLAVUS AND INTERACTION ANALYSIS WITH L-ASPARAGINE AND CEFOTAXIME

Objective: L-Asparaginase enzyme possesses a crucial role in the treatment of various hematologic malignancies. The current study focuses on homology modeling and interaction analysis of L-Asparaginase proteins belonging to Streptomyces albidoflavus (S. albidoflavus) with the essential ligand L-Asparagine and subsequent analysis with essential β-lactam antibiotic Cefotaxime. Methods: The process of understanding Asparaginase interactions primarily involved structure determination of WP_096097608, WP_095730301, which is achieved by GalaxyTBM, I-TASSER and SWISS-MODEL. Further, the S. albidoflavus Asparaginase proteins are subjected to GalaxySite and Autodock Vina of PyRx analysis. Results: The GalaxyTBM predicted structures of both the proteins are found promising on various validation studies. The two Asparaginase proteins exhibited high binding affinities of-6.8 and-6.5 kcal/mol with Cefotaxime and-5.1 and-4.9 kcal/mol towards Asparagine. The protein WP_096097608 residues forming hydrogen bonds with L-Asparagine are also analysed to involve in interaction with Cefotaxime on individual docking analysis. Conclusion: The current findings details the two S. albidoflavus Asparaginase proteins affinity towards L-Asparagine, hence can be assessed further for immunogenicity studies. In addition to the above findings, an attempt is made to find the L-Asparaginase binding possibilities with non-metals that identified an essential β-lactam antibiotic Cefotaxime to be an effective inhibitor. This study helps in understanding the interactions of L-Asparaginase with Cefotaxime, as intake of antibiotics between the phases of chemotherapy is observed to treat various infections and also as an antibiotic to microbes that utilize Asparaginase as a vital enzyme.

Solid-Phase Extraction Embedded Dialysis (SPEED), an Innovative Procedure for the Investigation of Microbial Specialized Metabolites

Solid-phase extraction embedded dialysis (SPEED technology) is an innovative procedure developed to physically separate in-situ, during the cultivation, the mycelium of filament forming microorganisms, such as actinomycetes and fungi, and the XAD-16 resin used to trap the secreted specialized metabolites. SPEED consists of an external nylon cloth and an internal dialysis tube containing the XAD resin. The dialysis barrier selects the molecular weight of the trapped compounds, and prevents the aggregation of biomass or macromolecules on the XAD beads. The external nylon promotes the formation of a microbial biofilm, making SPEED a biofilm supported cultivation process. SPEED technology was applied to the marine Streptomyces albidoflavus 19-S21, isolated from a core of a submerged Kopara sampled at 20 m from the border of a saltwater pond. The chemical space of this strain was investigated effectively using a dereplication strategy based on molecular networking and in-depth chemical analysis. The results highlight the impact of culture support on the molecular profile of Streptomyces albidoflavus 19-S21 secondary metabolites.

Production of Candicidin Isomers Is Essential for Biocontrol of Cucumber Rhizoctonia rot By Streptomyces albidoflavus W68

Diseases caused by soil-borne fungal pathogens result in significant crop yield losses and quality reduction. Streptomyces albidoflavus strain W68 is effective in controlling several soil-borne fungal diseases. To identify antifungal substances critical for biocontrol activity of W68, the genome of W68 was sequenced and a linear chromosome of 6.80 Mb was assembled. A total of 21 secondary metabolite biosynthesis gene clusters (BGCs), accounting for 12.27% of the genome, were identified. Core gene deletion mutants for each of all 8 BGCs for non-ribosomal peptide synthetases and polyketide synthases, were created. Among them, only the mutant lacking gene ctg1-5755 (the gene was renamed as fscDW68) in BGC 19, which shares 100% sequence similarity to the BGC for candicidin synthesis, showed obvious reduction in antifungal activity. A pot experiment revealed that biocontrol effects of the ΔfscDW68 mutant in Rhizoctonia rot of cucumber were also significantly compromised relative to W68. LC-MS analysis revealed that W68 but not ΔfscDW68 can produce candicidin isomers, indicating that the production of candicidin isomers is key for antifungal activity and biocontrol activity of S. albidoflavus W68. Importance This study provides the first report that candicidin-like secondary metabolites produced by microbial cells in natural soil environment can effectively control soil-borne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 is attributed to the production of candicidin isomers, suggesting gene clusters for candicidin-like compound biosynthesis might be used as molecular markers to screen and breed microbial strains for biocontrol agent development.

Genome Mining Reveals Secondary Metabolites of Antarctic Bacterium Streptomyces Albidoflavus ANT_B131 Related to Antimicrobial and Antiproliferative Activities

The antimicrobial resistance requires the urgent mining of new antimicrobials. Actinobacteria, specially Streptomyces genus, are responsible for production of numerous clinical antibiotics and anticancer agents. The use of genome mining can reveal the genetic potential of a strain to produce natural products, however the potential may not be express under laboratory conditions. In the present study, the Antarctic bacterium was taxonomically affiliated as Streptomyces albidoflavus, ANT_B131. The crude extracts showed antimicrobial activity against fungi, Gram-positive and Gram-negative bacteria and antiproliferative activity against five human tumor cell lines. Whole genome sequencing reveals a 6.96 Mb genome size and the genome mining showed 24 BGCs, representing 13.3% of the genome. The use of three culture media and extraction methods reveal the expression and recovery of 20% of the BGCs. The natural products identified were surugamide A, surugamide D, desferrioxamine B + Al, desferrioxamine E, and ectoine. This study reveals the potential of S. albidoflavus ANT_B131 as a natural product producer. Yet, the diversity of culture media and extraction methods could enhance the BGCs expression and recovery of natural products, and could be a new strategy to intensify the BGC expression of natural products.