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Genome-Guided Investigation Provides New Insights into Secondary Metabolites of Streptomyces parvulus SX6 from Aegiceras corniculatum Cover

Genome-Guided Investigation Provides New Insights into Secondary Metabolites of Streptomyces parvulus SX6 from Aegiceras corniculatum

Polish Journal of Microbiology
Volume 71 (2022): Issue 3 (September 2022)
By: Ngoc Tung Quach,  Thi Hanh Nguyen Vu,  Thi Lien Bui,  Anh Tuan Pham,  Thi Thu An Nguyen,  Thi Thanh Xuan Le,  Thi Thu Thuy Ta,  Pravin Dudhagara and  Quyet-Tien Phi  
Open Access
|Sep 2022

Figures & Tables

Fig. 1

Heatmap presenting antibacterial activity against at least one tested pathogenic bacteria of endophytic actinobacteria isolated from Aegiceras corniculatum. BC – Bacillus cereus ATCC® 11778™, PA – Pseudomonas aeruginosa ATCC® 9027™, MRSE – methicillin-resistant Staphylococcus epidermidis ATCC® 35984™, EA – Enterobacter aerogenes ATCC® 13048™, EC – Escherichia coli ATCC® 11105™, ST – Salmonella typhimurium ATCC® 14028™.
Heatmap presenting antibacterial activity against at least one tested pathogenic bacteria of endophytic actinobacteria isolated from Aegiceras corniculatum. BC – Bacillus cereus ATCC® 11778™, PA – Pseudomonas aeruginosa ATCC® 9027™, MRSE – methicillin-resistant Staphylococcus epidermidis ATCC® 35984™, EA – Enterobacter aerogenes ATCC® 13048™, EC – Escherichia coli ATCC® 11105™, ST – Salmonella typhimurium ATCC® 14028™.

Fig. 2

Identification of endophytic strain SX6. A) Scanning electron microscopy of hyphae of strain SX6 grown on ISP2 medium; B) phylogenetic tree based on 16S rRNA gene sequences of strain SX6 and closely related Streptomyces strains.
Identification of endophytic strain SX6. A) Scanning electron microscopy of hyphae of strain SX6 grown on ISP2 medium; B) phylogenetic tree based on 16S rRNA gene sequences of strain SX6 and closely related Streptomyces strains.

Fig. 3

Biological activities determined in the Streptomyces parvulus SX6 extract. A) Selective antibacterial activity against MRSE ATCC® 35984™ and Pseudomonas aeruginosa ATCC® 9027™; B) cytotoxic activity against A549, Hep3B, MCF-7, and HEK-293 cell lines; C) and D) antioxidant activities, including DPPH free radical scavenging and hydroxyl radical scavenging were determined in the SX6 extract. Mean values and SD of three independent experiments are shown and p-values were calculated by the Student’s unpaired two-tailed t-test by the graph prism software (nsp > 0.05, *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001).
Biological activities determined in the Streptomyces parvulus SX6 extract. A) Selective antibacterial activity against MRSE ATCC® 35984™ and Pseudomonas aeruginosa ATCC® 9027™; B) cytotoxic activity against A549, Hep3B, MCF-7, and HEK-293 cell lines; C) and D) antioxidant activities, including DPPH free radical scavenging and hydroxyl radical scavenging were determined in the SX6 extract. Mean values and SD of three independent experiments are shown and p-values were calculated by the Student’s unpaired two-tailed t-test by the graph prism software (nsp > 0.05, *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001).

Fig. 4

Genome characterization of Streptomyces parvulus SX6. A) Clusters of Orthologous Groups (COGs) of protein functions; B) whole genome-based phylogenetic classification of S. parvulus SX6. The numbers on the branches are GBDP pseudo-bootstrap support values of > 60% from 100 replications, with average branch support of 96.6%.
Genome characterization of Streptomyces parvulus SX6. A) Clusters of Orthologous Groups (COGs) of protein functions; B) whole genome-based phylogenetic classification of S. parvulus SX6. The numbers on the branches are GBDP pseudo-bootstrap support values of > 60% from 100 replications, with average branch support of 96.6%.

Fig. 5

Cryptic secondary metabolite biosynthetic gene clusters identified in the genome of Streptomyces parvulus SX6.
Cryptic secondary metabolite biosynthetic gene clusters identified in the genome of Streptomyces parvulus SX6.

Fig. 6

Biosynthetic pathway of daidzein and genistein in Streptomyces parvulus SX6. A) Using genome mining, the proposed biosynthetic pathways of daidzein and genistein present in S. parvulus SX6; B) identification of genes involved in daidzein and genistein biosynthesis across S. parvulus genomes; C) HPLC-DAD-MS chromatogram of reference compounds and the extract of mangrove endophytic S. parvulus SX6.
Biosynthetic pathway of daidzein and genistein in Streptomyces parvulus SX6. A) Using genome mining, the proposed biosynthetic pathways of daidzein and genistein present in S. parvulus SX6; B) identification of genes involved in daidzein and genistein biosynthesis across S. parvulus genomes; C) HPLC-DAD-MS chromatogram of reference compounds and the extract of mangrove endophytic S. parvulus SX6.

Features of the SX6 and other Streptomyces parvulus genomes_

SpeciesSize (Mb)GC (%)GenesCDSstRNAsrRNAs
S. parvulus SX67.6972.86,9526,7796811
S. parvulus JCM 40687.6971.56,8816,866663
S. parvulus 22977.1572.76,9516,7736618
S. parvulus LP037.7472.57,0306,832663
DOI: https://doi.org/10.33073/pjm-2022-034 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
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Language: English
Page range: 381 - 394
Submitted on: Mar 16, 2022
Accepted on: Jul 13, 2022
Published on: Sep 24, 2022
Published by: Polish Society of Microbiologists
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
genome mining,
plant-derived compounds,
secondary metabolites
Related subjects:
Life sciences,
Microbiology and virology

© 2022 Ngoc Tung Quach, Thi Hanh Nguyen Vu, Thi Lien Bui, Anh Tuan Pham, Thi Thu An Nguyen, Thi Thanh Xuan Le, Thi Thu Thuy Ta, Pravin Dudhagara, Quyet-Tien Phi, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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