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

Ngoc Tung Quach
Ngoc Tung Quach
, 
Thi Hanh Nguyen Vu
Thi Hanh Nguyen Vu
, 
Thi Lien Bui
Thi Lien Bui
, 
Anh Tuan Pham
Anh Tuan Pham
, 
Thi Thu An Nguyen
Thi Thu An Nguyen
, 
Thi Thanh Xuan Le
Thi Thanh Xuan Le
, 
Thi Thu Thuy Ta
Thi Thu Thuy Ta
, 
Pravin Dudhagara
Pravin Dudhagara
 et 
Quyet-Tien Phi
Quyet-Tien Phi
   | 24 sept. 2022
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Article Category: Original Paper
Publié en ligne: 24 sept. 2022
Pages: 381 - 394
Reçu: 16 mars 2022
Accepté: 13 juil. 2022
DOI: https://doi.org/10.33073/pjm-2022-034
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© 2022 Ngoc Tung Quach et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

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.

Species Size (Mb) GC (%) Genes CDSs tRNAs rRNAs
S. parvulus SX6 7.69 72.8 6,952 6,779 68 11
S. parvulus JCM 4068 7.69 71.5 6,881 6,866 66 3
S. parvulus 2297 7.15 72.7 6,951 6,773 66 18
S. parvulus LP03 7.74 72.5 7,030 6,832 66 3
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