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Journals
Polish Journal of Microbiology
Volume 71 (2022): Issue 3 (September 2022)
Open Access
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
and
Quyet-Tien Phi
Quyet-Tien Phi
| Sep 24, 2022
Polish Journal of Microbiology
Volume 71 (2022): Issue 3 (September 2022)
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Article Category:
Original Paper
Published Online:
Sep 24, 2022
Page range:
381 - 394
Received:
Mar 16, 2022
Accepted:
Jul 13, 2022
DOI:
https://doi.org/10.33073/pjm-2022-034
Keywords
genome mining
,
plant-derived compounds
,
secondary metabolites
© 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™.
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.
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).
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%.
Fig. 5
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.
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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