Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolation of Genomic DNA and Genome Sequencing
2.2. Genome Assembly and Annotation
2.3. Spectrometric Experiments
2.4. Identification of Secondary Metabolites and Molecular Network Analysis
2.5. Comparative analysis of the Strain JCM 3382 with 2061 Streptomyces Genomes
3. Results and Discussion
3.1. Summary of the S. nojiriensis JCM 3382 Genome
3.2. Genome-Mining-Based Identification of Secondary Metabolites Produced by the Strain JCM 3382
3.3. Distribution of Gene Clusters for Antibiotics across Streptomyces Genomes
3.4. Distribution of gabT1, yktC1, and gutB1 across 2062 Streptomyces Genomes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genomic Feature | Value |
---|---|
Size of the genome assembly (bp) | 9,022,916 |
GC content (%) | 71.98 |
Protein-coding genes/regions (bp) | 8103/7,869,321 |
tRNA/tmRNA/rRNA genes | 99/1/21 |
Genes assigned to COG categories | 7697 |
Complete BUSCOs (%) | 98.86 |
Region | Type | Most Similar Known Cluster | Similarity |
---|---|---|---|
Region 1 | Terpene | Avermitilol | 100.00% |
Region 2 | Lanthipeptide, PKS-like, Butyrolactone | Venezuelin | 100.00% |
Region 3 | Thiopeptide, LAP | Lactazole | 55.00% |
Region 4 | NRPS | Deimino-antipain | 66.00% |
Region 5 | T2PKS | Spore pigment | 58.00% |
Region 6 | NRPS | JBIR-126 (tambromycin) | 96.00% |
Region 7 | NRPS, T1PKS | Coelichelin | 72.00% |
Region 8 | Butyrolactone | Neocarzinostatin | 4.00% |
Region 9 | Siderophore | Desferrioxamin B | 100.00% |
Region 10 | T2PKS | Setomimycin | 100.00% |
Region 11 | RiPP-like | ||
Region 12 | NRPS, T1PKS | Bleomycin | 9.00% |
Region 13 | CDPS | BD-12 | 17.00% |
Region 14 | Siderophore | Ficellomycin | 3.00% |
Region 15 | Bacteriocin | ||
Region 16 | Terpene | Toxoflavin, Fervenulin | 14.00% |
Region 17 | Lanthipeptide | ||
Region 18 | Terpene | Hopene | 61.00% |
Region 19 | T1PKS, hglE-KS | ||
Region 20 | NRPS, NRPS-like | Kirromycin, Nojirimycin | 22.00% |
Region 21 | T1PKS | ECO-02301 | 75.00% |
Region 22 | Lanthipeptide | ||
Region 23 | NRPS-like | Lipstatin | 42.00% |
Region 24 | Terpene | ||
Region 25 | Terpene | Ebelactone | 5.00% |
Region 26 | Terpene | Monensin | 5.00% |
Region 27 | Melanin | Istamycin | 4.00% |
Region 28 | Siderophore | ||
Region 29 | T3PKS | Alkylresorcinol | 100.00% |
Region 30 | CDPS, NRPS-like |
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Park, J.-S.; Kim, D.-E.; Hong, S.-C.; Kim, S.-Y.; Kwon, H.C.; Hyun, C.-G.; Choi, J. Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces. Microorganisms 2021, 9, 1802. https://doi.org/10.3390/microorganisms9091802
Park J-S, Kim D-E, Hong S-C, Kim S-Y, Kwon HC, Hyun C-G, Choi J. Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces. Microorganisms. 2021; 9(9):1802. https://doi.org/10.3390/microorganisms9091802
Chicago/Turabian StylePark, Jin-Soo, Da-Eun Kim, Sung-Chul Hong, Seung-Young Kim, Hak Cheol Kwon, Chang-Gu Hyun, and Jaeyoung Choi. 2021. "Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces" Microorganisms 9, no. 9: 1802. https://doi.org/10.3390/microorganisms9091802