Analysis of Secondary Metabolite Synthesis Potential of Streptomyces fradiae sf106 Based on the Whole Genome and Non-Target Metabolomics and Exploration of the Biosynthesis of Tylosin
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain and Culture Conditions
2.2. Genomic DNA Extraction
2.3. Library Construction and Genome Sequencing
2.4. Genome Assembly and Annotation
2.5. Metabolite Extraction
2.6. (UHPLC–MS/MS) Analysis
2.7. Data Preprocessing and Annotation
3. Results
3.1. Systematic Evolution Analysis of Streptomyces fradiae sf106
3.2. The Genomic Overview and Annotation of Streptomyces fradiae sf106
3.3. Analysis of Mobile Genetic Elements
3.4. Prediction of Antibiotic Resistance Genes
3.5. Metabolic System Analysis
3.5.1. Carbohydrate-Active Enzyme Annotation
3.5.2. Secondary Metabolite Analysis
3.6. Preprocessing of Metabolite Expression Data
3.7. Metabolites KEGG Compounds Classification
3.8. Differential Metabolite Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Genome Size (kb) | GC Content (%) | CDS No. | tRNA No | rRNA No. | KEGG | GO | COG | NR | Pfam | Swiss-Prot |
---|---|---|---|---|---|---|---|---|---|---|---|
Streptomyces fradiae sf106 | 7351 | 73 | 6750 | 60 | 20 | 2300 | 3500 | 4950 | 6100 | 4860 | 3920 |
Sample Name | GI No. | Is No. | Prophage No. | CRISPR-Cas No. |
---|---|---|---|---|
Streptomyces fradiae sf106 | 12 | 5 | 1 | 13 |
Region | Type | From | To | Most Similar Known Cluster | Similarity | |
---|---|---|---|---|---|---|
Region 1 | redox-cofactor | 11,912 | 34,657 | Alanylclavam/2-hydroxymethylclavam/2-fomyloxymethyclavam/clavam-2-carboxylate | Other: Non-NRP beta- lactam | 12% |
Region 2 | T3PKS, terpene | 367,053 | 406,828 | endophenazine A/endophenazine B | Other: Phenazine | 38% |
Region 3 | NRPS | 670,555 | 724,534 | scabichelin | NRP | 20% |
Region 4 | NRPS-like, PKS-like, betalactone, T2PKS, RRE- containing | 1,232,101 | 1,317,375 | LL-D49194α1 (LLD) | Polyketide | 39% |
Region 5 | lanthipeptide-class-iii | 1,980,221 | 2,002,953 | SapB | RiPP: Lanthipeptide | 100% |
Region 6 | siderophore | 2,354,686 | 2,365,381 | |||
Region 7 | ectoine | 2,484,580 | 2,494,984 | ectoine | Other | 100% |
Region 8 | T3PKS | 3,482,933 | 3,524,030 | flaviolin | Other | 50% |
Region 9 | T1PKS | 3,545,272 | 3,626,176 | carrimycin | Polyketide | 55% |
Region 10 | NRPS-like, lassopeptide | 3,657,076 | 3,699,170 | citrulassin B | RiPP | 100% |
Region 11 | NRPS | 4,128,379 | 4,201,561 | isocomplestatin | NRP | 93% |
Region 12 | terpene | 4,360,731 | 4,379,029 | |||
Region 13 | RiPP-like, NRPS-like | 4,422,841 | 4,466,244 | nunapeptin/nunamycin | NRP | 14% |
Region 14 | lanthipeptide-class-i | 4,599,449 | 4,622,053 | |||
Region 15 | terpene | 4,728,801 | 4,752,252 | Terpene | 53% | |
Region 16 | terpene | 4,832,715 | 4,849,274 | |||
Region 17 | RRE-containing, LAP, thiopeptide | 4,936,167 | 4,971,075 | |||
Region 18 | siderophore | 5,095,314 | 5,106,980 | desferrioxamine | Other | 83% |
Region 19 | RiPP-like | 5,186,566 | 5,198,233 | |||
Region 20 | siderophore | 5,473,885 | 5,488,679 | ficellomycin | NRP | 3% |
Region 21 | lanthipeptide- class-i | 5,836,957 | 5,862,133 | tetrocarcin A | Polyketide | 4% |
Region 22 | terpene | 7,023,507 | 7,049,988 | isorenieratene | Terpene | 87% |
Reference | Similarity Score | Type | Compound(s) | Organism | |
---|---|---|---|---|---|
Cluster1 | BGC0001156.1 | 0.15 | Terpene | platencin | Streptomyces platensis |
Cluster2 | BGC0000674.1 | 0.71 | Terpene | (-)-δ-cadinene | Streptomyces clavuligerus ATCC 27064 |
Cluster3 | BGC0000426.1 | 0.42 | NRP | sevadicin | Paenibacillus larvae |
Cluster4 | BGC0000248.1 | 1.65 | Polyketide | naphtocyclinone | Streptomyces arenae |
Cluster5 | BGC0000551.1 | 0.47 | RiPP | SapB | Streptomyces coelicolor A3(2) |
Cluster6 | BGC0001572.1 | 0.34 | Other | desferrioxamine E | Pantoea agglomerans |
Cluster7 | BGC0000853.1 | 0.64 | Other | ectoine | Streptomyces anulatus |
Cluster8 | BGC0001310.1 | 0.46 | Terpene | naringenin | Streptomyces clavuligerus ATCC 27064 |
Cluster9 | BGC0000166.1 | 0.78 | Polyketide | tylactone | Streptomyces fradiae |
Cluster10 | BGC0001552.1 | 1.16 | RiPP | citrulassin F | Streptomyces avermitilis MA-4680 = NBRC 14893 |
Cluster11 | BGC0000326.1 | 0.41 | NRP | isocomplestatin | Streptomyces lavendulae |
Cluster12 | BGC0001910.1 | 0.28 | Terpene | cyslabdan | Streptomyces cyslabdanicus |
Cluster13 | BGC0000500.1 | 0.41 | RiPP | carnolysin A1, carnolysin A2 | Carnobacterium maltaromaticum |
Cluster14 | BGC0000544.1 | 0.19 | RiPP | planosporicin | Planomonospora alba |
Cluster15 | BGC0000648.1 | 0.34 | Terpene | carotenoid | Myxococcus xanthus |
Cluster16 | BGC0001910.1 | 0.34 | Terpene | cyslabdan | Streptomyces cyslabdanicus |
Cluster17 | BGC0001146.1 | 1.02 | RiPP | cyclothiazomycin C | Streptomyces sp. NRRL WC-3908 |
Cluster18 | BGC0001478.1 | 0.58 | Other | desferrioxamine E | Streptomyces sp. ID38640 |
Cluster19 | No matches found | ||||
Cluster 20 | BGC0001531.1 | 0.26 | Other | bisucaberin B | Tenacibaculum mesophilum |
Cluster21 | BGC0001727.1 | 0.23 | RiPP | paenilan | Paenibacillus polymyxa E681 |
Cluster22 | BGC0000664.1 | 0.42 | Terpene | isorenieratene | Streptomyces griseus subsp. griseus NBRC 13350 |
Ion Mode | All Peaks | Identified Metabolites | Metabolites in Library | Metabolites in KEGG |
---|---|---|---|---|
pos | 6480 | 970 | 697 | 229 |
neg | 8049 | 885 | 790 | 238 |
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Jia, C.; Ma, X.; Jiang, Y.; Cheng, S.; Yue, S.; Su, J. Analysis of Secondary Metabolite Synthesis Potential of Streptomyces fradiae sf106 Based on the Whole Genome and Non-Target Metabolomics and Exploration of the Biosynthesis of Tylosin. Fermentation 2023, 9, 866. https://doi.org/10.3390/fermentation9100866
Jia C, Ma X, Jiang Y, Cheng S, Yue S, Su J. Analysis of Secondary Metabolite Synthesis Potential of Streptomyces fradiae sf106 Based on the Whole Genome and Non-Target Metabolomics and Exploration of the Biosynthesis of Tylosin. Fermentation. 2023; 9(10):866. https://doi.org/10.3390/fermentation9100866
Chicago/Turabian StyleJia, Chenbo, Xian Ma, Yuting Jiang, Shanshan Cheng, Sijun Yue, and Jianyu Su. 2023. "Analysis of Secondary Metabolite Synthesis Potential of Streptomyces fradiae sf106 Based on the Whole Genome and Non-Target Metabolomics and Exploration of the Biosynthesis of Tylosin" Fermentation 9, no. 10: 866. https://doi.org/10.3390/fermentation9100866
APA StyleJia, C., Ma, X., Jiang, Y., Cheng, S., Yue, S., & Su, J. (2023). Analysis of Secondary Metabolite Synthesis Potential of Streptomyces fradiae sf106 Based on the Whole Genome and Non-Target Metabolomics and Exploration of the Biosynthesis of Tylosin. Fermentation, 9(10), 866. https://doi.org/10.3390/fermentation9100866