Pan-reactome analysis of Streptomyces strains reveals association and disconnection between primary and secondary metabolism
Authors/Creators
-
1.
Korea Advanced Institute of Science and Technology
-
2.
Technical University of Denmark
Description
Table S1.xlsx:
Details on genome data, biosynthetic gene cluster (BGC) statistics, and fastANI results for average nucleotide identity (ANI) among the 242 Streptomyces strains considered in this study.
Table S2.xlsx:
Details on all BGCs from antiSMASH among the 242 Streptomyces strains considered in this study and their corresponding gene cluster families (GCFs) from BiG-SCAPE.
Table S3.xlsx:
Validation results of genome-scale metabolic models (GEMs) for Streptomyces avermitilis MA-4680 and Streptomyces coelicolor A3(2) using phenotype microarray data, and for 20 Streptomyces strains using literature.
Table S4.xlsx:
Number of reactions, metabolites, and genes in the GEMs of the 242 Streptomyces strains.
Table S5.xlsx:
Jaccard similarities between presence vectors of reactions from the 242 Streptomyces GEMs and those of GCFs from BiG-SCAPE for the 242 Streptomyces strains.
Table S6.xlsx:
Summary of precursor requirements for all BGCs and the precursor biosynthetic capability of Streptomyces strains. A total of four categories were considered between the precursor producibility and precursor requirement.
Table S7.xlsx:
Metabolites and reactions suggested to be necessary for the biosynthesis of 20 secondary metabolite precursors according to the literature.
Table S8.xlsx:
List of genes predicted to be horizontally transferred among those within BGCs.
models_final_241108.zip:
SBML files of Streptomyces GEMs
Notes
This work was supported by National Research Foundation of Korea through the following programs: The Bio & Medical Technology Development Program (RS-2024-00509338); the ERC Center (2022R1A5A1033719); and the Development of next-generation biorefinery platform technologies for leading bio-based chemicals industry project (2022M3J5A1056072); and the Development of platform technologies of microbial cell factories for the next-generation biorefineries project (2022M3J5A1056117). This study was supported by the KAIST Cross-Generation Collaborative Lab project.
Files
models_final_241108.zip
Files
(83.5 MB)
| Name | Size | |
|---|---|---|
|
md5:4a39898987dd58e46a6919d4bf14b702
|
80.2 MB | Preview Download |
|
md5:650e1be3dafa8ee0455671c455a008c7
|
556.1 kB | Download |
|
md5:e602b0b9d42a928cc3b4498293b5c9bb
|
383.9 kB | Download |
|
md5:9aa9939405dbf588194a2b084e9018ce
|
24.8 kB | Download |
|
md5:bf0391de6af17eb0edc6262600ec1ad6
|
16.9 kB | Download |
|
md5:804385d26595b76b816ca28daacac08f
|
1.1 MB | Download |
|
md5:e5ea0215cc14a07248d5868118986cf9
|
32.3 kB | Download |
|
md5:4934d7200abf1d47b5be5efe105d2d6f
|
25.7 kB | Download |
|
md5:943edf7cf72765340612da85a9858fa6
|
1.1 MB | Download |