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Characterization and Engineering of Streptomyces griseofuscus DSM 40191 as a Potential Host for Heterologous Expression of Biosynthetic Gene Clusters

Supporting dataset for

Characterization and Engineering of Streptomyces griseofuscus DSM 40191 as a Potential Host for Heterologous Expression of Biosynthetic Gene Clusters

Tetiana Grena, Christopher M. Whitforda, Omkar S. Mohitea, Tue S. Jørgensena, Eftychia E. Kontoua, Julie B. Nielsena, Sang Yup Leea,b, Tilmann Webera#

a) The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark

b) Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Republic of Korea

Supplementary Data 1. Genome comparison data
Excel tables with gene annotations from NCBI GenBank and KEGG subsystems. Gene presence-absence table for genes across the pangenome of S. griseofuscus, S. coelicolor, S. venezuelae. The KEGG subsystem gene and reaction counts per organism.
Supplementary Data 2. Phenotype microarray data analysis with DuctApe
Excel tables with raw kinetic growth data across plates PM1 to PM4 with 2 replicates for S. griseofuscus, S. coelicolor, S. venezuelae. Biolog activity index (0 to 9) across 384 nutrients in each strain and comparison of number of active nutrients across the three strains.
Supplementary Data 3. Genotype phenotype mapping using the KEGG pathways
Excel tables with matrix of BioLog activity index across different KEGG nutrients mapped on to the KEGG pathways. Combined matrix with mean activity differences across three strains.

Supplementary Data 4. Genome scale metabolic models
The SMBL formatted genome-scale metabolic models of the three Streptomyces strains used in the study
Supplementary Data 5. Comparison of genome scale model based growth predictions and BioLog data
Excel table with list of reactions considered in the three genome scale models and comparison of in-silico growth prediction on different nutrients against BioLog data.

Supplementry Data 6. BGC comparison across Streptomyces using BiG-SCAPE
Information on BGCs detected in S. griseofuscus and information on the public genomes selected along with the BGCs selected for comparison. Similarity network data used for generation of Fig. 3 with information on nodes and edges.

Funding

NNF Center for Biosustainability (Internationaliseringsprogram)

Novo Nordisk Foundation

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Integration of Informatics and Metabolic Engineering for the discovery of Novel Antibiotics (IIMENA)

Novo Nordisk Foundation

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History

Related publications (DOI or link to DTU Orbit, DTU Findit)