Differential gene expression analysis of aclacinomycin producing Streptomyces galilaeus ATCC 31615 and its mutant
Sharifuzzaman, Md (2021-05-25)
Differential gene expression analysis of aclacinomycin producing Streptomyces galilaeus ATCC 31615 and its mutant
(25.05.2021)
Julkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty.
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Julkaisun pysyvä osoite on:
https://urn.fi/URN:NBN:fi-fe2021061537293
https://urn.fi/URN:NBN:fi-fe2021061537293
Tiivistelmä
Streptomyces from the genus Actinomycetales are soil bacteria known to have a complex secondary metabolism that is extensively regulated by environmental and genetic factors. Consequently they produce antibiotics that are unnecessary for their growth but are used as a defense mechanism to dispel cohabiting microorganisms. In addition to other isoforms Streptomyces galilaeus ATCC 31615 (WT) produces aclacinomycin A (Acl A), whereas its mutant strain HO42 (MT) is an overproducer of Acl B. Acl A is an anthracycline clinically approved for cancer chemotherapy and used in Japan and China. A better understanding of the how the different isoforms of Acl are made and investigations into a possible Acl recycling system would allow us to use metabolic engineering for the generation of a strain that produces higher quantities of Acl A with a clean production profile.
In this study, RNA-Seq data from the WT, and MT strains on the 1st (D1), 2nd (D2), 3rd (D3), and 4th (D4) day of their growth was used and differentially expressed genes (DEGs) were identified. Differential gene expression (DGE) analyses were carried out using Bioconductor R-packages i.e., Bowtie2, HTSeq, and edgeR embedded in Chipster. DEGs were further analyzed for gene ontology (GO) enrichment and mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
The number of significantly (P < 0.05) DEGs from the first analysis were 891 (D1), 1573 (D2), 1638 (D3), and 1392 (D4). However, DGE analysis by comparing RNA-Seq data within the strain gives two sets of gene list (WT and MT). The number of DEGs from WT were 915 (D1-D2), 810 (D2-D3), and 363 (D3-D4) and from the MT, there were 844 (D1-D2), 145 (D2-D3) and 170 (D3-D4). GO enrichment analysis of the DEGs between the strains showed significant enrichment in polysaccharide catabolic process, carbohydrate transport, cellular process, organic substance metabolic and biosynthetic process, catalytic activity, hydrolase, and oxidoreductase activity. Additionally, these DEGs were enriched from membrane origin. KEGG pathway analysis of the DEGs from both data sets showed that mutant strain had a lower number of mapped DEGs in carbon and fatty acid metabolism, metabolism of different amino acids. There were variations in some primary metabolic cycles, such as the TCA cycle, oxidative phosphorylation, glycolysis. ABC transporter, two-component system, nucleotide metabolism was also varied between the strain.
In this study, RNA-Seq data from the WT, and MT strains on the 1st (D1), 2nd (D2), 3rd (D3), and 4th (D4) day of their growth was used and differentially expressed genes (DEGs) were identified. Differential gene expression (DGE) analyses were carried out using Bioconductor R-packages i.e., Bowtie2, HTSeq, and edgeR embedded in Chipster. DEGs were further analyzed for gene ontology (GO) enrichment and mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
The number of significantly (P < 0.05) DEGs from the first analysis were 891 (D1), 1573 (D2), 1638 (D3), and 1392 (D4). However, DGE analysis by comparing RNA-Seq data within the strain gives two sets of gene list (WT and MT). The number of DEGs from WT were 915 (D1-D2), 810 (D2-D3), and 363 (D3-D4) and from the MT, there were 844 (D1-D2), 145 (D2-D3) and 170 (D3-D4). GO enrichment analysis of the DEGs between the strains showed significant enrichment in polysaccharide catabolic process, carbohydrate transport, cellular process, organic substance metabolic and biosynthetic process, catalytic activity, hydrolase, and oxidoreductase activity. Additionally, these DEGs were enriched from membrane origin. KEGG pathway analysis of the DEGs from both data sets showed that mutant strain had a lower number of mapped DEGs in carbon and fatty acid metabolism, metabolism of different amino acids. There were variations in some primary metabolic cycles, such as the TCA cycle, oxidative phosphorylation, glycolysis. ABC transporter, two-component system, nucleotide metabolism was also varied between the strain.