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Series GSE97637 Query DataSets for GSE97637
Status Public on Oct 16, 2019
Title Ribosome pausing at the AT-rich codons regulates the protein expression of secondary metabolite gene clusters in the Streptomyces tsukubaensis NRRL 18488
Organism Streptomyces tsukubensis
Experiment type Expression profiling by high throughput sequencing
Summary Streptomyces tsukubaensis NRRL 18488 is the preferred strain for the production of immunosuppressant agent tacrolimus (FK506). To take full advantage of its genetic potential, systematic understanding of secondary metabolism and related regulatory mechanisms is highly demanded. Here, to this end, we complete its 7.9 Mbp linear genome sequence followed by integrating with multi-omics measurements. With accurate reannotation of FK506 gene cluster, total 2,389 transcription start sites were determined by using primary transcriptome analysis. Integrated analysis of transcriptome and translatome data revealed that secondary metabolic gene clusters, especially FK506 cluster, undergo translational control with decrease in translational efficiency according to the growth. Furthermore, we demonstrated that SD motif has little correlation with ribosome pausing but AT-rich codons delay the translational elongation. Strong ribosome pausing was observed in the rare TTA codon in FK506 cluster. This comprehensive genome-scale analysis provides insight to the translational regulation of secondary metabolism in S. tsukubaensis.
Overall design Transcription abundance and ribosomal profiling analysis of Streptomyces tsukubaensis according to the growth phase
Contributor(s) Lee N, Jeong Y, Chung J, Lee YJ, Cho S, Palsson B, Cho B
Citation(s) 32385251
Submission date Apr 11, 2017
Last update date May 18, 2020
Contact name Namil Lee
Phone 821098633995
Organization name KAIST
Department Biological science
Lab Systems and Synthetic Biology Lab
Street address Daehakro
City Daejeon
ZIP/Postal code 34141
Country South Korea
Platforms (2)
GPL23281 Illumina HiSeq 2000 (Streptomyces tsukubensis)
GPL23282 Illumina MiSeq (Streptomyces tsukubensis)
Samples (18)
GSM2574047 RNA_E1
GSM2574048 RNA_E2
GSM2574049 RNA_T1
BioProject PRJNA382534
SRA SRP103795

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE97637_RAW.tar 480.0 Kb (http)(custom) TAR (of TXT)
GSE97637_Stsu_CDS_seq_2.txt.gz 1.9 Mb (ftp)(http) TXT
GSE97637_tsukubaensis_TSS.gff.gz 35.7 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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