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Series GSE118597 Query DataSets for GSE118597
Status Public on Mar 03, 2020
Title Transcriptome and translatome of Streptomyces avermitilis MA-4680
Organism Streptomyces avermitilis
Experiment type Expression profiling by high throughput sequencing
Summary The gram-positive bacterium, Streptomyces avermitilis holds industrial importance, which produces widely used anthelmintic agent, avermectin. Furthermore, S. avermitilis is generally considered as a prominent heterologous gene expression host for diverse secondary metabolites biosynthesis. However, despite of its industrial importance, it largely remains unknown how its genome is organized and regulated for timely gene expression. Here, we determined 1,601 transcription units (TU) encoded in its genome using the integrated analysis of high-throughput sequencing data including dRNA-Seq, Term-Seq, RNA-Seq, and Ribo-Seq. In addition to TU cataloguing, these information-rich results also revealed the presence of diverse regulatory elements for the transcriptional and translational control of individual TU, such as promoters, 5¢-UTRs, terminators, 3¢-UTRs, and riboswitches. The conserved promoter sequences for transcription initiation were identified from 2,361 transcription start sites as 5¢-TANNNT and 5¢-TGAC for -10 and -35 elements, respectively. Interestingly, the -35 element and spacer length between them were critical for transcriptional regulation of functionally distinct genes. Total 2,017 transcription termination sites were detected from Term-Seq analysis, revealing that stem structure formation is a prerequisite for transcription termination and that Rho-independent termination prevails in S. avermitilis. Lastly, the TU architecture suggests the presence of novel small RNAs and cis-regulatory elements in the genome. Our findings will serve as invaluable resources for comprehensive understanding on regulatory features of S. avermitilis. Moreover, it is anticipated the elevation of its potential as the heterologous expression host for diverse secondary metabolite biosynthesis.
Overall design Profiles of 5' termini of primary transcripts, 3' termini of whole transcripts, whole transcripts and ribosome protected RNA fragements of Streptomyces avermitilis were generated by deep sequencing using Illumina Hi-Seq 2500
Contributor(s) Lee Y, Jeong Y, Lee N, Hwang S, Kim W, Cho S, Palsson BO, Cho B
Citation(s) 32385251, 35062881
Submission date Aug 15, 2018
Last update date Jan 31, 2022
Contact name Yongjae Lee
Organization name KAIST
Street address 291 Daehak-ro
City Daejeon
ZIP/Postal code ASI|KR|KS015|DAEJEON
Country South Korea
Platforms (1)
GPL25453 Illumina HiSeq 2500 (Streptomyces avermitilis)
Samples (22)
GSM3334088 TSS_TAP_treated1
GSM3334089 TSS_TAP_treated2
GSM3334090 TSS_TAP_untreated1
BioProject PRJNA486172
SRA SRP158023

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE118597_RNA_DESeq2.txt.gz 424.1 Kb (ftp)(http) TXT
GSE118597_Ribo_DESeq2.txt.gz 421.3 Kb (ftp)(http) TXT
GSE118597_TSS.txt.gz 23.9 Kb (ftp)(http) TXT
GSE118597_Term.txt.gz 25.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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