System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus

Soonkyu Hwang, Namil Lee, Donghui Choe, Yongjae Lee, Woori Kim, Ji Hun Kim, Gahyeon Kim, Hyeseong Kim, Neung Ho Ahn, Byoung Hee Lee, Bernhard O. Palsson, Byung-Kwan Cho*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements governing gene expression related to primary and secondary metabolism in Streptomyces, system-level information remains limited. In this study, we integrated four multi-omics datasets from Streptomyces griseus NBRC 13350: RNA-seq, ribosome profiling, dRNA-seq, and Term-Seq, to analyze the regulatory elements of transcription and translation of differentially expressed genes during cell growth. With the functional enrichment of gene expression in different growth phases, one sigma factor regulon and four transcription factor regulons governing differential gene transcription patterns were found. In addition, the regulatory elements of transcription termination and post-transcriptional processing at transcript 3′-end positions were elucidated, including their conserved motifs, stem-loop RNA structures, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5′-UTR length, RNA structures at ribosome-bound sites, and codon usage were investigated. This comprehensive genetic information provides a foundational genetic resource for strain engineering to enhance secondary metabolite production in Streptomyces.

Original languageEnglish
Article number844200
JournalFrontiers in Bioengineering and Biotechnology
Volume10
Number of pages18
ISSN2296-4185
DOIs
Publication statusPublished - 2022

Keywords

  • Differential gene expression
  • Regulatory elements
  • Sigma factor
  • Streptomyces
  • Transcript 3′-end positions
  • Transcription factor

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