A genome-wide activity assessment of terminator regions in saccharomyces cerevisiae provides a "terminatome" toolbox

Mamoru Yamanishi, Yoichiro Ito, Reiko Kintaka, Chie Imamura, Satoshi Katahira, Akinori Ikeuchi, Hisao Moriya, Takashi Matsuyama

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

The terminator regions of eukaryotes encode functional elements in the 3′ untranslated region (3′-UTR) that influence the 3′-end processing of mRNA, mRNA stability, and translational efficiency, which can modulate protein production. However, the contribution of these terminator regions to gene expression remains unclear, and therefore their utilization in metabolic engineering or synthetic genetic circuits has been limited. Here, we comprehensively evaluated the activity of 5302 terminator regions from a total of 5880 genes in the budding yeast Saccharomyces cerevisiae by inserting each terminator region downstream of the PTDH3- green fluorescent protein (GFP) reporter gene and measuring the fluorescent intensity of GFP. Terminator region activities relative to that of the PGK1 standard terminator ranged from 0.036 to 2.52, with a mean of 0.87. We thus could isolate the most and least active terminator regions. The activities of the terminator regions showed a positive correlation with mRNA abundance, indicating that the terminator region is a determinant of mRNA abundance. The least active terminator regions tended to encode longer 3′-UTRs, suggesting the existence of active degradation mechanisms for those mRNAs. The terminator regions of ribosomal protein genes tended to be the most active, suggesting the existence of a common regulator of those genes. The ″terminatome″ (the genome-wide set of terminator regions) thus not only provides valuable information to understand the modulatory roles of terminator regions on gene expression but also serves as a useful toolbox for the development of metabolically and genetically engineered yeast.

Original languageEnglish
Pages (from-to)337-347
Number of pages11
JournalACS Synthetic Biology
Volume2
Issue number6
DOIs
Publication statusPublished - Jun 21 2013

Keywords

  • 3′-UTR
  • Saccharomyces cerevisiae
  • metabolic engineering
  • post-transcriptional regulation
  • terminatome
  • terminator

ASJC Scopus subject areas

  • Biomedical Engineering
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

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