Engineering artificial small RNAs for Conditional gene silencing in escherichia coli

Vandana Sharma, Asami Yamamura, Yohei Yokobayashi

Research output: Contribution to journalArticlepeer-review

66 Scopus citations


It has become increasingly evident that noncoding small RNAs (sRNAs) play a significant and global role in bacterial gene regulation. A majority of the trans-acting sRNAs in bacteria interact with the 50 untranslated region (UTR) and/ or the translation initiation region of the targeted mRNAs via imperfect base pairing, resulting in reduced translation efficiency and/or mRNA stability. Additionally, bacterial sRNAs often contain distinct scaffolds that recruit RNA chaperones such as Hfq to facilitate gene regulation. In this study, we describe a strategy to engineer artificial sRNAs that can regulate desired endogenous genes in Escherichia coli. Using a fluorescent reporter gene that was translationally fused to a native 50 mRNA leader sequence, active artificial sRNAs were screened from libraries in which natural sRNA scaffolds were fused to a randomized antisense domain. Artificial sRNAs that posttranscriptionally repress two endogenous genes ompF and fliC were isolated and characterized. We anticipate that the artificial sRNAs will be useful for dynamic control and fine-tuning of endogenous gene expression in bacteria for applications in synthetic biology.

Original languageEnglish (US)
Pages (from-to)6-13
Number of pages8
JournalACS Synthetic Biology
Issue number1
StatePublished - Jan 20 2012


  • Gene knockdown
  • Gene regulation
  • Noncoding RNA
  • RNA engineering
  • Small RNA
  • Translational regulation

ASJC Scopus subject areas

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


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