Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth

Emiko Noro, Masaru Mori, Gakuto Makino, Yuki Takai, Sumiko Ohnuma, Asako Sato, Masaru Tomita, Kenji Nakahigashi, Akio Kanai

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

A new screening system for artificial small RNAs (sRNAs) that inhibit the growth of Escherichia coli was constructed. In this system, we used a plasmid library to express RNAs of ∼120 nucleotides, each with a random 30-nucleotide sequence that can recognize its target mRNA(s). After approximately 60,000 independent colonies were screened, several plasmids that inhibited bacterial growth were isolated. To understand the inhibitory mechanism, we focused on one sRNA, S-20, that exerted a strong inhibitory effect. A time-course analysis of the proteome of S-20-expressing E. coli and a bioinformatic analysis were used to identify potential S-20 target mRNAs, and suggested that S-20 binds the translation initiation sites of several mRNAs encoding enzymes such as peroxiredoxin (osmC), glycyl-tRNA synthetase α subunit (glyQ), uncharacterized protein ygiM, and tryptophan synthase β chain (trpB). An in vitro translation analysis of chimeric luciferase-encoding mRNAs, each containing a potential S-20 target sequence, indicated that the translation of these mRNAs was inhibited in the presence of S-20. A gel shift analysis combined with the analysis of a series of S-20 mutants suggested that S-20 targets multiple mRNAs that are responsible for inhibiting E. coli growth. These data also suggest that S-20 acts like an endogenous sRNA and that E. coli can utilize artificial sRNAs.

Original languageEnglish
Pages (from-to)206-218
Number of pages13
JournalRNA Biology
Volume14
Issue number2
DOIs
Publication statusPublished - 2017 Feb 1

Fingerprint

RNA
Escherichia coli
Messenger RNA
Growth
Glycine-tRNA Ligase
Plasmids
Tryptophan Synthase
Peroxiredoxins
Protein Biosynthesis
Electrophoretic Mobility Shift Assay
Proteome
Computational Biology
Luciferases
Nucleotides
Enzymes
Proteins

Keywords

  • Artificial small RNA
  • Escherichia coli
  • growth inhibition
  • proteomic analysis
  • reporter assay
  • RNA-RNA interaction
  • target mRNA

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. / Noro, Emiko; Mori, Masaru; Makino, Gakuto; Takai, Yuki; Ohnuma, Sumiko; Sato, Asako; Tomita, Masaru; Nakahigashi, Kenji; Kanai, Akio.

In: RNA Biology, Vol. 14, No. 2, 01.02.2017, p. 206-218.

Research output: Contribution to journalArticle

Noro, Emiko ; Mori, Masaru ; Makino, Gakuto ; Takai, Yuki ; Ohnuma, Sumiko ; Sato, Asako ; Tomita, Masaru ; Nakahigashi, Kenji ; Kanai, Akio. / Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. In: RNA Biology. 2017 ; Vol. 14, No. 2. pp. 206-218.
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