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Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth
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...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Taylor & Francis
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324740/ https://www.ncbi.nlm.nih.gov/pubmed/27981881 http://dx.doi.org/10.1080/15476286.2016.1270001 |
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author | Noro, Emiko Mori, Masaru Makino, Gakuto Takai, Yuki Ohnuma, Sumiko Sato, Asako Tomita, Masaru Nakahigashi, Kenji Kanai, Akio |
author_facet | Noro, Emiko Mori, Masaru Makino, Gakuto Takai, Yuki Ohnuma, Sumiko Sato, Asako Tomita, Masaru Nakahigashi, Kenji Kanai, Akio |
author_sort | Noro, Emiko |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5324740 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Taylor & Francis |
record_format | MEDLINE/PubMed |
spelling | pubmed-53247402017-03-02 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 RNA Biol Research Paper 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. Taylor & Francis 2016-12-16 /pmc/articles/PMC5324740/ /pubmed/27981881 http://dx.doi.org/10.1080/15476286.2016.1270001 Text en © 2017 The Author(s). Published with license by Taylor & Francis Group, LLC http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The moral rights of the named author(s) have been asserted. |
spellingShingle | Research Paper 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 |
title | Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth |
title_full | Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth |
title_fullStr | Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth |
title_full_unstemmed | Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth |
title_short | Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth |
title_sort | systematic characterization of artificial small rna-mediated inhibition of escherichia coli growth |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324740/ https://www.ncbi.nlm.nih.gov/pubmed/27981881 http://dx.doi.org/10.1080/15476286.2016.1270001 |
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