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Identification of microRNA-Size, Small RNAs in Escherichia coli

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Abstract

Noncoding small regulatory RNA molecules control gene expression and microRNAs provide one of the best examples in eukaryotes. However, bacterial RNAs of comparable size to eukaryotic microRNAs have received little attention. Here, we demonstrate the existence of microRNA-size, small RNAs (msRNAs) in the model bacterium Escherichia coli. We examined the small RNAs in E. coli using a deep sequencing approach, and analyzed 33.2 million small RNA clone reads after size fractionation. Bioinformatic analysis of the whole set revealed more than 400 individual msRNA species. The cellular contents of selected highly expressed msRNAs were verified by quantitative RT-PCR and northern blotting. Although, the functional significance of these RNAs is unclear, their high abundance suggests that they may play specialized roles in bacteria, analogous to miRNAs in eukaryotes.

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Abbreviations

msRNA:

microRNA-size small RNA

E. coli :

Escherichia coli

miRNA:

microRNA

qRT-PCR:

Quantitative reverse transcription-PCR

siRNA:

Small interfering RNA

sRNA:

Small regulatory RNA

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Acknowledgments

The authors sincerely thank Dr. Scott Young at the National Institutes of Health (USA) and Geetha Kannan at the Johns Hopkins University for her critical reading of this manuscript. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2011-0028240 and 2011-0014086).

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Oral Microbiology, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Jung-gu, Daegu, 700-412, South Korea

    Sung-Min Kang, Ji-Woong Choi, Su-Hyung Hong & Heon-Jin Lee

  2. Department of Oral Biochemistry, School of Dentistry, Kyungpook National University, Daegu, South Korea

    Youngkyun Lee

  3. Brain Science and Engineering Institute, Kyungpook National University, Daegu, South Korea

    Heon-Jin Lee

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  1. Sung-Min Kang
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  2. Ji-Woong Choi
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  3. Youngkyun Lee
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  4. Su-Hyung Hong
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  5. Heon-Jin Lee
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Corresponding author

Correspondence to Heon-Jin Lee.

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Supporting information Table S1

Complete list of cloning profile data, including cloned sequence information (ID, representative clone sequence, location in the 5′- and 3′-strand duplex of each msRNA hairpin loop, clone count, extended sequence and hairpin formation)

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Kang, SM., Choi, JW., Lee, Y. et al. Identification of microRNA-Size, Small RNAs in Escherichia coli . Curr Microbiol 67, 609–613 (2013). https://doi.org/10.1007/s00284-013-0411-9

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  • DOI: https://doi.org/10.1007/s00284-013-0411-9

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