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Journal of Bacteriology, October 2004, p. 6689-6697, Vol. 186, No. 20
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.20.6689-6697.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

MicC, a Second Small-RNA Regulator of Omp Protein Expression in Escherichia coli

Shuo Chen,1,{dagger} Aixia Zhang,2,{dagger} Lawrence B. Blyn,1 and Gisela Storz2*

IBIS Therapeutics, ISIS Pharmaceuticals, Inc., Carlsbad, California,1 Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland2

Received 16 January 2004/ Accepted 9 June 2004

In a previous bioinformatics-based search for novel small-RNA genes encoded by the Escherichia coli genome, we identified a region, IS063, located between the ompN and ydbK genes, that encodes an ~100-nucleotide small-RNA transcript. Here we show that the expression of this small RNA is increased at a low temperature and in minimal medium. Twenty-two nucleotides at the 5' end of this transcript have the potential to form base pairs with the leader sequence of the mRNA encoding the outer membrane protein OmpC. The deletion of IS063 increased the expression of an ompC-luc translational fusion 1.5- to 2-fold, and a 10-fold overexpression of the small RNA led to a 2- to 3-fold repression of the fusion. Deletion and overexpression of the IS063 RNA also resulted in increases and decreases, respectively, in OmpC protein levels. Taken together, these results suggest that IS063 is a regulator of OmpC expression; thus, the small RNA has been renamed MicC. The antisense regulation was further demonstrated by the finding that micC mutations were suppressed by compensatory mutations in the ompC mRNA. MicC was also shown to inhibit ribosome binding to the ompC mRNA leader in vitro and to require the Hfq RNA chaperone for its function. We suggest that the MicF and MicC RNAs act in conjunction with the EnvZ-OmpR two-component system to control the OmpF/OmpC protein ratio in response to a variety of environmental stimuli.

* Corresponding author. Mailing address: NIH, Building 18T, Room 101, 18 Library Dr., MSC 5430, Bethesda, MD 20892-5430. Phone: (301) 402-0968. Fax: (301) 402-0078. E-mail: storz{at}helix.nih.gov.

{dagger} S.C. and A.Z. contributed equally to this study.

Journal of Bacteriology, October 2004, p. 6689-6697, Vol. 186, No. 20
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.20.6689-6697.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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