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A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide

Nature Structural & Molecular Biology volume 19, pages 105–112 (2012)Cite this article

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Abstract

Antisense RNAs (asRNAs) pair to RNAs expressed from the complementary strand, and their functions are thought to depend on nucleotide overlap with genes on the opposite strand. There is little information on the roles and mechanisms of asRNAs. We show that a cis asRNA acts in trans, using a domain outside its target complementary sequence. SprA1 small regulatory RNA (sRNA) and SprA1AS asRNA are concomitantly expressed in S. aureus. SprA1AS forms a complex with SprA1, preventing translation of the SprA1-encoded open reading frame by occluding translation initiation signals through pairing interactions. The SprA1 peptide sequence is within two RNA pseudoknots. SprA1AS represses production of the SprA1-encoded cytolytic peptide in trans, as its overlapping region is dispensable for regulation. These findings demonstrate that sometimes asRNA functional domains are not their gene-target complementary sequences, suggesting there is a need for mechanistic re-evaluation of asRNAs expressed in prokaryotes and eukaryotes.

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Figure 1: Genomic location, lengths, boundaries and expression of sprA1 and sprA1AS.
Figure 2: Detection of the interaction between SprA1 and SprA1AS in vivo and assessment of their binding constants.
Figure 3: Experimental and phylogenetic evidence for the pairings between SprA1AS and SprA1.
Figure 4: SprA1 and SprA1AS interact by their 5′ non-overlapping domains.
Figure 5: SprA1 recruits the S. aureus ribosomes and is translated in vitro, and SprA1AS hinders SprA1 translation by its 5′ non-overlapping domain.
Figure 6: SprA1AS cis-RNA acts in trans to downregulate SprA1-encoded peptide expression in vivo.
Figure 7: The SprA1-encoded peptide is lytic for human cells.

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Acknowledgements

We are thankful to S. Chabelskaya and M. Hallier for critical reading of the manuscript and comments. This study was supported by grant ANR-09-MIEN-030-01 from the Agence Nationale pour la Recherche to B.F. and funds from the Institut National de la Santé et de la Recherche Médicale, Brittany region (grant to N.S.) and from the French Department of Research and Education.

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  1. Laboratoire de Biochimie Pharmaceutique Inserm U835 Upres EA2311 Université de Rennes, Rennes, France

    Nour Sayed, Ambre Jousselin & Brice Felden

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  1. Nour Sayed
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  3. Brice Felden
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Contributions

N.S. and B.F. designed experiments, prepared samples, analyzed the data and wrote the manuscript. A.J. constructed the sRNA double mutant, did the Hfq experiment and participated in discussions and writing of the manuscript.

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Correspondence to Brice Felden.

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The authors declare no competing financial interests.

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Sayed, N., Jousselin, A. & Felden, B. A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide. Nat Struct Mol Biol 19, 105–112 (2012). https://doi.org/10.1038/nsmb.2193

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