Journal Article

Seed-based I<span class="smallCaps">nta</span>RNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

Andreas S. Richter, Christian Schleberger, Rolf Backofen and Claudia Steglich

in Bioinformatics

Volume 26, issue 1, pages 1-5
Published in print January 2010 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp609

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Motivation: Prochlorococcus possesses the smallest genome of all sequenced photoautotrophs. Although the number of regulatory proteins in the genome is very small, the relative number of small regulatory RNAs is comparable with that of other bacteria. The compact genome size of Prochlorococcus offers an ideal system to search for targets of small RNAs (sRNAs) and to refine existing target prediction algorithms.

Results: Target predictions for the cyanobacterial sRNA Yfr1 were carried out with INTARNA in Prochlorococcus MED4. The ultraconserved Yfr1 sequence motif was defined as the putative interaction seed. To study the impact of Yfr1 on its predicted mRNA targets, a reporter system based on green fluorescent protein (GFP) was applied. We show that Yfr1 inhibits the translation of two predicted targets. We used mutation analysis to confirm that Yfr1 directly regulates its targets by an antisense interaction sequestering the ribosome binding site, and to assess the importance of interaction site accessibility.

Contact: backofen@informatik.uni-freiburg.de; claudia.steglich@biologie.uni-freiburg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  3372 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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