Shewanella oneidensis cis-Regulatory RNA Structural Element Database

• Introduction

  The Database of cis-regulatory RNA structural elements in Shewanella oneidensis is generated by comparative analysis of several Shewanella genomes in the recent publication of Xu, Ji and Stormo, 2009 in PLOS Computational Biology .

  We applied RSSVM, the newly developed SVM based algorithm for RNA motif identification, to multiple Shewanella genomes and identified putative regulatory RNA motifs in the 5’-UTRs in S. oneidensis, an important bacterial organism with extraordinary respiratory and metal reducing abilities and great potentials for bioremediation. From 1002 sets of 5’-UTRs of orthologous operons, we identified 166 putative regulatory RNA motifs, including 17 of the 19 known RNA motifs from Rfam, additional 21 RNA motifs that are supported by literature evidence, 72 RNA motifs overlapping predicted transcription terminators or attenuators, and other candidate regulatory RNA motifs. Our study provides a list of promising novel regulatory RNA motifs potentially involved in post-transcriptional gene regulation. Combining with the previous cis-regulatory DNA motif study in S. oneidensis, this genome-wide discovery of cis-regulatory RNA motifs may offer more comprehensive views of gene regulation at a different level in this organism.

   

  To better serve the Shewanella research community, we not only provide the "Browse" page to serve as the supplementary materials for our publication, but also provide "Search" functions that allow users to retrieve useful information by gene, respectively.

   

• Citation

  If information in the supplementary material is used in work that is published, please cite:
   

  Xing Xu, Yongmei Ji, and Gary D. Stormo
  Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines

  PPLoS Comput Biol. 2009 Apr;5(4):e1000338. Epub 2009 Apr 3

    

• Collaboration

We are very excited about the fact that a large number of our predictions are supported by independent evidence and provide promising candidates for experimental validation.  If you think some of motifs are interesting and want to explore them further, collaborations are always very welcome.  Please contact us.

? 2008 Xing Xu, Yongmei Ji and Gary Stormo, Washington University School of Medicine.