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Open Access Research

Identification of cyanobacterial non-coding RNAs by comparative genome analysis

Ilka M Axmann1, Philip Kensche12, Jörg Vogel3, Stefan Kohl1, Hanspeter Herzel2 and Wolfgang R Hess14*

Author Affiliations

1 Humboldt-University, Department of Biology/Genetics, Chausseestrasse, D-Berlin, Germany

2 Humboldt-University, Institute for Theoretical Biology, Invalidenstrasse, Berlin, Germany

3 Max Planck Institute for Infection Biology, Schumannstrasse, Berlin, Germany

4 University Freiburg, Institute of Biology II/Experimental Bioinformatics, Schänzlestrasse, Freiburg, Germany

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Genome Biology 2005, 6:R73  doi:10.1186/gb-2005-6-9-r73

Published: 17 August 2005

Abstract

Background

Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the lifestyle of an ecologically successful marine microorganism. Small non-coding RNAs (ncRNAs) control a plethora of processes in eukaryotes as well as in bacteria; however, systematic searches for ncRNAs are still lacking for most eubacterial phyla outside the enterobacteria.

Results

Based on a computational prediction we show the presence of several ncRNAs (cyanobacterial functional RNA or Yfr) in several different cyanobacteria of the Prochlorococcus-Synechococcus lineage. Some ncRNA genes are present only in two or three of the four strains investigated, whereas the RNAs Yfr2 through Yfr5 are structurally highly related and are encoded by a rapidly evolving gene family as their genes exist in different copy numbers and at different sites in the four investigated genomes. One ncRNA, Yfr7, is present in at least seven other cyanobacteria. In addition, control elements for several ribosomal operons were predicted as well as riboswitches for thiamine pyrophosphate and cobalamin.

Conclusion

This is the first genome-wide and systematic screen for ncRNAs in cyanobacteria. Several ncRNAs were both computationally predicted and their presence was biochemically verified. These RNAs may have regulatory functions and each shows a distinct phylogenetic distribution. Our approach can be applied to any group of microorganisms for which more than one total genome sequence is available for comparative analysis.