MPI für Infektionsbiologie / RNA Biology |
|Identification of cyanobacterial non-coding RNAs by comparative genome analysis|
|Authors:||Axmann, Ilka M.; Kensche, Philip; Vogel, Jörg; Kohl, Stefan; Herzel, Hanspeter; Hess, Wolfgang R.|
|Date of Publication (YYYY-MM-DD):||2005|
|Title of Journal:||Genome Biology|
|Journal Abbrev.:||Genome Biol.|
|Issue / Number:||9|
|Sequence Number of Article:||R73|
|Copyright:||© 2005 Axmann et al.; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
|Abstract / Description:||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.
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.
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.
|Comment of the Author/Creator:||Supported by grants from the European Union (MARGENES, QLRT-2001-01226; Marine Genomics Europe, GOCE-CT-2004-505403) to W.R.H. and by an EMBO long-term fellowship to J.V.. We thank Carolin Adams for careful technical assistance, Alice Boit for discussion of RNA structural motifs and Martin Meixner of Molecular Biology Systems for sequencing a long chain of RACE fragments.|
|External Publication Status:||published|
|Version Comment:||Automatic journal name synchronization|
|Communicated by:||Hilmar Fünning|
|Affiliations:||MPI für Infektionsbiologie/RNA Biology|
|External Affiliations:||Humboldt Univ, Dept Biol Genet, Berlin, Germany.; Humboldt Univ, Inst Theoret Biol, Berlin, Germany.; Univ Freiburg, Inst Biol & Expt Bioinformat 2, Freiburg, Germany.|
|Identifiers:||ISI:000232301600007 [ID No:1] |
ISSN:1474-7596 [ID No:2]