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Open Access Highly Accessed Research article

A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti

Jan-Philip Schlüter1, Jan Reinkensmeier2, Svenja Daschkey3, Elena Evguenieva-Hackenberg4, Stefan Janssen2, Sebastian Jänicke3, Jörg D Becker5, Robert Giegerich2 and Anke Becker1*

Author Affiliations

1 Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany

2 Faculty of Technology, Bielefeld University, Bielefeld, Germany

3 Center for Biotechnology, Bielefeld University, Bielefeld, Germany

4 Institut für Mikrobiologie und Molekularbiologie, Gießen, Germany

5 Affymetrix Core Facility, Instituto Gulbenkian de Ciencia, Oeiras, Portugal

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BMC Genomics 2010, 11:245  doi:10.1186/1471-2164-11-245

Published: 17 April 2010

Abstract

Background

Small untranslated RNAs (sRNAs) are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti applying deep sequencing of cDNAs and microarray hybridizations.

Results

A total of 1,125 sRNA candidates that were classified as trans-encoded sRNAs (173), cis-encoded antisense sRNAs (117), mRNA leader transcripts (379), and sense sRNAs overlapping coding regions (456) were identified in a size range of 50 to 348 nucleotides. Among these were transcripts corresponding to 82 previously reported sRNA candidates. Enrichment for RNAs with primary 5'-ends prior to sequencing of cDNAs suggested transcriptional start sites corresponding to 466 predicted sRNA regions. The consensus σ70 promoter motif CTTGAC-N17-CTATAT was found upstream of 101 sRNA candidates. Expression patterns derived from microarray hybridizations provided further information on conditions of expression of a number of sRNA candidates. Furthermore, GenBank, EMBL, DDBJ, PDB, and Rfam databases were searched for homologs of the sRNA candidates identified in this study. Searching Rfam family models with over 1,000 sRNA candidates, re-discovered only those sequences from S. meliloti already known and stored in Rfam, whereas BLAST searches suggested a number of homologs in related alpha-proteobacteria.

Conclusions

The screening data suggests that in S. meliloti about 3% of the genes encode trans-encoded sRNAs and about 2% antisense transcripts. Thus, this first comprehensive screen for sRNAs applying deep sequencing in an alpha-proteobacterium shows that sRNAs also occur in high number in this group of bacteria.