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

BMC Genomics

Research Article

Jörg D Becker¹  Sebastian Jänicke²  Svenja Daschkey²  Stefan Janssen³  Jan Reinkensmeier³  Robert Giegerich³  Elena Evguenieva-Hackenberg⁴  Anke Becker⁵  Jan-Philip Schlüter⁵ 

[1] Affymetrix Core Facility, Instituto Gulbenkian de Ciencia, Oeiras, Portugal;Center for Biotechnology, Bielefeld University, Bielefeld, Germany;Faculty of Technology, Bielefeld University, Bielefeld, Germany;Institut für Mikrobiologie und Molekularbiologie, Gießen, Germany;Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany;

关键词: Deep Sequencing;    Antisense Transcript;    Ribosome Binding Site;    GATC Biotech;    sRNA Candidate;   

DOI  :  10.1186/1471-2164-11-245

 received in 2010-01-06, accepted in 2010-04-17,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundSmall 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.ResultsA 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Schlüter et al; licensee BioMed Central Ltd. 2010. This article is published under license to 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.