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Open Access Research article

Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021

Jan-Philip Schlüter12, Jan Reinkensmeier3, Melanie J Barnett4, Claus Lang4, Elizaveta Krol2, Robert Giegerich3, Sharon R Long4 and Anke Becker2*

Author Affiliations

1 Institute of Biology III, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany

2 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg, Germany

3 Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

4 Department of Biology, Stanford University, Stanford, CA, 94305, USA

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BMC Genomics 2013, 14:156  doi:10.1186/1471-2164-14-156

Published: 7 March 2013

Abstract

Background

Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important model organism, global characterization of genetic regulatory circuits has been hampered by a lack of information about transcription and promoters.

Results

Using an RNAseq approach and RNA populations representing 16 different growth and stress conditions, we comprehensively mapped S. meliloti transcription start sites (TSS). Our work identified 17,001 TSS that we grouped into six categories based on the genomic context of their transcripts: mRNA (4,430 TSS assigned to 2,657 protein-coding genes), leaderless mRNAs (171), putative mRNAs (425), internal sense transcripts (7,650), antisense RNA (3,720), and trans-encoded sRNAs (605). We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti σ factors σ70, σ54, σH1, σH2, σE1, σE2, and σE9). Altogether, we predicted 2,770 new promoter sequences, including 1,302 located upstream of protein coding genes and 722 located upstream of antisense RNA or trans-encoded sRNA genes. To validate promoter predictions for targets of the general stress response σ factor, RpoE2 (σE2), we identified rpoE2-dependent genes using microarrays and confirmed TSS for a subset of these by 5 RACE mapping.

Conclusions

By identifying TSS and promoters on a global scale, our work provides a firm foundation for the continued study of S. meliloti gene expression with relation to gene organization, σ factors and other transcription factors, and regulatory RNAs.

Keywords:
Transcription; RNAseq; Transcription start site; Promoter; Sigma factor; Sinorhizobium meliloti; mRNA; sRNA; Antisense RNA