Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti1021

BMC Genomics

Research Article

Jan Reinkensmeier¹  Robert Giegerich¹  Claus Lang²  Sharon R Long²  Melanie J Barnett²  Jan-Philip Schlüter³  Elizaveta Krol⁴  Anke Becker⁴ 

[1] Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany;Department of Biology, Stanford University, 94305, Stanford, CA, USA;Institute of Biology III, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany;LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg, Germany;LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg, Germany;

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

DOI  :  10.1186/1471-2164-14-156

 received in 2012-11-15, accepted in 2013-02-12,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundSinorhizobium 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.ResultsUsing 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.ConclusionsBy 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.

【 授权许可】

Unknown   
© Schlüter et al; licensee BioMed Central Ltd. 2013. 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.