title: Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021.
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.
authors.affiliation: Institute of Biology III, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
authors.forename: Jan-Philip
authors.initials: JP
authors.lastname: Schlüter
authors.forename: Jan
authors.initials: J
authors.lastname: Reinkensmeier
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Barnett
authors.forename: Claus
authors.initials: C
authors.lastname: Lang
authors.forename: Elizaveta
authors.initials: E
authors.lastname: Krol
authors.forename: Robert
authors.initials: R
authors.lastname: Giegerich
authors.forename: Sharon R
authors.initials: SR
authors.lastname: Long
authors.forename: Anke
authors.initials: A
authors.lastname: Becker
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping; D005798:Genes, Bacterial; D011401:Promoter Regions, Genetic; D012313:RNA / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism; D016962:Sinorhizobium meliloti / Q000235:genetics* / Q000378:metabolism; D013559:Symbiosis; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D001426:Bacterial Proteins; D012808:Sigma Factor; D014157:Transcription Factors; D012313:RNA