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@ARTICLE{Kranz:841893,
      author       = {Kranz, Angela and Busche, Tobias and Vogel, Alexander and
                      Usadel, Björn and Kalinowski, Jörn and Bott, Michael and
                      Polen, Tino},
      title        = {{RNA}seq analysis of α-proteobacterium {G}luconobacter
                      oxydans 621{H}},
      journal      = {BMC genomics},
      volume       = {19},
      number       = {1},
      issn         = {1471-2164},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {FZJ-2018-00190},
      pages        = {24},
      year         = {2018},
      note         = {Biotechnologie1},
      abstract     = {Background The acetic acid bacterium Gluconobacter oxydans
                      621H is characterized by its exceptional ability to
                      incompletely oxidize a great variety of carbohydrates in the
                      periplasm. The metabolism of this α-proteobacterium has
                      been characterized to some extent, yet little is known about
                      its transcriptomes and related data. In this study, we
                      applied two different RNAseq approaches. Primary
                      transcriptomes enriched for 5′-ends of transcripts were
                      sequenced to detect transcription start sites, which allow
                      subsequent analysis of promoter motifs, ribosome binding
                      sites, and 5´-UTRs. Whole transcriptomes were sequenced to
                      identify expressed genes and operon
                      structures.ResultsSequencing of primary transcriptomes of G.
                      oxydans revealed 2449 TSSs, which were classified according
                      to their genomic context followed by identification of
                      promoter and ribosome binding site motifs, analysis of
                      5´-UTRs including validation of predicted cis-regulatory
                      elements and correction of start codons. 1144 $(41\%)$ of
                      all genes were found to be expressed monocistronically,
                      whereas 1634 genes were organized in 571 operons. Together,
                      TSSs and whole transcriptome data were also used to identify
                      novel intergenic (18), intragenic (328), and antisense
                      transcripts (313).ConclusionsThis study provides deep
                      insights into the transcriptional landscapes of G. oxydans.
                      The comprehensive transcriptome data, which we made publicly
                      available, facilitate further analysis of promoters and
                      other regulatory elements. This will support future
                      approaches for rational strain development and targeted gene
                      expression in G. oxydans. The corrections of start codons
                      further improve the high quality genome reference and
                      support future proteome analysis.},
      cin          = {IBG-1 / IBG-2},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBG-1-20101118 / I:(DE-Juel1)IBG-2-20101118},
      pnm          = {581 - Biotechnology (POF3-581)},
      pid          = {G:(DE-HGF)POF3-581},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:29304737},
      UT           = {WOS:000419677900001},
      doi          = {10.1186/s12864-017-4415-x},
      url          = {https://juser.fz-juelich.de/record/841893},
}