title: Genome wide transcription start sites analysis of Xanthomonas campestris pv. campestris B100 with insights into the gum gene cluster directing the biosynthesis of the exopolysaccharide xanthan.
abstract: Xanthomonas campestris pv. campestris (Xcc) is the major producer of the exopolysaccharide xanthan, the commercially most important natural polysaccharide of microbial origin. The current work provides deeper insights into the yet uncharacterized transcriptomic features of the xanthan producing strain Xcc-B100. Towards this goal, RNA sequencing of a library based on the selective enrichment of the 5' ends of native transcripts was performed. This approach resulted in the genome wide identification of 3067 transcription start sites (TSSs) that were further classified based on their genomic positions. Among them, 1545 mapped upstream of an actively transcribed CDS and 1363 were classified as novel TSSs representing antisense, internal, and TSSs belonging to previously unidentified genomic features. Analyzing the transcriptional strength of primary and antisense TSSs revealed that in some instances antisense transcription seemed to be initiated at a higher level than its sense counterpart. Mapping the exact positions of TSSs aided in the identification of promoter consensus motifs, ribosomal binding sites, and enhanced the genome annotation of 159 in silico predicted translational start (TLS) sites. The global view on length distribution of the 5' untranslated regions (5'-UTRs) deduced from the data pointed to the occurrence of leaderless transcripts and transcripts with unusually long 5'-UTRs, in addition to identifying seven putative riboswitch elements for Xcc-B100. Concerning the biosynthesis of xanthan, we focused on the transcriptional organization of the gum gene cluster. Under the conditions tested, we present evidence for a complex transcription pattern of the gum genes with multiple TSSs and an obvious considerable role of antisense transcription. The gene gumB, encoding an outer membrane xanthan exporter, is presented here as an example for genes that possessed a strong antisense TSS.
authors.affiliation: Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Rabeaa S
authors.initials: RS
authors.lastname: Alkhateeb
authors.affiliation: Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany; Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Frank-Jörg
authors.initials: FJ
authors.lastname: Vorhölter
authors.affiliation: Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Rückert
authors.affiliation: Technologie Platform Genomics, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Almut
authors.initials: A
authors.lastname: Mentz
authors.affiliation: Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wibberg
authors.affiliation: Jungbunzlauer Austria AG, Pernhofen 1, 2064 Wulzeshofen, Austria.
authors.forename: Gerd
authors.initials: G
authors.lastname: Hublik
authors.affiliation: Abteilung für Proteom und Metabolomforschung, Fakultät für Biologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany. Electronic address: kniehaus@CeBiTec.Uni-Bielefeld.DE.
authors.forename: Karsten
authors.initials: K
authors.lastname: Niehaus
authors.affiliation: Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D005810:Multigene Family; D011135:Polysaccharides, Bacterial / Q000096:biosynthesis / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D024363:Transcription Initiation Site; D016959:Xanthomonas campestris / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D011135:Polysaccharides, Bacterial; D012329:RNA, Bacterial; C002563:xanthan gum
keywords: 5' enriched ends; RNA sequencing; Xanthomonads; plant pathogens; transcription start sites; xanthan biosynthesis.