title: The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
abstract: The complete genome sequence of the Xanthomonas campestris pv. campestris strain B100 was established. It consisted of a chromosome of 5,079,003bp, with 4471 protein-coding genes and 62 RNA genes. Comparative genomics showed that the genes required for the synthesis of xanthan and xanthan precursors were highly conserved among three sequenced X. campestris pv. campestris genomes, but differed noticeably when compared to the remaining four Xanthomonas genomes available. For the xanthan biosynthesis genes gumB and gumK earlier translational starts were proposed, while gumI and gumL turned out to be unique with no homologues beyond the Xanthomonas genomes sequenced. From the genomic data the biosynthesis pathways for the production of the exopolysaccharide xanthan could be elucidated. The first step of this process is the uptake of sugars serving as carbon and energy sources wherefore genes for 15 carbohydrate import systems could be identified. Metabolic pathways playing a role for xanthan biosynthesis could be deduced from the annotated genome. These reconstructed pathways concerned the storage and metabolization of the imported sugars. The recognized sugar utilization pathways included the Entner-Doudoroff and the pentose phosphate pathway as well as the Embden-Meyerhof pathway (glycolysis). The reconstruction indicated that the nucleotide sugar precursors for xanthan can be converted from intermediates of the pentose phosphate pathway, some of which are also intermediates of glycolysis or the Entner-Doudoroff pathway. Xanthan biosynthesis requires in particular the nucleotide sugars UDP-glucose, UDP-glucuronate, and GDP-mannose, from which xanthan repeat units are built under the control of the gum genes. The updated genome annotation data allowed reconsidering and refining the mechanistic model for xanthan biosynthesis.
authors.affiliation: Universität Bielefeld, Biologie VI (Genetik), Universitätsstr. 25, D-33615 Bielefeld, Germany.
authors.forename: Frank-Jörg
authors.initials: FJ
authors.lastname: Vorhölter
authors.forename: Susanne
authors.initials: S
authors.lastname: Schneiker
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Lutz
authors.initials: L
authors.lastname: Krause
authors.forename: Thomas
authors.initials: T
authors.lastname: Bekel
authors.forename: Olaf
authors.initials: O
authors.lastname: Kaiser
authors.forename: Burkhard
authors.initials: B
authors.lastname: Linke
authors.forename: Thomas
authors.initials: T
authors.lastname: Patschkowski
authors.forename: Christian
authors.initials: C
authors.lastname: Rückert
authors.forename: Joachim
authors.initials: J
authors.lastname: Schmid
authors.forename: Vishaldeep Kaur
authors.initials: VK
authors.lastname: Sidhu
authors.forename: Volker
authors.initials: V
authors.lastname: Sieber
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
authors.forename: Steven Alexander
authors.initials: SA
authors.lastname: Watt
authors.forename: Bernd
authors.initials: B
authors.lastname: Weisshaar
authors.forename: Anke
authors.initials: A
authors.lastname: Becker
authors.forename: Karsten
authors.initials: K
authors.lastname: Niehaus
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
mesh_terms: D016680:Genome, Bacterial; D008954:Models, Biological; D008969:Molecular Sequence Data; D011135:Polysaccharides, Bacterial / Q000096:biosynthesis*; D017422:Sequence Analysis, DNA; D016959:Xanthomonas campestris / Q000235:genetics* / Q000378:metabolism*
chemical_list: D011135:Polysaccharides, Bacterial; C002563:xanthan gum