The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis

• Published in: Journal of biotechnology 2008-03, Vol.134 (1), p.33-45
• Main Authors: Vorhölter, Frank-Jörg, Schneiker, Susanne, Goesmann, Alexander, Krause, Lutz, Bekel, Thomas, Kaiser, Olaf, Linke, Burkhard, Patschkowski, Thomas, Rückert, Christian, Schmid, Joachim, Sidhu, Vishaldeep Kaur, Sieber, Volker, Tauch, Andreas, Watt, Steven Alexander, Weisshaar, Bernd, Becker, Anke, Niehaus, Karsten, Pühler, Alfred
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Biotechnology; Carbohydrate metabolism; Carbohydrate uptake; Comparative genomics; Fundamental and applied biological sciences. Psychology; Genome, Bacterial; Models, Biological; Molecular Sequence Data; Nucleotide sugars synthesis genes; Polysaccharides, Bacterial - biosynthesis; Sequence Analysis, DNA; X. campestris pv. campestris genome sequence; Xanthan biosynthesis; Xanthomonas; Xanthomonas campestris; Xanthomonas campestris - genetics; Xanthomonas campestris - metabolism
• ISSN: 0168-1656; 1873-4863
• DOI: 10.1016/j.jbiotec.2007.12.013

The complete genome sequence of the Xanthomonas campestris pv. campestris strain B100 was established. It consisted of a chromosome of 5,079,003 bp, 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.