Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling

Schatschneider S, Vorhölter F-J, Rückert C, Becker A, Eisenreich W, Pühler A, Niehaus K (2011)
Molecular Genetics and Genomics 286(3-4): 247-259.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Abstract
To elucidate the biosynthetic pathways for all proteinogenic amino acids in Xanthomonas campestris pv. campestris, this study combines results obtained by in silico genome analysis and by 13C-NMR-based isotopologue profiling to provide a panoramic view on a substantial section of bacterial metabolism. Initially, biosynthesis pathways were reconstructed from an improved annotation of the complete genome of X. campestris pv. campestris B100. This metabolic reconstruction resulted in the unequivocal identification of biosynthesis routes for 17 amino acids in total: arginine, asparagine, aspartate, cysteine, glutamate, glutamine, histidine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine. Ambiguous pathways were reconstructed from the genome data for alanine, glycine, and isoleucine biosynthesis. 13C-NMR analyses supported the identification of the metabolically active pathways. The biosynthetic routes for these amino acids were derived from the precursor molecules pyruvate, serine, and pyruvate, respectively. By combining genome analysis and isotopologue profiling, a comprehensive set of biosynthetic pathways covering all proteinogenic amino acids was unraveled for this plant pathogenic bacterium, which plays an important role in biotechnology as a producer of the exopolysaccharide xanthan. The data obtained lay ground for subsequent functional analyses in post-genomics and biotechnology, while the innovative combination of in silico and wet lab technology described here is promising as a general approach to elucidate metabolic pathways.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Schatschneider S, Vorhölter F-J, Rückert C, et al. Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling. Molecular Genetics and Genomics. 2011;286(3-4):247-259.
Schatschneider, S., Vorhölter, F. - J., Rückert, C., Becker, A., Eisenreich, W., Pühler, A., & Niehaus, K. (2011). Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling. Molecular Genetics and Genomics, 286(3-4), 247-259. doi:10.1007/s00438-011-0639-7
Schatschneider, S., Vorhölter, F. - J., Rückert, C., Becker, A., Eisenreich, W., Pühler, A., and Niehaus, K. (2011). Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling. Molecular Genetics and Genomics 286, 247-259.
Schatschneider, S., et al., 2011. Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling. Molecular Genetics and Genomics, 286(3-4), p 247-259.
S. Schatschneider, et al., “Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling”, Molecular Genetics and Genomics, vol. 286, 2011, pp. 247-259.
Schatschneider, S., Vorhölter, F.-J., Rückert, C., Becker, A., Eisenreich, W., Pühler, A., Niehaus, K.: Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling. Molecular Genetics and Genomics. 286, 247-259 (2011).
Schatschneider, Sarah, Vorhölter, Frank-Jörg, Rückert, Christian, Becker, Anke, Eisenreich, Wolfgang, Pühler, Alfred, and Niehaus, Karsten. “Genome-enabled determination of amino acid biosynthesis in Xanthomonas campestris pv. campestris and identification of biosynthetic pathways for alanine, glycine, and isoleucine by 13C-isotopologue profiling”. Molecular Genetics and Genomics 286.3-4 (2011): 247-259.
This data publication is cited in the following publications:
This publication cites the following data publications:

10 Citations in Europe PMC

Data provided by Europe PubMed Central.

Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data.
Alkhateeb RS, Rückert C, Rupp O, Pucker B, Hublik G, Wibberg D, Niehaus K, Pühler A, Vorhölter FJ., J Biotechnol 253(), 2017
PMID: 28506932
Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.
Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ., Microbiology 163(8), 2017
PMID: 28795660
Unconventional membrane lipid biosynthesis in Xanthomonas campestris.
Aktas M, Narberhaus F., Environ Microbiol 17(9), 2015
PMID: 26119594
Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner-Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis.
Schatschneider S, Huber C, Neuweger H, Watt TF, Pühler A, Eisenreich W, Wittmann C, Niehaus K, Vorhölter FJ., Mol Biosyst 10(10), 2014
PMID: 25072918
Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100.
Schatschneider S, Persicke M, Watt SA, Hublik G, Pühler A, Niehaus K, Vorhölter FJ., J Biotechnol 167(2), 2013
PMID: 23395674
The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection.
Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R., Mol Plant Pathol 14(6), 2013
PMID: 23578314
Isotopically non-stationary metabolic flux analysis: complex yet highly informative.
Wiechert W, Nöh K., Curr Opin Biotechnol 24(6), 2013
PMID: 23623747
Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach.
Musa YR, Bäsell K, Schatschneider S, Vorhölter FJ, Becher D, Niehaus K., J Biotechnol 167(2), 2013
PMID: 23792782
A biosynthetic pathway of sesquiterpene lactones in Smallanthus sonchifolius and their localization in leaf tissues by MALDI imaging.
Lopes AA, Pina ES, Silva DB, Pereira AM, da Silva MF, Da Costa FB, Lopes NP, Pupo MT., Chem Commun (Camb) 49(85), 2013
PMID: 24042494
Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content.
Vandroemme J, Cottyn B, Baeyen S, De Vos P, Maes M., BMC Genomics 14(), 2013
PMID: 24274055

54 References

Data provided by Europe PubMed Central.

Cysteine biosynthesis in Trichomonas vaginalis involves cysteine synthase utilizing O-phosphoserine.
Westrop GD, Goodall G, Mottram JC, Coombs GH., J. Biol. Chem. 281(35), 2006
PMID: 16735516
Metabolic flux analysis using mass spectrometry.
Wittmann C., Adv. Biochem. Eng. Biotechnol. 74(), 2002
PMID: 11991183
Isoleucine biosynthesis in Leptospira interrogans serotype lai strain 56601 proceeds via a threonine-independent pathway.
Xu H, Zhang Y, Guo X, Ren S, Staempfli AA, Chiao J, Jiang W, Zhao G., J. Bacteriol. 186(16), 2004
PMID: 15292141
A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12.
Yang CR, Shapiro BE, Hung SP, Mjolsness ED, Hatfield GW., J. Biol. Chem. 280(12), 2005
PMID: 15657047

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 21853248
PubMed | Europe PMC

Search this title in

Google Scholar