Analysis of in vivo function of predicted isoenzymes-a metabolomic approach

OMICS A Journal of Integrative Biology

Volumn 16, Issue 12, 2012, Pages 668-680

  Choorapoikayil, Suma ^a,b   Schoepe, Jan ^a,c   Buchinger, Sebastian ^a,d   Schomburg, Dietmar ^a,e  

^a UNIVERSITY OF COLOGNE   (Germany)

^b HUBRECHT INSTITUTE   (Netherlands)

^c German Federal Institute of Hydrology ^*  (Belgium)

^d FEDERAL INSTITUTE OF HYDROLOGY   (Germany)

^e TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ISOENZYME; OXIDOREDUCTASE; SHIKIMIC ACID;

ARTICLE; CONSTANTS AND COEFFICIENTS; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; ENZYME INACTIVATION; HETEROLOGOUS EXPRESSION; IN VITRO STUDY; IN VIVO STUDY; METABOLOMICS; NONHUMAN; PRIORITY JOURNAL;

EID: 84870882122     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2012.0055     Document Type: Article

References (53)

1. Anton IA, and Coggins Jr. (1988). Sequencing and overexpression of the Escherichia coli aroE gene encoding shikimate dehydrogenase. Biochem J 249, 319-326.
2. Asakura Y, Kimura E, Usuda Y, et al. (2007). Altered metabolic flux due to deletion of odhA causes L-glutamate overproduction in Corynebacterium glutamicum. Appl Environ Microbiol 73, 1308-1319.
3. Baba T, Ara T, Hasegawa M, et al. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Systems Biol 2, 0008.
4. Barthelmes J, Ebeling C, Chang A, Schomburg I, and Schomburg D. (2007). BRENDA, AMENDA and FRENDA: The enzyme information system in 2007. Nucleic Acids Res 35, D511-514.
5. Becker D, Selbach M, Rollenhagen C, et al. (2006). Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 440, 303-307.
6. Becker SA, and Palsson BO. (2005). Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: An initial draft to the two-dimensional annotation. BMC Microbiol 5, 8.
7. Benach J, Lee I, Edstrom W, et al. (2003). The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase. J Biol Chem 278, 19176-19182.
8. Borner J, Buchinger S, and Schomburg D. (2007). A highthroughput method for microbial metabolome analysis using gas chromatography/mass spectrometry. Anal Biochem 367, 143-151.
9. Bro C, Regenberg B, Forster J, and Nielsen J. (2006). In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Engin 8, 102-111.
10. Caspi R, Foerster H, Fulcher CA, et al. (2006). MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 34, D511-516.
11. Chatterjee S, Schoepe J, Lohmer S, and Schomburg D. (2005). High level expression and single-step purification of hexahistidine-tagged L-2-hydroxyisocaproate dehydrogenase making use of a versatile expression vector set. Protein Express Purif 39, 137-143.
12. Chaudhuri S, and Coggins Jr. (1985). The purification of shikimate dehydrogenase from Escherichia coli. Biochem J 226, 217-223.
13. Claes WA, Puhler A, and Kalinowski J. (2002). Identification of two prpDBC gene clusters in Corynebacterium glutamicum and their involvement in propionate degradation via the 2- methylcitrate cycle. J Bacteriol 184, 2728-2739.
14. Coggins JR, Abell C, Evans LB, et al. (2003). Experiences with the shikimate-pathway enzymes as targets for rational drug design. Biochem Soc Trans 31, 548-552.
15. De Berardinis V, Vallenet D, Castelli V, et al. (2008). A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Systems Biol 4, 174.
16. De Graaf AA, Eggeling L, and Sahm H. (2001). Metabolic engineering for L-lysine production by Corynebacterium glutamicum. Adv Biochem Engin/Biotechnol 73, 9-29.
17. Duarte NC, Becker SA, Jamshidi N, et al. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 104, 1777-1782.
18. Durot M, Bourguignon PY, and Schachter V. (2009). Genomescale models of bacterial metabolism: Reconstruction and applications. FEMS Microbiol Rev 33, 164-190.
19. Eikmanns BJ, Follettie MT, Griot MU, and Sinskey AJ. (1989). The phosphoenolpyruvate carboxylase gene of Corynebacterium glutamicum: Molecular cloning, nucleotide sequence, and expression. Mol Gen Genet 218, 330-339.
20. Gourdon P, and Lindley ND. (1999). Metabolic analysis of glutamate production by Corynebacterium glutamicum. Metab Engin 1, 224-231.
21. Herrmann KM, and Weaver LM. (1999). The shikimate pathway. Ann Rev Plant Physiol Plant Mol Biol 50, 473-503.
22. Ikeda M, and Nakagawa S. (2003). The Corynebacterium glutamicum genome: Features and impacts on biotechnological processes. App Microbiol Biotechnol 62, 99-109.
23. Junker BH, Klukas C, and Schreiber F. (2006). VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinform 7, 109.
24. Kalinowski J, Bathe B, Bartels D, et al. (2003). The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol 104, 5-25.
25. Kanehisa M, Goto S, Kawashima S, Okuno Y, and Hattori M. (2004). The KEGG resource for deciphering the genome. Nucleic Acids Res 32, D277-280.
26. Kimura E. (2003). Metabolic engineering of glutamate production. Adv Biochem Engin/Biotechnol 79, 37-57.
27. Klamt S, and Gilles ED. (2004). Minimal cut sets in biochemical reaction networks. Bioinformatics (Oxford, England). 20, 226-234.
28. Krieger CJ, Zhang P, Mueller LA, et al., (2004). MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 32, D438-442.
29. Magalhaes ML, Pereira CP, Basso LA, and Santos DS. (2002). Cloning and expression of functional shikimate dehydrogenase (EC 1.1.1.25) from Mycobacterium tuberculosis H37Rv. Protein Express Purif 26, 59-64.
30. Michel G, Roszak AW, Sauve V, et al. (2003). Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities. J Biol Chem 278, 19463-19472.
31. Ohnishi J, and Ikeda M. (2006). Comparisons of potentials for Llysine production among different Corynebacterium glutamicum strains. Bio Biotechnol Biochem 70, 1017-1020.
32. Peters-Wendisch PG, Schiel B, Wendisch VF, et al. (2001). Pyruvate carboxylase is a major bottleneck for glutamate and lysine production by Corynebacterium glutamicum. J Mol Microbiol Biotechnol 3, 295-300.
33. Pinney JW, Shirley MW, McConkey GA, and Westhead DR. (2005). metaSHARK: Software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res 33, 1399-1409.
34. Price ND, Papin JA, Schilling CH, and Palsson BO. (2003). Genome-scale microbial in silico models: The constraintsbased approach. Trends Biotechnol 21, 162-169.
35. Quester S, and Schomburg D. (2011). EnzymeDetector: An integrated enzyme function prediction tool and database. BMC Bioinformat 12, 376.
36. Rahman SA, and Schomburg D. (2006). Observing local and global properties of metabolic pathways: 'Load points' and 'choke points' in the metabolic networks. Bioinformatics (Oxford, England) 22, 1767-1774.
37. Roessner U, Wagner C, Kopka J, Trethewey RN, and Willmitzer L. (2000). Technical advance: Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23, 131-142.
38. Schafer A, Kalinowski J, Simon R, Seep-Feldhaus AH, and Puhler A. (1990). High-frequency conjugal plasmid transfer from gram-negative Escherichia coli to various gram-positive coryneform bacteria. J Bacteriol 172, 1663-1666.
39. Schafer A, Tauch A, Jager W, Kalinowski J, Thierbach G, and Puhler A. (1994). Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: Selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145, 69-73.
40. Schoepe J, Niefind K, and Schomburg D. (2008). 1.6 angstroms structure of an NAD+ -dependent quinate dehydrogenase from Corynebacterium glutamicum. Acta Crystallograph D64, 803-809.
41. Selkov E, Maltsev N, Olsen GJ, Overbeek R, and Whitman WB. (1997). A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 197, GC11-26.
42. Singh S, Korolev S, Koroleva O, et al. (2005). Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae. J Biol Chem 280, 17101-17108.
43. Singh S, Stavrinides J, Christendat D, and Guttman DS. (2008). A phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass. Mol Biol Evol 25, 2221-2232.
44. Stein SE. (1999). An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J Am Soc Mass Spect 10, 770-781.
45. Strelkov S, Von Elstermann M, and Schomburg D. (2004). Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry. Biol Chem 385, 853-861.
46. Tauch A, Gotker S, Puhler A. Kalinowski J, and Thierbach G. (2002). The 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum encodes the aminoglycoside adenyltransferase gene cassette aadA9 and the regulated tetracycline efflux system Tet 33 flanked by active copies of the widespread insertion sequence IS6100. Plasmid 48, 117-129.
47. Teramoto H, Inui M, and Yukawa H. (2009). Regulation of expression of genes involved in quinate and shikimate utilization in Corynebacterium glutamicum. App Environ Microbiol 75, 3461-3468.
48. Tsoka S, Simon D, and Ouzounis CA. (2004). Automated metabolic reconstruction for Methanococcus jannaschii. Archaea (Vancouver, B.C) 1, 223-229.
49. Usuda Y, Tujimoto N, Abe C, et al. (1996). Molecular cloning of the Corynebacterium glutamicum ('Brevibacterium lactofermentum' AJ12036) odhA gene encoding a novel type of 2-oxoglutarate dehydrogenase. Microbiology (Reading, England) 142, 3347-3354.
50. Vandendool H, and Kratz PD. (1963). A generalization of the retention index system including linear temperature programmed gas-liquid partition chromatography. J Chromatog 11, 463-471.
51. Winzeler EA, Shoemaker DD, Astromof FA, et al. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (New York, N.Y) 285, 901-906.
52. Wu CH, Apweiler R, Bairoc, A, et al. (2006). The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res 34, D187-191.
53. Ye S, Von Delft F, Brooun A, Knuth MW, Swanson RV, McRee DE. (2003). The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode. J Bacteriol 185, 4144-4151.