Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001

Journal of Biotechnology

Volumn 161, Issue 1, 2012, Pages 42-48

  Zou, Wei ^a   Liu, Liming ^a,b   Zhang, Jing ^c   Yang, Haoru ^a   Zhou, Maoda ^a   Hua, Qiang ^b   Chen, Jian ^a  

^a JIANGNAN UNIVERSITY   (China)

^b EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^c SICHUAN UNIVERSITY OF SCIENCE AND ENGINEERING   (China)

Author keywords

2 keto l Gulonic acid; Genome scale metabolic model; Ketogulonicigenium vulgare; Sulfate metabolism; Vitamin C

Indexed keywords

COENZYME A; EXPERIMENTAL DATA; FERMENTATION CONDITIONS; GENOME ANNOTATION; GENOME-SCALE METABOLIC MODELS; GLUTATHIONES; INDUSTRIAL STRAIN; KETOGULONICIGENIUM VULGARE; L-CYSTEINE; L-METHIONINE; LITERATURE MINING; PHENOTYPIC FEATURES; PHYSIOLOGICAL CHARACTERISTICS; PRODUCTION EFFICIENCY; VALIDATED PLATFORM; VITAMIN C;

AMINO ACIDS; GENES; INDUSTRY; METABOLISM; PHYSIOLOGY; VITAMINS;

PHYSIOLOGICAL MODELS;

ASCORBIC ACID; COENZYME A; CYSTEINE; GLUTATHIONE; METHIONINE; SORBOSE; SULFATE;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; FERMENTATION; KETOGULONICIGENIUM VULGARE; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; RHODOBACTER;

ALPHAPROTEOBACTERIA; ASCORBIC ACID; INDUSTRIAL MICROBIOLOGY; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL;

KETOGULONICIGENIUM VULGARE;

EID: 84863474170     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2012.05.015     Document Type: Article

References (40)

1. Asakura A., Hoshino T. Isolation and characterization of a new Quinoprotein dehydrogenase, l-sorbose/l-sorbosone dehydrogenase. Bioscience, Biotechnology, and Biochemistry 1999, 63:46-53.
2. Asakura, A., Hoshino, T., Kiyasu, T., Shinjoh, M., 2000. Manufacture of l-ascorbic acid and d-erythorbic acid. United States Patent 6146860.
3. Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., Formsma K., Gerdes S., Glass E.M., Kubal M., Meyer F., Olsen G.J., Olson R., Osterman A.L., Overbeek R.A., McNeil L.K., Paarmann D., Paczian T., Parrello B., Pusch G.D., Reich C., Stevens R., Vassieva O., Vonstein V., Wilke A., Zagnitko O. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75.
4. Bremus C., Herrmann U., Bringer-Meyer S., Sahm H. The use of microorganisms in l-ascorbic acid production. Journal of Biotechnology 2006, 124:196-205.
5. Caspi R., Altman T., Dale J.M., Dreher K., Fulcher C.A., Gilham F., Kaipa P., Karthikeyan A.S., Kothari A., Krummenacker M., Latendresse M., Mueller L.A., Paley S., Popescu L., Pujar A., Shearer A.G., Zhang P., Karp P.D. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 2010, 38:D473-D479.
6. Feist A.M., Henry C.S., Reed J.L., Krummenacker M., Joyce A.R., Karp P.D., Broadbelt L.J., Hatzimanikatis V., Palsson B.O. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 2007, 3:121.
7. Hancock R.D., Viola R. Biotechnological approaches for l-ascorbic acid production. Trends in Biotechnology 2002, 20:299-305.
8. Henry C.S., Dejongh M., Best A.A., Frybarger P.M., Linsay B., Stevens R.L. High-throughput generation optimization and analysis of genome-scale metabolic models. Nature Biotechnology 2010, 28:977-982.
9. Jain E., Bairoch A., Duvaud S., Phan I., Redaschi N., Suzek B.E., Martin M.J., McGarvey P., Gasteiger E. Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 2009, 10:136.
10. Kanehisa M., Goto S., Furumichi M., Tanabe M., Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Research 2010, 38:D355-D360.
11. Kim, T.Y., Sohn, S.B., Kim, Y.B., Kim, W.J., Lee, S.Y. Recent advances in reconstruction and applications of genome-scale metabolic models. Current Opinion in Biotechnology,, in press. doi:10.1016/j.copbio.2011.10.007.
12. Leduc S., de Troostembergh J.C., Lebeault J.M. Folate requirements of the 2-keto-l-gulonic acid-producing strain Ketogulonigenium vulgare LMP P-20356 in l-sorbose/CSL medium. Applied Microbiology and Biotechnology 2004, 65:163-167.
13. Li Q., Diao J., Xiang B., Cao Z. Studies on metabolism of nitrogen source in fermentation of 2-keto-l-gulonic acid. Acta Microbiologica Sinica 1996, 36:19-24.
14. Liu L., Chen K., Zhang J., Liu J., Chen J. Gelatin enhances 2-keto-l-gulonic acid production based on Ketogulonigenium vulgare genome annotation. Journal of Biotechnology 2011, 156:182-187.
15. Liu L., Li Y., Zhang J., Zhou Z., Liu J., Li X., Zhou J., Du G., Wang L., Chen J. Complete genome sequence of the industrial strain Ketogulonicigenium vulgare WSH-001. Journal of Bacteriology 2011, 193:6108-6109.
16. Liu L.M., Agren R., Bordel S., Nielsen J. Use of genome-scale metabolic models for understanding microbial physiology. FEBS Letters 2010, 584:2556-2564.
17. Ma Q., Zhou J., Zhang W., Meng X., Sun J., Yuan Y.J. Integrated proteomic and metabolomic analysis of an artificial microbial community for two-step production of vitamin C. PLoS One 2011, 6:e26108.
18. Miyazaki T., Sugisawa T., Hoshino T. Pyrroloquinoline quinone-dependent dehydrogenases from Ketogulonicigenium vulgare catalyze the direct conversion of l-sorbosone to l-ascorbic acid. Applied and Environmental Microbiology 2006, 72:1487-1495.
19. Moriya Y., Itoh M., Okuda S., Yoshizawa A.C., Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research 2007, 35:W182-W185.
20. Orth J.D., Thiele I., Palsson B.O. What is flux balance analysis?. Nature Biotechnology 2010, 28:245-248.
21. Reed J.L., Vo T.D., Schilling C.H., Palsson B.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology 2003, 4:R54.
22. Reichstein T., Grüssner A. Eine ergiebige Synthese der l-Ascorbinsäure (C-Vitamin). Helvetica Chimica Acta 1934, 17:311-328.
23. Saier M.H., Yen M.R., Noto K., Tamang D.G., Elkan C. The Transporter Classification Database: recent advances. Nucleic Acids Research 2009, 37:D274-D278.
24. Scheer M., Grote A., Chang A., Schomburg I., Munaretto C., Rother M., Sohngen C., Stelzer M., Thiele J., Schomburg D. BRENDA the enzyme information system in 2011. Nucleic Acids Research 2011, 39:D670-D676.
25. Schellenberger J., Que R., Fleming R.M., Thiele I., Orth J.D., Feist A.M., Zielinski D.C., Bordbar A., Lewis N.E., Rahmanian S., Kang J., Hyduke D.R., Palsson B.O. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 2011, 6:1290-1307.
26. Sugisawa T., Miyazaki T., Hoshino T. Microbial production of l-ascorbic acid from d-sorbitol l-sorbose, l-gulose, and l-sorbosone by Ketogulonicigenium vulgare DSM 4025. Bioscience, Biotechnology, and Biochemistry 2005, 69:659-662.
27. Sugisawa T., Ojima S., Matzinger K.P., Hoshino T. Isolation and characterization of a new vitamin C producing enzyme (l-gulono-(-lactone dehydrogenase) of bacterial origin. Bioscience, Biotechnology, and Biochemistry 1995, 59:190-196.
28. Takagi Y., Sugisawa T., Hoshino T. Continuous 2-keto-l-gulonic acid fermentation from l-sorbose by Ketogulonigenium vulgare DSM 4025. Applied Microbiology and Biotechnology 2009, 82:1049-1056.
29. Thiele I., Palsson B.O. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocols 2010, 5:93-121.
30. Urbance J.W., Bratina B.J., Stoddard S.F., Schmidt T.M. Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov. which oxidize l-sorbose to 2-keto-l-gulonic acid. International Journal of Systematic and Evolutionary Microbiology 2001, 51:1059-1070.
31. Xiong X.H., Han S., Wang J.H., Jiang Z.H., Chen W., Jia N., Wei H.L., Cheng H., Yang Y.X., Zhu B., You S., He J.Y., Hou W., Chen M.X., Yu C.J., Jiao Y.H., Zhang W.C. Complete genome sequence of the bacterium Ketogulonicigenium vulgare Y25. Journal of Bacteriology 2011, 193:315-316.
32. Xu A., Yao J., Yu L., Lv S., Wang J., Yan B., Yu Z. Mutation of Gluconobacter oxydans and Bacillus megaterium in a two-step process of l-ascorbic acid manufacture by ion beam. Journal of Applied Microbiology 2004, 96:1317-1323.
33. Yang F., Jia Q., Xiong Z.H., Zhang X.B., Wu H.T., Zhao Y., Yang J., Zhu J.P., Dong J., Xue Y., Sun L.L., Shen Y., Jin Q. Complete genome analysis of Ketogulonigenium sp WB0104. Chinese Science Bulletin 2006, 51:941-945.
34. Yin, G.L., Tao, Z.X., Yan, Z.Z., Ning, W.Z., Wang, C.H., Wang, S.D., 1990. Fermentation process. United State Patent 4935359.
35. Yin G.L., Tao Z.X., Yu L.H., Wang D.S., Dan J.L., Yan Z.Z., Ning W.Z., Wang C.H., Wang S.D., Jiang H.F., Zhang X.D., Feng X.Y., Zhao Q., Wei W.Q. Studies on the production of vitamin C precursor-2-keto-l-gulonic acid from l-sorbose by fermentation I. isolation screening and identification of 2-keto-l-gulonic acid producing bacteria. Acta Microbiologica Sinica 1980, 20:246-251.
36. Zhang J., Liu J., Shi Z.P., Liu L.M., Chen J. Manipulation of B. megaterium growth for efficient 2-KLG production by K. vulgare. Process Biochemistry 2010, 45:602-606.
37. Zhang J., Zhou J., Liu J., Chen K., Liu L., Chen J. Development of chemically defined media supporting high cell density growth of Ketogulonicigenium vulgare and Bacillus megaterium. Bioresource Technology 2011, 102:4807-4814.
38. Zhang J., Zhou J., Liu L., Liu J., Chen K., Du G., Chen J. Enhancement of 2-keto-l-gulonic acid production using three-stage pH control strategy. Chinese Journal of Biotechnology 2010, 26:1263-1268.
39. Zhang J., Zhou J.W., Liu L.M., Liu J., Chen K.J., Du G.C., Chen J. Enhancement of 2-keto-l-gulonic acid production using three-stage pH control strategy. Chinese Journal of Biotechnology 2010, 26:1263-1268.
40. Zhou J., Ma Q., Yi H., Wang L., Song H., Yuan Y.-J. Metabolome profiling reveals metabolic cooperation between Bacillus megaterium and Ketogulonicigenium vulgare during induced swarm motility. Applied and Environmental Microbiology 2011, 77:7023-7030.