IAK692: A genome-scale metabolic model of Spirulina platensis C1

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Klanchui, Amornpan ^a   Khannapho, Chiraphan ^a   Phodee, Atchara ^b   Cheevadhanarak, Supapon ^b   Meechai, Asawin ^b  

^a NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^b KING MONGKUT'S UNIVERSITY OF TECHNOLOGY THONBURI   (Thailand)

Author keywords

Cyanobacteria; Flux balance analysis; Genome scale metabolic model; Metabolic network reconstruction; Spirulina platensis C1

Indexed keywords

ANIMALIA; ARTHROSPIRA SP.; CYANOBACTERIA; SPIRULINA; SPIRULINA PLATENSIS;

ARTICLE; AUTOTROPHY; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; HETEROTROPHY; METABOLISM; PHENOTYPE; REPRODUCIBILITY; SPIRULINA;

AUTOTROPHIC PROCESSES; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; HETEROTROPHIC PROCESSES; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PHENOTYPE; REPRODUCIBILITY OF RESULTS; SPIRULINA;

EID: 84862205997     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-71     Document Type: Article

References (56)

1. Pinero Estrada JE, Bermejo Bescos P, del Fresno AM V. Antioxidant activity of different fractions of Spirulina platensis protean extract. Farmaco 2001, 56:497-500. 10.1016/S0014-827X(01)01084-9, 11482785.
2. Tietze HW. Spirulina-Micro Food Macro Blessing 2004, Harald W. Tietz Publishing, Australia, 4.
3. Habib MAB, Parvin M, Huntington TC, Hasan MR. A review on culture, production and use of spirulina as food for humans and feeds for domestic animals and fish 2008, Food and agriculture organization of the united nations, , Retrieved November 20, 2011.
4. Kulshreshtha A, Zacharia AJ, Jarouliya U, Bhadauriya P, Prasad GB, Bisen PS. Spirulina in health care management. Current pharmaceutical biotechnology 2008, 9:400-405. 10.2174/138920108785915111, 18855693.
5. Ghirardi ML, Zhang L, Lee JW, Flynn T, Seibert M, Greenbaum E, Melis A. Microalgae: a green source of renewable H(2). Trends Biotechnol 2000, 18:506-511. 10.1016/S0167-7799(00)01511-0, 11102662.
6. Santillan C. Mass production of Spirulina. Experientia 1982, 38:40-43.
7. Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 2009, 7:129-143. 3119670, 19116616.
8. Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet 2006, 7:130-141. 10.1038/nrg1769, 16418748.
9. Patil KR, Akesson M, Nielsen J. Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol 2004, 15:64-69. 10.1016/j.copbio.2003.11.003, 15102469.
10. Palsson BO. System Biology: Determining the Capabilities of Reconstructed Networks 2006, Cambrige University Press, London/New York.
11. Kim HU, Kim TY, Lee SY. Metabolic flux analysis and metabolic engineering of microorganism. Molecular BioSystems 2008, 4:113-120. 10.1039/b712395g, 18213404.
12. Price ND, Reed JL, Palsson BO. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2:886-897. 10.1038/nrmicro1023, 15494745.
13. Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2007, 2:727-738. 10.1038/nprot.2007.99, 17406635.
14. Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 2011, 6:1290-1307. 10.1038/nprot.2011.308, 21886097.
15. Oberhardt MA, Palsson BO, Papin JA. Applications of genome-scale metabolic reconstructions. Molecular systems biology 2009, 5:320. 2795471, 19888215.
16. Durot M, Bourguignon PY, Schachter V. Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS microbiology reviews 2009, 33:164-190. 10.1111/j.1574-6976.2008.00146.x, 2704943, 19067749.
17. Osterlund T, Nookaew I, Nielsen J. Fifteen years of large scale metabolic modeling of yeast: Developments and impacts 2011, Biotechnology advances, .
18. Kim TY, Sohn SB, Kim YB. Kim WJ 2011, Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Opin Biotechnol, Lee SY.
19. Fu P. Genome-scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertion. Journal of Chemical Technology and Biotechnology 2008, 84(411):473-483.
20. Montagud A, Navarro E, Fernandez de Cordoba P, Urchueguia JF, Patil KR. Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC systems biology 2010, 4:156. 10.1186/1752-0509-4-156, 3009638, 21083885.
21. Yoshikawa K, Kojima Y, Nakajima T, Furusawa C, Hirasawa T, Shimizu H. Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803. Applied microbiology and biotechnology 2011, 92:347-358. 10.1007/s00253-011-3559-x, 21881889.
22. Meechai A, Pongakarakun S, Deshnium P, Cheevadhanarak S, Bhumiratana S. Metabolic flux distribution for gamma-linolenic acid synthetic pathways in Spirulina Platensis. Biotechnology and Bioprocess Engineering 2004, 9:506-513.
23. Cogne G, Gros JB, Dussap CG. Identification of a metabolic network structure representative of Arthrospira (spirulina) platensis metabolism. Biotechnol Bioeng 2003, 84:667-676. 10.1002/bit.10808, 14595779.
24. Cheevadhanarak S, Paithoonrangsarid K, Prommeenate P, Kaewngam W, Musigkain A, Tragoonrung S, Tabata S, Kaneko T, Chaijaruwanich J, Sangsrakru D, et al. Draft genome sequence of Arthrospira platensis C1 (PCC9438) 2012, 6. Standards in Genomic Sciences, North America.
25. Edwards JS, Ramakrishna R, Palsson BO. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng 2002, 77:27-36. 10.1002/bit.10047, 11745171.
26. Karp PD, Paley S, Romero P. The Pathway Tools software. Bioinformatics 2002, 18(Suppl 1):S225-232. 10.1093/bioinformatics/18.suppl_1.S225, 12169551.
27. Paley SM, Karp PD. The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res 2006, 34:3771-3778. 10.1093/nar/gkl334, 1557788, 16893960.
28. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
29. Mount DW. Using the Basic Local Alignment Search Tool (BLAST) 2007, CSH protocols, , pdb top17.
30. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-222. 10.1093/nar/gkp985, 2808889, 19920124.
31. Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 2008, 36:D623-631. 2238876, 17965431.
32. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-357. 10.1093/nar/gkj102, 1347464, 16381885.
33. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 2009, 37:D588-592. 10.1093/nar/gkn820, 2686525, 18984617.
34. Yang C, Hua Q, Shimizu K. Energetics and Carbon Metabolism During Growth of Microalgal Cells under Photoautotrophic, Mixotrophic and Cyclic Light-Autotrophic/Dark-Heterotrophic Condition. Biochemical Engineering Journal 2000, 6:87-102. 10.1016/S1369-703X(00)00080-2, 10959082.
35. Enzyme Nomenclature 1992: IUB Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes 1992, Academic, San Diego.
36. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. 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. 1911197, 17593909.
37. Forster J, Famili I, Fu P, Palsson BO, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome research 2003, 13:244-253. 10.1101/gr.234503, 420374, 12566402.
38. Chojnacka K, Noworyta A. Evaluation of Spirulina sp. growth in photoautotrophic, heterotrophic and mixotrophic cultures. Enzyme and Microbial Technology 2004, 34:461-465.
39. Lodi A, Binaghi L, Faveri DD, Carvalho JCM, Converti A. Fed-Batch Mixotrophic Cultivation ofArthrospira (Spirulina) Platensis(Cyanophycea) with Carbon Source Pulse Feeding. Annals of Microbiology 2005, 55(3):181-185.
40. Muhling M, Belay A, Whitton BA. ScreeningArtrospira(Spirulina) strains for Heterotrophy. Journal of Applied Phycology 2005, 17:129-135.
41. Marquez FJ, Sasaki K, Kakizono T, Nishio N, Nagai S. Growth characteristics of Spirulina platensis in mixotrophic and heterotrophic conditions. Journal of Fermentation and Bioengineering 1993, 76:408-410.
42. Milne CB, Eddy JA, Raju R, Ardekani S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC systems biology 2011, 5:130. 10.1186/1752-0509-5-130, 3212993, 21846360.
43. Nishikawa T, Gulbahce N, Motter AE. Spontaneous reaction silencing in metabolic optimization. PLoS computational biology 2008, 4:e1000236. 10.1371/journal.pcbi.1000236, 2582435, 19057639.
44. Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 2003, 5:264-276. 10.1016/j.ymben.2003.09.002, 14642354.
45. Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S. Experimental and computational assessment of conditionally essential genes in Escherichia coli. Journal of bacteriology 2006, 188:8259-8271. 10.1128/JB.00740-06, 1698209, 17012394.
46. Segre D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:15112-15117. 10.1073/pnas.232349399, 137552, 12415116.
47. Vonshak A. Laboratory Techniques for the Cultivation of Microalgae: CRC Handbook of Microalgae Mass Cultures 1986, CRC Press, Florida, USA.
48. Michel D, Gilles KA, Hamilton JK, Rebers PA, Smith F. Colorimetric Method for Determination of Sugars and Related Substances. Analytical Chemistry 1956, 28:350-356.
49. Franson M. Standard Methods for the Examination of Water and Wastewater, 20thedn.American Public Heath Association, American Water Works Association, Water Enviroment Federation 1998, United Book Press, Baltimore, Maryland, USA.
50. Nakamura Y, Kaneko T, Hirosawa M, Miyajima N, Tabata S. CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803. Nucleic Acids Res 1998, 26:63-67. 10.1093/nar/26.1.63, 147195, 9399802.
51. Ren Q, Chen K, Paulsen IT. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 2007, 35:D274-279. 10.1093/nar/gkl925, 1747178, 17135193.
52. Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Molecular systems biology 2006, 2:2006-0004. 1681510, 16788596.
53. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:1777-1782. 10.1073/pnas.0610772104, 1794290, 17267599.
54. Kauffman KJ, Prakash P, Edwards JS. Advances in flux balance analysis. Curr Opin Biotechnol 2003, 14:491-496. 10.1016/j.copbio.2003.08.001, 14580578.
55. Stephanopoulos GN, Aristidou AA, Nielsen J. Metabolic Engineering Principles and Methodologies 1998, Acadimic press, San Diego.
56. Keating SM, Bornstein BJ, Finney A, Hucka M. SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics 2006, 22:1275-1277. 10.1093/bioinformatics/btl111, 16574696.