Genome-scale analysis of the metabolic networks of oleaginous Zygomycete fungi

Gene

Volumn 521, Issue 1, 2013, Pages 180-190

  Vongsangnak, Wanwipa ^a   Ruenwai, Rawisara ^b   Tang, Xin ^c   Hu, Xinjie ^c   Zhang, Hao ^c   Shen, Bairong ^a   Song, Yuanda ^c   Laoteng, Kobkul ^d  

^a SOOCHOW UNIVERSITY   (China)

^b UNIVERSITY OF PHAYAO   (Thailand)

^c JIANGNAN UNIVERSITY   (China)

^d NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

Author keywords

Gene annotation; Genome scale metabolic network; Lipid; Metabolic function; Oleaginous fungi

Indexed keywords

FATTY ACID; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; STEROL;

ARTICLE; BIOINFORMATICS; COMPARATIVE STUDY; DATA ANALYSIS; FATTY ACID SYNTHESIS; FUNGAL METABOLISM; GENOMICS; LIPID METABOLISM; LIPID STORAGE; MORTIERELLA ALPINA; MUCOR CIRCINELLOIDES; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; STEROL SYNTHESIS; ZYGOMYCETES;

AMINO ACIDS; ENERGY METABOLISM; FATTY ACIDS; FUNGAL PROTEINS; GENOME, FUNGAL; LIPID METABOLISM; METABOLIC NETWORKS AND PATHWAYS; MORTIERELLA; MUCOR; NADP; PHYLOGENY;

FUNGI; MORTIERELLA ALPINA; MUCOR CIRCINELLOIDES;

EID: 84876699612     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.03.012     Document Type: Article

References (53)

1. Nielsen J. Systems biology of lipid metabolism: from yeast to human. FEBS Lett. 2009, 583:3905-3913.
2. Ageitos J.M., Vallejo J.A., Veiga-Crespo P., Villa T.G. Oily yeasts as oleaginous cell factories. Appl. Microbiol. Biotechnol. 2011, 90:1219-1227.
3. Ratledge C. Fatty acid biosynthesis in microorganisms being used for single cell oil production. Biochimie 2004, 86:807-815.
4. Ratledge C., Wynn J.P. The biochemistry and molecular biology of lipid accumulation in oleaginous microorganisms. Adv. Appl. Microbiol. 2002, 51:1-51.
5. Vorapreeda T., Thammarongtham C., Cheevadhanarak S., Laoteng K. Alternative routes of acetyl-CoA synthesis identified by comparative genomic analysis: involvement in lipid production of oleaginous yeast and fungi. Microbiology 2012, 158:217-228.
6. Botha A., Kock J.L.F., Coetzee D.J., Botes P.J. Physiological properties and fatty acid composition in Mucor circinelloides f. circinelloides. Antonie Van Leeuwenhoek 1997, 71:201-206.
7. Wang L., et al. Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One 2011, 6:e28319.
8. Vongsangnak W., et al. Genome-scale metabolic representation of Amycolatopsis balhimycina. Biotechnol. Bioeng. 2012, 109:1798-1807.
9. Quevillon E., et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005, 33:W116-W120.
10. Finn R.D., et al. The Pfam protein families database. Nucleic Acids Res. 2008, 36:D281-D288.
11. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004, 32:D277-D280.
12. Haft D.H., Selengut J.D., White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003, 31:371-373.
13. Lees J., Yeats C., Redfern O., Clegg A., Orengo C. Gene3D: merging structure and function for a thousand genomes. Nucleic Acids Res. 2010, 38:D296-D300.
14. Gough J., Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res. 2002, 30:268-272.
15. Sigrist C.J., et al. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res. 2010, 38:D161-D166.
16. Thomas P.D., et al. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003, 31:334-341.
17. Tatusov R.L., et al. The COG database: an updated version includes eukaryotes. BMC Bioinform. 2003, 4:41.
18. Schultz J., Milpetz F., Bork P., Ponting C.P. SMART, a simple modular architecture research tool: identification of signaling domains. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:5857-5864.
19. Wu C.H., et al. The protein information resource. Nucleic Acids Res. 2003, 31:345-347.
20. Attwood T.K., Beck M.E., Flower D.R., Scordis P., Selley J.N. The PRINTS protein fingerprint database in its fifth year. Nucleic Acids Res. 1998, 26:304-308.
21. Corpet F., Gouzy J., Kahn D. The ProDom database of protein domain families. Nucleic Acids Res. 1998, 26:323-326.
22. Nookaew I., et al. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst. Biol. 2008, 2:71.
23. Förster J., Famili I., Fu P., Palsson B.Ø., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003, 13:244-253.
24. Borodina I., Krabben P., Nielsen J. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res. 2005, 15:820-829.
25. Edwards J.S., Palsson B.Ø. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 2000, 1:1.
26. O'Connell B.T., Paznokas J.L. Glyoxylate cycle in Mucor racemosus. J. Bacteriol. 1980, 143:416-421.
27. Mysiakina I.S., Funtikova N.S. Activity of NAD-dependent isocitrate dehydrogenase, isocitrate lyase, and malate dehydrogenase in Mucor circinelloides var. lusitanicus INMI under different modes of nitrogen supply. Mikrobiologiia 2008, 77:453-459.
28. Wynn J.P., Ratledge C. Evidence that the rate-limiting step for the biosynthesis of arachidonic acid in Mortierella alpina is at the level of the 18:3 to 20:3 elongase. Microbiology 2000, 146:2325-2331.
29. Wynn J.P., bin Abdul Hamid A., Ratledge C. The role of malic enzyme in the regulation of lipid accumulation in filamentous fungi. Microbiology 1999, 145:1911-1917.
30. Vongsangnak W., Zhang Y., Chen W., Ratledge C., Song Y. Annotation and analysis of malic enzyme genes encoding for multiple isoforms in the fungus Mucor circinelloides CBS 277.49. Biotechnol. Lett. 2012, 34:941-947.
31. Zhang Y., Adams I.P., Ratledge C. Malic enzyme: the controlling activity for lipid production? Overexpression of malic enzyme in Mucor circinelloides leads to a 2.5-fold increase in lipid accumulation. Microbiology 2007, 153:2013-2025.
32. Li Y., Adams I.P., Wynn J.P., Ratledge C. Cloning and characterization of gene encoding a malic enzyme involved in anaerobic growth in Mucor circinelloides. Mycol. Res. 2005, 109:461-468.
33. Machida M., et al. Genome sequencing and analysis of Aspergillus oryzae. Nature 2005, 438:1157-1161.
34. Ratledge C. Regulation of lipid accumulation in oleaginous micro-organisms. Biochem. Soc. Trans. 2002, 30:1047-1050.
35. Wynn J.P., Hamid A.A., Li Y., Ratledge C. Biochemical events leading to the diversion of carbon into storage lipids in the oleaginous fungi Mucor circinelloides and Mortierella alpina. Microbiology 2001, 147:2857-2864.
36. Leonard A.E., Pereira S.L., Sprecher H., Huang Y.S. Elongation of long-chain fatty acids. Prog. Lipid Res. 2004, 43:36-54.
37. Parker-Barnes J.M., et al. Identification and characterization of an enzyme involved in the elongation of n-6 and n-3 polyunsaturated fatty acids. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:8284-8289.
38. Certik M., Shimizu S. Biosynthesis and regulation of microbial polyunsaturated fatty acid production. J. Biosci. Bioeng. 1999, 87:1-14.
39. Vicente G., et al. Direct transformation of fungal biomass from submerged cultures into biodiesel. Energy Fuel 2010, 24:3173-3178.
40. Beopoulos A., Chardot T., Nicaud J.M. Yarrowia lipolytica: a model and a tool to understand the mechanisms implicated in lipid accumulation. Biochimie 2009, 91:692-696.
41. Song Y., Wynn J.P., Li Y., Grantham D., Ratledge C. A pre-genetic study of the isoforms of malic enzyme associated with lipid accumulation in Mucor circinelloides. Microbiology 2001, 147:1507-1515.
42. Queiros O., Casal M., Althoff S., Moradas-Ferreira P., Leao C. Isolation and characterization of Kluyveromyces marxianus mutants deficient in malate transport. Yeast 1998, 14:401-407.
43. Srivastava A.K., Alexova R., Jeon Y.J., Kohli G.S., Neilan B.A. Assessment of salinity-induced photorespiratory glycolate metabolism in Anabaena sp. PCC 7120. Microbiology 2011, 157:911-917.
44. Weete J.D., Gandhi S.R. Biochemistry and molecular biology of fungal sterols. The Mycota III Biochemistry and Molecular Biology 1996, 421-438. Springer, Berlin, Germany. R. Brambl, G. Marzluf (Eds.).
45. Weete J.D., Gandhi S.R. Sterols and fatty acids of the Mortierellaceae: taxonomic implications. Mycologia 1999, 91:642-649.
46. David Nes W., Nichols S.D. Phytosterol biosynthesis pathway in Mortierella alpina. Phytochemistry 2006, 67:1716-1721.
47. Shimizu S., Kawashima H., Wada M., Yamada H. Occurrence of a novel sterol, 24,25-methylene cholest-5-en-3-beta-ol, in Mortierella alpina 1S-4. Lipids 1992, 27:481-483.
48. Safe S., Caldwell J. In vitro binding of sterols by extracts from Mucor rouxii cells grown under different environmental conditions. Can. J. Microbiol. 1976, 22:1163-1168.
49. Lübbehüsen T.L., Nielsen J., McIntyre M. Morphology and physiology of the dimorphic fungus Mucor circinelloides (syn. M. racemosus) during anaerobic growth. Mycol. Res. 2003, 107:223-230.
50. Vongsangnak W., Olsen P., Hansen K., Krogsgaard S., Nielsen J. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 2008, 9:245.
51. Andersen M.R., Nielsen M.L., Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol. Syst. Biol. 2008, 4:178.
52. Dobson P., et al. Further developments towards a genome-scale metabolic model of yeast. BMC Syst. Biol. 2010, 4:145.
53. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.