Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches

Systems and Synthetic Biology

Volumn 7, Issue 1-2, 2013, Pages 7-22

  Srivastava, Akriti ^a   Somvanshi, Pallavi ^b   Mishra, Bhartendu Nath ^a  

^a UNIVERSITY OF LUCKNOW   (India)

^b TERI UNIVERSITY   (India)

Author keywords

Carbohydrate; Pichia; Reconstruction; System biology

Indexed keywords

PICHIA; PICHIA PASTORIS;

EID: 84877051071     PISSN: 18725325     EISSN: 18725333     Source Type: Journal    
DOI: 10.1007/s11693-012-9102-2     Document Type: Article

References (43)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Ates O, Oner ET, Arga KY (2011) Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043. BMC Syst Biol 5: 12.
3. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LL (2005) The universal protein resource (UniProt). Nucleic Acids Res 33: 154-159.
4. Balamurugan G, Reddy VR, Suryanarayan VVS (2007) Pichia pastoris: a notable heterologous expression system for the production of foreign proteins-vaccines. IJBT 6: 175-186.
5. Bobrowicz P, Davidson RC, Li H, Potgeiter TI, Nett JH, Hamilton SR, Stadheim TA, Meile RG, Bobrowicz B, Mitchell T, Rausch S, Renfer E, Wildt S (2004) Engineering of an artificial glycosylation pathwayblocked in core oligosaccharide assembly in yeast Pichia pastoris: production of complex humanized glycoproteins with terminal galactose. Glycobiology 14(9): 757-766.
6. Boyer F, Viari A (2003) Ab initio reconstruction of metabolic pathways. Bioinformatics 19: 26-34.
7. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED (2012) Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res 40: 700-705.
8. Chung BKS, Selavarasu S, Camattari A, Ryu J, Lee H, Ahn J, Lee H, Lee DY (2010) Genome scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microb Cell Fact 9: 50.
9. Davidson RC, Bobrowicz P, Zha D. (2012) Metabolic engineering of a galactose assimilation pathway in the glycoengineered yeast Pichia pastoris. U. S. Patent 20120003695, January 5, 2012.
10. DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A (2007) Towards the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 8: 139.
11. Durot M, Bourguignon PY, Schachter V (2008) Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 33: 164-190.
12. Feist AM, Scholten JCM, Palsson BO, Brockman FJ, Ideker T (2006) Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. doi: 10. 1038/msb4100046.
13. Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO (2009) Reconstruction of biochemical networks in microbial organisms. Nat Rev Microbiol 7(2): 129-143.
14. Folger O, Jerby L, Frezza C, Gottleib E, Ruppin E, Shlomi T (2011) Predicting selective drug targets in cancer through metabolic networks. Mol Syst Biol 7: 501.
15. Forster J, Famili I, Fu P, Palsson BO, Nielsen J (2003) Genome scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13: 244-253.
16. Forth T, McConkey GA, Westhead DR (2010) MetNetMaker: a free and open source tool for the creation of novel metabolic networks in SBML format. Bioinformatics 26(18): 2352-2353.
17. Francke C, Seizen RJ, Teusink B (2005) Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol 13: 550-558.
18. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31: 3784-3788.
19. Ha S, Wang Y, Rustandi RR (2011) Biochemical and biophysical characterization of humanized IgG1 produced in Pichia pastoris. MAbs 3(5): 453-460.
20. Hu F, Li X, Lu J, Mao PH, Jin X, Rao B, Zheng P, Zhou YL, Liu SY, Ke T, Ma XD, Ma LX (2011) A visual method for direct selection of high-producing Pichia pastoris clones. BMC Biotechnol 11: 23.
21. Inan M, Meagher MM (2001) Non-repressing carbon sources for Alcohol Oxidase (AOX1) promoter of Pichia pastoris. J Biosci Bioeng 92(6): 585-589.
22. Jewison T, Knox C, Neveu V, Djoumbou Y, Guo AC, Lee J, Liu P, Mandal R, Krishnamurthy R, Sinelnikov I, Wilson M, Wishart DS (2012) YMDB: the yeast metabolome database. Nucleic Acids Res 40: 815-820.
23. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: 354-357.
24. Karp PD, Riley M, Paley SM, Pellegrini-toole A (2002) The metacyc database. Nucleic Acids Res 30: 59-61.
25. Kharchenko P, Vitkup D, Church GM (2004) Filling gaps in a metabolic network using expression information. Bioinformatics 20: 178-185.
26. Kuberl A, Schneider J, Thallinger GG, Anderl I, Wibberg D, Hajek T, Jaenicke S, Brinkrolf K, Goesmann A, Szczepanowski R, Puhler A, Schwab H, Gleider A, Pichler H (2011) High-quality genome sequence of Pichia pastoris CBS7435. J Biotechnol 154(4): 312-320.
27. Kumar VS, Dasika MS, Maranas CD (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8: 212.
28. Kurtzman CP (2005) Description of Komagataella phaffii sp. nov. and the transfer of Pichia pseudopastoris to the methylotrophic yeast genus Komagataella. Int J Syst Evol Microbiol 55: 973-976.
29. Mazurie A, Bonchev D, Schwikowski B, Buck GA (2010) Evolution of metabolic network organization. BMC Syst Biol 4: 59.
30. Milne CB, Eddy JA, Raju R, Ardekani S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND (2011) Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst Biol 5: 130.
31. Montagud A, Navarro E, de Cordoba PF, Urchueguia JF, Patil KR (2010) Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC Syst Biol 4: 156.
32. Notebaart RA, van Enckevort FHJ, Francke C, Seizen RJ, Teusink B (2006) Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics 7: 296.
33. Oberhardt MA, Palsson BO, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5: 320.
34. Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7: 238-251.
35. Schellenberger J, Park JO, Conrad TM, Palsson BO (2010) BiGG: a biochemical genetics and genomics knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11: 213.
36. Schutter KD, Lin YC, Tiels P, Hecke AV, Glinka S, Lehmann JW, Rouze P, de Peer YV, Callewaert N (2009) Genome sequence of recombinant protein production host Pichia pastoris. Nat Biotechnol 7: 561-566.
37. Seo S, Lewin HA (2009) Reconstruction of metabolic pathways for cattle genome. BMC Syst Biol 3: 33.
38. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
39. Thiele I, Palsson BO (2010) A protocol for generating a high quality genome-scale metabolic reconstruction. Nat Protoc 5(1): 93-121.
40. van Rensburg P, van Zyl WH, Pretorius IS (1998) Engineering yeast for efficient cellulose degradation. Yeast 14(1): 67-76.
41. Weidner M, Taupp M, Hallam SJ (2010). Expression of recombinant proteins in methylotrophic yeast Pichia pastoris. J Vis Exp. 36.
42. Yadava A, Ockenhouse CF (2003) Effect of codon optimization on expression levels of a functionally folded malaria vaccine candidate in prokaryotic and eukaryotic expression systems. Infect Immun 71(9): 4961-4969.
43. Zhang W, Liu C, Wang G, Ma Y, Zhang K, Zou S, Zhang M (2012) Comparison of expression in Saccharomyces cerevisiae of endoglucanase II from Trichoderma reesei and Endoglucanase I from Aspergillus aculeatus. BioResource 7(3): 4031-4045.