Improving functional annotation for industrial microbes: A case study with pichia pastoris

Trends in Biotechnology

Volumn 32, Issue 8, 2014, Pages 396-399

  Dikicioglu, Duygu ^a   Wood, Valerie ^a   Rutherford, Kim M ^a   McDowall, Mark D ^b   Oliver, Stephen G ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Italy)

Author keywords

Functional annotation; Industrial microbes; Komagataella pastoris; Pichia pastoris; Recombinant protein production

Indexed keywords

BACTERIA; BIOLOGY; ESCHERICHIA COLI; INDUSTRY;

FUNCTIONAL ANNOTATION; INDUSTRIAL MICROBES; PASTORIS; PICHIA PASTORIS; RECOMBINANT PROTEIN PRODUCTIONS;

YEAST;

BIOINFORMATICS; BIOTECHNOLOGY; DRUG INDUSTRY; GENE INTERACTION; GENE ONTOLOGY; GENE SEQUENCE; MICROBIAL COMMUNITY; NONHUMAN; PICHIA PASTORIS; PRIORITY JOURNAL; REVIEW; SYNTHETIC BIOLOGY; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PHYSIOLOGY; PICHIA; PROCEDURES;

ESCHERICHIA COLI; PICHIA PASTORIS; SACCHAROMYCES CEREVISIAE;

FUNGAL PROTEIN;

BIOTECHNOLOGY; FUNGAL PROTEINS; INDUSTRIAL MICROBIOLOGY; MOLECULAR SEQUENCE ANNOTATION; PICHIA;

EID: 84904703785     PISSN: 01677799     EISSN: 18793096     Source Type: Journal    
DOI: 10.1016/j.tibtech.2014.05.003     Document Type: Review

References (39)

1. Hazeu W., et al. The fine structure of microbodies in the yeast Pichia pastoris. Experientia 1975, 31:926-927.
2. Ellis S.B., et al. Isolation of alcohol oxidase and two other methanol regulatable genes from the yeast Pichia pastoris. Mol. Cell. Biol. 1985, 5:1111-1121.
3. Cregg J.M., et al. Pichia pastoris as a host system for transformations. Mol. Cell. Biol. 1985, 5:3376-3385.
4. Celik E., Calik P. Production of recombinant proteins by yeast cells. Biotechnol. Adv. 2012, 30:1108-1118.
5. Dunn W.A., et al. Pexophagy: the selective autophagy of peroxisomes. Autophagy 2005, 1:75-83.
6. Yamada Y., et al. The phylogenetic relationships of methanol-assimilating yeasts based on the partial sequences of 18S and 26S ribosomal RNAs: the proposal of Komagataella Gen. Nov. (Saccharomycetaceae). Biosci. Biotechnol. Biochem. 1995, 59:439-444.
7. Kurtzman C.P. Biotechnological strains of Komagataella (Pichia) pastoris are Komagataella phaffii as determined from multigene sequence analysis. J. Ind. Microbiol. Biotechnol. 2009, 36:1435-1438.
8. Mattanovich D., et al. Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris. Microb. Cell Fact. 2009, 8:29.
9. De Schutter K., et al. Genome sequence of the recombinant protein production host Pichia pastoris. Nat. Biotechnol. 2009, 27:561-566.
10. Küberl A., et al. High-quality genome sequence of Pichia pastoris CBS7435. J. Biotechnol. 2011, 154:312-320.
11. Rustici G., et al. ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Res. 2013, 41:D987-D990.
12. Barrett T., et al. NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res. 2013, 41:D991-D995.
13. Graf A., et al. Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays. BMC Genomics 2008, 9:390.
14. Hesketh A.R., et al. Investigating the physiological response of Pichia (Komagataella) pastoris GS115 to the heterologous expression of misfolded proteins using chemostat cultures. Appl. Microbiol. Biotechnol. 2013, 97:9747-9762.
15. Vanz A.L., et al. Physiological response of Pichia pastoris GS115 to methanol-induced high level production of the hepatitis B surface antigen: catabolic adaptation, stress responses, and autophagic processes. Microb. Cell Fact. 2012, 11:103.
16. Huang C-J., et al. A proteomic analysis of the Pichia pastoris secretome in methanol-induced cultures. Appl. Microbiol. Biotechnol. 2011, 90:235-247.
17. Ivashov V.A., et al. Lipidome and proteome of lipid droplets from the methylotrophic yeast Pichia pastoris. Biochim. Biophys. Acta 2013, 1831:282-290.
18. Dragosits M., et al. The effect of temperature on the proteome of recombinant Pichia pastoris. J. Proteome Res. 2009, 8:1380-1392.
19. Carnicer M., et al. Quantitative metabolomics analysis of amino acid metabolism in recombinant Pichia pastoris under different oxygen availability conditions. Microb. Cell Fact. 2012, 11:83.
20. Tredwell G.D., et al. The development of metabolomic sampling procedures for Pichia pastoris, and baseline metabolome data. PLoS ONE 2011, 6:e16286.
21. Klavins K., et al. Interlaboratory comparison for quantitative primary metabolite profiling in Pichia pastoris. Anal. Bioanal. Chem. 2013, 405:5159-5169.
22. 13C flux analysis. BMC Syst. Biol. 2013, 7:17.
23. Neubauer S., et al. U13C cell extract of Pichia pastoris - a powerful tool for evaluation of sample preparation in metabolomics. J. Sep. Sci. 2012, 35:3091-3105.
24. Celik E., et al. Metabolic flux analysis for recombinant protein production by Pichia pastoris using dual carbon sources: effects of methanol feeding rate. Biotechnol. Bioeng. 2010, 105:317-329.
25. Sohn S.B., et al. Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production. Biotechnol. J. 2010, 5:705-715.
26. Chung B.K., et al. Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microb. Cell Fact. 2010, 9:50.
27. Caspeta L., et al. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst. Biol. 2012, 6:24.
28. Kerrien S., et al. IntAct--open source resource for molecular interaction data. Nucleic Acids Res. 2007, 35:D561-D565.
29. Chatr-aryamontri A., et al. MINT: the Molecular INTeraction database. Nucleic Acids Res. 2007, 35:D572-D574.
30. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013, 41:D43-D47. The UniProt Consortium.
31. Pruitt K.D., et al. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 2009, 37:D32-D36.
32. Kersey P.J., et al. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 2012, 40:D91-D97.
33. Jensen L.J., et al. STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009, 37:D412-D416.
34. Kanehisa M., et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012, 40:D109-D114.
35. Ashburner M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
36. Skunca N., et al. Quality of computationally inferred gene ontology annotations. PLoS Comput. Biol. 2012, 8:e1002533.
37. Dimmer E.C., et al. The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 2012, 40:D565-D570.
38. Rutherford K.M., et al. Canto: an online tool for community literature curation. Bioinformatics 2014, 30:1791-1792.
39. Stark C., et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39:D698-D704.