A systems biology approach to optimising hosts for industrial protein production

Biotechnology Letters

Volumn 35, Issue 12, 2013, Pages 1961-1969

  Royle, Kate ^a   Kontoravdi, Cleo ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Chaperones; Enzyme production; Industrial proteins; Mathematical modelling; Molecular toolboxes; Recombinant protein production; Synthetic biology

Indexed keywords

CHAPERONES; ENZYME PRODUCTION; INDUSTRIAL PROTEINS; MOLECULAR TOOLBOXES; RECOMBINANT PROTEIN PRODUCTIONS; SYNTHETIC BIOLOGY;

BIOLOGY; INDUSTRY; MATHEMATICAL MODELS; RECOMBINANT PROTEINS;

OPTIMIZATION;

ENZYME; RECOMBINANT PROTEIN;

BIOLOGICAL MODEL; MICROBIOLOGY; REVIEW; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

ENZYMES; INDUSTRIAL MICROBIOLOGY; MODELS, BIOLOGICAL; RECOMBINANT PROTEINS; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

EID: 84887318841     PISSN: 01415492     EISSN: 15736776     Source Type: Journal    
DOI: 10.1007/s10529-013-1297-0     Document Type: Review

References (44)

1. Aggarwal S (2012) What's fueling the biotech engine-2011 to 2012. Nat Biotechnol 30: 1191-1197.
2. Carrera J, Rodrigo G, Singh V, Kirov B, Jaramillo A (2011) Empirical model and in vivo characterization of the bacterial response to synthetic gene expression show that ribosome allocation limits growth rate. Biotechnol J 6: 773-783.
3. Chen X, Liu YD, Flynn GC (2009) The effect of Fc glycan forms on human IgG2 antibody clearance in humans. Glycobiology 19: 240-249.
4. Chen BS, Hsu CY, Liou JJ (2011) Robust design of biological circuits: evolutionary systems biology approach. J Biomed Biotechnol 2011: 304236.
5. Credle JJ, Finer-Moore JS, Papa FR, Stroud RM, Walter P (2005) On the mechanism of sensing unfolded protein in the endoplasmic reticulum. Proc Natl Acad Sci USA 102: 18773-18784.
6. Demain AL, Vaishnav P (2009) Production of recombinant proteins by microbes and higher organisms. Biotechnol Adv 27: 297-306.
7. Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477: 471-476.
8. Ellis T, Wang X, Collins JJ (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol 27: 465-471.
9. Erguler K, Pieri M, Deltas C (2013) A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis. BMC Syst Biol 7: 16.
10. EvaluatePharma (2012) World preview 2018: embracing the patent cliff.
11. Foley PL, Shuler ML (2010) Considerations for the design and construction of a synthetic platform cell for biotechnological applications. Biotechnol Bioeng 105: 26-36.
12. Gardner BM, Walter P (2011) Unfolded proteins are Ire1-activating ligands that directly induce the unfolded protein response. Science 333: 1891-1894.
13. Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475: 324-332.
14. Heavner B, Smallbone K, Barker B, Mendes P, Walker L (2012) Yeast 5-an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 6: 55.
15. Hildebrandt S, Raden D, Petzold L, Robinson AS, Doyle FJ (2008) A top-down approach to mechanistic biological modeling: application to the single-chain antibody folding pathway. Biophys J 95: 3535-3558.
16. Inan M, Aryasomayajula D, Sinha J, Meagher MM (2006) Enhancement of protein secretion in Pichia pastoris by overexpression of protein disulfide isomerase. Biotechnol Bioeng 93: 771-778.
17. Jimenez del Val I, Nagy JM, Kontoravdi C (2011) A dynamic mathematical model for monoclonal antibody N-linked glycosylation and nucleotide sugar donor transport within a maturing Golgi apparatus. Biotechnol Prog 27: 1730-1743.
18. Kimata Y, Kohno K (2011) Endoplasmic reticulum stress-sensing mechanisms in yeast and mammalian cells. Curr Opin Cell Biol 23: 135-142.
19. Kimata Y, Kimata YI, Shimizu Y, Abe H, Farcasanu IC, Takeuchi M, Rose MD, Kohno K (2003) Genetic evidence for a role of BiP/Kar2 that regulates Ire1 in response to accumulation of unfolded proteins. Mol Biol Cell 14: 2559-2569.
20. Kimata Y, Oikawa D, Shimizu Y, Ishiwata-Kimata Y, Kohno K (2004) A role for BiP as an adjustor for the endoplasmic reticulum stress-sensing protein Ire1. J Cell Biol 167: 445-456.
21. Kobeissy FH, Guingab-Cagmat JD, Razafsha M, O'Steen L, Zhang Z, Hayes RL, Chiu W-T, Wang KKW (2011) Leveraging biomarker platforms and systems biology for rehabilomics and biologics effectiveness research. PM & R 3: S139-S147.
22. Kudla G, Murray AW, Tollervey D, Plotkin JB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255-258.
23. Love KR, Politano TJ, Panagiotou V, Jiang B, Stadheim TA, Love JC (2012) Systematic single-cell analysis of Pichia pastoris reveals secretory capacity limits productivity. PLoS ONE 7: e37915.
24. Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J (2011) In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol 29: 1114-1116.
25. Nevozhay D, Zal T, Balazsi G (2013) Transferring a synthetic gene circuit from yeast to mammalian cells. Nat Commun 4: 1451.
26. O'Brien EP, Vendruscolo M, Dobson CM (2012) Prediction of variable translation rate effects on cotranslational protein folding. Nat Commun 3: 868.
27. Oikawa D, Kitamura A, Kinjo M, Iwawaki T (2012) Direct association of unfolded proteins with mammalian ER stress sensor, Ire1β. PLoS ONE 7: e51290.
28. Pincus D, Chevalier MW, Aragon T, van Anken E, Vidal SE, El-Samad H, Walter P (2010) BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response. PLoS Biol 8: e1000415.
29. Powers ET, Powers DL, Gierasch LM (2012) FoldEco: a model for proteostasis in E. coli. Cell Rep 1: 265-276.
30. Racle J, Overney J, Hatzimanikatis V (2012) A computational framework for the design of optimal protein synthesis. Biotechnol Bioeng 109: 2127-2133.
31. Raden D, Hildebrandt S, Xu P, Bell E, Doyle FJ 3rd, Robinson AS (2005) Analysis of cellular response to protein overexpression. IEE Proc Syst Biol 152: 285-289.
32. Sekhar A, Lam HN, Cavagnero S (2012) Protein folding rates and thermodynamic stability are key determinants for interaction with the Hsp70 chaperone system. Protein Sci 21: 1489-1502.
33. Siller E, DeZwaan DC, Anderson JF, Freeman BC, Barral JM (2010) Slowing bacterial translation speed enhances eukaryotic protein folding efficiency. J Mol Biol 396: 1310-1318.
34. Storms ZJ, Brown T, Sauvageau D, Cooper DG (2012) Self-cycling operation increases productivity of recombinant protein in Escherichia coli. Biotechnol Bioeng 109: 2262-2270.
35. Sunley K, Butler M (2010) Strategies for the enhancement of recombinant protein production from mammalian cells by growth arrest. Biotechnol Adv 28: 385-394.
36. Tyson JJ, Baumann WT, Chen C, Verdugo A, Tavassoly I, Wang Y, Weiner LM, Clarke R (2011) Dynamic modelling of oestrogen signalling and cell fate in breast cancer cells. Nat Rev Cancer 11: 523-532.
37. van den Berg BA, Reinders MJT, Hulsman M, Wu L, Pel HJ, Roubos JA, de Ridder D (2012) Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger. PLoS ONE 7: e45869.
38. Walter P, Ron D (2011) The unfolded protein response: from stress pathway to homeostatic regulation. Science 334: 1081-1086.
39. Warne T, Serrano-Vega MJ, Tate CG, Schertler GFX (2009) Development and crystallization of a minimal thermostabilised G protein-coupled receptor. Protein Expr Purif 65: 204-213.
40. Welch M, Govindarajan S, Ness JE, Villalobos A, Gurney A, Minshull J, Gustafsson C (2009) Design parameters to control synthetic gene expression in Escherichia coli. PLoS ONE 4: 10.
41. Whyteside G, Alcocer MJC, Kumita JR, Dobson CM, Lazarou M, Pleass RJ, Archer DB (2011) Native-state stability determines the extent of degradation relative to secretion of protein variants from Pichia pastoris. PLoS ONE 6: e22692.
42. Wiseman RL, Powers ET, Buxbaum JN, Kelly JW, Balch WE (2007) An adaptable standard for protein export from the endoplasmic reticulum. Cell 131: 809-821.
43. Xu P, Raden D, Doyle FJ III, Robinson AS (2005) Analysis of unfolded protein response during single-chain antibody expression in Saccaromyces cerevisiae reveals different roles for BiP and PDI in folding. Metab Eng 7: 269-279.
44. Zhou M, Guo J, Cha J, Chae M, Chen S, Barral JM, Sachs MS, Liu Y (2013) Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 495: 111-115.