Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 18, 2013, Pages 7229-7234

  Yi, Li ^a   Gebhard, Mark C ^b   Li, Qing ^a   Taft, Joseph M ^a   Georgiou, George ^a,b   Iverson, Brent L ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b The University of Texas at Austin   (United States)

Author keywords

Directed evolution; Method; Protein engineering

Indexed keywords

ABELSON KINASE; AGA2 RECEPTOR; CYSTEINE PROTEINASE; EPITOPE; HYBRID PROTEIN; PROTEIN VARIANT; RECEPTOR; TOBACCO ETCH VIRUS PROTEASE; UNCLASSIFIED DRUG;

ARTICLE; COMBINATORIAL LIBRARY; ENDOPLASMIC RETICULUM; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN STRUCTURE; SINGLE CELL ANALYSIS; YEAST CELL;

COMBINATORIAL CHEMISTRY TECHNIQUES; ENDOPEPTIDASES; ENDOPLASMIC RETICULUM; FLOW CYTOMETRY; HUMANS; KINETICS; MUTANT PROTEINS; PROTEIN ENGINEERING; RECOMBINANT FUSION PROTEINS; SACCHAROMYCES CEREVISIAE; SINGLE-CELL ANALYSIS; SUBSTRATE SPECIFICITY;

HEPATITIS C VIRUS; TOBACCO ETCH VIRUS;

EID: 84876919211     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1215994110     Document Type: Article

References (37)

1. Marnett AB, Craik CS (2005) Papa's got a brand new tag: Advances in identification of proteases and their substrates. Trends Biotechnol 23(2):59-64. (Pubitemid 40127337)
2. Overall CM, Blobel CP (2007) In search of partners: Linking extracellular proteases to substrates. Nat Rev Mol Cell Biol 8(3):245-257.
3. Schilling O, Overall CM (2008) Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat Biotechnol 26(6):685-694. (Pubitemid 351809596)
4. Chanalia P, Gandhi D, Jodha D, Singh J (2011) Applications of microbial proteases in pharmaceutical industry: An overview. Rev Med Microbiol 22(4):96-101.
5. Gupta R, Beg QK, Lorenz P (2002) Bacterial alkaline proteases: Molecular approaches and industrial applications. Appl Microbiol Biotechnol 59(1):15-32. (Pubitemid 34809671)
6. Wehr MC, et al. (2006) Monitoring regulated protein-protein interactions using split TEV. Nat Methods 3(12):985-993. (Pubitemid 44782697)
7. Collen D, Lijnen HR (1991) Basic and clinical aspects of fibrinolysis and thrombolysis. Blood 78(12):3114-3124.
8. Craik CS, Page MJ, Madison EL (2011) Proteases as therapeutics. Biochem J 435(1):1-16.
9. Drag M, Salvesen GS (2010) Emerging principles in protease-based drug discovery. Nat Rev Drug Discov 9(9):690-701.
10. Gray DC, Mahrus S, Wells JA (2010) Activation of specific apoptotic caspases with an engineered small-molecule-activated protease. Cell 142(4):637-646.
11. Waugh DS (2011) An overview of enzymatic reagents for the removal of affinity tags. Protein Expr Purif 80(2):283-293.
12. Hedstrom L, Szilagyi L, Rutter WJ (1992) Converting trypsin to chymotrypsin: The role of surface loops. Science 255(5049):1249-1253.
13. Lim EJ, et al. (2007) Swapping the substrate specificities of the neuropeptidases neurolysin and thimet oligopeptidase. J Biol Chem 282(13):9722-9732. (Pubitemid 47104597)
14. Sellamuthu S, et al. (2008) Engineering of protease variants exhibiting altered substrate specificity. Biochem Biophys Res Commun 371(1):122-126.
15. Varadarajan N, Rodriguez S, Hwang BY, Georgiou G, Iverson BL (2008) Highly active and selective endopeptidases with programmed substrate specificities. Nat Chem Biol 4(5):290-294. (Pubitemid 351550889)
16. Verhoeven KD, Altstadt OC, Savinov SN (2012) Intracellular detection and evolution of site-specific proteases using a genetic selection system. Appl Biochem Biotechnol 166(5):1340-1354.
17. Villa JP, Bertenshaw GP, Bond JS (2003) Critical amino acids in the active site of meprin metalloproteinases for substrate and peptide bond specificity. J Biol Chem 278(43):42545-42550. (Pubitemid 37310527)
18. Aharoni A, Amitai G, Bernath K, Magdassi S, Tawfik DS (2005) High-throughput screening of enzyme libraries: Thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. Chem Biol 12(12):1281-1289. (Pubitemid 41779468)
19. Gould SM, Tawfik DS (2005) Directed evolution of the promiscuous esterase activity of carbonic anhydrase II. Biochemistry 44(14):5444-5452. (Pubitemid 40489983)
20. Varadarajan N, Georgiou G, Iverson BL (2008) An engineered protease that cleaves specifically after sulfated tyrosine. Angew Chem Int Ed Engl 47(41):7861-7863.
21. Varadarajan N, Pogson M, Georgiou G, Iverson BL (2009) Proteases that can distinguish among different post-translational forms of tyrosine engineered using multicolor flow cytometry. J Am Chem Soc 131(50):18186-18190.
22. Yoo TH, Pogson M, Iverson BL, Georgiou G (2012) Directed evolution of highly selective proteases by using a novel FACS-based screen that capitalizes on the p53 regulator MDM2. ChemBioChem 13(5):649-653.
23. Pogson M, Georgiou G, Iverson BL (2009) Engineering next generation proteases. Curr Opin Biotechnol 20(4):390-397.
24. Daugherty PS (2007) Protein engineering with bacterial display. Curr Opin Struct Biol 17(4):474-480.
25. Stevens RC (2000) Design of high-throughput methods of protein production for structural biology. Structure 8(9):R177-R185.
26. Kapust RB, et al. (2001) Tobacco etch virus protease: Mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng 14(12):993-1000. (Pubitemid 34137240)
27. Phan J, et al. (2002) Structural basis for the substrate specificity of tobacco etch virus protease. J Biol Chem 277(52):50564-50572. (Pubitemid 36042215)
28. Boulware KT, Jabaiah A, Daugherty PS (2010) Evolutionary optimization of peptide substrates for proteases that exhibit rapid hydrolysis kinetics. Biotechnol Bioeng 106(3):339-346.
29. Dougherty WG, Carrington JC, Cary SM, Parks TD (1988) Biochemical and mutational analysis of a plant virus polyprotein cleavage site. EMBO J 7(5):1281-1287.
30. Kostallas G, Löfdahl PA, Samuelson P (2011) Substrate profiling of tobacco etch virus protease using a novel fluorescence-assisted whole-cell assay. PLoS ONE 6(1):e16136.
31. Pelham HR, Hardwick KG, Lewis MJ (1988) Sorting of soluble ER proteins in yeast. EMBO J 7(6):1757-1762.
32. Semenza JC, Hardwick KG, Dean N, Pelham HR (1990) ERD2, a yeast gene required for the receptor-mediated retrieval of luminal ER proteins from the secretory pathway. Cell 61(7):1349-1357.
33. Boder ET, Wittrup KD (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15(6):553-557. (Pubitemid 27251573)
34. Bloom JD, Arnold FH (2009) In the light of directed evolution: Pathways of adaptive protein evolution. Proc Natl Acad Sci USA 106(Suppl 1):9995-10000.
35. Khersonsky O, Tawfik DS (2010) Enzyme promiscuity: A mechanistic and evolutionary perspective. Annu Rev Biochem 79:471-505.
36. O'Loughlin TL, Greene DN, Matsumura I (2006) Diversification and specialization of HIV protease function during in vitro evolution. Mol Biol Evol 23(4):764-772.
37. Varadarajan N, Gam J, Olsen MJ, Georgiou G, Iverson BL (2005) Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity. Proc Natl Acad Sci USA 102(19):6855-6860. (Pubitemid 40675406)