Yeast-based bioproduction of disulfide-rich peptides and their cyclization via asparaginyl endopeptidases

Kuok Yap, Junqiao Du, Fabian B. H. Rehm, Shyn Ric Tang, Yan Zhou, Jing Xie, Conan K. Wang, Simon J. de Veer, Linda H. L. Lua, Thomas Durek, David J. Craik

Published: 2021-02-16 DOI: 10.1038/s41596-020-00483-0

Pichia pastoris

cyclic peptides

asparaginyl endopeptidases

bioproduction

enzymatic cyclization

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Supplementary information

Supplementary Information

Supplementary Figs. 1–3.

Reporting Summary

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Colgrave, M. L. & Craik, D. J. Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: the importance of the cyclic cystine knot. Biochemistry 43, 5965–5975 (2004).
Colgrave, M. L., Korsinczky, M. J., Clark, R. J., Foley, F. & Craik, D. J. Sunflower trypsin inhibitor-1, proteolytic studies on a trypsin inhibitor peptide and its analogs. Biopolymers 94, 665–672 (2010).
Isidro-Llobet, A. et al. Sustainability challenges in peptide synthesis and purification: from R&D to production. J. Org. Chem. 84, 4615–4628 (2019).
Merrifield, R. B. Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J. Am. Chem. Soc. 85, 2149–2154 (1963).
Yap, K. et al. An environmentally sustainable biomimetic production of cyclic disulfide-rich peptides. Green Chem. 22, 5002–5016 (2020).
Cheneval, O. et al. Fmoc-based synthesis of disulfide-rich cyclic peptides. J. Org. Chem. 79, 5538–5544 (2014).
El Hamdaoui, Y. et al. Periplasmic expression of 4/7 α-conotoxin TxIA analogues in E. coli favours ribbon isomer formation—suggestion of a binding mode at the α7 nAChR. Front. Pharmacol 10, 577 (2019).
Gasser, B. et al. Pichia pastoris: protein production host and model organism for biomedical research. Future Microbiol. 8, 191–208 (2013).
Pokoj, S. et al. Pichia pastoris is superior to E. coli for the production of recombinant allergenic non-specific lipid-transfer proteins. Protein Expr. Purif. 69, 68–75 (2010).
Cregg, J. M., Vedvick, T. S. & Raschke, W. C. Recent advances in the expression of foreign genes in Pichia pastoris. Biotechnology 11, 905–910 (1993).
Cregg, J. M., Cereghino, J. L., Shi, J. & Higgins, D. R. Recombinant protein expression in Pichia pastoris. Mol. Biotechnol. 16, 23–52 (2000).
Gassler, T. et al. The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2. Nat. Biotechnol. 38, 210–216 (2020).
Poon, S. et al. Co-expression of a cyclizing asparaginyl endopeptidase enables efficient production of cyclic peptides in planta. J. Exp. Bot. 69, 633–641 (2018).
Jagadish, K. et al. Recombinant expression and phenotypic screening of a bioactive cyclotide against α‐synuclein‐induced cytotoxicity in baker’s yeast. Angew. Chem. Int. Ed 54, 8390–8394 (2015).
Li, Y., Aboye, T., Breindel, L., Shekhtman, A. & Camarero, J. A. Efficient recombinant expression of SFTI‐1 in bacterial cells using intein‐mediated protein trans‐splicing. Pept. Sci. 106, 818–824 (2016).
Toplak, A., Nuijens, T., Quaedflieg, P. J., Wu, B. & Janssen, D. B. Peptiligase, an enzyme for efficient chemoenzymatic peptide synthesis and cyclization in water. Adv. Synth. Catal. 358, 2140–2147 (2016).
Antos, J. M. et al. A straight path to circular proteins. J. Biol. Chem. 284, 16028–16036 (2009).
Du, J. et al. A bifunctional asparaginyl endopeptidase efficiently catalyzes both cleavage and cyclization of cyclic trypsin inhibitors. Nat. Commun. 11, 1575 (2020).
Harris, K. S. et al. Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase. Nat. Commun. 6, 10199 (2015).
Nguyen, G. K. et al. Butelase 1 is an Asx-specific ligase enabling peptide macrocyclization and synthesis. Nat. Chem. Biol. 10, 732–738 (2014).
Lin-Cereghino, G. P. et al. The effect of alpha-mating factor secretion signal mutations on recombinant protein expression in Pichia pastoris. Gene 519, 311–317 (2013).
Cabral, K. M., Almeida, M. S., Valente, A. P., Almeida, F. C. & Kurtenbach, E. Production of the active antifungal Pisum sativum defensin 1 (Psd1) in Pichia pastoris: overcoming the inefficiency of the STE13 protease. Protein Expr. Purif. 31, 115–122 (2003).
Yang, R. et al. Engineering a catalytically efficient recombinant protein ligase. J. Am. Chem. Soc. 139, 5351–5358 (2017).
Tolner, B., Smith, L., Begent, R. H. & Chester, K. A. Production of recombinant protein in Pichia pastoris by fermentation. Nat. Protoc. 1, 1006–1021 (2006).
Armishaw, C. J., Dutton, J. L., Craik, D. J. & Alewood, P. F. Establishing regiocontrol of disulfide bond isomers of α‐conotoxin ImI via the synthesis of N‐to‐C cyclic analogs. Peptide Sci. 94, 307–313 (2010).
Lovelace, E. S. et al. Stabilization of α-conotoxin AuIB: influences of disulfide connectivity and backbone cyclization. Antioxid. Redox Signal. 14, 87–95 (2011).
Lovelace, E. S. et al. Cyclic MrIA: a stable and potent cyclic conotoxin with a novel topological fold that targets the norepinephrine transporter. J. Med. Chem. 49, 6561–6568 (2006).
Dawson, P. E., Muir, T. W., Clark-Lewis, I. & Kent, S. B. Synthesis of proteins by native chemical ligation. Science 266, 776–779 (1994).
Jia, X. Y. et al. Semienzymatic cyclization of disulfide-rich peptides using sortase A. J. Biol. Chem. 289, 6627–6638 (2014).
Wu, Z., Guo, X. & Guo, Z. Sortase A-catalyzed peptide cyclization for the synthesis of macrocyclic peptides and glycopeptides. ChemComm 47, 9218–9220 (2011).
Schmidt, M. et al. Efficient enzymatic cyclization of disulfide‐rich peptides by using peptide ligases. ChemBioChem 20, 1524–1529 (2019).
Schmidt, M. et al. Omniligase‐1: a powerful tool for peptide head‐to‐tail cyclization. Adv. Synth. Catal. 359, 2050–2055 (2017).
Hemu, X., Qiu, Y., Nguyen, G. K. & Tam, J. P. Total synthesis of circular bacteriocins by butelase 1. J. Am. Chem. Soc. 138, 6968–6971 (2016).
Nguyen, G. K., Hemu, X., Quek, J. P. & Tam, J. P. Butelase-mediated macrocyclization of d-amino-acid-containing peptides. Angew. Chem. Int. Ed. Engl. 55, 12802–12806 (2016).
Johnson, B. H. & Hecht, M. H. Recombinant proteins can be isolated from E. coli cells by repeated cycles of freezing and thawing. Biotechnology 12, 1357–1360 (1994).
Feliu, J., Cubarsi, R. & Villaverde, A. Optimized release of recombinant proteins by ultrasonication of E. coli cells. Biotechnol. Bioeng. 58, 536–540 (1998).
Rehm, F. B. H. et al. Site-specific sequential protein labeling catalyzed by a single recombinant ligase. J. Am. Chem. Soc. 141, 17388–17393 (2019).
Rehm, F. B. H., Tyler, T. J., Yap, K., Durek, T. & Craik, D. J. Improved asparaginyl ligase‐catalyzed transpeptidation via selective nucleophile quenching. Angew. Chem. Int. Ed. http://doi.org/10.1002/anie.202013584 (2020).

Yeast-based bioproduction of disulfide-rich peptides and their cyclization via asparaginyl endopeptidases

Supplementary information

Supplementary Information

Reporting Summary

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