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In situ detection of protein interactions for recombinant therapeutic enzymes
  • +8
  • Mojtaba Samoudi,
  • Chih-Chung Kuo,
  • Caressa Robinson,
  • Km Shams-Ud-DohaOrcid,
  • Song-Min Schinn,
  • Stefan Kol,
  • Linus Weiss,
  • Sara Petersen Bjørn,
  • Bjørn Voldborg,
  • Alexandre Rosa Campos,
  • Nathan Lewis
Mojtaba Samoudi
University of California San Diego
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Chih-Chung Kuo
University of California San Diego
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Caressa Robinson
University of California San Diego
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Km Shams-Ud-Doha
Orcid
Sanford Burnham Prebys Medical Discovery Institute
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Song-Min Schinn
University of California San Diego
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Stefan Kol
Technical University of Denmark
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Linus Weiss
Eberhard Karls University Tübingen
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Sara Petersen Bjørn
DTU Biosustain
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Bjørn Voldborg
DTU Biosustain
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Alexandre Rosa Campos
Sanford Burnham Prebys Medical Discovery Institute
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Nathan Lewis
University of California, San Diego
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Peer review status:IN REVISION

13 May 2020Submitted to Biotechnology and Bioengineering
15 May 2020Assigned to Editor
15 May 2020Submission Checks Completed
18 May 2020Reviewer(s) Assigned
14 Jun 2020Review(s) Completed, Editorial Evaluation Pending
14 Jun 2020Editorial Decision: Revise Major

Abstract

Despite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and post-translational modifications (PTMs). Here we aimed to identify the machinery supporting recombinant protein secretion by measuring the protein-protein interaction (PPI) networks of four different recombinant proteins (SERPINA1, SERPINC1, SERPING1 and SeAP) with various PTMs and structural motifs using the proximity-dependent biotin identification (BioID) method. We identified PPIs associated with specific features of the secreted proteins using a Bayesian statistical model, and found proteins involved in protein folding, disulfide bond formation and N-glycosylation were positively correlated with the corresponding features of the four model proteins. Among others, oxidative folding enzymes showed the strongest association with disulfide bond formation, supporting their critical roles in proper folding and maintaining the ER stability. Knock down of ERP44, a measured interactor with the highest fold change, led to the decreased secretion of SERPINC1, which relies on its extensive disulfide bonds. Proximity-dependent labeling successfully identified the transient interactions supporting synthesis of secreted recombinant proteins and refined our understanding of key molecular mechanisms of the secretory pathway during recombinant protein production.