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Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

Morgane Boone (UGent) , Pathmanaban Ramasamy (UGent) , Jasper Zuallaert (UGent) , Robbin Bouwmeester (UGent) , Berre Van Moer (UGent) , Davy Maddelein (UGent) , Demet Turan (UGent) , Niels Hulstaert (UGent) , Hannah Eeckhaut (UGent) , Elien Vandermarliere (UGent) , et al.
(2021) NATURE COMMUNICATIONS. 12(1).
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Abstract
While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >10(5) protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies. The exact protein features that control passage through the eukaryotic secretory system remain largely unknown. Here the authors report SECRiFY which they use to evaluate the secretory potential of polypeptides on a proteome-wide scale in yeast, revealing a role for flexibility and intrinsic disorder.
Keywords
General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, ENDOPLASMIC-RETICULUM, BINDING-SPECIFICITY, HUMAN-ANTIBODIES, GLOBAL ANALYSIS, QUALITY-CONTROL, EXPRESSION, SURFACE, PREDICTION, LIBRARY, TRANSFORMATION

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MLA
Boone, Morgane, et al. “Massively Parallel Interrogation of Protein Fragment Secretability Using SECRiFY Reveals Features Influencing Secretory System Transit.” NATURE COMMUNICATIONS, vol. 12, no. 1, 2021, doi:10.1038/s41467-021-26720-y.
APA
Boone, M., Ramasamy, P., Zuallaert, J., Bouwmeester, R., Van Moer, B., Maddelein, D., … Callewaert, N. (2021). Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-021-26720-y
Chicago author-date
Boone, Morgane, Pathmanaban Ramasamy, Jasper Zuallaert, Robbin Bouwmeester, Berre Van Moer, Davy Maddelein, Demet Turan, et al. 2021. “Massively Parallel Interrogation of Protein Fragment Secretability Using SECRiFY Reveals Features Influencing Secretory System Transit.” NATURE COMMUNICATIONS 12 (1). https://doi.org/10.1038/s41467-021-26720-y.
Chicago author-date (all authors)
Boone, Morgane, Pathmanaban Ramasamy, Jasper Zuallaert, Robbin Bouwmeester, Berre Van Moer, Davy Maddelein, Demet Turan, Niels Hulstaert, Hannah Eeckhaut, Elien Vandermarliere, Lennart Martens, Sven Degroeve, Wesley De Neve, Wim Vranken, and Nico Callewaert. 2021. “Massively Parallel Interrogation of Protein Fragment Secretability Using SECRiFY Reveals Features Influencing Secretory System Transit.” NATURE COMMUNICATIONS 12 (1). doi:10.1038/s41467-021-26720-y.
Vancouver
1.
Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, et al. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. NATURE COMMUNICATIONS. 2021;12(1).
IEEE
[1]
M. Boone et al., “Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit,” NATURE COMMUNICATIONS, vol. 12, no. 1, 2021.
@article{8754771,
  abstract     = {{While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >10(5) protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.

The exact protein features that control passage through the eukaryotic secretory system remain largely unknown. Here the authors report SECRiFY which they use to evaluate the secretory potential of polypeptides on a proteome-wide scale in yeast, revealing a role for flexibility and intrinsic disorder.}},
  articleno    = {{6414}},
  author       = {{Boone, Morgane and Ramasamy, Pathmanaban and Zuallaert, Jasper and Bouwmeester, Robbin and Van Moer, Berre and Maddelein, Davy and Turan, Demet and Hulstaert, Niels and Eeckhaut, Hannah and Vandermarliere, Elien and Martens, Lennart and Degroeve, Sven and De Neve, Wesley and Vranken, Wim and Callewaert, Nico}},
  issn         = {{2041-1723}},
  journal      = {{NATURE COMMUNICATIONS}},
  keywords     = {{General Physics and Astronomy,General Biochemistry,Genetics and Molecular Biology,General Chemistry,ENDOPLASMIC-RETICULUM,BINDING-SPECIFICITY,HUMAN-ANTIBODIES,GLOBAL ANALYSIS,QUALITY-CONTROL,EXPRESSION,SURFACE,PREDICTION,LIBRARY,TRANSFORMATION}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{16}},
  title        = {{Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit}},
  url          = {{http://doi.org/10.1038/s41467-021-26720-y}},
  volume       = {{12}},
  year         = {{2021}},
}
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