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Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis

Shuai Zheng, Lise C. Noack, Ouda Khammy, Andreas De Meyer (UGent) , Ghazanfar Abbas Khan, Nancy De Winne (UGent) , Dominique Eeckhout (UGent) , Daniël Van Damme (UGent) and Staffan Persson
(2025) NATURE COMMUNICATIONS. 16(1).
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Abstract
Knowledge about how and where proteins interact provides a pillar for cell biology. Protein proximity-labeling has emerged as an important tool to detect protein interactions. Biotin-related proximity labeling approaches are by far the most commonly used but may have labeling-related drawbacks. Here, we use pupylation-based proximity labeling (PUP-IT) as a tool for protein interaction detection in plants. We show that PUP-IT readily confirmed protein interactions for several known protein complexes across different types of plant hosts and that the approach increased detection of specific interactions as compared to biotin-based proximity labeling systems. To further demonstrate the power of PUP-IT, we used the system to identify protein interactions of the protein complex that underpin cellulose synthesis in plants. Apart from known complex components, we identified the ARF-GEF BEN1 (BFA-VISUALIZED ENDOCYTIC TRAFFICKING DEFECTIVE1). We show that BEN1 contributes to cellulose synthesis by regulating both clathrin-dependent and -independent endocytosis of the cellulose synthesis protein complex from the plasma membrane. Our results highlight PUP-IT as a powerful proximity labeling system to identify protein interactions in plant cells.
Keywords
PROTEIN, ENDOCYTOSIS, MECHANISM, IMMUNITY, PLATFORM, GENES

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MLA
Zheng, Shuai, et al. “Pupylation-Based Proximity Labeling Reveals Regulatory Factors in Cellulose Biosynthesis in Arabidopsis.” NATURE COMMUNICATIONS, vol. 16, no. 1, 2025, doi:10.1038/s41467-025-56192-3.
APA
Zheng, S., Noack, L. C., Khammy, O., De Meyer, A., Khan, G. A., De Winne, N., … Persson, S. (2025). Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis. NATURE COMMUNICATIONS, 16(1). https://doi.org/10.1038/s41467-025-56192-3
Chicago author-date
Zheng, Shuai, Lise C. Noack, Ouda Khammy, Andreas De Meyer, Ghazanfar Abbas Khan, Nancy De Winne, Dominique Eeckhout, Daniël Van Damme, and Staffan Persson. 2025. “Pupylation-Based Proximity Labeling Reveals Regulatory Factors in Cellulose Biosynthesis in Arabidopsis.” NATURE COMMUNICATIONS 16 (1). https://doi.org/10.1038/s41467-025-56192-3.
Chicago author-date (all authors)
Zheng, Shuai, Lise C. Noack, Ouda Khammy, Andreas De Meyer, Ghazanfar Abbas Khan, Nancy De Winne, Dominique Eeckhout, Daniël Van Damme, and Staffan Persson. 2025. “Pupylation-Based Proximity Labeling Reveals Regulatory Factors in Cellulose Biosynthesis in Arabidopsis.” NATURE COMMUNICATIONS 16 (1). doi:10.1038/s41467-025-56192-3.
Vancouver
1.
Zheng S, Noack LC, Khammy O, De Meyer A, Khan GA, De Winne N, et al. Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis. NATURE COMMUNICATIONS. 2025;16(1).
IEEE
[1]
S. Zheng et al., “Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis,” NATURE COMMUNICATIONS, vol. 16, no. 1, 2025.
@article{01JJNGDH7Z570WP8FMNS68K6HH,
  abstract     = {{Knowledge about how and where proteins interact provides a pillar for cell biology. Protein proximity-labeling has emerged as an important tool to detect protein interactions. Biotin-related proximity labeling approaches are by far the most commonly used but may have labeling-related drawbacks. Here, we use pupylation-based proximity labeling (PUP-IT) as a tool for protein interaction detection in plants. We show that PUP-IT readily confirmed protein interactions for several known protein complexes across different types of plant hosts and that the approach increased detection of specific interactions as compared to biotin-based proximity labeling systems. To further demonstrate the power of PUP-IT, we used the system to identify protein interactions of the protein complex that underpin cellulose synthesis in plants. Apart from known complex components, we identified the ARF-GEF BEN1 (BFA-VISUALIZED ENDOCYTIC TRAFFICKING DEFECTIVE1). We show that BEN1 contributes to cellulose synthesis by regulating both clathrin-dependent and -independent endocytosis of the cellulose synthesis protein complex from the plasma membrane. Our results highlight PUP-IT as a powerful proximity labeling system to identify protein interactions in plant cells.}},
  articleno    = {{872}},
  author       = {{Zheng, Shuai and Noack, Lise C. and Khammy, Ouda and De Meyer, Andreas and Khan, Ghazanfar Abbas and De Winne, Nancy and Eeckhout, Dominique and Van Damme, Daniël and Persson, Staffan}},
  issn         = {{2041-1723}},
  journal      = {{NATURE COMMUNICATIONS}},
  keywords     = {{PROTEIN,ENDOCYTOSIS,MECHANISM,IMMUNITY,PLATFORM,GENES}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{11}},
  title        = {{Pupylation-based proximity labeling reveals regulatory factors in cellulose biosynthesis in Arabidopsis}},
  url          = {{http://doi.org/10.1038/s41467-025-56192-3}},
  volume       = {{16}},
  year         = {{2025}},
}
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