4D-DIA proteomics reveals distinct proteolytic landscapes induced by mechanical stress, Agrobacterium, and a viral capsid precursor
- 1Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, Chongqing, China
- 2School of Life Science, Southwest University, Chongqing, China
Abstract
Nicotiana benthamiana is a widely used platform for plant molecular farming, yet recombinant protein yields are frequently compromised by the host’s innate defense mechanisms, particularly proteolytic degradation. While the general effects of Agroinfiltration are known, the distinct contributions of mechanical injury, bacterial perception, and product-specific stress remain poorly resolved. Here we utilized high-depth 4D-DIA proteomics to dissect the host response across three dimensions: physical stress (buffer infiltration), pathogen-associated stress (Agrobacterium), and product-associated stress (GFP vs. the FMDV capsid precursor P1_2A). We demonstrate that buffer infiltration is not a neutral event but an independent inducer of cell wall remodeling and oxidative stress. By filtering out these background effects, we defined a core Agrobacterium-responsive proteome characterized by a growth-defense trade-off. We also expanded the known protease repertoire of N. benthamiana to 1,505 enzymes through improved genomic annotation. We found that the expression of the FMDV capsid precursor P1_2A was associated with a distinct and more pronounced protease profile compared to soluble GFP, characterized by the upregulation of subtilases and cysteine proteases. These findings suggest that host proteolytic responses vary with the recombinant cargo, a factor worth considering when designing engineering strategies for the production of complex biopharmaceuticals in plants.
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BibTeX
@article{tang20264ddia,
title = {{4D-DIA proteomics reveals distinct proteolytic landscapes induced by mechanical stress, Agrobacterium, and a viral capsid precursor}},
author = {You Tang and Xiaoping Qiu and Xinli Ye and Xiaorui Ma and Yilin Mao and Qiwei Yang and Yike Chen and Yiming Sun and Lijun Zhu},
journal = {PLOS One},
year = {2026},
month = sep,
doi = {10.1371/journal.pone.0356905},
url = {https://doi.org/10.1371/journal.pone.0356905},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - 4D-DIA proteomics reveals distinct proteolytic landscapes induced by mechanical stress, Agrobacterium, and a viral capsid precursor
AU - You Tang
AU - Xiaoping Qiu
AU - Xinli Ye
AU - Xiaorui Ma
AU - Yilin Mao
AU - Qiwei Yang
AU - Yike Chen
AU - Yiming Sun
AU - Lijun Zhu
PY - 2026
DA - 2026/09/11
JO - PLOS One
DO - 10.1371/journal.pone.0356905
UR - https://doi.org/10.1371/journal.pone.0356905
AB - Nicotiana benthamiana is a widely used platform for plant molecular farming, yet recombinant protein yields are frequently compromised by the host’s innate defense mechanisms, particularly proteolytic degradation. While the general effects of Agroinfiltration are known, the distinct contributions of mechanical injury, bacterial perception, and product-specific stress remain poorly resolved. Here we utilized high-depth 4D-DIA proteomics to dissect the host response across three dimensions: physical stress (buffer infiltration), pathogen-associated stress (Agrobacterium), and product-associated stress (GFP vs. the FMDV capsid precursor P1_2A). We demonstrate that buffer infiltration is not a neutral event but an independent inducer of cell wall remodeling and oxidative stress. By filtering out these background effects, we defined a core Agrobacterium-responsive proteome characterized by a growth-defense trade-off. We also expanded the known protease repertoire of N. benthamiana to 1,505 enzymes through improved genomic annotation. We found that the expression of the FMDV capsid precursor P1_2A was associated with a distinct and more pronounced protease profile compared to soluble GFP, characterized by the upregulation of subtilases and cysteine proteases. These findings suggest that host proteolytic responses vary with the recombinant cargo, a factor worth considering when designing engineering strategies for the production of complex biopharmaceuticals in plants.
SN - 1932-6203
ER -