@article{low_zinc_2025,
	title = {{ZINC} {FINGER} {PROTEIN2} suppresses funiculus lignification to ensure seed loading efficiency in \textit{{Arabidopsis}}},
	volume = {60},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580725000620},
	doi = {10.1016/j.devcel.2025.01.021},
	abstract = {The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.},
	number = {12},
	urldate = {2026-01-30},
	journal = {Developmental Cell},
	author = {Low, Pui Man and Kong, Que and Blaschek, Leonard and Ma, Zhiming and Lim, Peng Ken and Yang, Yuzhou and Quek, Trisha and Lim, Cuithbert J. R. and Singh, Sanjay K. and Crocoll, Christoph and Engquist, Ellen and Thorsen, Jakob S. and Pattanaik, Sitakanta and Tee, Wan Ting and Mutwil, Marek and Miao, Yansong and Yuan, Ling and Xu, Deyang and Persson, Staffan and Ma, Wei},
	month = jun,
	year = {2025},
	keywords = {ZINC FINGER PROTEIN2, funiculus, secondary cell wall biosynthesis, transcription factor, transcriptional repression},
	pages = {1719--1729.e6},
}

The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.

@article{zheng_pupylation-based_2025,
	title = {Pupylation-{Based} {Proximity} {Labeling} {Unravels} a {Comprehensive} {Protein} and {Phosphoprotein} {Interactome} of the {Arabidopsis} {TOR} {Complex}},
	volume = {12},
	copyright = {© 2025 The Author(s). Advanced Science published by Wiley-VCH GmbH},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202414496},
	doi = {10.1002/advs.202414496},
	abstract = {Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein–protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.},
	language = {en},
	number = {19},
	urldate = {2026-01-30},
	journal = {Advanced Science},
	author = {Zheng, Shuai and Blaschek, Leonard and Pottier, Delphine and Dijkhof, Luuk Robin Hoegen and Özmen, Beyza and Lim, Peng Ken and Tan, Qiao Wen and Mutwil, Marek and Hauser, Alexander Sebastian and Persson, Staffan},
	year = {2025},
	note = {\_eprint: https://advanced.onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202414496},
	keywords = {AlphaFold, PUP-IT, proximity labeling, sugar signaling, target of rapamycin},
	pages = {2414496},
}

Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein–protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.

@article{ozmen_proximity_2025,
	title = {Proximity labeling techniques for protein–protein interaction mapping in plants},
	volume = {301},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925825023518},
	doi = {10.1016/j.jbc.2025.110501},
	abstract = {Protein–protein interactions (PPIs) are fundamental to understanding cellular processes, serving as the cornerstone of biological signaling, structural organization, and metabolic regulation. However, capturing PPIs in living organisms remains a significant challenge, particularly in complex and compartmentalized cellular environments. Research in this area has been greatly accelerated by the invention of proximity labeling (PL) techniques. By employing engineered enzymes capable of tagging proteins and other molecules in vivo, PL allows real-time mapping of biomolecular interactions within native environments. In plants, the implementation of PL presents unique challenges but has nonetheless emerged as a powerful tool. Here, we summarize the mechanisms, strengths, and weaknesses of different enzyme-based PL methods. We also highlight key considerations to optimize PL experiments in plants and propose targets for development to further improve their efficiency and flexibility.},
	number = {8},
	urldate = {2026-01-30},
	journal = {Journal of Biological Chemistry},
	author = {Özmen, Beyza and Blaschek, Leonard and Ogden, Michael and San Segundo, Marcos and Persson, Staffan and Zheng, Shuai},
	month = aug,
	year = {2025},
	keywords = {TOR complex, cellulose, plants, protein-protein interactions (PPIs), proximity labeling (PL)},
	pages = {110501},
}

Protein–protein interactions (PPIs) are fundamental to understanding cellular processes, serving as the cornerstone of biological signaling, structural organization, and metabolic regulation. However, capturing PPIs in living organisms remains a significant challenge, particularly in complex and compartmentalized cellular environments. Research in this area has been greatly accelerated by the invention of proximity labeling (PL) techniques. By employing engineered enzymes capable of tagging proteins and other molecules in vivo, PL allows real-time mapping of biomolecular interactions within native environments. In plants, the implementation of PL presents unique challenges but has nonetheless emerged as a powerful tool. Here, we summarize the mechanisms, strengths, and weaknesses of different enzyme-based PL methods. We also highlight key considerations to optimize PL experiments in plants and propose targets for development to further improve their efficiency and flexibility.

@article{holloway-phillips_rethinking_2026,
	title = {Rethinking the {2H} fingerprint of carbohydrates: a novel proxy for plant metabolism and performance},
	volume = {249},
	issn = {1469-8137},
	shorttitle = {Rethinking the {2H} fingerprint of carbohydrates},
	doi = {10.1111/nph.70845},
	abstract = {The intricate architecture of plant metabolic networks and the dynamic fluxes of elements through these networks are fundamental determinants of how carbon (C) is partitioned among growth, reproduction, storage, respiration and the synthesis of secondary metabolites. While these C fluxes are critical to cellular function and plant life, their routine measurement remains a significant challenge. This review aimed to highlight the substantial potential of hydrogen (H) isotopes of plant carbohydrates to bridge this methodological gap by serving as a flux-based proxy for primary C metabolism. This potential is demonstrated from both a theoretical perspective and by summarising available evidence at the whole-molecule and position-specific levels. The utility of this proxy is significant for understanding species' metabolic plasticity, assessing plant responses to environmental change and selecting superior metabolic phenotypes in agriculture and forestry. However, for this proxy to be fully realised, several fundamental questions remain. This includes the identification of specific metabolic reactions associated with isotopic variation and their relationship to plant performance. We outline several approaches to advance the development of an H-isotope based plant metabolic proxy for plant performance.},
	language = {eng},
	number = {4},
	journal = {The New Phytologist},
	author = {Holloway-Phillips, Meisha and Lehmann, Marco M. and Tcherkez, Guillaume and Werner, Roland A. and Nelson, Daniel B. and Baan, Jochem and Cernusak, Lucas A. and Cormier, Marc-Andre and Diao, Haoyu and Gessler, Arthur and Guidi, Claudia and Hugger, Selina and Ladd, S. Nemiah and Martínez-Sancho, Elisabet and Niittylä, Totte and Saurer, Matthias and Schuler, Philipp and Vitali, Valentina and Wieloch, Thomas and Kahmen, Ansgar},
	month = feb,
	year = {2026},
	keywords = {Carbohydrate Metabolism, Carbon, Deuterium, Plants, carbohydrates, hydrogen stable isotopes, isotope fractionation, metabolic flux analysis, plant C metabolism, plant physiology},
	pages = {1623--1643},
}

The intricate architecture of plant metabolic networks and the dynamic fluxes of elements through these networks are fundamental determinants of how carbon (C) is partitioned among growth, reproduction, storage, respiration and the synthesis of secondary metabolites. While these C fluxes are critical to cellular function and plant life, their routine measurement remains a significant challenge. This review aimed to highlight the substantial potential of hydrogen (H) isotopes of plant carbohydrates to bridge this methodological gap by serving as a flux-based proxy for primary C metabolism. This potential is demonstrated from both a theoretical perspective and by summarising available evidence at the whole-molecule and position-specific levels. The utility of this proxy is significant for understanding species' metabolic plasticity, assessing plant responses to environmental change and selecting superior metabolic phenotypes in agriculture and forestry. However, for this proxy to be fully realised, several fundamental questions remain. This includes the identification of specific metabolic reactions associated with isotopic variation and their relationship to plant performance. We outline several approaches to advance the development of an H-isotope based plant metabolic proxy for plant performance.

@article{ma_pangenome_2026,
	title = {A pangenome insight into the genome divergence and flower color diversity among {Rhododendron} species},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-025-12461-5},
	doi = {10.1186/s12864-025-12461-5},
	abstract = {The Rhododendron genus (Rhododendron L.), recognized as the most extensive woody plant genus in the Northern Hemisphere, captivates with its strikingly beautiful corollas and variety of flower colors. In addition, the Rhododendron genus exhibits a complex evolutionary history and substantial species diversification. To comprehensively understand the genomic complexity and flower color diversity within this genus, comparative genomics has emerged as a promising approach, enabling analysis at a super-species level.},
	language = {en},
	urldate = {2026-01-09},
	journal = {BMC Genomics},
	author = {Ma, Hai-Yao and Nie, Shuai and Liu, Hai-Bo and Shi, Tian-Le and Zhao, Shi-Wei and Chen, Zhao-Yang and Bao, Yu-Tao and Li, Zhi-Chao and Mao, Jian-Feng},
	month = jan,
	year = {2026},
	keywords = {DNA Transposable Elements, Evolution, Molecular, Flower color, Flowers, Gene duplication, Gene loss, Genetic Variation, Genome, Plant, Genomics, Phylogeny, Pigmentation, Retroelements, Rhododendron, Transposable element},
}

The Rhododendron genus (Rhododendron L.), recognized as the most extensive woody plant genus in the Northern Hemisphere, captivates with its strikingly beautiful corollas and variety of flower colors. In addition, the Rhododendron genus exhibits a complex evolutionary history and substantial species diversification. To comprehensively understand the genomic complexity and flower color diversity within this genus, comparative genomics has emerged as a promising approach, enabling analysis at a super-species level.