@article{kumar_shape_2025,
	title = {“{Shape} of {Cell}”—{An} {Auxin} and {Cell} {Wall} {Duet}},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70294},
	doi = {10.1111/ppl.70294},
	abstract = {Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.},
	language = {en},
	number = {3},
	urldate = {2025-06-13},
	journal = {Physiologia Plantarum},
	author = {Kumar, Vinod and Yadav, Sandeep and Heymans, Adrien and Robert, Stéphanie},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70294},
	keywords = {auxin, cell shape, cell wall, cytoskeleton, mechanical stress},
	pages = {e70294},
}

Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.

@article{liu_genomic_2025,
	title = {Genomic insights into the evolution of {Chinese} sweetgum and its autumn leaf coloration},
	volume = {198},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf218},
	doi = {10.1093/plphys/kiaf218},
	abstract = {Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.},
	number = {2},
	urldate = {2025-06-13},
	journal = {Plant Physiology},
	author = {Liu, Ping-Li and Jing, Zhao-Yang and Zhang, Ren-Gang and Chen, Ye and Zhu, Zhixin and Zhang, Xi and Jiang, Chen-Kun and Li, Ruili and Xie, Jian-Bo and Niu, Shihui and Zhang, Jinfeng and Kong, Lisheng and Zhao, Jian and Ma, Yongpeng and Zeisler-Diehl, Viktoria V and Schreiber, Lukas and Karahara, Ichirou and Mao, Jian-Feng and Jiao, Yuannian and Ge, Song and Lin, Jinxing},
	month = jun,
	year = {2025},
	pages = {kiaf218},
}

Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.

@article{zeng_mutations_2025,
	title = {Mutations in the floral regulator gene {HUA2} restore flowering to the {Arabidopsis} trehalose 6-phosphate synthase1 (tps1) mutant},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf225},
	doi = {10.1093/plphys/kiaf225},
	abstract = {Plant growth and development are regulated by many factors, including carbohydrate availability and signaling. Trehalose 6-phosphate (T6P), which is synthesized by TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), is positively associated with and functions as a signal that informs the cell about the carbohydrate status. Mutations in TPS1 negatively affect the growth and development of Arabidopsis (Arabidopsis thaliana), and complete loss-of-function alleles are embryo-lethal, which can be overcome using inducible expression of TPS1 (GVG::TPS1) during embryogenesis. Using EMS mutagenesis in combination with genome re-sequencing, we have identified several alleles in the floral regulator gene HUA2 that restore flowering in tps1-2 GVG::TPS1. Genetic analyses using a HUA2 T-DNA insertion allele, hua2-4, confirmed this finding. RNA-seq analyses demonstrated that hua2-4 has widespread effects on the tps1-2 GVG::TPS1 transcriptome, including key genes and pathways involved in regulating flowering. Higher order mutants combining tps1-2 GVG::TPS1 and hua2-4 with alleles in the key flowering time regulators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and FLOWERING LOCUS C (FLC) were constructed to analyze the role of HUA2 during floral transition in tps1-2 in more detail. Our findings demonstrate that loss of HUA2 can restore flowering in tps1-2 GVG::TPS1, in part through activation of FT, with contributions from the upstream regulators SOC1 and FLC. Interestingly, we found that mutation of FLC is sufficient to induce flowering in tps1-2 GVG::TPS1. Furthermore, we observed that mutations in HUA2 modulate carbohydrate signaling and that this regulation might contribute to flowering in hua2-4 tps1-2 GVG::TPS1.},
	urldate = {2025-06-13},
	journal = {Plant Physiology},
	author = {Zeng, Liping and Zacharaki, Vasiliki and van Es, Sam W and Wang, Yanwei and Schmid, Markus},
	month = jun,
	year = {2025},
	pages = {kiaf225},
}

Plant growth and development are regulated by many factors, including carbohydrate availability and signaling. Trehalose 6-phosphate (T6P), which is synthesized by TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1), is positively associated with and functions as a signal that informs the cell about the carbohydrate status. Mutations in TPS1 negatively affect the growth and development of Arabidopsis (Arabidopsis thaliana), and complete loss-of-function alleles are embryo-lethal, which can be overcome using inducible expression of TPS1 (GVG::TPS1) during embryogenesis. Using EMS mutagenesis in combination with genome re-sequencing, we have identified several alleles in the floral regulator gene HUA2 that restore flowering in tps1-2 GVG::TPS1. Genetic analyses using a HUA2 T-DNA insertion allele, hua2-4, confirmed this finding. RNA-seq analyses demonstrated that hua2-4 has widespread effects on the tps1-2 GVG::TPS1 transcriptome, including key genes and pathways involved in regulating flowering. Higher order mutants combining tps1-2 GVG::TPS1 and hua2-4 with alleles in the key flowering time regulators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), and FLOWERING LOCUS C (FLC) were constructed to analyze the role of HUA2 during floral transition in tps1-2 in more detail. Our findings demonstrate that loss of HUA2 can restore flowering in tps1-2 GVG::TPS1, in part through activation of FT, with contributions from the upstream regulators SOC1 and FLC. Interestingly, we found that mutation of FLC is sufficient to induce flowering in tps1-2 GVG::TPS1. Furthermore, we observed that mutations in HUA2 modulate carbohydrate signaling and that this regulation might contribute to flowering in hua2-4 tps1-2 GVG::TPS1.

@article{faleiro_assessment_2025,
	title = {Assessment of the impact of biodegradable lignin nanoparticles encapsulating {IAA} on tomato development: from seed to fruit},
	volume = {25},
	issn = {1471-2229},
	shorttitle = {Assessment of the impact of biodegradable lignin nanoparticles encapsulating {IAA} on tomato development},
	url = {https://doi.org/10.1186/s12870-025-06539-1},
	doi = {10.1186/s12870-025-06539-1},
	abstract = {Polymeric nanoparticles have emerged as promising nanocarriers for plant growth regulators (PGRs) in agriculture, enhancing plant growth and boosting fruit and cereal yields. Among these, lignin nanoparticles (LNPs) stand out due to their biodegradability and low production cost. However, few studies have evaluated the biological effects of LNPs encapsulating PGRs — particularly their dose-dependent impacts across the entire plant life cycle. Therefore, our study aims to evaluate the efficiency of lignin nanoparticles (LNPs) encapsulating indole-3-acetic acid (IAA) compared with free application of the hormone. We employed a multidisciplinary approach to comprehensively assess the impacts of different LNPs-IAA concentrations. Germination tests and morphometric analyses were conducted, along with anatomical analyses of seeds, seedlings, and vegetative organs using light microscopy. Confocal microscopy analyses to examine LNP uptake and translocation. Additionally, leaf gas exchange parameters and photosynthetic pigment levels were measured. The lignin nanoparticles were also characterized in terms of length, polydispersity index, zeta potential and encapsulation efficiency. All variables were subjected to normality tests, variance analysis, and post-hoc tests. Structural analysis revealed that LNP application did not alter overall plant anatomy architecture, except for inducing differences in xylem area among vegetative organs. Additionally, LNPs were rapidly absorbed by seeds in less than 5 h and were transported exclusively via the apoplastic pathway. The composition of lignin nanoparticles influenced germination rates and time. Application with lower concentrations showed minimal statistical significance, whereas higher concentrations exhibited phytotoxic effects. Thus, our study highlights the critical importance of optimizing nanocarrier concentrations for plant growth enhancement, demonstrating that lignin nanoparticles (LNPs) represent a promising nanoformulation for bioactive compound encapsulation.},
	number = {1},
	urldate = {2025-06-13},
	journal = {BMC Plant Biology},
	author = {Faleiro, Rodrigo and Tessmer, Magda Andreia and Santo Pereira, Anderson Espirito and Fraceto, Leonardo Fernandes and Rampasso, Marcelle Sanches and Miranda, Marcela Trevenzoli and Pissolato, Maria Dolores and Cassola, Fábio and Ribeiro, Rafael Vasconcelos and Mayer, Juliana Lischka Sampaio},
	month = jun,
	year = {2025},
	keywords = {Crop science, Encapsulation, Nanotechnology, Plant growth regulators, Sustainability},
	pages = {768},
}

Polymeric nanoparticles have emerged as promising nanocarriers for plant growth regulators (PGRs) in agriculture, enhancing plant growth and boosting fruit and cereal yields. Among these, lignin nanoparticles (LNPs) stand out due to their biodegradability and low production cost. However, few studies have evaluated the biological effects of LNPs encapsulating PGRs — particularly their dose-dependent impacts across the entire plant life cycle. Therefore, our study aims to evaluate the efficiency of lignin nanoparticles (LNPs) encapsulating indole-3-acetic acid (IAA) compared with free application of the hormone. We employed a multidisciplinary approach to comprehensively assess the impacts of different LNPs-IAA concentrations. Germination tests and morphometric analyses were conducted, along with anatomical analyses of seeds, seedlings, and vegetative organs using light microscopy. Confocal microscopy analyses to examine LNP uptake and translocation. Additionally, leaf gas exchange parameters and photosynthetic pigment levels were measured. The lignin nanoparticles were also characterized in terms of length, polydispersity index, zeta potential and encapsulation efficiency. All variables were subjected to normality tests, variance analysis, and post-hoc tests. Structural analysis revealed that LNP application did not alter overall plant anatomy architecture, except for inducing differences in xylem area among vegetative organs. Additionally, LNPs were rapidly absorbed by seeds in less than 5 h and were transported exclusively via the apoplastic pathway. The composition of lignin nanoparticles influenced germination rates and time. Application with lower concentrations showed minimal statistical significance, whereas higher concentrations exhibited phytotoxic effects. Thus, our study highlights the critical importance of optimizing nanocarrier concentrations for plant growth enhancement, demonstrating that lignin nanoparticles (LNPs) represent a promising nanoformulation for bioactive compound encapsulation.

@article{gran_unravelling_2025,
	title = {Unravelling the dynamics of seed-stored {mRNAs} during seed priming},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70098},
	doi = {10.1111/nph.70098},
	abstract = {Seed priming is a pre-sowing treatment that enables more efficient and uniform seed germination; however, it negatively affects seed longevity. In this work, the mRNA dynamics underlying a hydropriming treatment have been investigated. Polysome profiling was performed on seeds during different stages of hydropriming. Ribosome nascent chain complex sequencing (RNC-seq) elucidated transcriptomic and translatomic changes during the priming treatment. In contrast to mature dry seeds, hydroprimed seeds contain more mRNA-ribosome complexes, suggesting that the mRNAs that need to be translated during germination are already associated with ribosomes in the primed seeds, leading to a quicker restart of translation and thus faster germination upon re-imbibition. As a result of priming, seeds lose part of their stress-related transcriptome. This work highlights genes that might play a role in increasing the rate of germination after priming.},
	language = {en},
	urldate = {2025-03-28},
	journal = {New Phytologist},
	author = {Gran, Patricija and Visscher, Tessa W. and Bai, Bing and Nijveen, Harm and Mahboubi, Amir and Bakermans, Lars L. and Willems, Leo A. J. and Bentsink, Leónie},
	month = mar,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70098},
	keywords = {Arabidopsis thaliana, RNC-seq, germination, hydropriming, longevity, mRNA dynamics, polysome profiling, seeds},
}

Seed priming is a pre-sowing treatment that enables more efficient and uniform seed germination; however, it negatively affects seed longevity. In this work, the mRNA dynamics underlying a hydropriming treatment have been investigated. Polysome profiling was performed on seeds during different stages of hydropriming. Ribosome nascent chain complex sequencing (RNC-seq) elucidated transcriptomic and translatomic changes during the priming treatment. In contrast to mature dry seeds, hydroprimed seeds contain more mRNA-ribosome complexes, suggesting that the mRNAs that need to be translated during germination are already associated with ribosomes in the primed seeds, leading to a quicker restart of translation and thus faster germination upon re-imbibition. As a result of priming, seeds lose part of their stress-related transcriptome. This work highlights genes that might play a role in increasing the rate of germination after priming.