@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{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{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.

@incollection{pesquet_bulk_2024,
	address = {New York, NY},
	title = {Bulk and {In} {Situ} {Quantification} of {Coniferaldehyde} {Residues} in {Lignin}},
	isbn = {978-1-0716-3477-6},
	url = {https://doi.org/10.1007/978-1-0716-3477-6_14},
	doi = {10.1007/978-1-0716-3477-6_14},
	abstract = {Lignin is a group of cell wall localised heterophenolic polymers varying in the chemistry of the aromatic and aliphatic parts of its units. The lignin residues common to all vascular plants have an aromatic ring with one para hydroxy group and one meta methoxy group, also called guaiacyl (G). The terminal function of the aliphatic part of these G units, however, varies from alcohols, which are generally abundant, to aldehydes, which represent a smaller proportion of lignin monomers. The proportions of aldehyde to alcohol G units in lignin are, nevertheless, precisely controlled to respond to environmental and development cues. These G aldehyde to alcohol unit proportions differ between each cell wall layer of each cell type to fine-tune the cell wall biomechanical and physico-chemical properties. To precisely determine changes in lignin composition, we, herein, describe the various methods to detect and quantify the levels and positions of G aldehyde units, also called coniferaldehyde residues, of lignin polymers in ground plant samples as well as in situ in histological cross-sections.},
	language = {en},
	urldate = {2026-01-30},
	booktitle = {Xylem: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Pesquet, Edouard and Blaschek, Leonard and Takahashi, Junko and Yamamoto, Masanobu and Champagne, Antoine and {Nuoendagula} and Subbotina, Elena and Dimotakis, Charilaos and Bacisk, Zoltán and Kajita, Shinya},
	editor = {Agusti, Javier},
	year = {2024},
	keywords = {Coniferaldehyde residues, In situ quantitative chemical imaging, Lignin, Pyrolysis-GC/MS, Raman microspectroscopy, Thioacidolysis-GC/MS, Wiesner test, Xylem cell types},
	pages = {201--226},
}

Lignin is a group of cell wall localised heterophenolic polymers varying in the chemistry of the aromatic and aliphatic parts of its units. The lignin residues common to all vascular plants have an aromatic ring with one para hydroxy group and one meta methoxy group, also called guaiacyl (G). The terminal function of the aliphatic part of these G units, however, varies from alcohols, which are generally abundant, to aldehydes, which represent a smaller proportion of lignin monomers. The proportions of aldehyde to alcohol G units in lignin are, nevertheless, precisely controlled to respond to environmental and development cues. These G aldehyde to alcohol unit proportions differ between each cell wall layer of each cell type to fine-tune the cell wall biomechanical and physico-chemical properties. To precisely determine changes in lignin composition, we, herein, describe the various methods to detect and quantify the levels and positions of G aldehyde units, also called coniferaldehyde residues, of lignin polymers in ground plant samples as well as in situ in histological cross-sections.

@article{blaschek_functional_2024,
	title = {Functional {Complexity} on a {Cellular} {Scale}: {Why} {In} {Situ} {Analyses} {Are} {Indispensable} for {Our} {Understanding} of {Lignified} {Tissues}},
	volume = {72},
	issn = {0021-8561},
	shorttitle = {Functional {Complexity} on a {Cellular} {Scale}},
	url = {https://doi.org/10.1021/acs.jafc.4c01999},
	doi = {10.1021/acs.jafc.4c01999},
	abstract = {Lignins are a key adaptation that enables vascular plants to thrive in terrestrial habitats. Lignin is heterogeneous, containing upward of 30 different monomers, and its function is multifarious: It provides structural support, predetermined breaking points, ultraviolet protection, diffusion barriers, pathogen resistance, and drought resilience. Recent studies, carefully characterizing lignin in situ, have started to identify specific lignin compositions and ultrastructures with distinct cellular functions, but our understanding remains fractional. We summarize recent works and highlight where further in situ lignin analysis could provide valuable insights into plant growth and adaptation. We also summarize strengths and weaknesses of lignin in situ analysis methods.},
	number = {24},
	urldate = {2024-07-01},
	journal = {Journal of Agricultural and Food Chemistry},
	publisher = {American Chemical Society},
	author = {Blaschek, Leonard and Serk, Henrik and Pesquet, Edouard},
	month = jun,
	year = {2024},
	pages = {13552--13560},
}

Lignins are a key adaptation that enables vascular plants to thrive in terrestrial habitats. Lignin is heterogeneous, containing upward of 30 different monomers, and its function is multifarious: It provides structural support, predetermined breaking points, ultraviolet protection, diffusion barriers, pathogen resistance, and drought resilience. Recent studies, carefully characterizing lignin in situ, have started to identify specific lignin compositions and ultrastructures with distinct cellular functions, but our understanding remains fractional. We summarize recent works and highlight where further in situ lignin analysis could provide valuable insights into plant growth and adaptation. We also summarize strengths and weaknesses of lignin in situ analysis methods.

@article{pedersen_cellulose_2023,
	series = {“{Celebrating} 15 {Years} of {Publication}” {Special} {Issue}},
	title = {Cellulose synthesis in land plants},
	volume = {16},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205222004506},
	doi = {10.1016/j.molp.2022.12.015},
	abstract = {All plant cells are surrounded by a cell wall that provides cohesion, protection, and a means of directional growth to plants. Cellulose microfibrils contribute the main biomechanical scaffold for most of these walls. The biosynthesis of cellulose, which typically is the most prominent constituent of the cell wall and therefore Earth’s most abundant biopolymer, is finely attuned to developmental and environmental cues. Our understanding of the machinery that catalyzes and regulates cellulose biosynthesis has substantially improved due to recent technological advances in, for example, structural biology and microscopy. Here, we provide a comprehensive overview of the structure, function, and regulation of the cellulose synthesis machinery and its regulatory interactors. We aim to highlight important knowledge gaps in the field, and outline emerging approaches that promise a means to close those gaps.},
	number = {1},
	urldate = {2026-01-30},
	journal = {Molecular Plant},
	author = {Pedersen, Gustav B. and Blaschek, Leonard and Frandsen, Kristian E. H. and Noack, Lise C. and Persson, Staffan},
	month = jan,
	year = {2023},
	keywords = {cellulose microfibrils, cellulose synthases, cytoskeleton, membrane proteins, plant cell wall, protein interaction},
	pages = {206--231},
}

All plant cells are surrounded by a cell wall that provides cohesion, protection, and a means of directional growth to plants. Cellulose microfibrils contribute the main biomechanical scaffold for most of these walls. The biosynthesis of cellulose, which typically is the most prominent constituent of the cell wall and therefore Earth’s most abundant biopolymer, is finely attuned to developmental and environmental cues. Our understanding of the machinery that catalyzes and regulates cellulose biosynthesis has substantially improved due to recent technological advances in, for example, structural biology and microscopy. Here, we provide a comprehensive overview of the structure, function, and regulation of the cellulose synthesis machinery and its regulatory interactors. We aim to highlight important knowledge gaps in the field, and outline emerging approaches that promise a means to close those gaps.

@article{blaschek_different_2023,
	title = {Different combinations of laccase paralogs nonredundantly control the amount and composition of lignin in specific cell types and cell wall layers in {Arabidopsis}},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koac344},
	doi = {10.1093/plcell/koac344},
	abstract = {Vascular plants reinforce the cell walls of the different xylem cell types with lignin phenolic polymers. Distinct lignin chemistries differ between each cell wall layer and each cell type to support their specific functions. Yet the mechanisms controlling the tight spatial localization of specific lignin chemistries remain unclear. Current hypotheses focus on control by monomer biosynthesis and/or export, while cell wall polymerization is viewed as random and nonlimiting. Here, we show that combinations of multiple individual laccases (LACs) are nonredundantly and specifically required to set the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12, and 17 by generating quadruple and quintuple loss-of-function mutants. Loss of these LACs in different combinations led to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers. Moreover, we showed that LAC-mediated lignification has distinct functions in specific cell types, waterproofing fibers, and strengthening vessels. Altogether, we propose that the spatial control of lignin chemistry depends on different combinations of LACs with nonredundant activities immobilized in specific cell types and cell wall layers.},
	number = {2},
	urldate = {2026-01-30},
	journal = {The Plant Cell},
	author = {Blaschek, Leonard and Murozuka, Emiko and Serk, Henrik and Ménard, Delphine and Pesquet, Edouard},
	month = feb,
	year = {2023},
	pages = {889--909},
}

Vascular plants reinforce the cell walls of the different xylem cell types with lignin phenolic polymers. Distinct lignin chemistries differ between each cell wall layer and each cell type to support their specific functions. Yet the mechanisms controlling the tight spatial localization of specific lignin chemistries remain unclear. Current hypotheses focus on control by monomer biosynthesis and/or export, while cell wall polymerization is viewed as random and nonlimiting. Here, we show that combinations of multiple individual laccases (LACs) are nonredundantly and specifically required to set the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12, and 17 by generating quadruple and quintuple loss-of-function mutants. Loss of these LACs in different combinations led to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers. Moreover, we showed that LAC-mediated lignification has distinct functions in specific cell types, waterproofing fibers, and strengthening vessels. Altogether, we propose that the spatial control of lignin chemistry depends on different combinations of LACs with nonredundant activities immobilized in specific cell types and cell wall layers.

@article{menard_plant_2022,
	title = {Plant biomechanics and resilience to environmental changes are controlled by specific lignin chemistries in each vascular cell type and morphotype},
	volume = {34},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koac284},
	doi = {10.1093/plcell/koac284},
	abstract = {The biopolymer lignin is deposited in the cell walls of vascular cells and is essential for long-distance water conduction and structural support in plants. Different vascular cell types contain distinct and conserved lignin chemistries, each with specific aromatic and aliphatic substitutions. Yet, the biological role of this conserved and specific lignin chemistry in each cell type remains unclear. Here, we investigated the roles of this lignin biochemical specificity for cellular functions by producing single cell analyses for three cell morphotypes of tracheary elements, which all allow sap conduction but differ in their morphology. We determined that specific lignin chemistries accumulate in each cell type. Moreover, lignin accumulated dynamically, increasing in quantity and changing in composition, to alter the cell wall biomechanics during cell maturation. For similar aromatic substitutions, residues with alcohol aliphatic functions increased stiffness whereas aldehydes increased flexibility of the cell wall. Modifying this lignin biochemical specificity and the sequence of its formation impaired the cell wall biomechanics of each morphotype and consequently hindered sap conduction and drought recovery. Together, our results demonstrate that each sap-conducting vascular cell type distinctly controls their lignin biochemistry to adjust their biomechanics and hydraulic properties to face developmental and environmental constraints.},
	number = {12},
	urldate = {2026-01-30},
	journal = {The Plant Cell},
	author = {Ménard, Delphine and Blaschek, Leonard and Kriechbaum, Konstantin and Lee, Cheng Choo and Serk, Henrik and Zhu, Chuantao and Lyubartsev, Alexander and {Nuoendagula} and Bacsik, Zoltán and Bergström, Lennart and Mathew, Aji and Kajita, Shinya and Pesquet, Edouard},
	month = dec,
	year = {2022},
	pages = {4877--4896},
}

The biopolymer lignin is deposited in the cell walls of vascular cells and is essential for long-distance water conduction and structural support in plants. Different vascular cell types contain distinct and conserved lignin chemistries, each with specific aromatic and aliphatic substitutions. Yet, the biological role of this conserved and specific lignin chemistry in each cell type remains unclear. Here, we investigated the roles of this lignin biochemical specificity for cellular functions by producing single cell analyses for three cell morphotypes of tracheary elements, which all allow sap conduction but differ in their morphology. We determined that specific lignin chemistries accumulate in each cell type. Moreover, lignin accumulated dynamically, increasing in quantity and changing in composition, to alter the cell wall biomechanics during cell maturation. For similar aromatic substitutions, residues with alcohol aliphatic functions increased stiffness whereas aldehydes increased flexibility of the cell wall. Modifying this lignin biochemical specificity and the sequence of its formation impaired the cell wall biomechanics of each morphotype and consequently hindered sap conduction and drought recovery. Together, our results demonstrate that each sap-conducting vascular cell type distinctly controls their lignin biochemistry to adjust their biomechanics and hydraulic properties to face developmental and environmental constraints.

@article{blaschek_phenoloxidases_2021,
	title = {Phenoloxidases in {Plants}—{How} {Structural} {Diversity} {Enables} {Functional} {Specificity}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.754601/full},
	doi = {10.3389/fpls.2021.754601},
	abstract = {The metabolism of polyphenolic polymers is essential to the development and response to environmental changes of organisms from all kingdoms of life, but shows particular diversity in plants. In contrast to other biopolymers, whose polymerisation is catalysed by homologous gene families, polyphenolic metabolism depends on phenoloxidases, a group of heterogeneous oxidases that share little beyond the eponymous common substrate. In this review, we provide an overview of the differences and similarities between phenoloxidases in their protein structure, reaction mechanism, substrate specificity, and functional roles. Using the example of laccases, we also performed a meta-analysis of enzyme kinetics, a comprehensive phylogenetic analysis and machine-learning based protein structure modelling to link functions, evolution, and structures in this group of phenoloxidases. With these approaches, we generated a framework to explain the reported functional differences between paralogs, while also hinting at the likely diversity of yet undescribed laccase functions. Altogether, this review provides a basis to better understand the functional overlaps and specificities between and within the three major families of phenoloxidases, their evolutionary trajectories, and their importance for plant primary and secondary metabolism.},
	language = {English},
	urldate = {2026-01-30},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Blaschek, Leonard and Pesquet, Edouard},
	month = oct,
	year = {2021},
	keywords = {Bayesian phylogeny, Laccase, Lignin, Peroxidase, Polyphenol oxidase, Polyphenolic polymers, Protein modelling},
}

The metabolism of polyphenolic polymers is essential to the development and response to environmental changes of organisms from all kingdoms of life, but shows particular diversity in plants. In contrast to other biopolymers, whose polymerisation is catalysed by homologous gene families, polyphenolic metabolism depends on phenoloxidases, a group of heterogeneous oxidases that share little beyond the eponymous common substrate. In this review, we provide an overview of the differences and similarities between phenoloxidases in their protein structure, reaction mechanism, substrate specificity, and functional roles. Using the example of laccases, we also performed a meta-analysis of enzyme kinetics, a comprehensive phylogenetic analysis and machine-learning based protein structure modelling to link functions, evolution, and structures in this group of phenoloxidases. With these approaches, we generated a framework to explain the reported functional differences between paralogs, while also hinting at the likely diversity of yet undescribed laccase functions. Altogether, this review provides a basis to better understand the functional overlaps and specificities between and within the three major families of phenoloxidases, their evolutionary trajectories, and their importance for plant primary and secondary metabolism.

@article{blaschek_cellular_2020,
	title = {Cellular and {Genetic} {Regulation} of {Coniferaldehyde} {Incorporation} in {Lignin} of {Herbaceous} and {Woody} {Plants} by {Quantitative} {Wiesner} {Staining}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00109/full},
	doi = {10.3389/fpls.2020.00109},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Blaschek, Leonard and Champagne, Antoine and Dimotakis, Charilaos and {Nuoendagula} and Decou, Raphaël and Hishiyama, Shojiro and Kratzer, Susanne and Kajita, Shinya and Pesquet, Edouard},
	month = mar,
	year = {2020},
	pages = {109},
}

@article{blaschek_determining_2020,
	title = {Determining the {Genetic} {Regulation} and {Coordination} of {Lignification} in {Stem} {Tissues} of {Arabidopsis} {Using} {Semiquantitative} {Raman} {Microspectroscopy}},
	volume = {8},
	url = {https://doi.org/10.1021/acssuschemeng.0c00194},
	doi = {10.1021/acssuschemeng.0c00194},
	abstract = {Lignin is a phenolic polymer accumulating in the cell walls of specific plant cell types to confer unique properties such as hydrophobicity, mechanical strengthening, and resistance to degradation. Different cell types accumulate lignin with specific concentration and composition to support their specific roles in the different plant tissues. Yet the genetic mechanisms controlling lignin quantity and composition differently between the different lignified cell types and tissues still remain poorly understood. To investigate this tissue-specific genetic regulation, we validated both the target molecular structures as well as the linear semiquantitative capacity of Raman microspectroscopy to characterize the total lignin amount, S/G ratio, and coniferyl alcohol content in situ directly in plant biopsies. Using the optimized method on stems of multiple lignin biosynthesis loss-of-function mutants revealed that the genetic regulation of lignin is tissue specific, with distinct genes establishing nonredundant check-points to trigger specific compensatory adjustments affecting either lignin composition and/or cell wall polymer concentrations.},
	number = {12},
	urldate = {2026-01-30},
	journal = {ACS Sustainable Chemistry \& Engineering},
	publisher = {American Chemical Society},
	author = {Blaschek, Leonard and {Nuoendagula} and Bacsik, Zoltán and Kajita, Shinya and Pesquet, Edouard},
	month = mar,
	year = {2020},
	pages = {4900--4909},
}

Lignin is a phenolic polymer accumulating in the cell walls of specific plant cell types to confer unique properties such as hydrophobicity, mechanical strengthening, and resistance to degradation. Different cell types accumulate lignin with specific concentration and composition to support their specific roles in the different plant tissues. Yet the genetic mechanisms controlling lignin quantity and composition differently between the different lignified cell types and tissues still remain poorly understood. To investigate this tissue-specific genetic regulation, we validated both the target molecular structures as well as the linear semiquantitative capacity of Raman microspectroscopy to characterize the total lignin amount, S/G ratio, and coniferyl alcohol content in situ directly in plant biopsies. Using the optimized method on stems of multiple lignin biosynthesis loss-of-function mutants revealed that the genetic regulation of lignin is tissue specific, with distinct genes establishing nonredundant check-points to trigger specific compensatory adjustments affecting either lignin composition and/or cell wall polymer concentrations.

@article{yamamoto_importance_2020,
	title = {Importance of {Lignin} {Coniferaldehyde} {Residues} for {Plant} {Properties} and {Sustainable} {Uses}},
	volume = {13},
	copyright = {© 2020 The Authors. Published by Wiley-VCH GmbH},
	issn = {1864-564X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cssc.202001242},
	doi = {10.1002/cssc.202001242},
	abstract = {Increases in coniferaldehyde content, a minor lignin residue, significantly improves the sustainable use of plant biomass for feed, pulping, and biorefinery without affecting plant growth and yields. Herein, different analytical methods are compared and validated to distinguish coniferaldehyde from other lignin residues. It is shown that specific genetic pathways regulate amount, linkage, and position of coniferaldehyde within the lignin polymer for each cell type. This specific cellular regulation offers new possibilities for designing plant lignin for novel and targeted industrial uses.},
	language = {en},
	number = {17},
	urldate = {2026-01-30},
	journal = {ChemSusChem},
	author = {Yamamoto, Masanobu and Blaschek, Leonard and Subbotina, Elena and Kajita, Shinya and Pesquet, Edouard},
	year = {2020},
	note = {\_eprint: https://chemistry-europe.onlinelibrary.wiley.com/doi/pdf/10.1002/cssc.202001242},
	keywords = {analytical methods, biomass, coniferaldehyde, mutagenesis, polymers},
	pages = {4400--4408},
}

Increases in coniferaldehyde content, a minor lignin residue, significantly improves the sustainable use of plant biomass for feed, pulping, and biorefinery without affecting plant growth and yields. Herein, different analytical methods are compared and validated to distinguish coniferaldehyde from other lignin residues. It is shown that specific genetic pathways regulate amount, linkage, and position of coniferaldehyde within the lignin polymer for each cell type. This specific cellular regulation offers new possibilities for designing plant lignin for novel and targeted industrial uses.