Single-Cell and Spatial Multi-Omics Reveal Mechanical Stress Driving Heterogeneous Xylem Development in Populus [Spatial metabolomics_LCM]
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Liquid Chromatography MS - positive - direct infusion, Liquid Chromatography MS - negative - direct infusion
PROVIDER: MTBLS12561 | MetaboLights | 2025-06-16
REPOSITORIES: MetaboLights
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Negative_Blank_1.mzML | Mzml | |||
| Negative_Blank_2.mzML | Mzml | |||
| Negative_Blank_3.mzML | Mzml | |||
| Negative_Blank_4.mzML | Mzml | |||
| Negative_Blank_5.mzML | Mzml |
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Project description:Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.
2025-06-17 | GSE295131 | GEO
Project description:Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.
2025-06-16 | MTBLS12601 | MetaboLights
Project description:Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.
2025-06-18 | PXD064017 | Pride
Project description:Xylem, the predominant tissue for structural support, forms tension wood with G-layer-rich fibers under mechanical stress. Despite being recognized over a century ago, three key biological questions remained unclear: (1) Are fibers in normal and tension wood distinct cells due to morphological differences? (2) Do tension wood fibers arise from different lineages? (3) What are the key genes regulating tension wood formation? We conducted single-cell RNA-seq on normal, tension and opposite xylem. Fibers in normal and tension wood belong to the same cell type and lineage. Differential developmental speed and cell-type ratio in tension and opposite xylem were further validated by spatial transcriptomics and metabolomics. Phosphoproteomics uncovered mechanical sensing mechanisms conserved between stems and roots across angiosperms. We identified a group of genes involved in the cell fate transition in tension wood. The knowledge on the heterogeneity of cell development offers insights for optimizing biomass production and bioenergy yield.
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Project description:The within-tree variation in wood properties constitutes an exceptional model to study the mechanisms that adjust the different biosynthetic pathways providing substrates with the massive and variable demands of different biosynthetic reactions of cell wall polymers. Although a few genes have been reported as differentially expressed in differentiating compression wood compared to normal or opposite wood, the expression of a larger set of genes is expected to change due the broad range of features that distinguish this reaction wood. By combining the construction of different cDNA libraries with microarray analyses, using samples from different Pinus pinaster provenances collected in different years and geographic locations, we have identified a total of 496 genes that change their expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Consistent with the well-known structural and chemical characteristics of compression wood, a large number of genes involved in the biosynthesis of cell wall components were shown to be up-regulated during compression wood differentiation, including genes involved in synthesis of cellulose, hemicellulose, lignin and lignans. In particular, further analysis of a set of these genes involved in providing S-adenosylmethionine, ammonium recycling, lignin and lignans biosynthesis showed parallel expression profiles to levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. The comparative transcriptomic analysis of compression and opposite wood formation in this work have revealed a broad spectrum of coordinated transcriptional modulation of biosynthetic reactions for different cell wall polymers associated to within-tree variations in softwood structure and composition. In particular, it suggest the occurrence of a mechanism that modulates at transcriptional level genes encoding enzymes involved in S-adenosylmethionine synthesis and ammonium assimilation with coniferyl alcohol demand for lignin and lignan synthesis, as a key metabolic requirement in cells undergoing lignification. Two-condition experiment including dye-swap experiments, Compression Differentiating Xylem vs. Opposite Differentiating Xylem. Biological replicates: 4 compression xylem, 4 opposite xylew, harvested from four different individual pine trees. Two replicates per array.
2012-05-05 | E-GEOD-37678 | biostudies-arrayexpress
Project description:The within-tree variation in wood properties constitutes an exceptional model to study the mechanisms that adjust the different biosynthetic pathways providing substrates with the massive and variable demands of different biosynthetic reactions of cell wall polymers. Although a few genes have been reported as differentially expressed in differentiating compression wood compared to normal or opposite wood, the expression of a larger set of genes is expected to change due the broad range of features that distinguish this reaction wood. By combining the construction of different cDNA libraries with microarray analyses, using samples from different Pinus pinaster provenances collected in different years and geographic locations, we have identified a total of 496 genes that change their expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Consistent with the well-known structural and chemical characteristics of compression wood, a large number of genes involved in the biosynthesis of cell wall components were shown to be up-regulated during compression wood differentiation, including genes involved in synthesis of cellulose, hemicellulose, lignin and lignans. In particular, further analysis of a set of these genes involved in providing S-adenosylmethionine, ammonium recycling, lignin and lignans biosynthesis showed parallel expression profiles to levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. The comparative transcriptomic analysis of compression and opposite wood formation in this work have revealed a broad spectrum of coordinated transcriptional modulation of biosynthetic reactions for different cell wall polymers associated to within-tree variations in softwood structure and composition. In particular, it suggest the occurrence of a mechanism that modulates at transcriptional level genes encoding enzymes involved in S-adenosylmethionine synthesis and ammonium assimilation with coniferyl alcohol demand for lignin and lignan synthesis, as a key metabolic requirement in cells undergoing lignification. Two-condition experiment including dye-swap experiments, Compression Differentiating Xylem vs. Opposite Differentiating Xylem. Biological replicates: 4 compression xylem, 4 opposite xylew, harvested from four different individual pine trees. Two replicates per array.
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Project description:The plant xylem tissue is responsible for water transportation, mechanical support and lateral growth, and can be utilized as wood. The seed plant xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells, including tracheids in gymnosperms and vessel elements and libriform fibers in angiosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. Here we show that the radial and axial systems of stem-differentiating xylem are differentially conserved across four divergent woody angiosperms. Through transcriptomic profiling of single cells and cell-type regions isolated by laser capture microdissection, we identified cell types corresponding to single-cell clusters in Populus trichocarpa. Cross-species analyses of single-cell trajectories demonstrated highly conserved development in ray lineages across angiosperms. While the core eudicots P. trichocarpa and Eucalyptus grandis share nearly identical fusiform cell lineages, the tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed character, exhibited an expression pattern highly similar to that of vessel elements. It suggests that water transportation, instead of mechanical support, is the dominant feature of tracheary elements. Furthermore, we found that the more basal angiosperm Liriodendron chinense has a distinct fusiform lineage. This evo-developmental framework of xylem cell lineages provides a comprehensive understanding of the formation of the most abundant tissue on Earth.
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Project description:Currently little is known about the genetic mechanisms regulating the vascular cambium or the secondary growth of stems. We show here that the Populus Class I KNOX homeobox gene ARBORKNOX2 (ARK2) regulates both cell division in the cambium region and the differentiation of daughter cells in secondary xylem and phloem. ARK2 is expressed in the shoot apical meristem, and the vascular cambium region, reflecting some overlap in the regulation of these meristems. ARK2 is expressed broadly in the cambium region and in differentiating lignified cells types before becoming progressively restricted to the cambium. Populus overexpressing ARK2 present stem phenotypes with precocious cambium formation, delayed differentiation of cambium daughter cells, a wider cambium region, and ultimately less phloem fibers and secondary xylem. In contrast, Populus expressing RNAi or amicroRNA that target ARK2 transcripts present precocious differentiation of secondary phloem fibers and xylem, and ultimately more secondary xylem tissue and thicker secondary cell walls in phloem fibers and secondary xylem cells. These phenotypes in turn correlate with changes in the expression of genes affecting cell division, auxin, and cell wall synthesis and lignification that indicate that ARK2 primarily affects woody tissue development by regulation of cell differentiation. Notably, wood properties associated with secondary cell wall synthesis are negatively associated with ARK2 expression, including lignin and cellulose content. Together, our results suggest that ARK2 functions primarily by negatively regulating cell differentiation during secondary growth. We propose that ARK2 may identify a co-evolved regulatory module that influences complex wood properties relevant to ecological, industrial, and biofuels applications.
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Project description:<p>Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.</p><p><br></p><p><strong>UPLC-MS assay of Wood ring and extraxylary tissue</strong> is reported in the current study <strong>MTBLS1797</strong>.</p><p><strong>GC-MS assay of Wood ring and extraxylary tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1796' rel='noopener noreferrer' target='_blank'><strong>MTBLS1796</strong></a>.</p><p><strong>UPLC-MS assay of Wood fibre and ray cell tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1831' rel='noopener noreferrer' target='_blank'><strong>MTBLS1831</strong></a>.</p>
2020-09-01 | MTBLS1797 | MetaboLights
Project description:<p>Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.</p><p><br></p><p><strong>GC-MS assay of Wood ring and extraxylary tissue</strong> is reported in the current study <strong>MTBLS1796</strong>.</p><p><strong>UPLC-MS assay of Wood ring and extraxylary tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1797' rel='noopener noreferrer' target='_blank'><strong>MTBLS1797</strong></a>.</p><p><strong>UPLC-MS assay of Wood fibre and ray cell tissue</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1831' rel='noopener noreferrer' target='_blank'><strong>MTBLS1831</strong></a>.</p>
2020-09-01 | MTBLS1796 | MetaboLights