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Plant metabolism : zoom in to the single-cell level

Nikolaos Ntelkis (UGent) , C. Robin Buell and Alain Goossens (UGent)
(2025) PLANT PHYSIOLOGY. 199(1).
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Abstract
Plant specialized metabolism is intricately regulated and often compartmentalized at the cell-type level. Understanding where and when metabolites accumulate is essential for uncovering their function, biosynthesis, and regulation. Historically, studies have inferred metabolite localization based on the expression patterns of genes encoding biosynthetic enzymes, but these approaches fall short due to the complexity of metabolite transport and the discrepancy between transcript, protein, and metabolite abundance. Recent advances in mass spectrometry imaging, single-cell transcriptomics, and multi-omics have enabled the direct visualization and quantification of metabolites and gene expression at cellular resolution. These technologies have revealed striking cell type- and organ-specific patterns of metabolite accumulation, as well as the underlying transcriptional and chromatin regulatory networks. In this review, we describe case studies in several model and medicinal plant species that highlight the roles of rare or specialized cell types in specialized metabolite biosynthesis and the importance of spatiotemporal regulation. In addition, we discuss why it is becoming increasingly important to transition from single- to multi-omics approaches. As new tools continue to evolve, the regulation of plant metabolism will be uncovered at higher resolution, enabling precise pathway discovery and metabolic engineering for agriculture, biotechnology, and medicine.
Keywords
ARTEMISIA-ANNUA, MONOTERPENE BIOSYNTHESIS, ALKALOID BIOSYNTHESIS, TRANSCRIPTION FACTOR, GLANDULAR TRICHOMES, SIEVE ELEMENTS, S-CELLS, PATHWAY, TRANSLOCATION, PEPPERMINT

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Citation

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MLA
Ntelkis, Nikolaos, et al. “Plant Metabolism : Zoom in to the Single-Cell Level.” PLANT PHYSIOLOGY, vol. 199, no. 1, 2025, doi:10.1093/plphys/kiaf375.
APA
Ntelkis, N., Buell, C. R., & Goossens, A. (2025). Plant metabolism : zoom in to the single-cell level. PLANT PHYSIOLOGY, 199(1). https://doi.org/10.1093/plphys/kiaf375
Chicago author-date
Ntelkis, Nikolaos, C. Robin Buell, and Alain Goossens. 2025. “Plant Metabolism : Zoom in to the Single-Cell Level.” PLANT PHYSIOLOGY 199 (1). https://doi.org/10.1093/plphys/kiaf375.
Chicago author-date (all authors)
Ntelkis, Nikolaos, C. Robin Buell, and Alain Goossens. 2025. “Plant Metabolism : Zoom in to the Single-Cell Level.” PLANT PHYSIOLOGY 199 (1). doi:10.1093/plphys/kiaf375.
Vancouver
1.
Ntelkis N, Buell CR, Goossens A. Plant metabolism : zoom in to the single-cell level. PLANT PHYSIOLOGY. 2025;199(1).
IEEE
[1]
N. Ntelkis, C. R. Buell, and A. Goossens, “Plant metabolism : zoom in to the single-cell level,” PLANT PHYSIOLOGY, vol. 199, no. 1, 2025.
@article{01K4W599SGY3PP38WKEWVV4JM6,
  abstract     = {{Plant specialized metabolism is intricately regulated and often compartmentalized at the cell-type level. Understanding where and when metabolites accumulate is essential for uncovering their function, biosynthesis, and regulation. Historically, studies have inferred metabolite localization based on the expression patterns of genes encoding biosynthetic enzymes, but these approaches fall short due to the complexity of metabolite transport and the discrepancy between transcript, protein, and metabolite abundance. Recent advances in mass spectrometry imaging, single-cell transcriptomics, and multi-omics have enabled the direct visualization and quantification of metabolites and gene expression at cellular resolution. These technologies have revealed striking cell type- and organ-specific patterns of metabolite accumulation, as well as the underlying transcriptional and chromatin regulatory networks. In this review, we describe case studies in several model and medicinal plant species that highlight the roles of rare or specialized cell types in specialized metabolite biosynthesis and the importance of spatiotemporal regulation. In addition, we discuss why it is becoming increasingly important to transition from single- to multi-omics approaches. As new tools continue to evolve, the regulation of plant metabolism will be uncovered at higher resolution, enabling precise pathway discovery and metabolic engineering for agriculture, biotechnology, and medicine.}},
  articleno    = {{kiaf375}},
  author       = {{Ntelkis, Nikolaos and Buell, C. Robin and Goossens, Alain}},
  issn         = {{0032-0889}},
  journal      = {{PLANT PHYSIOLOGY}},
  keywords     = {{ARTEMISIA-ANNUA,MONOTERPENE BIOSYNTHESIS,ALKALOID BIOSYNTHESIS,TRANSCRIPTION FACTOR,GLANDULAR TRICHOMES,SIEVE ELEMENTS,S-CELLS,PATHWAY,TRANSLOCATION,PEPPERMINT}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{20}},
  title        = {{Plant metabolism : zoom in to the single-cell level}},
  url          = {{http://doi.org/10.1093/plphys/kiaf375}},
  volume       = {{199}},
  year         = {{2025}},
}
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