Novel Cell-Type-Specific Drought-Responsive Proteins in Root Tips of Field-Grown Perennial Switchgrass

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Abstract
The plant root tip is a highly specialized region where cells transition from stem cells to differentiated types and respond to environmental cues. Yet, cell-type-specific proteomic responses to abiotic stress in field-grown plants remain poorly understood. This study generated proteomes for five root-tip cell types in switchgrass (Panicum virgatum), including (1) quiescent center and stem cell niche (Quc), (2) protodermal epidermal cells in the meristematic zone (PEC), (3) epidermal cells in the transition and elongation zones (Epi), (4) peripheral root cap cells (PRC) and (5) columella root cap cells (Col), and characterized their drought-responsive profiles. Root tips from seven-year-old field-grown “Alamo” plants under well-watered or long-term drought conditions were analyzed using laser capture microdissection (LCM) coupled with nanoPOTS and nano-LC-MS. In well-watered samples, 6336–6640 proteins were quantified per cell type, and principal component analysis confirmed distinct proteomic identities. Drought-stressed samples, collected from fewer cells per type, yielded 1109–3298 proteins, with 4,493 proteins quantified overall and 935 shared across all cell types. After median normalization of peptide abundance, differentially abundant proteins (DAPs) were identified using Welch’s t test (|log2FC| > 1, adjusted p ≤ 0.05), revealing cell-type-specific drought responses, with the largest numbers of DAPs in Quc and Col cells. DAPs were associated with phytohormone biosynthesis and signaling (auxin, cytokinin, jasmonic acid), DNA repair and mitosis (notably enriched in Quc), and metabolic pathways involving amino acids, carbohydrates, and lipids. Stress-responsive proteins generally increased, whereas proteins linked to translation decreased across all cell types. Overall, this work provides the first spatially resolved, cell-type-specific root-tip proteomes from field-grown switchgrass, offering new insight into distinct cellular strategies underlying drought tolerance.
Funding Information
  • Environmental Molecular Sciences Laboratory (60294)
  • National Institute of Food and Agriculture (2020-69008-32761)
  • National Institute of Food and Agriculture (2022-38821-37339)

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