{
  "abstract": "Organelle retrograde signaling studies have exclusively relied on bulk tissues, obscuring cell-type specificity, spatial organization, and heterogeneity within cell types. Here, we use single-nucleus and spatial RNA sequencing to define the cellular and spatial architecture of mitochondrial stress signaling in Arabidopsis thaliana. Inhibition of the mitochondrial electron transport chain by antimycin A and myxothiazol rapidly redistributed nuclei among transcriptional states within epidermal, leaf pavement, and mesophyll lineages, revealing that mitochondrial dysfunction reshapes cell identity trajectories rather than eliciting a uniform response. Stress-associated clusters were already present at low frequency in untreated samples, but the numbers of cells increased following stress treatments, suggesting that stress increases the proportion of nuclei occupying pre-existing transcriptional states. Gene-level analyses revealed distinct temporal dynamics and variable cell-state penetrance of mitochondrial stress markers and identified broadly responsive genes absent from earlier marker sets. Spatial transcriptomics resolved tissue-scale responses, spanning from pan-tissue induction to cell-type- and cluster-restricted activation, and uncovered pronounced adaxial–abaxial polarity in gene expression. Cell identity and spatial inferences were supported by extensive experimental validation using a custom 465-probe 10× Xenium panel and 52 promoter-GFP reporter lines. Together, these data provide a high-resolution framework for organelle-to-nucleus signaling and a resource of cell-type markers and spatial maps to dissect mitochondrial stress signaling and its integration with developmental and environmental pathways.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "name": "Yanqiao Zhu",
      "orcid": "0000-0002-8860-2692"
    },
    {
      "name": "Minxuan Li",
      "orcid": "0009-0004-0216-0371"
    },
    {
      "name": "Jiahao Li",
      "orcid": "0009-0008-9661-968X"
    },
    {
      "name": "Rijad Sarić",
      "orcid": "0000-0002-7554-2555"
    },
    {
      "name": "Feiran Han",
      "orcid": "0009-0003-3087-2459"
    },
    {
      "name": "Xinxin Zhou",
      "orcid": "0009-0005-6008-7229"
    },
    {
      "name": "Xiachao Wang",
      "orcid": "0009-0006-6011-5872"
    },
    {
      "name": "Yuhua Liu",
      "orcid": "0009-0009-8865-8715"
    },
    {
      "name": "Chi Zhang",
      "orcid": "0009-0001-3537-5836"
    },
    {
      "name": "Huixia Shou",
      "orcid": "0000-0001-6890-5672"
    },
    {
      "name": "Ghazanfar Abbas Khan",
      "orcid": "0000-0001-5629-0682"
    },
    {
      "name": "Mathew G Lewsey",
      "orcid": "0000-0002-2631-4337"
    },
    {
      "name": "James Whelan",
      "orcid": "0000-0001-5754-025X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0gk4qmccxvh8y.bib",
  "cited_by": 0,
  "doi": "10.1093/plcell/koag308",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13714915/",
  "id": "0gk4qmccxvh8y",
  "issns": [
    "1040-4651",
    "1532-298X"
  ],
  "landing_url": "https://doi.org/10.1093/plcell/koag308",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01210"
    ],
    [
      "heading",
      "Research Article"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7221044311",
  "pdf_url": "https://academic.oup.com/plcell/advance-article-pdf/doi/10.1093/plcell/koag308/71720505/koag308.pdf",
  "pmcid": "PMC13714915",
  "pmid": "42848931",
  "published": "2026-10-08",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/0gk4qmccxvh8y.ris",
  "sources": [
    {
      "first_seen": "2026-11-01T12:22:19Z",
      "native_id": "PMC13714915",
      "source": "pmc",
      "url": "https://doi.org/10.1093/plcell/koag308"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Spatial and single-nucleus transcriptomic profiling reveal polarity and intracellular responses to mitochondrial dysfunction",
  "title_text": "Spatial and single-nucleus transcriptomic profiling reveal polarity and intracellular responses to mitochondrial dysfunction",
  "type": "peer-reviewed",
  "updated_at": "2026-11-01T12:22:19Z",
  "url": "https://research.draconitic.com/paper/0gk4qmccxvh8y",
  "venue": "The Plant Cell",
  "versions": []
}