ArticlePlant physiology2010
Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses.
Article in Plant physiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 180 papers, 2 of them syntheses that pooled it.
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Who cites it
180 citing papers in PubMed, 2 syntheses or guidelines pooled it, 373 citations in OpenAlex.
- Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis.Functional & integrative genomics · 2020Pooled it
- Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach.BMC plant biology · 2015Pooled it
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- A synthetic ERFVII-dependent circuit in yeast sheds light on the regulation of early hypoxic responses of plants.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structural variation drives rhizome innovation and adaptive divergence in sister Medicago species.Journal of integrative plant biology · 2026Article
- Waterlogging and hypoxia in plant abiotic stress.Frontiers in plant science · 2026Review
- GLARE: discovering hidden patterns in spaceflight transcriptome using representation learning.NPJ microgravity · 2025Article
- Identification of Quantitative Trait Loci and Candidate Genes Involved in Rice Seedling Growth Under Hypoxic Stress.International journal of molecular sciences · 2025Article
- Mangrove-Derived Endophytic Bacteria Enhance Growth, Yield, and Stress Resilience in Rice.International journal of molecular sciences · 2025Article
- Detecting Environmental Stress In Situ Using Molecular Data: A Case Study with the Filamentous Green AlgaMicroorganisms · 2025Article
- Oxygen supply is a prerequisite for response to aluminum in cultured cells of tobacco (Nicotiana tabacum).Plant & cell physiology · 2025Article
- Physiological, biochemical, and transcriptomic responses to waterlogging stress in Panicum bisulcatum, an emerging weed in rice fields.BMC plant biology · 2025Article
- Metabolite Profile and Metabolic Network Analysis of Walnuts (Metabolites · 2025Article
- ERFVIIs as transducers of oxygen-sensing in the evolution of land plant response to hypoxia.Molecular plant · 2025Article
- Oxygen sensing and plant adaptation to flooding in a changing climate.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
120 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput technology has facilitated genome-scale analyses of transcriptomic adjustments in response to environmental perturbations with an oxygen deprivation component, such as transient hypoxia or anoxia, root waterlogging, or complete submergence. We showed previously that Arabidopsis (Arabidopsis thaliana) seedlings elevate the levels of hundreds of transcripts, including a core group of 49 genes that are prioritized for translation across cell types of both shoots and roots. To recognize low-oxygen responses that are evolutionarily conserved versus species specific, we compared the transcriptomic reconfiguration in 21 organisms from four kingdoms (Plantae, Animalia, Fungi, and Bacteria). Sorting of organism proteomes into clusters of putative orthologs identified broadly conserved responses associated with glycolysis, fermentation, alternative respiration, metabolite transport, reactive oxygen species amelioration, chaperone activity, and ribosome biogenesis. Differentially regulated genes involved in signaling and transcriptional regulation were poorly conserved across kingdoms. Strikingly, nearly half of the induced mRNAs of Arabidopsis seedlings encode proteins of unknown function, of which over 40% had up-regulated orthologs in poplar (Populus trichocarpa), rice (Oryza sativa), or Chlamydomonas reinhardtii. Sixteen HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes, including four that are Arabidopsis specific, were ectopically overexpressed and evaluated for their effect on seedling tolerance to oxygen deprivation. This allowed the identification of HUPs coregulated with genes associated with anaerobic metabolism and other processes that significantly enhance or reduce stress survival when ectopically overexpressed. These findings illuminate both broadly conserved and plant-specific low-oxygen stress responses and confirm that plant-specific HUPs with limited phylogenetic distribution influence low-oxygen stress endurance.
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