Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA.
Plant Physiol. 2010 Mar;152(3):1484-500. doi: 10.1104/pp.109.151845. Epub 2010 Jan 22.
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.
高通量技术促进了大规模的转录组分析，以研究环境胁迫（如短暂缺氧或缺氧、根系水淹或完全淹没）对转录组的影响。我们之前表明，拟南芥（Arabidopsis thaliana）幼苗会提高数百个转录本的水平，包括一组核心基因，这些基因在茎和根的所有细胞类型中都被优先翻译。为了识别进化上保守和物种特异性的低氧反应，我们比较了来自四个界（植物界、动物界、真菌界和细菌界）的 21 种生物的转录组重排。将生物体的蛋白质组分类为假定的同源物簇，确定了与糖酵解、发酵、替代呼吸、代谢物运输、活性氧缓解、伴侣活性和核糖体生物发生广泛相关的保守反应。参与信号转导和转录调控的差异调节基因在不同界之间的保守性较差。引人注目的是，拟南芥幼苗中近一半的诱导 mRNA 编码未知功能的蛋白质，其中超过 40%的在杨树（Populus trichocarpa）、水稻（Oryza sativa）或莱茵衣藻（Chlamydomonas reinhardtii）中有上调的同源物。16 个缺氧反应未知蛋白（HYPOXIA-RESPONSIVE UNKNOWN PROTEIN，HUP）基因，包括 4 个是拟南芥特有的，被异位过表达，并评估其对幼苗耐受缺氧的影响。这使得与厌氧代谢和其他过程相关的基因及其核心调控基因得以确定，当异位过表达时，这些基因显著增强或降低了应激生存能力。这些发现阐明了广泛保守和植物特异性的低氧应激反应，并证实了具有有限系统发生分布的植物特异性 HUP 影响低氧应激耐力。
