Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses
Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses
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对低氧胁迫转录组调整的跨王国比较凸显了植物的保守反应和特异反应
DOI：
10.1104/pp.109.151845
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发表时间：
2010-03-01
期刊：
影响因子：
7.4
通讯作者：
Bailey-Serres, Julia
中科院分区：
文献类型：
--
作者：
Mustroph, Angelika;Lee, Seung Cho;Bailey-Serres, Julia
高通量技术促进了对转录调节的基因组规模分析，以响应环境扰动和缺氧成分，如瞬时缺氧或缺氧、根淹水或完全淹没。我们之前的研究表明，拟南芥(Arabitopsis Thaliana)幼苗可以上调数百种转录本的水平，其中包括一组由49个基因组成的核心组，这些基因被优先用于在茎和根的细胞类型之间进行翻译。为了识别进化上保守的低氧反应与物种特异性的反应，我们比较了来自四个物种(植物、动物、真菌和细菌)的21种生物的转录重组。对生物体蛋白质组进行分类，确定了与糖酵解、发酵、交替呼吸、代谢物运输、活性氧物种改善、伴侣活性和核糖体生物发生相关的广泛保守的反应。涉及信号和转录调控的差异调控基因在不同王国之间保守程度很低。值得注意的是，在拟南芥幼苗诱导的mRNAs中，近一半编码功能未知的蛋白质，其中40%以上在杨树、水稻或莱茵衣藻中上调表达。16个低氧反应未知蛋白(HUP)基因，包括4个拟南芥特有的基因，被异位过表达，并评价了它们对幼苗耐缺氧的影响。这使得可以识别与厌氧代谢和其他过程相关的基因共同调节的HUPs，当异位过度表达时，这些过程可以显着增强或降低应激存活。这些发现阐明了广泛保守的和植物特有的低氧胁迫反应，并证实了植物特有的HUP具有有限的系统发育分布影响低氧胁迫的耐受性。
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.