Complementary Proteome and Transcriptome Profiling in Phosphate-deficient Arabidopsis Roots Reveals Multiple Levels of Gene Regulation
Complementary Proteome and Transcriptome Profiling in Phosphate-deficient Arabidopsis Roots Reveals Multiple Levels of Gene Regulation
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DOI：
10.1074/mcp.m112.020461
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发表时间：
2012-11-01
影响因子：
7
通讯作者：
Schmidt, Wolfgang
中科院分区：
文献类型：
--
作者：
Lan, Ping;Li, Wenfeng;Schmidt, Wolfgang
在许多农业生态系统中，磷酸盐（P-i）缺乏会损害植物生长和生产力，导致作物产量严重降低。为了揭示新的方面，在适应P-i饥饿，我们研究了P-i缺乏诱导的变化在转录组和蛋白质组分布在拟南芥根之间的相关性。使用基于穷举串联质谱的鸟枪蛋白质组学和全基因组RNA测序来产生几乎完整的表达mRNA和蛋白质目录，我们可靠地鉴定了13，298种蛋白质和24，591种转录物，356种蛋白质和3106种mRNA的子集在P-i缺乏症期间差异表达。最引人注目的变化被注意到的基因参与P-i收购和过程中，要么释放P-i或旁路P-i/ATP消耗代谢步骤，例如在膜脂质重塑和糖酵解碳通量。对于高度上调的基因，mRNA及其编码蛋白的丰度之间的一致性通常较高，但分析也揭示了mRNA/蛋白对中的许多不一致变化，表明转录和转录后过程的不同调节。特别地，在P-i缺乏时蛋白质丰度的降低与相应mRNA的变化不密切相关。在某些情况下，仅在蛋白质水平上观察到基因活性的上调，为适应Pi缺乏的关键过程增添了新的方面。我们的结论是，对蛋白质和转录本丰度变化的综合测量和解释对于生成对环境刺激反应至关重要的成分的完整清单是强制性的。Molecular & Cellular Proteomics 11：10.1074/mcp. M112.020461，1156-1166，2012.
Phosphate (P-i) deficiency impairs plant growth and productivity in many agricultural ecosystems, causing severe reductions in crop yield. To uncover novel aspects in acclimation to P-i starvation, we investigated the correlation between P-i deficiency-induced changes in transcriptome and proteome profiles in Arabidopsis roots. Using exhaustive tandem mass spectrometry-based shotgun proteomics and whole-genome RNA sequencing to generate a nearly complete catalog of expressed mRNAs and proteins, we reliably identified 13,298 proteins and 24,591 transcripts, subsets of 356 proteins and 3106 mRNAs were differentially expressed during P-i deficiency. Most dramatic changes were noticed for genes involved in P-i acquisition and in processes that either liberate P-i or bypass P-i/ATP-consuming metabolic steps, for example during membrane lipid remodeling and glycolytic carbon flux. The concordance between the abundance of mRNA and its encoded protein was generally high for highly up-regulated genes, but the analysis also revealed numerous discordant changes in mRNA/protein pairs, indicative of divergent regulation of transcription and post-transcriptional processes. In particular, a decreased abundance of proteins upon P-i deficiency was not closely correlated with changes in the corresponding mRNAs. In several cases, up-regulation of gene activity was observed solely at the protein level, adding novel aspects to key processes in the adaptation to P-i deficiency. We conclude that integrated measurement and interpretation of changes in protein and transcript abundance are mandatory for generating a complete inventory of the components that are critical in the response to environmental stimuli. Molecular & Cellular Proteomics 11: 10.1074/mcp.M112.020461, 1156-1166, 2012.