Integrated Analysis of Protein Abundance, Transcript Level, and Tissue Diversity To Reveal Developmental Regulation of Maize

The differentiation and subsequent development of plant tissues or organs are tightly regulated at multiple levels, including the transcriptional, posttranscriptional, translational, and posttranslational levels. Transcriptomes define many of the tissue-specific gene expression patterns in maize, and some key genes and their regulatory networks have been established at the transcriptional level. In this study, the sequential window acquisition of all theoretical spectra–mass spectrometry technique was employed as a quantitative proteome assay of four representative maize tissues, and a set of high-confidence proteins was identified. Integrated analysis of the proteome and transcriptome revealed that protein abundance was positively correlated with mRNA level with weak to moderate correlation coefficients, but the abundance of key proteins for function or architecture in a given tissue was closely tempospatially regulated at the transcription level. A subset of differentially expressed proteins, specifically tissue-specific highly expressed proteins, was identified, for example, reproductive structure and flower development-related proteins in tassel and ear, lipid and fatty acid biosynthetic process-related proteins in immature embryo, and inorganic substance and oxidation reduction responsive proteins in root, potentially revealing the physiology, morphology, and function of each tissue. Furthermore, we found many new proteins in specific tissues that were highly correlated with their mRNA levels, in addition to known key factors. These proteome data provide new perspective for understanding many aspects of maize developmental biology. Raw proteomics data are available via ProteomeXchange with identifier PXD008464.植物组织或器官的分化与后续发育，受到转录水平、转录后水平、翻译水平及翻译后水平等多个层面的严格调控。转录组可阐释玉米诸多组织特异性基因表达模式，目前已有部分关键基因及其调控网络在转录层面得到阐明。本研究采用全理论谱序贯窗口采集-质谱技术（sequential window acquisition of all theoretical spectra-mass spectrometry），对四种典型玉米组织开展定量蛋白质组学检测，成功鉴定得到一组高置信度蛋白质。通过蛋白质组与转录组的整合分析发现，蛋白质丰度与mRNA水平呈正相关，相关系数介于弱至中等区间；但特定组织中行使功能或构成结构的关键蛋白质丰度，在转录层面受到紧密的时空调控。本研究鉴定得到一批差异表达蛋白质，其中尤以组织特异性高表达蛋白质为代表：例如雄穗与雌穗中与生殖结构及花发育相关的蛋白质、未成熟胚中参与脂质与脂肪酸生物合成过程的蛋白质，以及根系中响应无机物质与氧化还原反应的蛋白质，这些蛋白质或可揭示各组织的生理、形态与功能特征。此外，除已知的关键调控因子外，我们还在特定组织中发现了一批与自身mRNA水平高度相关的新型蛋白质。本研究获得的蛋白质组数据，为解析玉米发育生物学的诸多方面提供了全新视角。原始蛋白质组学数据可通过ProteomeXchange数据库获取，登录编号为PXD008464。