Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA.
Plant Physiol. 2010 Mar;152(3):1219-50. doi: 10.1104/pp.109.152694. Epub 2010 Jan 20.
Chloroplasts in differentiated bundle sheath (BS) and mesophyll (M) cells of maize (Zea mays) leaves are specialized to accommodate C(4) photosynthesis. This study provides a reconstruction of how metabolic pathways, protein expression, and homeostasis functions are quantitatively distributed across BS and M chloroplasts. This yielded new insights into cellular specialization. The experimental analysis was based on high-accuracy mass spectrometry, protein quantification by spectral counting, and the first maize genome assembly. A bioinformatics workflow was developed to deal with gene models, protein families, and gene duplications related to the polyploidy of maize; this avoided overidentification of proteins and resulted in more accurate protein quantification. A total of 1,105 proteins were assigned as potential chloroplast proteins, annotated for function, and quantified. Nearly complete coverage of primary carbon, starch, and tetrapyrole metabolism, as well as excellent coverage for fatty acid synthesis, isoprenoid, sulfur, nitrogen, and amino acid metabolism, was obtained. This showed, for example, quantitative and qualitative cell type-specific specialization in starch biosynthesis, arginine synthesis, nitrogen assimilation, and initial steps in sulfur assimilation. An extensive overview of BS and M chloroplast protein expression and homeostasis machineries (more than 200 proteins) demonstrated qualitative and quantitative differences between M and BS chloroplasts and BS-enhanced levels of the specialized chaperones ClpB3 and HSP90 that suggest active remodeling of the BS proteome. The reconstructed pathways are presented as detailed flow diagrams including annotation, relative protein abundance, and cell-specific expression pattern. Protein annotation and identification data, and projection of matched peptides on the protein models, are available online through the Plant Proteome Database.
玉米叶片中分化的束鞘（BS）和叶肉（M）细胞中的叶绿体专门适应 C（4）光合作用。本研究提供了一种方法，可定量重建代谢途径、蛋白质表达和体内平衡功能如何在 BS 和 M 叶绿体中分布。这为细胞特化提供了新的见解。实验分析基于高精度质谱、光谱计数的蛋白质定量以及第一个玉米基因组组装。开发了一种生物信息学工作流程来处理与玉米多倍体相关的基因模型、蛋白质家族和基因复制；这避免了蛋白质的过度鉴定，并导致更准确的蛋白质定量。总共鉴定了 1105 种潜在的叶绿体蛋白，对其进行了功能注释和定量。几乎完全涵盖了初级碳、淀粉和四吡咯代谢，以及脂肪酸合成、类异戊二烯、硫、氮和氨基酸代谢的极好覆盖，这表明在淀粉生物合成、精氨酸合成、氮同化以及硫同化的初始步骤中存在定量和定性的细胞类型特异性特化。BS 和 M 叶绿体蛋白质表达和体内平衡机制的广泛概述（超过 200 种蛋白质）表明 M 和 BS 叶绿体之间存在定性和定量差异，以及 BS 增强的专门伴侣 ClpB3 和 HSP90 的水平，这表明 BS 蛋白质组的积极重塑。重建的途径以详细的流程图呈现，包括注释、相对蛋白质丰度和细胞特异性表达模式。蛋白质注释和鉴定数据以及匹配肽在蛋白质模型上的投影可通过植物蛋白质组数据库在线获得。
