C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism
C4GEM, a Genome-Scale Metabolic Model to Study C4 Plant Metabolism
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DOI：
10.1104/pp.110.166488
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发表时间：
2010-12-01
期刊：
影响因子：
7.4
通讯作者：
Nielsen, Lars Keld
中科院分区：
文献类型：
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作者：
Dal'Molin, Cristiana Gomes de Oliveira;Quek, Lake-Ee;Nielsen, Lars Keld
C-4禾本科植物（如玉米[Zea mays]、甘蔗[Escherichum officinarum]和高粱[Sorghum bicolor]）的叶形成了经典的Kranz叶解剖结构。与C-3植物不同，C-4植物中的光合CO2固定在叶肉（M）中进行，固定过程分布在两种细胞类型之间，M细胞和束鞘（BS）细胞。在这里，我们开发了一个C-4基因组规模的模型（C4 GEM）的调查流量分布在M和BS细胞在C-4光合作用。据我们所知，C4 GEM是第一个大规模的代谢模型，它封装了两种不同细胞类型之间的代谢相互作用。C4 GEM基于拟南芥（Arabidopsis thaliana）模型（AraGEM），但已通过添加负责代表三种不同C-4亚型（NADP-ME [苹果酸酶]，NAD-ME和磷酸烯醇丙酮酸羧激酶）的反应和转运蛋白进行了扩展。C4 GEM已被验证能够合成47种生物质组分，由1，588个独特反应，1，755种代谢产物，83种细胞器间转运蛋白和29种外部转运蛋白（包括通过胞间连丝的转运）组成。普通C-4模型中的反应与注释良好的C-4物种（NADP-ME亚型）相关：高粱中有3，557个基因，玉米中有11，623个基因，甘蔗中有3，881个基因。在高粱、玉米和甘蔗中，未分配给基因的基本反应的数量分别为131、135和156。采用通量平衡分析法研究了C-4光合作用过程中M和BS细胞的代谢活性。我们的模拟与叶绿体蛋白质组学研究是一致的，C4 GEM预测经典的C-4光合作用途径及其在M和BS细胞器功能的主要影响。该模型还突出了三种不同C-4亚型的光系统I和光系统II周围代谢活动的差异。还探讨了CO2泄漏的影响。C4 GEM是一个可行的框架，在计算机上分析细胞之间的合作M和BS细胞在光合作用，并可用于探索C4植物代谢。
Leaves of C-4 grasses (such as maize [Zea mays], sugarcane [Saccharum officinarum], and sorghum [Sorghum bicolor]) form a classical Kranz leaf anatomy. Unlike C-3 plants, where photosynthetic CO2 fixation proceeds in the mesophyll (M), the fixation process in C-4 plants is distributed between two cell types, the M cell and the bundle sheath (BS) cell. Here, we develop a C-4 genome-scale model (C4GEM) for the investigation of flux distribution in M and BS cells during C-4 photosynthesis. C4GEM, to our knowledge, is the first large-scale metabolic model that encapsulates metabolic interactions between two different cell types. C4GEM is based on the Arabidopsis (Arabidopsis thaliana) model (AraGEM) but has been extended by adding reactions and transporters responsible to represent three different C-4 subtypes (NADP-ME [for malic enzyme], NAD-ME, and phosphoenolpyruvate carboxykinase). C4GEM has been validated for its ability to synthesize 47 biomass components and consists of 1,588 unique reactions, 1,755 metabolites, 83 interorganelle transporters, and 29 external transporters (including transport through plasmodesmata). Reactions in the common C-4 model have been associated with well-annotated C-4 species (NADP-ME subtypes): 3,557 genes in sorghum, 11,623 genes in maize, and 3,881 genes in sugarcane. The number of essential reactions not assigned to genes is 131, 135, and 156 in sorghum, maize, and sugarcane, respectively. Flux balance analysis was used to assess the metabolic activity in M and BS cells during C-4 photosynthesis. Our simulations were consistent with chloroplast proteomic studies, and C4GEM predicted the classical C-4 photosynthesis pathway and its major effect in organelle function in M and BS. The model also highlights differences in metabolic activities around photosystem I and photosystem II for three different C-4 subtypes. Effects of CO2 leakage were also explored. C4GEM is a viable framework for in silico analysis of cell cooperation between M and BS cells during photosynthesis and can be used to explore C-4 plant metabolism.