Ehlting Jürgen, Sauveplane Vincent, Olry Alexandre, Ginglinger Jean-François, Provart Nicholas J, Werck-Reichhart Danièle
Institute of Plant Molecular Biology, Centre National de la Recherche Scientifique UPR 2357, Université Louis Pasteur, 28 rue Goethe, 67000 Strasbourg, France.
BMC Plant Biol. 2008 Apr 23;8:47. doi: 10.1186/1471-2229-8-47.
Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s) is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism.
We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here.
The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.
首批植物基因组测序结果显示，细胞色素P450已进化成为次生代谢中最大的酶家族。然而，具有已明确生化功能的P450酶的比例非常小。如果P450的多样化反映了化学多样性的进化，这表明我们对植物代谢的理解出乎意料地匮乏。我们认为，对基因表达进行广泛分析可能有助于了解P450酶的功能，并突出植物代谢中被忽视的方面。
我们创建了一个综合数据库“CYPedia”，该数据库基于公开的Affymetrix ATH1微阵列表达数据，描述了拟南芥四个数据集中的P450基因表达情况：器官和组织、应激反应、激素反应以及突变体。然后将P450表达与4130个重新注释的基因（预计参与植物代谢）的表达相结合，进行共表达分析。基于来自不同途径注释数据库的共表达基因注释，确定了共表达途径。对大多数具有已知功能的P450进行了预测验证。在此以与质体功能/光合作用以及苯丙烷类、三萜类和茉莉酸代谢相关的P450的共表达结果为例进行说明。
本文介绍的大规模假设生成工具为植物代谢中许多P450的新途径、意外功能和调控网络提供了线索。现在，科学界可以利用这些线索，通过反向遗传学、生物化学和代谢谱分析等方法，对所提出的功能进行实验验证。
