|An, Yong-qiang - Charles|
Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2010
Publication Date: 11/9/2010
Citation: Guttikonda, S.K., Joshi, T., Bisht, N., Chen, H., An, Y., Pandey, S., Xu, D., Yu, O. 2010. Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. Biomed Central (BMC) Plant Biology. 10:243. Interpretive Summary: Cytochrome P450 monooxygenases (P450s) are enzymes encoded by many genes in plants, and perform diverse biological functions by generating many metabolic compounds that are important to plant growth and agricultural production. However, the specific functions for most of the P450 genes are unknown. To gain insight into the function of each soybean P450 gene and the underlying regulatory networks that control their expression we conducted a genome-wide characterization of P450 genes and examined their expression patterns across diverse biological conditions. Our analysis of the recently published soybean genome sequence identified a large number of P450 genes and further classified them into distinct groups. Analyzing gene expression profiles for diverse soybean tissue/organ types and for a variety of stress treatments, revealed that P450 genes are subjected to differential regulation with respects to tissue type or stress response. Genome-wide co-expression analysis revealed that a number of P450 genes co-expresses with genes involved in nitrogen-fixing nodule and root development. These co-expression patterns suggest a role for some P450 genes in nodule and root developmental processes. The systematic and comprehensive results generated for the soybean P450 genes enable soybean researchers to design effective strategies to validate their individual functions and to ultimately utilize these important genes for soybean quality, seed composition, and productivity improvement.
Technical Abstract: Cytochrome P450 monooxygenases (P450s) catalyze oxidation of various substrates using oxygen and NAD(P)H. Plant P450s are involved in the biosynthesis of primary and secondary metabolites performing diverse biological functions. The recent availability of soybean genome sequence allows us to identify and analyze putative soybean P450s on a genomic scale. It has been hypothesized that genes co-expressing across a wide range of conditions are likely to have related functions. Therefore co-expression analysis of available soybean microarray and Illumina sequencing based transcriptome data should offer a great strategy for functional annotation of the soybean P450 gene family. Our studies of the soybean genome identified 332 full-length P450 genes and 372 pseudogenes. Of the full-length sequences, 201 genes belong to A-type and 131 to non A-type. The genes in these two categories have been further classified into 23 and 25 gene families respectively. In addition, using 28 publicly available microarray libraries containing organ-specific information, a number of tissue-specific P450s were identified. On the Affymetrix soybean genome GeneChip used in this study, a total of 178 probe sets were found to correspond to 108 individual P450 genes. Similarly, stress responsive soybean P450s were retrieved from 99 microarray soybean libraries. We also utilized Illumina transcriptome sequencing technology to analyze the expressions of all 332 soybean P450 genes. This dataset contains total RNAs isolated from nodules, roots, root tips, leaves, flowers, greenpods, apical meristem, mock-inoculated and Bradyrhizobium japonicum-infected root hair cells. The tissue-specific expression patterns of these P450 genes were determined, and the expression of representative genes was confirmed by qRT-PCR. We performed co-expression analysis on many of the 108 P450 genes identified from the Affymetrix arrays. This analysis confirmed that CYP93C5 (isoflavone synthase) is coexpressed with several isoflavonoid-related metabolic enzymes. We then focused on nodulation-induced P450s and found that CYP728H1 was co-expressed with genes involved in phenylpropanoid metabolism. Similarly, CYP736A34 was highly coexpressed with lipoxygenase, lectin and CYP83D1, all of which are involved in root and nodule development. Genomic scale analysis of P450s in soybean provides many unique features of important enzymes that have largely unknown functions. Our work presented here could provide important lead towards functional studies of soybean P450s and their underlying regulatory networks through integrating approaches of reverse genetics, biochemistry, and metabolic profiling tools. The identification of nodule-specific P450s and their further exploitation may help us to better understand the intriguing process of soybean and rhizobium interaction.