Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 7/15/2013
Publication Date: 8/23/2013
Citation: Guo, R., Xu, X., Bassett, C.L., Li, X., Zheng, Y., Gao, M., Wang, X. 2013. Genome-wide identification, evolutuionary and expression analysis of aspartic proteases gene superfamily in grape. Biomed Central (BMC) Genomics. 14:554. Interpretive Summary: Plants have to adapt to changes in their environment, particularly when such changes can be harmful. As a result, they have evolved complex networks of genes that respond to environmental threats and help the plant survive. Among these ‘stress-responsive’ genes are those encoding a large family of proteases which specifically degrade target proteins. Although this family has been studied in model plants, there is virtually no information about the composition, structure or expression of these genes in grape. The current manuscript describes 50 such genes and compares their sequence and structure to other model plants. In addition, the expression of these genes in response to environmental and plant hormone signals is thoroughly documented. Information from these studies lays the foundation for strategies to improve the survival of grape plants under adverse environmental conditions and protect the US grape industry from unnecessary crop loss.
Technical Abstract: Aspartic proteases (APs) are a large family of proteolytic enzymes in vertebrates, plants, yeast, nematodes, parasites, fungi, and viruses. In plants, they are involved in many biological processes, such as plant senescence, stress response, programmed cell death, and reproduction. Prior to the present study, no grape AP gene had been reported and research on woody species was very limited. In this study, a total of 50 AP genes (VvAP) were identified in the grape genome, and the ASP domain of 20 of them was found to be incomplete. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family, while synteny analysis between grape and Arabidopsis demonstrated that several grape AP genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of lineages that led to grape and Arabidopsis. Analysis of the complete set of VvAP genes is presented, including phylogenetic relationships between grape and Arabidopsis, as well as within grape, classification, exon/intron structure, and protein structure. Moreover, the expression profiles of VvAP genes in six tissues, as well as under various stresses and hormone treatments, were conducted. Twenty-seven VvAP genes were expressed in at least one of the six tissues examined; 18 VvAPs were detected that responded to at least one abiotic stress, 12 VvAPs responded to powdery mildew infection, and most of the VvAPs responded to SA and ABA treatments. Furthermore, integrated synteny analysis coupled with a phylogenetic tree was used to identify orthologous AP genes between grape and Arabidopsis. This approach is expected to provide a new starting point for investigating the function of grape genes by comparing orthologous genes between grape and Arabidopsis. The genome-wide identification, evolutionary and expression analyses of grape AP genes provides a framework for future analysis of AP genes and their roles in stress response. Application of integrated synteny analysis with phylogenetic tree assessment may provide a novel insights for investigating the functions of less well-studied genes by deriving information from their better understood orthologoues.