Abstract
BackgroundAspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cell death, and reproduction. Prior to the present study, no grape AP gene(s) had been reported, and their research on woody species was very limited.ResultsIn this study, a total of 50 AP genes (VvAP) were identified in the grape genome, among which 30 contained the complete ASP domain. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family. Additional 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 grape and Arabidopsis. Phylogenetic relationships of the 30 VvAPs with the complete ASP domain and their Arabidopsis orthologs, as well as their gene and protein features were analyzed and their cellular localization was predicted. Moreover, expression profiles of VvAP genes in six different tissues were determined, and their transcript abundance under various stresses and hormone treatments were measured. Twenty-seven VvAP genes were expressed in at least one of the six tissues examined; nineteen VvAPs 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 and phylogenetic analysis identified orthologous AP genes between grape and Arabidopsis, providing a unique starting point for investigating the function of grape AP genes.ConclusionsThe genome-wide identification, evolutionary and expression analyses of grape AP genes provide a framework for future analysis of AP genes in defining their roles during stress response. Integrated synteny and phylogenetic analyses provide novel insight into the functions of less well-studied genes using information from their better understood orthologs.
Highlights
Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms
The following Arabidopsis genes were selected for predicting the function of their orthologous counterparts in grape: Constitutive disease resistance gene 1 (CDR1) (NP_198319, which plays a crucial role in activating resistance of Arabidopsis against microbial pathogens) [11]; Promotion of cell survival gene 1 (PCS1) (NP_195839, the PROMOTION of CELL SURVIVAL 1 gene, which encodes an aspartic protease with an important role in determining the fate of both male and female gametophytes and excessive cell death of developing embryos) [19]; and Aspartic protease in guard cell 1 (ASPG1) (NP_188478, the ASPARTIC PROTEASE IN GUARD CELL 1 gene whose over expression conferred drought avoidance via abscisic acid (ABA)-dependent signalling in Arabidopsis) [20]
We examined the segmentally duplicated blocks within the grape genome and found that there were 9 pairs of grape AP genes associated with segmental duplications (Figure 1), VvAP10/VvAP34, VvAP16/VvAP44, VvAP40/VvAP18, VvAP42/VvAP17, VvAP27/VvAP45, VvAP32/VvAP21, VvAP13/VvAP25, VvAP22/VvAP14, including two tandemly duplicated genes (VvAP22 and VvAP34) (Additional file 3)
Summary
Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. Aspartic proteinases (APs; EC 3.4.23) are widely distributed among living organisms, being found in plants, yeast, nematodes, parasites, fungi and even viruses. These enzymes have been extensively studied and constitute one of the four superfamilies of proteolytic enzymes [1,2,3]. Typical plant AP preproteins contain a C-terminal domain of approximately 50–100 amino acids (called the plant specific insert, PSI) which is removed during protein maturation Neither their sequences nor structures share significant homology with animal or microbial APs; the PSI domain is homologous with the precursor of mammalian saposins [8]. Atypical APs display intermediate features between the typical and nucellin-like sequences [7]
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