Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape

• Published in: PloS one 2013-03, Vol.8 (3), p.e59358-e59358
• Main Authors: Hou, Hongmin, Li, Jun, Gao, Min, Singer, Stacy D, Wang, Hao, Mao, Linyong, Fei, Zhangjun, Wang, Xiping, Unver, Turgay
• Format: Article
• Language: English
• Subjects: Abiotic stress; Agriculture; Algae; Amino Acid Sequence; Angiosperms; Arabidopsis; Arabidopsis thaliana; Base Sequence; Binding sites; Biology; Bore; Chromosome Mapping; Cluster Analysis; Corn; Data mining; Data processing; Deoxyribonucleic acid; Developmental stages; DNA; DNA binding proteins; DNA microarrays; DNA, Complementary - genetics; fruiting; Gene expression; Gene Expression Profiling; gene expression regulation; Genes; Genome Components - genetics; Genome, Plant - genetics; Genomes; Genomics; Germplasm; Grapes; Homology; Horticulture; Laboratories; microarray technology; microRNA; MicroRNAs - genetics; miRNA; Molecular Sequence Data; Multigene Family - genetics; nucleotide sequences; Organs; Oryza; Phase transitions; Phylogeny; Plant biology; Plant genetics; Plant Leaves - genetics; Plant Leaves - metabolism; Polymerase chain reaction; Proteins; Real-Time Polymerase Chain Reaction; reverse transcriptase polymerase chain reaction; Ribonucleic acid; Rice; RNA; Sequence Alignment; Sequence Analysis, DNA; Species Specificity; Subgroups; Synteny; Synteny - genetics; Tidal bores; Transcription (Genetics); Transcription factors; Transcription Factors - genetics; Trends; Vitis - genetics; Vitis vinifera; Zinc; Zinc finger proteins
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0059358

The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis , rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157 , function in grapevine. Eighteen SBP-box gene family members were identified in Vitis vinifera , twelve of which bore sequences that were complementary to miRNA156/157 . Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis . Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis ‘Shang-24’ revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses. The results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop.