Kim Joung Sug, Chae Songhwa, Jun Kyong Mi, Pahk Yoon-Mok, Lee Tae-Ho, Chung Pil Joong, Kim Yeon-Ki, Nahm Baek Hie
Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, Republic of Korea.
Genomics Genetics Institute, GreenGene BioTech Inc., Yongin, Kyonggido, 449-728, Republic of Korea.
Rice (N Y). 2017 Dec;10(1):16. doi: 10.1186/s12284-017-0155-4. Epub 2017 Apr 26.
Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis.
Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic leucine zipper transcription factor involved in the regulation of rice seed maturation. OsSMF1 (previously called RISBZ1 or OsbZIP58) is known to interact with GCN4 motifs (TGA(G/C)TCA) to regulate seed storage protein synthesis, and it functions as a key regulator of starch synthesis. Quadruple 9-mer-based PBM analysis and electrophoretic mobility shift assay revealed that OsSMF1 bound to the GCN4 (TGA(G/C)TCA), ACGT (CCACGT(C/G)), and ATGA (GGATGAC) motifs with three different affinities. We predicted 44 putative OsSMF1 target genes using data obtained from both the PBM and RiceArrayNet. Among these putative target genes, 18, 21, and 13 genes contained GCN4, ACGT, and ATGA motifs within their 1-kb promoter regions, respectively. Among them, six genes encoding major grain filling proteins and transcription factors were chosen to confirm the activation of their expression in vivo. OsSMF1 was shown to bind directly to the promoters of Os03g0168500 (GCN4 motif), patatin-like gene (GCN4 motif), α-globulin (ACGT motif), rice prolamin box-binding factor (RPBF) (ATGA motif), and ONAC024 (GCN4 and ACGT motifs) and to regulate their expression.
The results of this study suggest that OsSMF1 is one of the key transcription factors that functions in a wide range of seed developmental processes with different specific binding affinities for the three DNA-binding motifs.
空间和时间特异性表达模式主要在转录水平上由基因启动子调控。因此，识别转录因子的结合基序对于更好地理解与胚胎发生相关的网络很重要。
在此，我们使用蛋白质结合微阵列（PBM）来识别OsSMF1的结合基序，OsSMF1是一种参与水稻种子成熟调控的碱性亮氨酸拉链转录因子。已知OsSMF1（以前称为RISBZ1或OsbZIP58）与GCN4基序（TGA(G/C)TCA）相互作用以调节种子贮藏蛋白合成，并且它作为淀粉合成的关键调节因子发挥作用。基于四重9聚体的PBM分析和电泳迁移率变动分析表明，OsSMF1以三种不同亲和力与GCN4（TGA(G/C)TCA）、ACGT（CCACGT(C/G)）和ATGA（GGATGAC）基序结合。我们使用从PBM和RiceArrayNet获得的数据预测了44个假定的OsSMF1靶基因。在这些假定的靶基因中，分别有18、21和13个基因在其1 kb启动子区域内包含GCN4、ACGT和ATGA基序。其中，选择了六个编码主要灌浆蛋白和转录因子的基因来确认其在体内表达的激活。结果表明，OsSMF1直接结合到Os03g0168500（GCN4基序）、类patatin基因（GCN4基序）、α-球蛋白（ACGT基序）、水稻醇溶蛋白盒结合因子（RPBF）（ATGA基序）和ONAC024（GCN4和ACGT基序）的启动子上并调节它们的表达。
本研究结果表明，OsSMF1是关键转录因子之一，在广泛的种子发育过程中发挥作用，对三种DNA结合基序具有不同的特异性结合亲和力。
