Identification of GCC-box and TCC-box motifs in the promoters of differentially expressed genes in rice (Oryza sativa L.): Experimental and computational approaches

Abstract

The transcription factor selectively binds with the cis -regulatory elements of the promoter and regulates the differential expression of genes. In this study, we aimed to identify and validate the presence of GCC-box and TCC-box motifs in the promoters of upregulated differentially expressed genes (UR-DEGs) and downregulated differentially expressed genes (DR-DEGs) under anoxia using molecular beacon probe (MBP) based real-time PCR. The GCC-box motif was detected in UR-DEGs ( DnaJ and 60S ribosomal protein L7 genes), whereas, the TCC-box was detected in DR-DEGs ( DnaK and CPuORF11 genes). In addition, the mechanism of interaction of AP2/EREBP family transcription factor (LOC_Os03g22170) with GCC-box promoter motif present in DnaJ gene (LOC_Os06g09560) and 60S ribosomal protein L7 gene (LOC_Os08g42920); and TCC-box promoter motif of DnaK gene (LOC_Os02g48110) and CPuORF11 gene (LOC_Os02g01240) were explored using molecular dynamics (MD) simulations analysis including binding free energy calculations, principal component analyses, and free energy landscapes. The binding free energy analysis revealed that AP2/EREBP model residues such as Arg68, Arg72, Arg83, Lys87, and Arg90 were commonly involved in the formation of hydrogen bonds with GCC and TCC-box promoter motifs, suggesting that these residues are critical for strong interaction. The movement of the entire protein bound to DNA was restricted, confirming the stability of the complex. This study provides comprehensive binding information and a more detailed view of the dynamic interaction between proteins and DNA.

Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci

“…Overexpression of ERF1 in Arabidopsis by the 35S CaMV promoter results in enhanced heat tolerance and up‐regulation of heat tolerance genes (Cheng et al , 2013). Depending on the stress conditions, ERFs activate a specific set of stress response genes by binding to the cis‐acting GCC box or its substitute TCC box and DRE elements which are also present in the HSFA2 promoter (Yang et al , 2015; Prajapati et al , 2019; Xie et al , 2019). In summary, our data suggest that SA187‐induced thermotolerance could be mediated via EIN3 ‐regulated expression of ERF s that subsequently act on HSFA2 (Fig 7).…”

motifNet: A Neural Network Approach for Learning Functional Sequence Patterns in mRNA

“…We suspected this fragment is related with GCC-box (sequence with GCCGCC pattern). It is reported by Prajapati et al (2019) that GCC-box is an essential sequence for enhancement of gene expression.…”