Identification and analysis of regulatory elements in the germin and germin-like proteins family promoters in rice

Germins and germin-like proteins constitute a ubiquitous family of plant proteins and have a role in the defense against pathogen attacks. In the present work the Oryza sativa germin-like protein 1 (OsGLP1) and putative germin A (OsGerA) promoter regions of five Pakistani rice varieties were analyzed for variations in expression regulation of these promoters and similarity with others germin and germin-like protein promoters. Phylogenetic analyses showed that the studied OsGLP1 promoters were tightly clustered around the ancestral group while putative OsGerA clustered around the descendant group. HADDOCK was used for docking selected transcription factors (TFs) with its corresponding regulatory elements, for determining the most stable interaction with the highest probability of hydrogen bonding between them. TATA box binding protein (TBP) elements mainly existed on the 3' regions very near the gene, while far regions of promoters mostly lacked such elements. This study showed that TBP not only binds to (-30) TATA box element, but also binds to a wide range of elements at different rates, positioned on about a thousand base pairs upstream region of germin and germin-like genes. Arginine was found to be the most reactive residue in TFs, while adenine was the most sensitive in regulatory elements.