In Silico Analysis of the Lateral Organ Junction (LOJ) Gene and Promoter of Arabidopsis Thaliana

Article type: Research Article

Authors: Saha, Dipnarayan | Prasad, Anand M. | Sujatha, Thankeswaran P. | Kumar, Vajinder | Jain, Pradeep K. | Bhat, Sripad R. | Srinivasan, Ramamurthy

Affiliations: National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India

Note: [] Corresponding author. Tel.: +91 11 25841787; Fax: +91 11 25843984; E-mail: srinivasan53@gmail.com

Abstract: A T-DNA based promoter trapped mutant has led to the identification of a novel lateral organ junction specific promoter upstream of the pentatricopeptide repeat (PPR) protein coding gene LOJ in Arabidopsis thaliana by our laboratory. Various in silico based prediction tools are employed to characterize the upstream sequence of the LOJ gene. Out of numerous cis-elements detected in the LOJ promoter a few are considered important based on the expression pattern of the LOJ gene. These elements would provide a basis for designing experiments for more accurate promoter function annotation. A comparative search for conserved elements in the 5'-upstream region of few genes involved in lateral organ development and meristem related expression reveals few common relevant regulatory motifs. The coding region of the LOJ gene is intron-less and contains 19 PPR units. Based on in silico analysis, LOJ protein is predicted to be hydrophobic in nature and targeted to mitochondria. A partial 3D model of the LOJ protein has been suggested using a homology-based modeling program.

Keywords: Arabidopsis thaliana, Lateral Organ Junction gene, LOJ, pentatricopeptide repeat protein, promoter, cis-acting elements, in silico analysis

Journal: In Silico Biology, vol. 7, no. 1, pp. 7-19, 2007