Open Access Research

Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses

Tahereh Deihimi1, Ali Niazi1, Mansour Ebrahimi2, Kimia Kajbaf1, Somaye Fanaee1, Mohammad Reza Bakhtiarizadeh3 and Esmaeile Ebrahimie45*

Author Affiliations

1 Institute of Biotechnology, Shiraz University, Shiraz, Iran

2 Department of Biology & Bioinformatics Research Group, University of Qom, Qom, Iran

3 Department of Animal Science, University of Tehran, Karaj, Iran

4 Department of Crop Production & Plant Breeding, College of Agriculture, Shiraz University, 71441, Shiraz, Iran

5 School of Molecular & Biomedical Science, The University of Adelaide, Adelaide, SA, Australia

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SpringerPlus 2012, 1:30  doi:10.1186/2193-1801-1-30

Published: 5 October 2012

Abstract

Regarding the possible multiple functions of a specific gene, finding the alternative roles of genes is a major challenge. Huge amount of available expression data and the central role of the promoter and its regulatory elements provide unique opportunely to address this issue. The question is that how the expression data and promoter analysis can be applied to uncover the different functions of a gene. A computational approach has been presented here by analysis of promoter regulatory elements, coexpressed gene as well as protein domain and prosite analysis. We applied our approach on Thaumatin like protein (TLP) as example. TLP is of group 5 of pathogenesis related proteins which their antifungal role has been proved previously. In contrast, Osmotin like proteins (OLPs) are basic form of TLPs with proved role only in abiotic stresses. We demonstrated the possible outstanding homolouges involving in both biotic and abiotic stresses by analyzing 300 coexpressed genes for each Arabidopsis TLP and OLP in biotic, abiotic, hormone, and light microarray experiments based on mutual ranking. In addition, promoter analysis was employed to detect transcription factor binding sites (TFBs) and their differences between OLPs and TLPs. A specific combination of five TFBs was found in all TLPs presenting the key structure in functional response of TLP to fungal stress. Interestingly, we found the fungal response TFBs in some of salt responsive OLPs, indicating the possible role of OLPs in biotic stresses. Thirteen TFBS were unique for all OLPs and some found in TLPs, proposing the possible role of these TLPs in abiotic stresses. Multivariate analysis showed the possibility of estimating models for distinguishing biotic and abiotic functions of TIPs based on promoter regulatory elements. This is the first report in identifying multiple roles of TLPs and OLPs in biotic and abiotic stresses. This study provides valuable clues for screening and discovering new genes with possible roles in tolerance against both biotic and abiotic stresses. Interestingly, principle component analysis showed that promoter regulatory elements of TLPs and OLPs are more variable than protein properties reinforcing the prominent role of promoter architecture in determining gene function alteration.

Keywords:
Promoter analysis; Domain and prosite analysis; Gene expression; Multivariate analysis; Thaumatin like proteins; Stress