In silico analysis of high affinity potassium transporter (HKT) isoforms in different plants

Aquatic Biosystems

Mahbobeh Zamani Babgohari²  Esmaeil Ebrahimie¹  Ali Niazi² 

[1] School of Molecular & Biomedical Science, The University of Adelaide, Adelaide, Australia

[2] Biotechnology Institute, Shiraz University, Shiraz, Iran

关键词: Pathway discovery;    In silico synteny;    Regulatory elements;    Promoter;    Gene network;    HKT;   

Others  :  1089033
DOI  :  10.1186/2046-9063-10-9

 received in 2014-01-29, accepted in 2014-09-10,  发布年份 2014

【 摘 要 】

Background

High affinity potassium transporters (HKTs) are located in the plasma membrane of the vessels and have significant influence on salt tolerance in some plants. They exclude Na⁺ from the parenchyma cells to reduce Na⁺ concentration. Despite many studies, the underlying regulatory mechanisms and the exact functions of HKTs within different genomic backgrounds are relatively unknown. In this study, various bioinformatics techniques, including promoter analysis, identification of HKT-surrounding genes, and construction of gene networks, were applied to investigate the HKT regulatory mechanism.

Results

Promoter analysis showed that rice HKTs carry ABA response elements. Additionally, jasmonic acid response elements were detected on promoter region of TmHKT1;5. In silico synteny highlighted several unknown and new loci near rice, Arabidopsis thaliana and Physcomitrella patent HKTs, which may play a significant role in salt stress tolerance in concert with HKTs. Gene network prediction unravelled that crosstalk between jasmonate and ethylene reduces AtHKT1;1 expression. Furthermore, antiporter and transferase proteins were found in AtHKT1;1 gene network. Interestingly, regulatory elements on the promoter region of HKT in wild genotype (TmHKT1;5) were more frequent and variable than the ones in cultivated wheat (TaHKT1;5) which provides the possibility of rapid response and better understanding of environmental conditions for wild genotype.

Conclusion

Detecting ABA and jasmonic acid response elements on promoter regions of HKTs provide valuable clues on underlying regulatory mechanisms of HKTs. In silico synteny and pathway discovery indicated several candidates which act in concert with HKTs in stress condition. We highlighted different arrangement of regulatory elements on promoter region of wild wheat (TmHKT1;5) compared to bread wheat (TaHKT1;5) in this study.

【 授权许可】

   
2014 Zamani Babgohari et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

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