Genome-wide analysis and identification of genes related to potassium transporter families in rice (Oryza sativa L.)

Amrutha, R N and Sekhar, P N and Varshney, R K and Kishor, P B K (2007) Genome-wide analysis and identification of genes related to potassium transporter families in rice (Oryza sativa L.). Plant Science, 172 (4). pp. 708-721. ISSN 0168-9452

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Abstract

Potassium (K+) is an important macronutrient and the most abundant cation in higher plants which plays a key role in various cellular processes. Its accumulation from soil and its distribution throughout diverse plant tissues is mediated by transporter proteins. In plants, different transport systems are known to be involved in the uptake and release of K+ from the cells. Though most of the information about the putative K+ transporters and their phylogenetic relationships is available in Arabidopsis, it is not the best model for plants with agronomic applications. Recent completion of rice genome sequencing project offered the opportunity to make an inventory of all putative K+ transporter proteins. More than 5% of the rice genome appears to encode membrane transport proteins. Unfortunately, several hundreds of putative transporter proteins have not yet been assigned to any families or subfamilies or functions. Therefore, phylogenetic relationships of many K+ transporters in rice are analyzed since rice is considered as a model plant because of its high degree of co-linearity with other cereals. Phylogenetic analysis of all K+ transporters in rice revealed that they fall into five major branches. Phylogenetic trees of each family define the evolutionary relationships of the members to each other. In each family, closely related isoforms and separate subfamilies existed, indicating possible redundancies and specialized functions. The HAK family is represented by 26 genes and formed the tightest and most distinct branch in the phylogenetic tree. Around 14 genes with conserved P-loop were found in K+ channel family out of which 11 genes belong to 1P/6TM (Shaker-type), and three genes to the 2P/4TM (ORK-type). On searching rice genome, it was found that nine genes belonged to Trk family. In rice, K+/H+ antiporter family is represented by a single gene. Comparative analysis of rice K+ channels with that of Arabidopsis, wheat and maize revealed that while cereals are closely related, Arabidopsis appeared quite distant from rice.

Item Type:	Article
Divisions:	UNSPECIFIED
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Potassium, Ion transporters, Salt stress, Oryza sativa, Genome analysis
Subjects:	Others > Genetics and Genomics
Depositing User:	Library ICRISAT
Date Deposited:	21 Oct 2011 10:53
Last Modified:	21 Oct 2011 10:53
URI:	http://oar.icrisat.org/id/eprint/3012
Official URL:	http://dx.doi.org/10.1016/j.plantsci.2006.11.019
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	We gratefully acknowledge the financial support from the Department of Science and Technology, New Delhi, India and to Prof. Bhujanga Rao, Director, Centre for Distance Education, Osmania University, Hyderabad for providing the Bioinformatics facilities.
Links:	Author

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