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

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.

Phylogeny of the Plant Salinity Tolerance Related HKT Genes

“…This study showed A. thaliana HKT gene was placed in group IV separated from O. sativa or T. aestivum. Comparative analysis of rice K+ channels also revealed that Arabidopsis is quite distant from rice (Amrutha et al, 2007). There was very high sequence variation among HKT-related genes (overall pairwise mean distance was 1.13).…”

“…Phylogenetic trees of each family define the evolutionary relationships of the members to each other. In each family, closely related isoforms and separate subfamilies of K + transporters existed, indicating possible redundancies and specialized functions (Amrutha et al, 2007). To meet this challenge of world hunger, it is important to understand the mechanisms of salt tolerance to utilize the unused salt-affected land.…”

Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters

“…Manual Bock et al, 2006), while transporter genes account for approximately 5% of all rice (Oryza sativa) genes (Amrutha et al, 2007).…”

Relationships between foliar carbon isotope composition and elements of C3 species in grasslands of Inner Mongolia, China

“…Phosphorus (P) can affect photosynthesis indirectly through its effects on Calvin cycle enzymes and enzymes related to the synthesis of protein, RNA, and DNA (Walker et al 2014(Walker et al , 1986Warren and Adams 2002). Potassium (K) plays an important role related to stomatal behavior, enzyme activity, photosynthesis, and osmotic adjustment (Amrutha et al 2007;Si et al 2015). Further, foliar element ratios, e.g., C/N (foliar carbon:nitrogen ratio), C/P (foliar carbon:phosphorus ratio), and N/P (foliar nitrogen:phosphorus ratio), are also key traits of ecological relevance and link with d 13 C through their correlation with water use efficiency (WUE).…”