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Pak. J. Bot., 48(1): 57-65, 2016.

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BIO-INFORMATIC ANALYSIS OF A VACUOLAR Na⁺/H⁺ ANTIPORTER (ALaNHX) FROM THE SALT RESISTANT GRASS AELUROPUS LAGOPOIDES

MUHAMMAD ZAHEER AHMED^1*, AKIRA KIKUCHI², KAZUO N. WATANABE² AND M. AJMAL KHAN^{1, 3}

Abstract: Sodium-hydrogen antiporter (NHX) protein regulates the trans-membrane transport of Na⁺ in higher plants. Vacuolar-NHX is a type of NHX protein located on tonoplast and minimizes the accumulation of Na⁺ in cytoplasm by compartmentalizing into vacuole especially in salt tolerant plants. In Aeluropus lagopoides, AlaNHX [NCBI: GU199336, Vacuolar-NHX] plays a vital role for efficient Na⁺ sequestration into the vacuole and helps in plant survival in saline areas. Therefore, sequence analysis, structural analysis and modeling of AlaNHX were performed through bioinformatics tools. Homology of AlaNHX was 99% similar with the Na⁺/H⁺ antiporter of Aeluropus littoralis. Sequence of AlaNHX consisted of 2353 bp including 337 bp of un-translated regions (UTR) at 5΄ and 393 at 3΄ end. In addition, AlaNHX have an “open reading frame” (ORF) of 1623 bp which translated into 59.4 KDa protein containing 540 amino acids (Leucine + Serine contributed in 22% of peptide chain). AlaNHX protein consists of 10 transmembrane domains (TMD; 3 primary and 7 secondary protein structural type) and a long (95 amino acids) carboxyl terminal end in cytoplasmic region. In addition, 3, 5, 7 and 8 TMD regions of AlaNHX were highly conserved. Different glycosylation, phosphorylation and myristoylation sites were also found in AlaNHX protein. Three-dimensional (3D) structure analysis revealed that this protein may be classified as stable and of hydrophobic nature containing a significant proportion of alpha helices. In this study, a three-dimensional structure of AlaNHX protein was predicted by using in-silico3D homology modeling technique. This study provides baseline information for understanding the importance of NHX protein structure in salinity resistance of grasses. This information could help in improving salinity tolerance in salt sensitive grasses through genetic engineering.

Key words: Aeluropus lagopoides; Homology modeling; Na⁺/H⁺ antiporter; Structural analysis.

¹Institute of Sustainable Halophyte Utilization (ISHU), University of Karachi, Karachi-75270, Pakistan

²Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, Ibaraki, 305-8572, Japan

³Qatar Shell Professorial Chair of Sustainable Development, Department of International Affairs,

College of Arts and Sciences, Qatar University, PO Box 2713, Doha, Qatar

^* Corresponding author’s: e-mail. mzahmed@uok.edu.pk