In-silico characterization and comparative study of iron and zinc regulatory gene families NAS, YSL and ZIP in cereal crops
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Date
2021-02
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G.B. Pant University of Agriculture and Technology, Pantnagar - 263145 (Uttarakhand)
Abstract
Micronutrient deficiency, especially iron and zinc deficiency in diet is a major reason of malnutrition in developing countries. Most of the population in developing countries is dependent on their staple crops as a source for their nutrition. Hence, developing biofortified crop varieties can be a promising way to overcome malnutrition of these minerals. Lack of genetic variation in major staples like rice and wheat is a major drawback in biofortification by conventional breeding method. Bioinformatics tools can be used as an alternative in biofortification of food grains. Iron homeostasis is a process by which the availability of iron is properly maintained in the plant body. In order to regulate this process a number of genes play a key role. Among these nicotinamine synthase (NAS), yellow stripe like (YSL) protein and zinc transporter protein (ZIP) are the most important and largely reported genes in cereal crops for iron and zinc uptake, transport and its storage. The comparative study of these iron homeostasis genes in related species helps to describe the evolutionary relationship, their nucleotide and amino acid profiling along with motif regions. During the present investigation in silico identification, characterization and comparative study of three iron homeostasis gene families viz. NAS, YSL and ZIP is conducted in five major cereal crops namely rice, wheat, maize, barley and barn yard millet. Various physico-chemical parameters such as molecular weight, isoelectric point, and aliphatic index are computed. Nicotinamine synthase gene (NAS), yellow- stripe like (YSL) protein and ZIP (ZRT-IRT) like proteins are involved in metal transport in plants. The respective sequences are retrieved from NCBI database in fasta format and different analysis are carried out. Phylogenetic tree is constructed using neighbour joining method for all the three groups together (NAS, YSL and ZIP genes) and individually for the three groups and the results are analyzed. Multiple sequence alignment study showed that amino acids namely glycine and phenylalanine are evolutionary conserved among these gene families. Phylogenetic analysis revealed that NAS and YSL gene family divided into two clusters A and B. On the other hand, the genes belonging to ZIP family divided into three clusters namely A, B and C. Conserved domain search explained that AdoMet_MTases superfamily with seven domain hits found in NAS gene family, YSL gene family contain OPT superfamily having four domain hits and ZIP gene family having five domain hits of ZIP superfamily.
Physicochemical analysis is done using PROTPARAM tool. Target P-1.1 is used to determine the sub – cellular location of proteins. Some of the proteins are signal peptide, few are mitochondrial transfer peptide, while the analysis of most of the proteins show that they belong to some other location other than signal peptide, mitochondrial transfer peptide, chloroplast transfer peptide and thylakoid luminal transfer peptide. Secondary structure is predicted using Chou- Fasman secondary structure prediction software. Comparing the average percentage of secondary structure it was found that, alpha helix is the most predominant conformation revealing the higher level of conservation and stability of protein structure. Highest percentage of alpha helix was detected in ZIP family and beta strand found in YSL whereas highest percentage of turn was found in NAS gene family. The information generated out of this comparative study of iron homeostasis regulatory genes in cereal crops may be helpful for better understanding of iron homeostasis in cereals which may subsequently be utilized for iron and zinc biofortification in cereal crops.