Transcriptome wide identification and characterization of starch branching enzyme in finger millet

Rajhans Tyagi; Apoorv Tiwari; Vijay Kumar Garg; Sanjay Gupta

doi:10.6026/97320630013179

Transcriptome wide identification and characterization of starch branching enzyme in finger millet

Bioinformation. 2017 Jun 30;13(6):179-184. doi: 10.6026/97320630013179. eCollection 2017.

Authors

Rajhans Tyagi¹, Apoorv Tiwari^{2

3}, Vijay Kumar Garg², Sanjay Gupta¹

Affiliations

¹ Uttarakhand Technical University, Dehradun, Uttarakhand, 248007, India.
² Sam Higginbottom University of Agriculture, Technology And Sciences (SHUATS), Allahabad, 211007, India.
³ Dept of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India.

Abstract

Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and play an important role in determining the structure and physical properties of starch granules. Multiple SBEs are involved in starch biosynthesis in plants. Finger millet is calcium rich important serial crop belongs to grass family and the transcriptome data of developing spikes is available on NCBI. In this study it was try to find out the gene sequence of starch branching enzyme and annotate the sequence and submit the sequence for further use. Rice SBE sequence was taken as reference and for characterization of the sequence different in silico tools were used. Four domains were found in the finger millet Starch branching enzyme like alpha amylase catalytic domain from 925 to2172 with E value 0, N-terminal Early set domain from 634 to 915 with E value 1.62 e-42, Alpha amylase, C-terminal all-beta domain from 2224 to 2511 with E value 5.80e-24 and 1,4-alpha-glucan-branching enzyme from 421 to 2517 with E value 0. Major binding interactions with the GLC (alpha-d-glucose), CA (calcium ion), GOL (glycerol), TRS (2-amino-2-hydroxymethylpropane- 1, 3-diol), MG (magnesium ion) and FLC (citrate anion) are fond with different residues. It was found in the phylogenetic study of the finger millet SBE with the 6 species of grass family that two clusters were form A and B. In cluster A, finger millet showed closeness with Oryzasativa and Setariaitalica, Sorghum bicolour and Zea mays while cluster B was formed with Triticumaestivum and Brachypodium distachyon. The nucleotide sequence of Finger millet SBE was submitted to NCBI with the accession no KY648913 and protein structure of SBE of finger millet was also submitted in PMDB with the PMDB id - PM0080938. This research presents a comparative overview of Finger millet SBE and includes their properties, structural and functional characteristics, and recent developments on their post-translational regulation.

Keywords: CDS; Domain; Finger millet; NCBI; PMDB; SBE.