Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Tyagi, Rajhans, Tiwari, Apoorv, Garg, Vijay Kumar, Gupta, Sanjay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5512855/
https://www.ncbi.nlm.nih.gov/pubmed/28729759
http://dx.doi.org/10.6026/97320630013179
_version_ 1783250543490105344
author Tyagi, Rajhans
Tiwari, Apoorv
Garg, Vijay Kumar
Gupta, Sanjay
author_facet Tyagi, Rajhans
Tiwari, Apoorv
Garg, Vijay Kumar
Gupta, Sanjay
author_sort Tyagi, Rajhans
collection PubMed
description 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.
format Online
Article
Text
id pubmed-5512855
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Biomedical Informatics
record_format MEDLINE/PubMed
spelling pubmed-55128552017-07-20 Transcriptome wide identification and characterization of starch branching enzyme in finger millet Tyagi, Rajhans Tiwari, Apoorv Garg, Vijay Kumar Gupta, Sanjay Bioinformation Hypothesis 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. Biomedical Informatics 2017-06-30 /pmc/articles/PMC5512855/ /pubmed/28729759 http://dx.doi.org/10.6026/97320630013179 Text en © 2017 Biomedical Informatics http://creativecommons.org/licenses/by/3.0/ This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
spellingShingle Hypothesis
Tyagi, Rajhans
Tiwari, Apoorv
Garg, Vijay Kumar
Gupta, Sanjay
Transcriptome wide identification and characterization of starch branching enzyme in finger millet
title Transcriptome wide identification and characterization of starch branching enzyme in finger millet
title_full Transcriptome wide identification and characterization of starch branching enzyme in finger millet
title_fullStr Transcriptome wide identification and characterization of starch branching enzyme in finger millet
title_full_unstemmed Transcriptome wide identification and characterization of starch branching enzyme in finger millet
title_short Transcriptome wide identification and characterization of starch branching enzyme in finger millet
title_sort transcriptome wide identification and characterization of starch branching enzyme in finger millet
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5512855/
https://www.ncbi.nlm.nih.gov/pubmed/28729759
http://dx.doi.org/10.6026/97320630013179
work_keys_str_mv AT tyagirajhans transcriptomewideidentificationandcharacterizationofstarchbranchingenzymeinfingermillet
AT tiwariapoorv transcriptomewideidentificationandcharacterizationofstarchbranchingenzymeinfingermillet
AT gargvijaykumar transcriptomewideidentificationandcharacterizationofstarchbranchingenzymeinfingermillet
AT guptasanjay transcriptomewideidentificationandcharacterizationofstarchbranchingenzymeinfingermillet