Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs

Archana Pal Negi; Ratnesh Singh; Anupma Sharma; Vishal Singh Negi

doi:10.1016/j.compbiolchem.2020.107306

Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs

Comput Biol Chem. 2020 Jun 10:87:107306. doi: 10.1016/j.compbiolchem.2020.107306. Online ahead of print.

Authors

Archana Pal Negi¹, Ratnesh Singh², Anupma Sharma², Vishal Singh Negi³

Affiliations

¹ School of Sciences, PP Savani University, Surat, Gujarat, 394125, India.
² Texas A&M Agrilife Research, Dallas, TX, 75252, USA.
³ School of Sciences, PP Savani University, Surat, Gujarat, 394125, India. Electronic address: vishal.negi@ppsu.ac.in.

PMID: 32559639
DOI: 10.1016/j.compbiolchem.2020.107306

Abstract

High mobility group (HMG) proteins are the major architectural proteins. Among HMG proteins, High Mobility Group A (HMGA) is characterized by AT-hook (ATH) motifs, which have an affinity for AT-rich DNA. In this study, we characterized the plant HMGAs from the Poaceae family using in silico methods. The protein sequences for rice HMGAs were retrieved and the corresponding orthologs from grasses were extracted. The phylogenetic analysis identified three major evolutionary clades of grass HMGAs and their ATH motif analysis revealed that HMGAs from clade 1 and 2, except for clade 2 HMGAs, are devoid of high-affinity DNA-binding domain. The clade 2 HMGAs also displayed a highly conserved length of all the spacers and the length of the C-terminal tail following the last ATH. Moreover, the C-terminal tail in clade 2 HMGAs is smaller than HMGAs from any other clade. Unlike clade 2, other clades of Poaceae HMGAs displayed high variability in the length of spacers. Despite several differences among HMGAs of different clades in Poaceae, the H1/H5 domain was found to be highly conserved. This study has revealed the detailed analyses of Poaceae HMGAs and it will be useful for further investigation aiming at the determination of precise biological functions and molecular mechanisms of grass HMGAs.

Keywords: AT-hook; H1/H5 domain; HMGA; Poaceae; RGRP motifs.