Contents lists available at ScienceDirect Computational Biology and Chemistry journal homepage: www.elsevier.com/locate/cbac Research Article Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs Archana Pal Negi a , Ratnesh Singh b , Anupma Sharma b , Vishal Singh Negi a, * a School of Sciences, PP Savani University, Surat, Gujarat, 394125, India b Texas A&M Agrilife Research, Dallas, TX, 75252, USA ARTICLE INFO Keywords: HMGA Poaceae AT-hook RGRP motifs H1/H5 domain 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. 1. Introduction High mobility group (HMG) proteins are the non-histone chromo- somal proteins, which were initially discovered in mammalian cells and named based on their electrophoretic mobility. Subsequent extensive research on HMG proteins identified different functional motifs and therefore, a systematic way to name HMG proteins was devised in 2001 based on the guidelines endorsed by the mouse and human gene no- menclature committees, and on consultations with the NCBI and the MESH Section at the National Library of Medicine (Bustin, 2001). These guidelines classified HMG proteins into three different families namely High Mobility Group Box (HMGB), High Mobility Group Nucleosome- binding (HMGN), and High Mobility Group A (HMGA) based on their functional motifs HMG-box, Nucleosome-binding domain, and AT-hook motif, respectively (Table S1, Supplementary materials). HMG proteins, irrespective of the family they belong to, are major architectural proteins of the cell and are known to interact with a wide range of proteins and DNA, thereby influence various biological func- tions in cell (Reeves, 2001). HMGA, like other HMG proteins, is in- volved in various protein-protein interactions and also in protein-DNA interactions. HMGA homologs are widespread and are known to occur in mammals, yeasts, insects, plants, and birds (Bustin and Reeves, 1996; Reeves and Beckerbauer, 2001). In mammals, the HMGA proteins are characterized by three conserved DNA-binding domains known as AT- hooks (Reeves and Nissen, 1990) and a carboxy-terminal acidic tail. The AT-hook motifs are dominated by positively charged amino acid re- sidues while the C-terminal tail of HMGA proteins is rich in negatively charged residues (Cleynen and Van de Ven, 2008). These AT-hook domains can recognize and bind to the minor groove of AT-rich DNA (Thanos and Maniatis, 1992). Humans have 2 HMGA homologs- HMGA1 (Uniprot ID P17096) and HMGA2 (Uniprot ID P52926), which are located in chromosomes 6 and 12, respectively. Although both the homologs of mammalian HMGAs has three AT-hook motifs, the spacing between the AT-hooks varies (Table S2, Supplementary materials), which can influence the conformation of bound DNA substrates in different ways, thereby affecting numerous biological functions (Cleynen and Van de Ven, 2008). HMGAs in mammals are well studied (Cleynen and Van de Ven, 2008) because of their involvement in a myriad of biological functions such as chromatin remodeling (Reeves and Wolffe, 1996; Strauss and Varshavsky, 1984), transcription activation (Bellard et al., 1989; Chau et al., 2000; Elton et al., 1987; Giancotti et al., 1996; Shannon et al., https://doi.org/10.1016/j.compbiolchem.2020.107306 Received 30 June 2019; Received in revised form 4 June 2020; Accepted 9 June 2020 ⁎ Corresponding author at: PP Savani University, NH 8, GETCO, Kosamba, Dhamdod, Surat, Gujarat, 394125, India. E-mail address: vishal.negi@ppsu.ac.in (V.S. Negi). Computational Biology and Chemistry 87 (2020) 107306 Available online 10 June 2020 1476-9271/ © 2020 Published by Elsevier Ltd. T