Among major reactive oxygen species (ROS), hydrogen peroxide (H2O2) exhibits dual roles in plant metabolism. Low levels of H2O2 modulate many biological/physiological processes in plants; whereas, its high level can cause damage to cell structures, having severe consequences. Thus, steady-state level of cellular H2O2 must be tightly regulated. Glutathione peroxidases (GPX) and ascorbate peroxidase (APX) are two major ROS-scavenging enzymes which catalyze the reduction of H2O2 in order to prevent potential H2O2-derived cellular damage. Employing bioinformatics approaches, this study presents a comparative evaluation of both GPX and APX in 18 different plant species, and provides valuable insights into the nature and complex regulation of these enzymes. Herein, (a) potential GPX and APX genes/proteins from 18 different plant species were identified, (b) their exon/intron organization were analyzed, (c) detailed information about their physicochemical properties were provided, (d) conserved motif signatures of GPX and APX were identified, (e) their phylogenetic trees and 3D models were constructed, (f) protein-protein interaction networks were generated, and finally (g) GPX and APX gene expression profiles were analyzed. Study outcomes enlightened GPX and APX as major H2O2-scavenging enzymes at their structural and functional levels, which could be used in future studies in the current direction.

Solanum tuberosum genome analysis revealed 12 StSULTR genes encoding 18 transcripts. Among genes annotated at group level ( StSULTR I-IV), group III members formed the largest SULTRs-cluster and were potentially involved in biotic/abiotic stress responses via various regulatory factors, and stress and signaling proteins. Employing bioinformatics tools, this study performed genome-wide identification and expression analysis of SULTR (StSULTR) genes in potato (Solanum tuberosum L.). Very strict homology search and subsequent domain verification with Hidden Markov Model revealed 12 StSULTR genes encoding 18 transcripts. StSULTR genes were mapped on seven S. tuberosum chromosomes. Annotation of StSULTR genes was also done as StSULTR I-IV at group level based mainly on the phylogenetic distribution with Arabidopsis SULTRs. Several tandem and segmental duplications were identified between StSULTR genes. Among these duplications, Ka/Ks ratios indicated neutral nature of mutations that might not be causing any selection. Two segmental and one-tandem duplications were calculated to occur around 147.69, 180.80 and 191.00 million years ago (MYA), approximately corresponding to the time of monocot/dicot divergence. Two other segmental duplications were found to occur around 61.23 and 67.83 MYA, which is very close to the origination of monocotyledons. Most cis-regulatory elements in StSULTRs were found associated with major hormones (such as abscisic acid and methyl jasmonate), and defense and stress responsiveness. The cis-element distribution in duplicated gene pairs indicated the contribution of duplication events in conferring the neofunctionalization/s in StSULTR genes. Notably, RNAseq data analyses unveiled expression profiles of StSULTR genes under different stress conditions. In particular, expression profiles of StSULTR III members suggested their involvement in plant stress responses. Additionally, gene co-expression networks of these group members included various regulatory factors, stress and signaling proteins, and housekeeping and some other proteins with unknown functions.

IntroductionTranscriptional control of biological processes including development, differentiation, growth, and metabolism is related to specific cis-regulatory regions of genes. Additionally, transcription factor activities affect gene expression level (Zhang et al., 2008). In Arabidopsis thaliana, 1500 possible specific transcription factors were detected and approximately 45% of these are accepted as plant-specific transcription factors (Riechmann et al., 2000). These transcription factors were classified based on their DNA-binding domains (Yamasaki et al., 2008). Growth-regulating factor (GRF) genes are plant-specific transcription factors that are distributed in all genomes of seed plants (Kim et al., 2003). These genes may regulate growth and development of leaves and cotyledons (Kim and Kende, 2004). In general, GRF family proteins contain 2 conserved regions: the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains (van der Knaap et al., 2000;Kim et al., 2003;Zhang et al., 2008). The QLQ domain is similar to the N-terminal part of the yeast SWI2/SNF2 protein, which is located with the SWI/SNF chromatin-remodeling complex in yeast (Treich et al., 1995), that may play a role in protein-protein interactions (Kim et al., 2003;Choi et al., 2004). The WRC domain contains a functional nuclear localization signal and putative zinc finger motifs with 1 His and 3 Cys residues (van der Knaap et al., 2000). Recently, GRF-interacting factor (GIF) family proteins that interact with the QLQ domain of GRF proteins in Arabidopsis have been identified (Kim and Kende, 2004). GIF genes connect with some mice CREST-related transcription coactivators including calcium signaling mechanisms (Aizawa et al., 2004) and proteins of the GIF family have a conserved domain named SNH or SSXT (Kim and Kende, 2004).GRF genes were found to comprise 9 and 12 members in Arabidopsis and rice, respectively (Kim et al., 2003;Choi et al., 2004). The GRF family proteins of Arabidopsis (AtGRF) and rice (OsGRF) contain the same characteristic regions of the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains. Many AtGRF genes are expressed in growing and developing tissues, including

Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme catalyzing the dismutation of superoxide radical to hydrogen peroxide and dioxygen. To date, four types of SODs--Cu/ZnSOD, MnSOD, FeSOD, and NiSOD--have been identified. In this study, SOD proteins of Brachypodium distachyon (L.) Beauv. were screened by utilization of bioinformatics approaches. According to our results, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found to be in basic and acidic character, respectively. Domain analyzes of SOD proteins revealed that iron/manganese SOD and copper/zinc SOD were within studied SOD proteins. Based on the seconder structure analyzes, Mn/FeSODs and Cu/ZnSODs of B. distachyon were found as having similar sheets, turns and coils. Although helical structures were noticed in the types of Mn/FeSODs, no the type of Cu/ZnSODs were identified having helical structures. The predicted binding sites of Fe/MnSODs and Cu/ZnSODs were confirmed for having His-His-Asp-His and His-His-His-Asp-Ser residues with different positions, respectively. The 3D structure analyzes of SODs revealed that some structural divergences were observed in patterns of SODs domains. Based on phylogenetic analysis, Mn/FeSODs were found to have similarities whereas Cu/ZnSODs were clustered independently in phylogenetic tree.

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