New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis

Abstract

The TIFY gene family, a key plant-specific transcription factor (TF) family, is involved in diverse biological processes including plant defense and growth regulation. Despite TIFY proteins being reported in some plant species, a genome-wide comparative and comprehensive analysis of TIFY genes in plant species can reveal more details. In the current study, the members of the TIFY gene family were significantly increased by the identification of 18 and six new members using maize and tomato reference genomes, respectively. Thus, a genome-wide comparative analysis of the TIFY gene family between 48 tomato (Solanum lycopersicum, a dicot plant) genes and 26 maize (Zea mays, a monocot plant) genes was performed in terms of sequence structure, phylogenetics, expression, regulatory systems, and protein interaction. The identified TIFYs were clustered into four subfamilies, namely, TIFY-S, JAZ, ZML, and PPD. The PPD subfamily was only detected in tomato. Within the context of the biological process, TIFY family genes in both studied plant species are predicted to be involved in various important processes, such as reproduction, metabolic processes, responses to stresses, and cell signaling. The Ka/Ks ratios of the duplicated paralogous gene pairs indicate that all of the duplicated pairs in the TIFY gene family of tomato have been influenced by an intense purifying selection, whereas in the maize genome, there are three duplicated blocks containing Ka/Ks > 1, which are implicated in evolution with positive selection. The amino acid residues present in the active site pocket of TIFY proteins partially differ in each subfamily, although the Mg or Ca ions exist heterogeneously in the centers of the active sites of all the predicted TIFY protein models. Based on the expression profiles of TIFY genes in both plant species, JAZ subfamily proteins are more associated with the response to abiotic and biotic stresses than other subfamilies. In conclusion, globally scrutinizing and comparing the maize and tomato TIFY genes showed that TIFY genes play a critical role in cell reproduction, plant growth, and responses to stress conditions, and the conserved regulatory mechanisms may control their expression.

The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis

“…The variations in subcellular localization may occur due to various factors, such as proteinprotein interaction and post-translational modifications [36,64]. The prediction of 3D structure and pocket site of proteins can provide valuable information about protein function based on ligand-binding sites [65,66]. In the present study, the cysteine, proline, lysine, leucine, serine, and threonine were frequently predicted as the key binding residues in the structure of GASA proteins, in which proline, serine, and leucine are known as the amino acid residues associated with responses to environmental stimuli [65,67].…”

Magnesium transporter Gene Family: Genome-Wide Identification and Characterization in Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum of Family Malvaceae

“…In addition, MGTs have been speculated to regulate the downstream pathways related to response to abiotic stresses by interacting with Ca 2+ sensors [83]. Our findings revealed that the MGT duplicated gene pair could have diverse expression patterns, suggesting that these genes probably under some modifications or insertion/deletion in their sequence, CDS, or promoter regions have received novel functions [71,84]. Modifications, such as gains and losses of cis elements in promoters between duplicated gene pairs, e.g., parent and daughter genes, could occur after duplication events, affecting the expression levels [85,86].…”

“…In previous studies, 62 MGTs in Camelina sativa [12], 41 MGTs in Triticum turgidum [12], 12 MGTs in Zea mays [70], 16 MGTs in Pyrus bretschneideri [23], 36 MGTs in Brassica napus [25], 12 MGTs in Fagaria vesca [27], and 8 MGTs in Poncirus trifoliata [24] were characterized. The number of MGTs is probably correlated with polyploidy events and genome size [12,71]. The prediction of the pI value of MGT proteins illustrated that CcMGTs are more acidophilic proteins than TcMGTs and GhMGTs, indicating that CcMGTs are mostly active under acidic conditions (pI < 6.50).…”

“…Notably, a gene cluster of three MRS2/TcMGT genes, namely TcMGT013, TcMGT14, and TcMGT15, was observed in chromosome 6, providing an avenue for further molecular investigations in cacao. In addition, the K a /K s ratios in most duplicated genes were less than one, suggesting that MGTs have evolved slowly under a purifying selection [54,71]. The comparisons between structures of MGT proteins revealed that NIPA proteins include the conserved structures with more transmembrane regions.…”

Hormone Profiles and Antioxidant Activity of Cultivated and Wild Tomato Seedlings under Low-Temperature Stress

“…Furthermore, the alteration of membrane conformation can cause oxidative stress by rapidly inducing reactive oxygen species (ROS), and then, the concentration of cryoprotective compounds increases in the cytoplasmic matrix [2,6,7]. However, plants use various mechanisms, including morphological and structural modifications, as well as biochemical mechanisms to modulate cellular homoeostasis to reduce low, nonfreezing temperature-induced damage [2,8,9]. Approximately 10% of the genes in Arabidopsis are involved in the response to cold stress and are known as cold-regulated (COR) genes [10,11].…”