In Silico and Transcription Analysis of Trehalose-6-phosphate Phosphatase Gene Family of Wheat: Trehalose Synthesis Genes Contribute to Salinity, Drought Stress and Leaf Senescence

Abstract

Trehalose-6-phosphate phosphatase (TPP) genes take part in trehalose metabolism and also in stress tolerance, which has been well documented in many species but poorly understood in wheat. The present research has identified a family of 31 TPP genes in Triticum aestivum L. through homology searches and classified them into five clades by phylogenetic tree analysis, providing evidence of an evolutionary status with Hordeum vulgare, Brachypodium distachyon and Oryza sativa. The exon-intron distribution revealed a discrete evolutionary history and projected possible gene duplication occurrences. Furthermore, different computational approaches were used to analyze the physical and chemical properties, conserved domains and motifs, subcellular and chromosomal localization, and three-dimensional (3-D) protein structures. Cis-regulatory elements (CREs) analysis predicted that TaTPP promoters consist of CREs related to plant growth and development, hormones, and stress. Transcriptional analysis revealed that the transcription levels of TaTPPs were variable in different developmental stages and organs. In addition, qRT-PCR analysis showed that different TaTPPs were induced under salt and drought stresses and during leaf senescence. Therefore, the findings of the present study give fundamental genomic information and possible biological functions of the TaTPP gene family in wheat and will provide the path for a better understanding of TaTPPs involvement in wheat developmental processes, stress tolerance, and leaf senescence.

Imperative role of trehalose metabolism and trehalose‐6‐phosphate signaling on salt stress responses in plants

“…In plants, trehalose is synthesized in two steps: first, TREHALOSE‐6‐PHOSPHATE SYNTHASE (TPS) catalyzes the conversion of UDP‐glucose and glucose‐6‐phosphate to T6P; and second, TREHALOSE‐6‐PHOSPHATE PHOSPHATASE (TPP) catalyzes the conversion of T6Pto trehalose (Mu et al, 2016; Figure 1). In addition to providing a route for the production of trehalose, TPS and TPP serve as signaling molecules in higher plants by modulating a variety of plant metabolic and developmental processes (Islam et al, 2021). T6P has been proposed as a proxy for carbohydrate status in plants.…”

Insights into the bioinformatics and transcriptional analysis of the Elongator complexes (ELPs) Gene Family of wheat: TaELPs contribute to wheat abiotic stress tolerance and leaf senescence

“…The aliphatic amino acid index ranged from 79.35 to 101.83 and the instability index ranged from 31.37 to 53.49. The high aliphatic amino acid index of the protein sequence indicates that it can play a role in a wide temperature range, while the instability index indicates whether the protein is stable or unstable [35]. Among them, 6 genes were stable (instability index < 40), and the remaining TaELPs genes were unstable (instability index > 40) [36].…”

“…The ORFs of TaELPs ranged from 753 to 3978 bp and the protein length ranged from 250 to 1325 amino acids. The molecular weights of TaELPs ranged from 27.05 to 147.31 KDa, and according to the predicted isoelectric point (PI) values, the PI ranged from 5.30 to 8.97, of which 6 genes were found to be basic (> 7) and 12 genes were found to be acidic (< 7) [35]. The aliphatic amino acid index and instability index were calculated.…”

“…The differences in the types and numbers of conserved motifs in wheat ELP proteins re ected the structural diversity of these proteins, indicating that they might have different biological functions. We used SWISS-MODEL to further identify 3-D models of TaELPs proteins [35,43] and the 3-D structure reveals a few key residues linked to biological processes or intended outcomes, (Figure S1). For TaELP1-A, TaELP1-B and TaELP1-D proteins, 3-D structures were analyzed using the template "6qk7.1.B", a template that describes Elongator complex protein 2.…”

“…Group III contained four core cis-acting elements, among which, CAAT-box and TATA-box appear most frequently in all TaELPs genes, indicating that they play an important role in transcription initiation. TATA-box (including TATA and ATTATA-box) and CAAT-box cis-elements are promoter-associated elements that function at the initiation of transcription [35]. Group IV was plant growth and development-related CAREs, including cis-elements involved in seed-speci c expression (AAGAA-motif, RY-element), cis-acting elements involved in cell cycle regulation (MSA-like), and meristem expression associated cis-regulatory elements (CAT-box) and several other CAREs associated with cell division.…”