Genome-wide Identification, Expression Profiling and Promoter Analysis of Trehalose-6-Phosphate Phosphatase Gene Family
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RESEARCH ARTICLE
Genome‑wide Identification, Expression Profiling and Promoter Analysis of Trehalose‑6‑Phosphate Phosphatase Gene Family in Rice Md Mustafizur Rahman1 · Md Mizanor Rahman1 · Joon‑Seob Eom1 · Jong‑Seong Jeon1 Received: 12 July 2020 / Revised: 24 August 2020 / Accepted: 25 August 2020 © Korean Society of Plant Biologist 2020
Abstract Trehalose-6-phosphate phosphatase (TPP) plays a key role in trehalose metabolism in plants. Here, we performed comprehensive in silico analyses and identified 12 OsTPPs (Oryza sativa TPPs) utilizing various bioinformatics tools. Phylogenetic tree, accomplished with OsTPPs and TPPs from 11 monocot and dicot species, was divided mainly into two clades, each clade containing six OsTPPs. Exon–intron distribution was related to phylogenetic clades. All OsTPPs are distributed within nine chromosomes (chr.), except Chr. 1, Chr. 5 and Chr. 11. OsTPPs were found to be stable in nature according to the 3-D structure prediction. Cis-regulatory elements (CREs) were also analyzed using 2 kb upstream of start codon for each gene to predict their biological functions. We categorized all CREs in five distinct groups based on core elements, stress response, cellular development, hormonal regulation, and unknown function, distributed in a range of 3–14 CREs in each group. Interestingly, our expression analysis showed that OsTPPs were more upregulated in response to drought and cold stresses compared to salt stress. Abundance of stress-related CREs found signifies TPPs’ possible role in stress response, which may facilitate to find related transcription factors and unveil complex molecular mechanisms during stress response. Keywords Cis-regulatory elements · Gene expression · In silico · Rice · Trehalose-6-phosphate phosphatase
Introduction Trehalose is a non-reducing disaccharide composed of two molecules of α-glucose, widely distributed in yeast, bacteria, fungi, animals, insects and plants (Elbein et al. 2003; Lunn et al. 2014). Previously, trehalose was thought to be present in only a few desiccation-tolerant plants (Bianchi et al. 1991; Drennan et al. 1993; Albini et al. 1994), but eventually discovered in Arabidopsis (Arabidopsis thaliana) with the identification of two enzymes, namely, Trehalose6-phosphate synthase (TPS) (Blázquez et al. 1998) and Trehalose-6-phosphate phosphatase (TPP) (Vogel et al. 1998). Md Mustafizur Rahman and Md Mizanor Rahman contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12374-020-09279-x) contains supplementary material, which is available to authorized users. * Jong‑Seong Jeon [email protected] 1
Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
Trehalose biosynthesis in plants as well as in other organisms, except the vertebrates, occurs in two main steps incorporating two catalytic enzymes TPS and TPP. In the first step, Trehalose-6-phosphate (T6P), a phosphorylated intermediate, is synthesized from Uridine dip
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