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Genome-wide Identification, Expression Profiling and Promoter Analysis of Trehalose-6-Phosphate Phosphatase Gene Family in Rice

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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.

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Acknowledgments

This work was supported by grants from the Next Generation BioGreen 21 program (PJ013138), Rural Development Administration, and the Brain Pool Program (2019H1D3A2A01102257) and the Basic Research Lab program (Project No. 2018R1A4A1025158), National Research Foundation of Korea.

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Author notes

  1. Md Mustafizur Rahman and Md Mizanor Rahman contributed equally to this work.

Authors and Affiliations

  1. Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea

    Md Mustafizur Rahman, Md Mizanor Rahman, Joon-Seob Eom & Jong-Seong Jeon

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  1. Md Mustafizur Rahman
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  2. Md Mizanor Rahman
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  3. Joon-Seob Eom
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  4. Jong-Seong Jeon
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Contributions

JJ conceived and designed the experiments. MR, MR, and JE performed the experiments and analyzed the data. MR, MR, JE, and JJ wrote the paper.

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Correspondence to Jong-Seong Jeon.

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Electronic supplementary material

Supplementary Fig. 1. General information of cis-regulatory elements. (A) Histogram representing the frequencies of different sequence lengths of Cis-Regulatory Elements (CREs) in all OsTPP promoters. (B) Histogram showing frequencies of CREs identified using PlantCARE in positive and negative strands of OsTPPs. (C) Pie chart depicting the distribution of identified motifs in CREs of OsTPPs, based on their biological functions. a, Core CREs; b, Stress related CREs; c, Cellular developmental related CREs; d, Hormonal regulation related CREs; e, Unknown CREs.

Supplementary Fig. 2. Schematic representation of Cis-Regulatory Elements (CREs). Promoter sequences (2 kb upstream of start codon) of 12 OsTPPs were analyzed using PlantCARE database. Different colors and shapes of markers represent various CREs. (A) Core CREs. (B) Stress related CREs. (C) Cellular development related CREs. (D) Hormonal regulation related CREs. (E) Unknown CREs.

Supplementary Fig. 3. Expression heat map and gene distance matrix of OsTPPs. (A) Heat map representing OsTPPs expression during different developmental stages. (B) Gene Distance Matrix, Pearson correlation according to mRNA expression using MeV.

Supplementary Fig. 4. Frequency of different CREs in each OsTPP. CRE, Cis-regulatory elements; SrCREs, Stress related CREs; CdCREs, Cellular development related CREs; HrCREs, Hormonal regulation related CREs.

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Rahman, M.M., Rahman, M.M., Eom, JS. et al. Genome-wide Identification, Expression Profiling and Promoter Analysis of Trehalose-6-Phosphate Phosphatase Gene Family in Rice. J. Plant Biol. 64, 55–71 (2021). https://doi.org/10.1007/s12374-020-09279-x

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  • DOI: https://doi.org/10.1007/s12374-020-09279-x

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