Genomic Characterization and Expression Analysis of the SnRK Family Genes in Dendrobium officinale Kimura et Migo (Orchidaceae).

Yue Wang,Aizhong Liu

doi:10.3390/plants10030479

Abstract

Sucrose non-fermenting1-related protein kinases (SnRKs) are a type of Ser/Thr protein kinases, and they play an important role in plant life, especially in metabolism and responses to environmental stresses. However, there is limited information on SnRK genes in Dendrobium officinale. In the present research, a total of 36 DoSnRK genes were identified based on genomic data. These DoSnRKs could be grouped into three subfamilies, including 1 member of DoSnRK1, 7 of DoSnRK2, and 28 of DoSnRK3. The gene structure analysis of DoSnRK genes showed that 17 members had no introns, while 16 members contained six or more introns. The conserved domains and motifs were found in the same subfamily. The various cis-elements present in the promoter regions showed that DoSnRK genes could respond to stresses and hormones. Furthermore, the expression patterns of DoSnRK genes in eight tissues were investigated according to RNA sequencing data, indicating that multiple DoSnRK genes were ubiquitously expressed in these tissues. The transcript levels of DoSnRK genes after drought, MeJA, and ABA treatments were analyzed by quantitative real-time PCR and showed that most DoSnRK genes could respond to these stresses. Therefore, genomic characterization and expression analyses provide valuable information on DoSnRK genes for further understanding the functions of SnRKs in plants.

Highlights

Protein kinases are important regulators in response to stresses that can activate downstream genes in different signal pathways through phosphorylation [1,2]
Because the genome of D. officinale is presently assembled to the scaffold level, these 36 DoSnRK
DoSnRK genes included the ABA-responsive element (ABRE) motif that can respond to abscisic acid (ABA). These results suggest that these cis-elements in their promoter regions of DoSnRK genes play a role in response to stress

Summary

Introduction

Protein kinases are important regulators in response to stresses that can activate downstream genes in different signal pathways through phosphorylation [1,2]. One of the well-known kinases is the sucrose nonfermenting (SNF1) kinase that is widely found in living organisms, including the SNF1 protein in yeast, the AMP-activated protein kinase (AMPK) in mammals, and the sucrose non-fermenting1-related protein kinase (SnRK). SnRK proteins can be divided into three subfamilies based on the sequences and structures, including SnRK1, SnRK2, and SnRK3 [10,11]. The SnRK1 subfamily contains a highly conserved protein kinase (Pkinase) domain at the N-terminus, which is the homolog of SNF1 in yeast and AMPKs in mammals [3].

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Discussion

Conclusion