Genome-Wide Characterization and Expression Analysis of KH Family Genes Response to ABA and SA in Arabidopsis thaliana.

Yanjie Zhang,Yu Ma,Guanglin Li,Ruiqi Liu

doi:10.3390/ijms23010511

Yanjie Zhang, Yu Ma + Show 2 more

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https://doi.org/10.3390/ijms23010511

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Abstract

K-homologous (KH) family is a type of nucleic acid-binding protein containing the KH domain and has been found to affect splicing and transcriptional regulation. However, KH family genes haven’t been investigated in plant species systematically. In this study, we identified 30 genes that belonged to the KH family based on HMM of the KH domain in Arabidopsis thaliana. Phylogenetic tree analysis showed that the KH family is grouped into three subgroups. Synteny analysis showed that AtKH9 and AtKH29 have the conserved synteny relationship between A. thaliana and the other five species. The AtKH9 and AtKH29 were located in the cytoplasm and nucleus. The seed germination rates of the mutants atkh9 and atkh29 were higher than wild-type after abscisic acid (ABA) and salicylic acid (SA) treatments. In addition, the expression of ABA-related genes, such as ABRE-binding factor 2 (ABF2), ABRE-binding factor 4 (ABF4), and delta 1-pyrroline-5-carboxylate synthase (P5CS), and an SA-related gene pathogenesis-related proteins b (PR1b) were downregulated after ABA and SA treatments, respectively. These results suggested that atkh9 and atkh29 mutants inhibit the effect of ABA and SA on seed germination. In conclusion, our results provide valuable information for further exploration of the function of KH family genes and propose directions and ideas for the identification and characterization of KH family genes in other plants.

Highlights

K-homologous (KH) family belongs to nucleic acid-binding protein containing KH domain, KH domain is first identified in human Heterogeneous Nuclear RibonucleoproteinK protein [1,2]
Thirty KH family genes identified in A. thaliana were named from AtKH1 to AtKH30
We found that twentyCucumis sativus, 34 KH family genes in Oryza sativa, 45 KH family genes in Solanum two gene pairs were found in synteny blocks between A. thaliana and B. rapa (AtKH3lycopersicum, 62 KH family genes in Zea mays were obtained, respectively (TableAtKH10S2)

Summary

Introduction

K-homologous (KH) family belongs to nucleic acid-binding protein containing KH domain, KH domain is first identified in human Heterogeneous Nuclear Ribonucleoprotein. K (hnRNPK) protein [1,2]. The hnRNPK was discovered early in humans containing three conserved KH domains. The KH domain is composed of approximately 70 amino acids and is present in archaea, bacteria, and eukaryotes [1,3]. KH domain can bind to RNA or DNA [4,5], and exists in different types of proteins, which play important roles in biological processes, including splicing, transcriptional regulation [6,7,8,9]. KH family genes haven’t been investigated in plant species systematically

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