Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin β Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses

Ya Xu,Pan Zhao,Ning Liu,Naiqin Zhong,Lu Liu,Jing Tong,Hongji Zhang

doi:10.3390/ijms21030931

Abstract

In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin β/Importin (KPNβ or Impβ) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in response to pathogen attack and environmental cues. Although achievements on understanding the roles of several KPNβs have been obtained from model plant Arabidopsis thaliana, comprehensive analysis of potato KPNβ gene family is yet to be elucidated. In our genome-wide identifications, a total of 13 StKPNβ (Solanum tuberosum KPNβ) genes were found in the genome of the doubled monoploid S. tuberosum Group Phureja DM1-3. Sequence alignment and conserved domain analysis suggested the presence of importin-β N-terminal domain (IBN_N, PF08310) or Exporin1-like domain (XpoI, PF08389) at N-terminus and HEAT motif at the C-terminal portion in most StKPNβs. Phylogenetic analysis indicated that members of StKPNβ could be classified into 16 subgroups in accordance with their homology to human KPNβs, which was also supported by exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis and quantitative real-time PCR experiments revealed that, except StKPNβ3d and StKPNβ4, almost all StKPNβs were ubiquitously expressed in all tissues analyzed, whereas transcriptional levels of several StKPNβs were increased upon biotic/abiotic stress or phytohormone treatments, reflecting their potential roles in plant growth, development or stress responses. Furthermore, we demonstrated that silencing of StKPNβ3a, a SA- and H2O2-inducible KPNβ genes led to increased susceptibility to environmental challenges, implying its crucial roles in plant adaption to abiotic stresses. Overall, our results provide molecular insights into StKPNβ gene family, which will serve as a strong foundation for further functional characterization and will facilitate potato breeding programs.

Highlights

Unlike the prokaryotic ancestors, the nucleus of eukaryotic cells is surrounded by double layers of lipid membranes, called the nuclear envelope (NE), which provides a controlled barrier between nucleoplasm and cytoplasm [1,2,3]
The nucleocytoplasmic transport machinery is composed of a variety of nuclear transport factors: (1) Karyopherin/Importin α (KPN α), which recognize cargo protein with nuclear localization signal (NLS) or nuclear export signal (NES); (2) Karyopherin/Importin β (KPNβ), which binds to KNPα and mediates cargo import into or export out of the nucleus; (3) A small GTPase Ran, which binds to KPNβ and drive directional nucleocytoplasmic transport of cargo-α/β/Ran complex by the RanGTP-RanGDP gradient across the NE [6,7,8,9,10,11]
One possible pseudogene (PGSC0003DMG400029568) was removed from our analysis because its expression could not be detected in all samples and conditions examined in subsequent expression analysis, its protein sequence is identical to KPNβ3d

Summary

Introduction

The nucleus of eukaryotic cells is surrounded by double layers of lipid membranes, called the nuclear envelope (NE), which provides a controlled barrier between nucleoplasm and cytoplasm [1,2,3]. The selective transportation of macromolecules across NE provides the eukaryotic cell with essential and additional benefits in regulating exchange of genetic information in response to the changing environments [4,5,6]. The nucleocytoplasmic transport machinery is composed of a variety of nuclear transport factors: (1) Karyopherin/Importin α (KPN α), which recognize cargo protein with nuclear localization signal (NLS) or nuclear export signal (NES); (2) Karyopherin/Importin β (KPNβ), which binds to KNPα and mediates cargo import into or export out of the nucleus; (3) A small GTPase Ran, which binds to KPNβ and drive directional nucleocytoplasmic transport of cargo-α/β/Ran complex by the RanGTP-RanGDP gradient across the NE [6,7,8,9,10,11]. In addition to collaborate with KPNα in nucleocytoplasmic transport, the KPNβ family of nuclear transport factors can mediate, by directly recognizing NLS/NES with cargos, most macromolecular transport across NE. Previous experiments have demonstrated that at least 11 human KPNβs and 10 yeast KPNβs can regulate nucleocytoplasmic transport [13]

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Discussion

Conclusion