Genome-wide identification, structure characterization, and expression pattern profiling of aquaporin gene family in cucumber

Yong-Xing Zhu,Yi-Qin He,Ning Liu,Dong-Fang Ma,Yu-Chen Xia,Xiao-Kang Zhou,Yang He,Hai-Jun Gong,Lei Yang,Jie Yang,Jun-Liang Yin

doi:10.1186/s12870-019-1953-1

Yong-Xing Zhu, Yi-Qin He + Show 9 more

Open Access

https://doi.org/10.1186/s12870-019-1953-1

Copy DOI

Abstract

BackgroundAquaporin (AQP) proteins comprise a group of membrane intrinsic proteins (MIPs) that are responsible for transporting water and other small molecules, which is crucial for plant survival under stress conditions including salt stress. Despite the vital role of AQPs, little is known about them in cucumber (Cucumis sativus L.).ResultsIn this study, we identified 39 aquaporin-encoding genes in cucumber that were separated by phylogenetic analysis into five sub-families (PIP, TIP, NIP, SIP, and XIP). Their substrate specificity was then assessed based on key amino acid residues such as the aromatic/Arginine (ar/R) selectivity filter, Froger’s positions, and specificity-determining positions. The putative cis-regulatory motifs available in the promoter region of each AQP gene were analyzed and results revealed that their promoter regions contain many abiotic related cis-regulatory elements. Furthermore, analysis of previously released RNA-seq data revealed tissue- and treatment-specific expression patterns of cucumber AQP genes (CsAQPs). Three aquaporins (CsTIP1;1, CsPIP2;4, and CsPIP1;2) were the most transcript abundance genes, with CsTIP1;1 showing the highest expression levels among all aquaporins. Subcellular localization analysis in Nicotiana benthamiana epidermal cells revealed the diverse and broad array of sub-cellular localizations of CsAQPs. We then performed RNA-seq to identify the expression pattern of CsAQPs under salt stress and found a general decreased expression level of root CsAQPs. Moreover, qRT-PCR revealed rapid changes in the expression levels of CsAQPs in response to diverse abiotic stresses including salt, polyethylene glycol (PEG)-6000, heat, and chilling stresses. Additionally, transient expression of AQPs in N. benthamiana increased leaf water loss rate, suggesting their potential roles in the regulation of plant water status under stress conditions.ConclusionsOur results indicated that CsAQPs play important roles in response to salt stress. The genome-wide identification and primary function characterization of cucumber aquaporins provides insight to elucidate the complexity of the AQP gene family and their biological functions in cucumber.

Highlights

Aquaporin (AQP) proteins comprise a group of membrane intrinsic proteins (MIPs) that are responsible for transporting water and other small molecules, which is crucial for plant survival under stress conditions including salt stress
Identification and classification of cucumber aquaporin genes Sequence homology analysis and protein domain validation using Pfam led to the identification of 41 aquaporin-like genes in cucumber (Table 1)
Consistent with RNA-seq data obtained from National Center for Biotechnology Information (NCBI), RNAseq data generated in our research suggested that

Summary

Introduction

Aquaporin (AQP) proteins comprise a group of membrane intrinsic proteins (MIPs) that are responsible for transporting water and other small molecules, which is crucial for plant survival under stress conditions including salt stress. Aquaporins (AQPs) are a family of small (21 to 34 kDa) channelforming transmembrane proteins that belong to the membrane intrinsic proteins (MIPs) family. They have been shown to act as multifunctional channels that transport water and many small molecules such as ammonia (NH3), carbon dioxide (CO2), nitric oxide (NO), formamide, glycerol, hydrogen peroxide (H2O2), and metalloids such as silicon and boron [5]

Methods

Results

Discussion

Conclusion