Genome-Wide Analyses of the Soybean F-Box Gene Family in Response to Salt Stress.

Qi Jia,Zhi-Xia Xiao,Song Sun,Kang-Jing Liang,Hon-Ming Lam,Fuk-Ling Wong

doi:10.3390/ijms18040818

Abstract

The F-box family is one of the largest gene families in plants that regulate diverse life processes, including salt responses. However, the knowledge of the soybean F-box genes and their roles in salt tolerance remains limited. Here, we conducted a genome-wide survey of the soybean F-box family, and their expression analysis in response to salinity via in silico analysis of online RNA-sequencing (RNA-seq) data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) to predict their potential functions. A total of 725 potential F-box proteins encoded by 509 genes were identified and classified into 9 subfamilies. The gene structures, conserved domains and chromosomal distributions were characterized. There are 76 pairs of duplicate genes identified, including genome-wide segmental and tandem duplication events, which lead to the expansion of the number of F-box genes. The in silico expression analysis showed that these genes would be involved in diverse developmental functions and play an important role in salt response. Our qRT-PCR analysis confirmed 12 salt-responding F-box genes. Overall, our results provide useful information on soybean F-box genes, especially their potential roles in salt tolerance.

Highlights

Organisms have developed multiple regulatory mechanisms to coordinate their life processes in response to internal or external stimuli
Protein degradation via the ubiquitin/26S proteasome system (UPS) is an important post-translational regulatory mechanism, which is highly conserved in eukaryotes [1]
The UPS catalyzes the covalent attachment of multiple ubiquitins to the target substrate, which causes the substrate to be recognized by the 26S proteasome for proteolysis

Summary

Introduction

Organisms have developed multiple regulatory mechanisms to coordinate their life processes in response to internal or external stimuli. Protein degradation via the ubiquitin/26S proteasome system (UPS) is an important post-translational regulatory mechanism, which is highly conserved in eukaryotes [1]. The UPS catalyzes the covalent attachment of multiple ubiquitins to the target substrate, which causes the substrate to be recognized by the 26S proteasome for proteolysis. Ubiquitination includes sequential actions of three proteins: E1s (ubiquitin-activating enzymes), E2s (ubiquitin-conjugating enzymes) and E3s (ubiquitin protein ligases), of which E3s are the most diverse group, offering an extensive range of substrate selection [2]. The first three subunits form a scaffold to assemble a diverse group of F-box proteins which confer the specificity for the target substrates to be degraded [5,6]

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