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Genome-Wide Analysis of Soybean Vacuolar Processing Enzyme Gene Family Reveals Their Roles in Plant Development and Response to Stress Conditions

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Abstract

Vacuolar processing enzymes (VPEs) are important proteases for the processing and maturation of vacuolar proteins. The VPEs in model plant Arabidopsis have been well researched. However, less is known about this gene family in the crop plant soybean (Glycine max). This study performed genome-wide identification of soybean VPE genes and 7 members were isolated. Their sequence information was firstly collected, and then phylogenetic relationship, chromosome distribution, gene duplication, conserved motifs as well as gene structure were analyzed for further insight into this gene family. The 7 GmVPEs were located on 6 chromosomes, and their encoding proteins were classified into three groups. Collinearity analysis indicated that 5 GmVPEs were involved in gene duplication events and they have undergone purifying selection during evolution. Conserved motif and gene structure analysis revealed the similarity and diversity among the sequences of different GmVPEs. To uncover the possible functions of soybean VPEs, cis-acting elements and TF binding sites on their promoters were identified, the results implied soybean VPE genes might participate in various biological processes and transcriptional regulation pathways. Through analyzing the RNA-Seq data, expression of the soybean VPE genes were found to exhibit spatiotemporal differences, with some being expressed almost ubiquitously, while others being expressed uniquely in seed. Finally, the expression profile analysis indicated that two VPE members, namely GmVPE4 and GmVPE7, likely play key roles in plant response to both biotic and abiotic stresses.

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Data Availability

Data used or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

This research was funded by National Natural Science Foundation of China (32201730) and the funding project of Northeast Geological S&T Innovation Center of China Geological Survey (QCJJ2022-44).

Funding

This research was funded by National Natural Science Foundation of China (32201730) and the funding project of Northeast Geological S&T Innovation Center of China Geological Survey (QCJJ2022-44).

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Authors and Affiliations

  1. Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Shenyang, 110044, China

    Xiangbo Duan, Ke Zhang, Yang Yu & Zhouli Liu

  2. Northeast Geological S&T Innovation Center of China Geological Survey, Shenyang, 110000, China

    Zhouli Liu

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Contributions

X. D. and Y. Y. conceived and designed the work; Y. Y. and Z. L. contributed to funding acquisition and supervision; X. D. and K. Z. collected the experimental data and conducted bioinformatic analysis; X. D. wrote the original draft; K. Z., Y. Y., and Z. L. revised and edited the manuscript. All authors have read and agreed the published version of the manuscript.

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Correspondence to Yang Yu.

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Duan, X., Zhang, K., Yu, Y. et al. Genome-Wide Analysis of Soybean Vacuolar Processing Enzyme Gene Family Reveals Their Roles in Plant Development and Response to Stress Conditions. J Plant Growth Regul (2024). https://doi.org/10.1007/s00344-024-11309-8

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