Genome-wide identification of the Glycine max (soybean) aspartate kinase (AK) gene family and functional analysis of the GmAK6 gene in seed amino acid metabolism
Aug 2026· Frontiers in Plant Science· Vol 17· 0 citations· 45 references
Medicine
TL;DR
It is suggested that GmAK6 plays a regulatory role in amino acid metabolism during seed development and highlight the functional importance of AK genes in soybean.
Abstract
Introduction Aspartate kinase (AK) functions as a key regulatory enzyme in seed development and amino acid metabolism in plants. Although soybean (Glycine max) is a model high protein crop rich in essential amino acids, systematic characterization of its AK gene family remains limited. Methods To identify AK family genes at the genome wide level and analyze their functions, we performed a comprehensive bioinformatic analysis of the soybean genome, including phylogenetic reconstruction, promoter cis element prediction, transcriptomic profiling, and subcellular localization via GFP fusion assays. Functional validation was conducted using GmAK6 overexpressing transgenic soybean lines, with amino acid profiles quantified by HPLC. Results A total of 16 GmAK genes were identified, unevenly distributed across 10 chromosomes, with segmental duplication as the primary evolutionary driver of family expansion. Promoter analysis revealed that nearly half of the cis acting elements are associated with phytohormone signaling (e.g., jasmonic acid, abscisic acid) and abiotic stress responses (e.g., wounding, low temperature). Transcriptomic data showed distinct spatiotemporal expression patterns, with GmAK5 and GmAK6 significantly upregulated during seed development. GmAK6 was localized to chloroplasts. Amino acid profiling of GmAK6 overexpressing seeds demonstrated increased accumulation of methionine, threonine, and cysteine, alongside reduced levels of glutamate and proline. Discussion These results suggest that GmAK6 plays a regulatory role in amino acid metabolism during seed development and highlight the functional importance of AK genes in soybean.
This study elucidates the multifaceted roles of GmCXE31 in coordinating soybean salt tolerance, lipid metabolism and agronomic traits, providing theoretical and genetic resources for salt-tolerant and high-quality soybean molecular breeding.
Zhaohao Guo, Xin-Yu Wang, Tianyu Wang et al.· Plant Science· 0 citations
This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members.
The Oxidative Stress 3 (OXS3) gene family encodes plant-specific proteins that play crucial roles in abiotic stress tolerance and chromatin remodeling. However, genome-wide identification and characterization of the OXS3 gene family in soybean have not been systematically conducted. Here, we identified 19 GmOXS3 genes from the soybean genome. Phylogenetic analysis assigned these genes to three subfamilies (I–III). Members within the same subfamily exhibited conserved motif compositions. The promoter regions of GmOXS3 genes contained various cis-acting regulatory elements associated with stress and phytohormone responses. Analysis of transcriptome data revealed that GmOXS3 genes exhibited different expression patterns in various organs. RT-qPCR further confirmed their differential expression under salt and alkaline stresses, with the most pronounced up-regulation observed for GmOXS3-1 and GmOXS3-14 under alkaline stress. Among them, GmOXS3-1 was further characterized, and it negatively regulates alkaline tolerance in soybean hairy roots. These results provide a foundation for elucidating GmOXS3-1-mediated alkaline stress signaling and highlight its potential as a breeding target for improving alkaline tolerance.
Xi Chen, Nai-Ze Mu, Ling-Shan Ren et al.· Agronomy· 0 citations
Background: Soybean is an important crop with multiple uses for oil, food, and feed, providing 50% of the vegetable protein and 20% of the edible oil in the world. The WD40 family genes play crucial regulatory roles in growth, development, secondary metabolism, and stress responses. However, the definition of WD40 family genes in soybean remained unclear, which limited their application potential in genetic improvement. Methods: To identify soybean WD40 family members and screen candidate genes for breeding improvement, this study performed genome-wide identification of the soybean WD40 gene family via bioinformatic approaches based on the latest Williams 82 reference genome (Wm82.a6.v1). Meanwhile, the function of the family gene GmWD40-257 regulating seed quality was analyzed. Results: The results showed that a total of 458 GmWD40 genes were identified, which were distributed on the 20 chromosomes. Subcellular localization showed that most members were mainly concentrated in the nucleus, chloroplast, and cytoplasm. Phylogenetic tree analysis divided the 458 GmWD40 genes into eight groups. Synteny analysis identified 160 syntenic genes between soybean and Arabidopsis thaliana. Conserved motif analysis identified ten core motifs. The promoter regions of GmWD40 contained 19 types of cis-acting elements. Functional analysis revealed that the nonsense mutation of GmWD40-257 significantly reduced the content of oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while significantly increasing the contents of protein, γ-tocopherol and δ-tocopherol. Conclusions: A total of 458 members of the WD40 gene family were identified in soybean. Among these, GmWD40-257 was found to positively regulate the contents of soybean oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while negatively regulating the contents of soybean protein, γ-tocopherol and δ-tocopherol.
Hui Chen, Sunlei Ding, Hai-Yan Bi et al.· Genes· 0 citations
A novel component of the maize nitrogen-signaling network is uncovered and provide a candidate gene for further functional studies on low-nitrogen adaptation in maize.
A comprehensive genome-wide identification and characterization of the maize TALE gene family were conducted using bioinformatics approaches, followed by an investigation of their transcriptional responses to low-phosphorus (LP) stress, providing valuable insights into the evolutionary characteristics and potential biological functions.
Xian-Ting Huang, Shuang Li, Li-Tao Yi et al.· Plants· 0 citations
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