Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis

Int J Mol Sci. 2021 May 18;22(10):5294. doi: 10.3390/ijms22105294.


Although spinach (Spinacia oleracea L.) is considered to be one of the most nutrient-rich leafy vegetables, it is also a potent accumulator of anti-nutritional oxalate. Reducing oxalate content would increase the nutritional value of spinach by enhancing the dietary bioavailability of calcium and other minerals. This study aimed to investigate the proposed hypothesis that a complex network of genes associated with intrinsic metabolic and physiological processes regulates oxalate homeostasis in spinach. Transcriptomic (RNA-Seq) analysis of the leaf and root tissues of two spinach genotypes with contrasting oxalate phenotypes was performed under normal physiological conditions. A total of 2308 leaf- and 1686 root-specific differentially expressed genes (DEGs) were identified in the high-oxalate spinach genotype. Gene Ontology (GO) analysis of DEGs identified molecular functions associated with various enzymatic activities, while KEGG pathway analysis revealed enrichment of the metabolic and secondary metabolite pathways. The expression profiles of genes associated with distinct physiological processes suggested that the glyoxylate cycle, ascorbate degradation, and photorespiratory pathway may collectively regulate oxalate in spinach. The data support the idea that isocitrate lyase (ICL), ascorbate catabolism-related genes, and acyl-activating enzyme 3 (AAE3) all play roles in oxalate homeostasis in spinach. The findings from this study provide the foundation for novel insights into oxalate metabolism in spinach.

Keywords: isocitrate lyase; oxalate; spinach; transcriptomics.

MeSH terms

  • Gene Expression / genetics
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Plant / genetics
  • Oxalates / metabolism*
  • Plant Leaves / metabolism
  • Plant Roots / metabolism
  • RNA-Seq / methods
  • Spinacia oleracea / genetics*
  • Spinacia oleracea / metabolism*
  • Spinacia oleracea / physiology
  • Transcriptome / genetics


  • Oxalates