Multi-omics approach highlights new targets for amino acid composition change in maize kernels

Maize (Zea mays) is among the most productive of cereal grains and is a staple crop for humans and livestock globally. Carbohydrates comprise ∼70% of maize kernels. Nevertheless, the crop is a major protein source in many developing countries (Watson, 2003; Flint-Garcia et al., 2009; Wu and Messing, 2014). Maize kernels are deficient in multiple essential amino acids required for human and animal health and survival. Therefore, the reliance on maize for protein is not ideal and has been the subject of interest for amino acid biofortification. Studies to enhance the amino acid content of maize have yet to be successful, likely because the expression of specific proteins is not sufficient to alter kernel amino acid composition.

The genetic and metabolic origins of seed amino acid composition are complex. Previous work suggests the deficiency of essential amino acids in seeds is due to high abundance of seed storage proteins. Seed storage proteins constitute more than 60% of the total amino acid composition of seeds and are poor in several essential amino acids, including lysine, methionine, and tryptophan (Shewry and Halford, 2002; Shewry, 2007; Larkins, 2017). Studies have endeavored to reduce or eliminate seed storage proteins in an attempt to increase the levels of essential amino acids without success. These investigations highlight that seeds maintain their protein levels and amino acid composition despite significant alterations to the proteome (Schmidt et al., 2011; Morton et al., 2016). This phenomenon, called proteomic rebalancing, is a conserved yet poorly understood mechanism and indicates greater complexity in the regulation of seed amino acid composition.

In a recent study published in this journal, Shrestha et al. (2021) utilized a multi-omics approach to elucidate the genes and biological processes underlying the regulation of amino acid composition in maize kernels. The approaches included a genome-wide association study (GWAS) to identify candidate genes involved in variation of protein-bound amino acids and a weighted gene correlation network analysis to associate protein expression with amino acid composition during kernel development and maturation. Independently, the two approaches yielded thousands of genes of interest, but when used in combination, the two techniques identified 80 overlapping candidate genes highly likely to be involved in the regulation of amino acid composition in kernels that could be targeted in future work.

The authors also employed a time course experiment of kernel development and maturation and showed that the relative composition of amino acids changes over time (Shrestha et al., 2021). In their analysis, leucine, isoleucine, valine, tyrosine, and proline levels were higher toward kernel maturation and desiccation. Inversely, the relative compositions of alanine, asparagine, aspartic acid, glutamine, glutamic acid, histidine, and lysine decreased during kernel development and maturation. These results are consistent with findings that seed storage proteins present in kernels are commonly rich in leucine and proline and poor in lysine. Shrestha et al. (2021) revealed that proteins that decrease in abundance toward kernel maturation were associated with translation and gene expression, especially of ribosomal proteins. The reduction in protein levels and lower levels of gene expression are expected as the seed prepares for desiccation and dormancy. Inversely, seed maturation is also characterized by massive synthesis and accumulation of seed storage proteins. These findings support translational reprogramming occurring during seed development and maturation, shaping amino acid composition and leading to the degradation of unnecessary proteins until a starchy endosperm remains (Sabelli and Larkins, 2009; Larkins, 2017).

Shrestha et al. (2021) revealed a substantial reduction in ∼50% of the proteome during kernel development, with a specific reduction in essential amino acids. This study supports the view that proteomic rebalancing is due to translational instead of transcriptional regulation (Schmidt et al., 2011; Morton et al., 2016) and shows that translational machinery, such as ribosomal proteins, is key to the regulation of seed amino acid composition. The large reduction in proteins during kernel development and maturation is of great interest and highlights potential avenues to amino acid biofortification. Future research can work toward targeting the proteins that decrease during kernel maturation instead of the abundant and, seemingly perturbation resistant, seed storage proteins in an attempt to increase the essential amino acid levels in maize.

Conflict of interest statement. None declared.