High-resolution mass spectrometry approach for proteomic and metabolomic analyses of fast neutron-mediated high-protein soybean seeds

Authors: Islam, Nazrul; Krishnan, Hari; Slovin, Janet; LI, ZENGLU - University Of Georgia; TAREQ, FAKIR - University Of Maryland; Luthria, Devanand; Natarajan, Savithiry

Submitted to: Journal of Agricultural and Food Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/25/2025
Publication Date: 3/5/2025
Citation: Islam, N., Krishnan, H.B., Slovin, J.P., Li, Z., Tareq, F., Luthria, D.L., Natarajan, S.S. 2025. High-resolution mass spectrometry approach for proteomic and metabolomic analyses of fast neutron-mediated high-protein soybean seeds. Journal of Agricultural and Food Chemistry. 73(11):6993-7002. https://doi.org/10.1021/acs.jafc.5c00375.
DOI: https://doi.org/10.1021/acs.jafc.5c00375

Interpretive Summary: Soybean provides the best alternative source of proteins for human consumption and animal feed. High-protein soybean without sacrificing yield may provide high-quality soybean products. However, detailed knowledge of all metabolic pathways for protein biosynthesis in soybeans is limited. We used cutting-edge technology for protein and metabolite profiling to identify metabolic pathways in high protein fast neutron soybean mutant lacking 137 genes. In this study, we identified a relationship among kinases, ubiquitin-proteasome system, and molecular chaperones. We demonstrated that the molecular chaperones play a critical role in rectifying the misfolded peptides and reassembling them to form a functional protein. The development of value-added seed traits using advanced metabolic engineering techniques can be achieved by further exploring this information.

Technical Abstract: Soybean provides a good source of vegetable protein and edible oil. The use of advanced technology to optimize growing conditions/alter genetic composition to produce value-added soybeans has been intensified since the inception of genome sequencing in 2010. Fast neutron (FN) radiation is widely accepted as one of the advanced techniques of genetic modification due to its ability to produce a variety of genetic variations. In this investigation, we conducted proteomic and metabolomic profiling of a high-protein soybean mutant developed through fast neutron mutagenesis with 137 genes and wild soybeans. The tandem tag-based protein profiling of the mutant and the wild type identified 6,098 proteins of which 175 proteins showed increased content, and 239 proteins showed decreased content in the mutant seeds. Using LC-MS-based metabolomic profiling, we identified 610 metabolites, of which 294 metabolites showed increased and 157 showed decreased content in the mutant seeds. By integrating proteomic and metabolomic profiling, we identified a relationship among deleted genes, ubiquitin-proteasome system, and molecular chaperones. Our findings indicate that some of the deleted genes are related to decreased content of ubiquitin-proteasome system and increased content of heat shock proteins based molecular chaperones. We anticipate that molecular chaperones are critical in rectifying misfolded peptides and reassembling them to form a functional protein, contributing to the mutant seeds' overall protein content. The development of value-added seed traits using advanced metabolic engineering techniques can be achieved by further exploring this information.