Submitted to: Journal of Proteomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 29, 2013
Publication Date: January 16, 2014
Repository URL: http://handle.nal.usda.gov/10113/58341
Citation: Smith-Hammond, C., Swatek, K.N., Johnston, M.L., Thelen, J.J., Miernyk, J.A. 2014. Initial description of the developing soybean seed protein-Lys-Ne-acetylome. Journal of Proteomics. 96:56-66. Interpretive Summary: A method was developed to measure chemical modification of soybean proteins. Results using this method were compared with two older methods and found to be significantly improved. Proteins that were modified were identified by genomic DNA sequence analysis, and separated into 11 different groups. The largest group contained proteins involved in growth, respiration, and primary metabolism. A method was developed to determine the spatial location of the chemically modified proteins, and the results obtained using this method were compared with results obtained through use of a computational bioinformatics method. Results from this study will be useful to both breeders and molecular biologists in their efforts to develop a line of soybeans that have a modified biochemical composition. They will additionally be useful to scientists who study the effects of chemical modifications on all aspects of plant biology.
Technical Abstract: Characterization of the myriad protein posttranslational modifications (PTM) is a key aspect of proteome profiling. While there have been previous studies of the developing soybean seed phospho-proteome, herein we present the first analysis of protein Lys-Ne-acetylation (PKA) in this system. In recent years there have been reports that PKA is widespread, affecting thousands of proteins in diverse species from bacteria to mammals. Recently, a preliminary description of the protein lysine-acetylome from the reference plant Arabidopsis thaliana has been reported. Using a combination of immunoenrichment and mass spectrometry-based techniques, we have identified 190 sites of lysine acetylation in 120 distinct proteins from developing soybean (Glycine max (L.) Merr., cv. Jack) cotyledons, which more than doubles the number of known plant Ne-lysine-acetylation sites. Results of functional annotation indicate acetyl-proteins are involved with a host of cellular activities. In addition to the histones, and other proteins involved in RNA synthesis and processing, acetyl-proteins participate in signaling, protein folding, and a plethora of metabolic processes. Results from in silico localization indicate that lysine-acetylated proteins are present in all major subcellular compartments. In toto, our results establish that developing soybean cotyledons will be a useful system for functional analysis of PKA.