Proteomic analysis of pecan (Carya illinoinensis) nut development

Authors: CLERMONT, KRISTEN - Oak Ridge Institute For Science And Education (ORISE); GRAHAM, CHARLES - Noble Research Institute; Lloyd, Steven; Grimm, Casey; RANDALL, JENNIFER - New Mexico State University; Mattison, Chris

Submitted to: Foods
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2023
Publication Date: 2/17/2023
Citation: Clermont, K., Graham, C., Lloyd, S.W., Grimm, C.C., Randall, J., Mattison, C.P. 2023. Proteomic analysis of pecan (Carya illinoinensis) nut development. Foods. 12:866. https://doi.org/10.3390/foods12040866.
DOI: https://doi.org/10.3390/foods12040866

Interpretive Summary: Pecan (Carya illinoinensis) nuts are high in good fats, antioxidants, micronutrients, and protein. While protein content can vary, pecan nuts usually contain 5 to 12 % protein. However, the identity and amount of individual proteins within a pecan nut is thought to vary. Modern protein characterization methods and bio-informatics tools were used to evaluate the identity of proteins accumulating during development in ‘Desirable’ and ‘Sumner’ pecan cultivars. The analysis was able to distinguish 1,267 different protein spots and identify 556 of them. Surprisingly there was little variation between the two cultivars, and only 26 protein spots accumulated to different levels between the two cultivars. The most rapid accumulation of proteins occurred during mid-September, and pecan allergens were first observed to accumulate during late September. These results provide a link between gene expression and protein accumulation that can be used in the future to allow trait-specific analyses of pecan proteins to enable reduced allergen content, improved sensory or nutritional qualities, increased tolerance to salinity or other abiotic or biotic stresses, seed hardiness, and seed viability.

Technical Abstract: Pecan (Carya illinoinensis) nuts are an economically valuable crop native to the United States and Mexico. Pecan kernels progress through multiple stages of development, and a proteomic summary of protein accumulation during pecan development is presented here. Pecan nuts from Sumner and Desirable pecan cultivars were collected at six time points throughout kernel filling. Computerized comparisons of soluble protein extracts via 2-D gel and gel-free, label-free proteomic analyses elucidated the accumulation of individual proteins during kernel filling. Rapid overall protein accumulation occurred in mid-September during the transition from the gel stage to the dough stage of kernel filling. 2-D gel electrophoresis distinguished 1,267 protein spots, and shotgun proteomics analysis identified 556 proteins. Pecan allergens Car i 1 and Car i 2 were first observed to accumulate during the dough stage in late September. The peptide QCCQQLSQMEEQCQCEGLR and the peptides NFLAGQNNIINQLER and VFSNDILVAALNTPR were identified as potential markers of Car i 1 and Car i 2, respectively. While overall protein accumulation and diversity increased through the dough stage, the incidence of observed peptides for Heterodimerization Activity (GO:0046982) and DNA Binding (GO:0003677) Gene Ontology (GO) terms decreased significantly from early to late development. Protein profiles were largely similar between the two cultivars; however, 26 protein spots were differentially accumulated between the two cultivars based on 2-D gel analyses. The results of this investigation provide a foundation for more focused trait-specific proteomic analyses of pecans that may include reduced allergen content, improved polyphenol or lipid content, increased tolerance to salinity or other abiotic or biotic stresses, seed hardiness, and seed viability.