Soy and fermented soy are popular and recognized as a health food among Koreans. Since soy proteins are known to be protease resistant, even to pepsin and pancreatin, it is hypothesized that soy proteins may interact with the intestinal tract and trigger certain physiological reactions. To test this hypothesis, mice were fed diets supplemented with soy, Chunkukjang, or casein. The differentially expressed proteins were analyzed using 2-D gels and identified by peptide mass fingerprinting using mass spectrometry. The majority of the differentially expressed proteins could be functionally grouped into metabolic enzymes and calcium-binding proteins. The differential protein expression by the soy-fed groups was also verified based on a representative protein, tropomyosin, using a Western blotting analysis. In addition, the soy-fed groups exhibited a taller villi structure. Therefore, this study suggests that soy proteins can be an effective nutrient and physiological stimulant for the intestines.

Nuts are one of the most common sources of allergies in individuals of all ages. In order for a particular protein to render an allergic reaction, it must resist proteolytic digestion by intestinal enzymes. In this study, three well-known allergenic nuts, almonds, cashew nuts, and peanuts, were used as samples, and enzyme digestion with Bacillus protease and porcine pepsin was tested. A proteomic approach using two-dimensional gel electrophoresis and an MS/MS analysis was applied to visualize and identify the proteins that were resistant to enzyme digestion. Among the 150 protein spots tested, 42 proteins were assigned functions. Due to the lack of genomic databases, 41% of the identified proteins were grouped as hypothetical. However, 12% of them were well-known allergens, including AraH. The remainder were grouped as storage, enzymes, and binding proteins.

Bacillus subtilis and Bacillus amyloliquefaciens are closely related species that share a similar genomic background, and are both known to secrete large amounts of proteins directly into a medium. The extracellular proteomes of two strains of Bacillus subtilis and two strains of Bacillus amyloliquefaciens were compared by 2-D gel electrophoresis during the late exponential growth phase. The relative abundance of some minor protein spots varied among the four strains of Bacillus. Over 123 spots of extracellular proteins were visualized on the gel for B. subtilis CH 97, 68 spots for B. subtilis 3-5, 230 spots for B. amyloliquefaciens CH 51, and 60 spotsfor B. amyloliquefaciens 86-1. 2D gel electrophoresis images of the four Bacillus strains showed significantly different protein profiles. Consistent with the 2D gel electrophoretic analysis, most of the B. subtilis proteins differed from the proteases secreted by the B. amyloliquefaciensstrains. Among the proteins identified from B. subtilis, approximately 50% were cytoplasmic and 30% were canonically extracellular proteins. The secreted protein profiles for B. subtilis CH 97 and B. subtilis 3-5 were quite different, as were the profiles for B. amyloliquefaciens CH 51 and 86-1. The four proteomes also differed in the major protein composition. The B. subtilis CH 97 and B. amyloliquefaciens CH 51 proteomes both contained large amounts of secreted hydrolytic enzymes. Among the four strains, B. subtilis 3-5 secreted the least number of proteins. Therefore, even closely related bacteria in terms of genomic sequences can still have significant differences in their physiology and proteome layout.