Taking advantage of nonspecific trypsin cleavages for the identification of seed storage proteins in cereals

Zein based-nanoparticles loaded botanical pesticides in pest control: An enzyme stimuli-responsive approach aiming sustainable agriculture

Nanoencapsulation of biopesticides is an important strategy to increase the efficiency of these compounds, reducing losses and adverse effects on non-target organisms. This study describes the preparation and characterisation of zein nanoparticles containing the botanical compounds limonene and carvacrol, responsive to proteolytic enzymes present in the insects guts. The spherical nanoparticles, prepared by the anti-solvent precipitation method, presented in the nanoparticle tracking analysis (NTA) a concentration of 4.7 × 10¹² ± 1.3 × 10¹¹ particles.mL^-1 and an average size of 125 ± 2 nm. The formulations showed stability over time, in addition to not being phytotoxic to Phaseolus vulgaris plants. In vivo tests demonstrated that formulations of zein nanoparticles containing botanical compounds showed higher mortality to Spodoptera frugiperda larvae. In addition, the FTIC probe (fluorescein isothiocyanate) showed wide distribution in the larvae midgut, as well as being identified in the feces. The trypsin enzyme, as well as the enzymatic extract from insects midgut, was effective in the degradation of nanoparticles containing the mixture of botanical compounds, significantly reducing the concentration of nanoparticles and the changes in size distribution. The zein degradation was confirmed by the disappearance of the protein band in the electrophoresis gel, by the formation of the lower molecular weight fragments and also by the greater release of FTIC after enzymes incubation. In this context, the synthesis of responsive nanoparticles has great potential for application in pest management, increasing the selectivity and specificity of the system and contributing to a more sustainable agriculture.

Nonspecific cleavages arising from reconstitution of trypsin under mildly acidic conditions

Tryptic digestion of proteins followed by liquid chromatography with tandem mass spectrometry analysis is an extensively used approach in proteomics research and biopharmaceutical product characterization, owing to the high level of cleavage fidelity produced with this technique. However, nonspecific trypsin cleavages have been frequently reported and shown to be related to a number of digestion conditions and predigestion sample treatments. In this work, we reveal that, for a number of commercial trypsins, reconstitution and storage conditions can have a significant impact on the occurrence of trypsin nonspecific cleavages. We analyzed the tryptic digestion of a variety of biotherapeutics, using trypsins reconstituted under different conditions. The results indicate that, for many commercial trypsins, commonly recommended reconstitution/storage conditions (mildly acidic, e.g., 50 mM acetic acid, 1 mM HCl) can actually promote nonspecific trypsin activities, which are time dependent and can be as high as 20% in total relative abundance. In contrast, using water for reconstitution and storage can effectively limit nonspecific cleavages to 1%. Interestingly, the performances of different commercial trypsins were found to be quite distinct in their levels of nonspecific cleavages and responses to the two reconstitution conditions. Our findings demonstrate the importance of choosing the appropriate trypsin for tryptic digestion and the necessity of assessing the impact of trypsin reconstitution and storage on nonspecific cleavages. We advocate for manufacturers of commercial trypsins to reevaluate manufacturing processes and reconstitution/storage conditions to provide good cleavage specificity.

Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation

High specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation.

METHODS

In this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less-complex Escherichia coli lysates to improve the sensitivity of detecting low-abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry.

RESULTS

Trypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2-h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16-h protocol.

CONCLUSIONS

The significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low-abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2-h protocol can potentially be a replacement for the traditional 16-h protocol.

Comparative genome-wide analysis of codon usage of different bacterial species infecting Oryza sativa

Oryza sativa is vastly affected by microbial pathogen, causing blight-related diseases, which in turn deplete the growth and productivity of rice. In this study, we analyzed four bacterial rice pathogen genomes and reported on their codon usage that might have greater implication in mutation-related research. Differential codon usage indices, such as codon adaptation index (CAI), codon bias index (CBI), effective number of codons (ENc), relative synonymous codon usage (RSCU), correspondence analysis (COA), and parity plots, were applied on coding sequences of Pseudomonas fuscovaginae, Pseudomonas syringae, Xanthomonas oryzae, and Pseudomonas avenae speices. The RSCU results proposed a high-frequency usage of CUG and CGC that codes for leucine and arginine in all of the species. The CBI and CAI values between the genomes range from 0.17 to 0.3 and from 0.26 to 0.35, respectively, indicating a direct proportionality between these indexes. The mean ENc value of P. avenae coding sequence showed high codon bias compared with other genomes. The axis I variation from COA analysis shows a mean value of 42.28% codon variations in these bacterial species. Correlation studies between axis I and ENc-GC3, along with CAI and CBI, suggested the presence of nucleotide bias and mutational pressure as major forces for codon bias within these species. Hence, certain genes with high CAI-CBI have been correlated for better gene expression. Our study highlights the importance of nucleotide biasness, mutation pressure, and natural selection in shaping protein-coding genes in these four rice-affecting bacteria. This would further help in investigating the evolution of pathogenic gene families, which may direct research toward synthetic genes that could be suppressed or overrepresented based on their codon usage pattern toward pathogenicity.

Identification of chickpea seed proteins resistant to simulated in vitro human digestion

Proteins and peptides able to resist gastrointestinal digestion and reach the intestinal mucosa have the potential to influence human health. Chickpea (Cicer arietinum L.) seed proteins are able to resist cooking (86.9% total protein) and/or in vitro simulated human digestion (15.9% total protein resists soaking, cooking and digestion with pepsin and pancreatin). To identify and characterize proteins resisting digestion we made use of different MS methodologies. The efficiency of several proteases (trypsin, AspN, chymotrypsin and LysC) was tested, and two technologies were employed (MALDI-MS/MS and LC-nESI-MS/MS). Digestion with trypsin and AspN were most successful for the identification of seed proteins. When analyzed by MALDI- MS/MS, trypsin allowed the identification of at least one protein in 60% of the polypeptide bands, while AspN allows the identification in 48%. The use of LC-nESI-MS/MS, allowed the identification of much more proteins/polypeptides from digested seeds (232 vs 17 using trypsin). The majority of the proteins found to be able to resist simulated digestion were members of the 7S vicilin and 11S legumin seed storage protein classes, which are reported to contain bio-active functions. In addition, we have found proteins that had not yet been described as potentially able to cause an impact on human health.

SIGNIFICANCE

This is the first proteomic study to analyze the effect of processing and simulated human gastrointestinal digestion on the proteome of chickpea seed. Chickpea is reported to have anti-nutritional effects as well as nutraceutical properties, so the identification and characterization of the proteins able to resist digestion is crucial to understand the targets underlying such properties.

Controlling nonspecific trypsin cleavages in LC-MS/MS-based shotgun proteomics using optimized experimental conditions

The highlight of this study is the efficient control of nonspecific trypsin cleavages in shotgun proteomics and N-glycoproteomics using optimized experimental conditions, which greatly increased the specificity of trypsin.

Maize IgE binding proteins: each plant a different profile?

Background

Allergies are nearly always triggered by protein molecules and the majority of individuals with documented immunologic reactions to foods exhibit IgE hypersensitivity reactions. In this study we aimed to understand if natural differences, at proteomic level, between maize populations, may induce different IgE binding proteins profiles among maize-allergic individuals. We also intended to deepen our knowledge on maize IgE binding proteins.

Results

In order to accomplish this goal we have used proteomic tools (SDS-PAGE and 2-D gel electrophoresis followed by western blot) and tested plasma IgE reactivity from four maize-allergic individuals against four different protein fractions (albumins, globulins, glutelins and prolamins) of three different maize cultivars. We have observed that maize cultivars have different proteomes that result in different IgE binding proteins profiles when tested against plasma from maize-allergic individuals. We could identify 19 different maize IgE binding proteins, 11 of which were unknown to date. Moreover, we found that most (89.5%) of the 19 identified potential maize allergens could be related to plant stress.

Conclusions

These results lead us to conclude that, within each species, plant allergenic potential varies with genotype. Moreover, considering the stress-related IgE binding proteins identified, we hypothesise that the environment, particularly stress conditions, may alter IgE binding protein profiles of plant components.

In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics

Partially tryptic peptides are often identified in shotgun proteomics using trypsin as the proteolytic enzyme; however, their sources have been controversial. Herein, we investigate the impact of in-source fragmentation on shotgun proteomics profiling of three biological samples: a standard protein mixture, a mouse brain tissue homogenate, and mouse plasma. Because the in-source fragments of peptide ions have the same LC elution time as their parental peptides, partially tryptic peptide ions from in-source fragmentation can be distinguished from other partially tryptic peptides based on their elution time differences from those computationally predicted data. The percentage of partially tryptic peptide identifications resulting from in-source fragmentation in a standard protein digest was observed to be ∼60%. In more complex mouse brain or plasma samples, in-source fragmentation contributed to a lesser degree of 1-3% of all identified peptides due to the limited dynamic range of LC-MS/MS measurements. The other major source of partially tryptic peptides in complex biological samples is presumably proteolytic cleavage by endogenous proteases in the samples. Our work also provides a method to identify such proteolytic-derived partially tryptic peptides due to endogenous proteases in the samples by removing in-source fragmentation artifacts from the identified peptides.