A generic approach for "shotgun" analysis of the soluble proteome of plant cell suspension cultures

Peptidomic profiling of endogenous peptides in the spleens of mouse models of Graves' disease

Background

Graves' disease (GD) is a common autoimmune thyroid disorder. The pathogenesis of GD involves an autoimmune response to the A subunit of the human thyrotropin receptor (hTSHR), although the specific mechanisms are not fully elucidated.

Methods

This study established a GD model by immunizing BALB/c mice with a recombinant adenovirus expressing the hTSHR A subunit. Spleen tissues were collected and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify differentially expressed peptides (DEPs). Gene Ontology (GO) analysis and KEGG pathway analysis were further utilized to annotate the functions of these DEPs. Additionally, peptide bioactivity prediction and molecular docking studies were conducted using Alphafold and Pymol software, respectively, to assess the binding affinity of specific peptides to the hTSHR A subunit.

Results

The GD mouse model was successfully established, and 1,428 DEPs were identified in the spleen, with 368 upregulated and 1,060 downregulated. Functional analysis indicated that these DEPs are mainly involved in cellular endocytosis, regulation of gene expression, and nucleocytoplasmic transport. Notably, molecular docking studies revealed that the abnormally highly expressed peptide HG2A-24aa demonstrated potential bioactivity and strong binding affinity with hTSHR-289aa.

Conclusion

The specific bioactive peptides may play key roles in the pathogenesis of GD, particularly HG2A-24aa, which may have a significant role in the MHC II antigen presentation pathway mediated by the hTSHR A subunit.

Didehydrophenylalanine, an abundant modification in the beta subunit of plant polygalacturonases

The structure and the activity of proteins are often regulated by transient or stable post- translational modifications (PTM). Different from well-known, abundant modifications such as phosphorylation and glycosylation some modifications are limited to one or a few proteins across a broad range of related species. Although few examples of the latter type are known, the evolutionary conservation of these modifications and the enzymes responsible for their synthesis suggest an important physiological role. Here, the first observation of a new, fold-directing PTM is described. During the analysis of alfalfa cell wall proteins a -2Da mass shift was observed on phenylalanine residues in the repeated tetrapeptide FxxY of the beta-subunit of polygalacturonase. This modular protein is known to be involved in developmental and stress-responsive processes. The presence of this modification was confirmed using in-house and external datasets acquired by different commonly used techniques in proteome studies. Based on these analyses it was found that all identified phenylalanine residues in the sequence FxxY of this protein were modified to α,β-didehydro-Phe (ΔPhe). Besides showing the reproducible identification of ΔPhe in different species arguments that substantiate the fold-determining role of ΔPhe are given.