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Seed germination is an important aspect of the plant life cycle, during which, reactive oxygen species (ROS) accumulate. The accumulation of ROS results in an increase in protein oxidation of which carbonylation is the most canonical one. However, there is insufficient information concerning protein oxidation, especially carbonylation and its contribution to seed germination. In this study, biotin hydrazide labeled chromatography combined with sequential window acquisition of all theoretical fragment ion spectra (SWATH) method was used to analyze the dynamic pattern of protein carbonylation in rice embryos during germination. A total of 1872 unique proteins were quantified, among which 288 carbonylated peptides corresponding to 144 proteins were determined based on the filtering through mass shifts of modified amino acids. In addition, 66 carbonylated proteins were further analyzed based on their carbonylation intensity in four stages of germination. These identified carbonylated proteins were mainly involved in maintaining the levels of ROS, abscisic acid and seed reserves. Remarkably, a peroxiredoxin was found with 23 unique carbonylated peptides, and the expression of which was consistent with its increased activity. This study describes the dynamic pattern of carbonylated proteins during seed germination, and may help to further understand the biochemical mechanisms on this process.

Thylakoid membrane complexes of rice (Oryza sativa L.) play crucial roles in growth and crop production. Understanding of protein interactions within the complex would provide new insights into photosynthesis. Here, a new “Double-Strips BN/SDS-PAGE” method was employed to separate thylakoid membrane complexes in order to increase the protein abundance on 2D-gels and to facilitate the identification of hydrophobic transmembrane proteins. A total of 58 protein spots could be observed and subunit constitution of these complexes exhibited on 2D-gels. The generality of this new approach was confirmed using thylakoid membrane from spinach (Spinacia oleracea) and pumpkin (Cucurita spp). Furthermore, the proteins separated from rice thylakoid membrane were identified by the mass spectrometry (MS). The stromal ridge proteins PsaD and PsaE were identified both in the holo- and core- PSI complexes of rice. Using molecular dynamics simulation to explore the recognition mechanism of these subunits, we showed that salt bridge interactions between residues R19 of PsaC and E168 of PasD as well as R75 of PsaC and E91 of PsaD played important roles in the stability of the complex. This stromal ridge subunits interaction was also supported by the subsequent analysis of the binding free energy, the intramolecular distances and the intramolecular energy.

Retinoid X receptor (RXR) antagonists, including some environmental endocrine disruptors, have a teratogenic effect on vertebrate embryos. To investigate the toxicological mechanism on the protein expression level, a quantitative proteomic study was conducted to analyze the proteome alterations of zebrafish (Danio rerio) embryos exposed to gradient concentrations of a representative RXR antagonist UVI3003. Using isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling coupled nano high-performance liquid chromatography-tandem mass spectrometry (nano HPLC-MS/MS), in total 6592 proteins were identified, among which 195 proteins were found to be differentially expressed by more than a two-fold change in exposed groups compared with the control. Gene ontology analysis showed that these differential proteins were mostly involved in anatomical structure development, biosynthetic process, ion binding and oxidoreductase activity. Moreover, the biological pathways of translation, lipoprotein metabolism, cell survival and gluconeogenesis were intensively inhibited after exposure. Some significantly downregulated proteins such as apolipoprotein A-I and vitellogenin and upregulated proteins such as calcium activated nucleotidase 1b, glutathione S-transferase and glucose 6-dehydrogenases showed a strong dose-dependent response. The results provided new insight into the molecular details of RXR antagonist-induced teratogenicity and added novel information of pathways and potential biomarkers for evaluation of RXR interfering activity.