A Strategy for Screening Monoclonal Antibodies for Arabidopsis Flowers

Antibody array-based proteome approach reveals proteins involved in grape seed development

Grape (Vitis vinifera) is one of the most widely cultivated fruits globally, primarily used for processing and fresh consumption. Seedless grapes are favored by consumers for their convenience, making the study of seedlessness a subject of great interest to scientists. To identify regulators involved in this process in grape, a monoclonal antibody (mAb)-array-based proteomics approach, which contains 21,120 mAbs, was employed for screening proteins/antigens differentially accumulated in grape during development. Differences in antigen signals were detected between seeded and seedless grapes revealing the differential accumulation of 2,587 proteins. After immunoblotting validation, 71 antigens were further immunoprecipitated and identified by mass spectrometry (MS). An in planta protein-protein interaction (PPI) network of those differentially accumulated proteins was established using mAb antibody by immunoprecipitation (IP)-MS, which reveals the alteration of pathways related to carbon metabolism and glycolysis. To validate our result, a seedless-related protein, DUF642 domain-containing protein (VvDUF642), which is functionally uncharacterized in grapes, was ectopically overexpressed in tomato (Solanum lycopersicum "MicroTom") and led to a reduction in seed production. PPI network indicated that VvDUF642 interacts with pectin acetylesterase (VvPAE) in grapes, which was validated by BiFC and Co-IP. As anticipated, overexpression of VvPAE substantially reduced seed production in tomato. Moreover, S. lycopersicum colourless non-ripening expression was altered in VvDUF642- and VvPAE-overexpressing plants. Taken together, we provided a high-throughput method for the identification of proteins involved in the seed formation process. Among those, VvDUF642 and VvPAE are potential targets for breeding seedless grapes and other important fruits in the future.

FaMYB9 is involved in the regulation of C6 volatile biosynthesis in strawberry

The large-scale untargeted proteomic and metabolomic studies were conducted in strawberry (Fragaria × ananassa) cv. Akihime fruit at five developmental stages. We found that some C6 volatiles highly contributed to the enrichment of volatiles at the red stage of strawberry fruit. We found that 12 genes involved in LOX pathway for volatile biosynthesis showed multiple patterns in protein abundance during fruit development and ripening, and 9 out of the 12 genes exhibited a significant increase in their relative expression levels at the red stage of fruit. We also found that the MYB9 gene (FaMYB9) expression level was positively correlated with the content of C6 volatiles (R = 0.989) and with the relative expression level and protein abundance of FaLOX5 at different strawberry fruit developmental stages (R = 0.954). The interaction between FaMYB9 and FaLOX5 was detected by yeast two-hybrid, co-immunoprecipitation (Co-IP), bimolecular fluorescence complementation (BiFC), and immunofluorescence (IF) analyses. Transient silencing of FaMYB9 delayed the fruit development and ripening, resulting in a significant decrease in the contents of C6 volatiles, while overexpression of FaMYB9 increased the fruit development and ripening and the contents of C6 volatiles in Akihime fruit. Therefore, FaMYB9 is positively involved in C6 volatile biosynthesis.

Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model

Peach (Prunus persica) is a typical climacteric fruit that produces ethylene rapidly during ripening, and its fruit softens quickly. Stony hard peach cultivars, however, do not produce large amounts of ethylene, and the fruit remains firm until fully ripe, thus differing from melting flesh peach cultivars. To identify the key proteins involved in peach fruit ripening, an antibody-based proteomic analysis was conducted. A mega-monoclonal antibody (mAb) library was generated and arrayed on a chip (mAbArray) at a high density, covering ~4950 different proteins of peach. Through the screening of peach fruit proteins with the mAbArray chip, differentially expressed proteins recognized by 1587 mAbs were identified, and 33 corresponding antigens were ultimately identified by immunoprecipitation and mass spectrometry. These proteins included not only important enzymes involved in ethylene biosynthesis, such as ACO1, SAHH, SAMS, and MetE, but also novel factors such as NUDT2. Furthermore, protein-protein interaction analysis identified a metabolon containing SAHH and MetE. By combining the antibody-based proteomic data with the transcriptomic and metabolic data, a mathematical model of ethylene biosynthesis in peach was constructed. Simulation results showed that MetE is an important regulator during peach ripening, partially through interaction with SAHH.