Global ubiquitinome analysis reveals the role of E3 ubiquitin ligase FaBRIZ in strawberry fruit ripening

Abstract

Ubiquitination is an important post-translational modification that mediates protein degradation in eukaryotic cell, participating in multiple biological processes. However, the profiling of protein ubiquitination and the function of this crucial modification in fruit ripening remain largely unknown. In this study, we found that suppression of proteasome by the inhibitor MG132 retarded strawberry fruit ripening. By using K-ɛ-GG antibody enrichment combined with high-resolution mass spectrometry, we performed a comprehensive ubiquitinome analysis in strawberry fruit. We identified 2947 ubiquitination sites for 2878 peptides within 1487 proteins, which are involved in a variety of cellular functions. The lysine at position 48 (K48)-linked poly-ubiquitin chains appeared to be the most prevalent types of modification among the identified ubiquitinated proteins. A large number of ubiquitination sites exhibited altered ubiquitination levels after proteasome inhibition, including those within ripening-related proteins associated with sugar and acid metabolism, cell wall metabolism, anthocyanin synthesis, and ABA biosynthesis and signaling. We further demonstrated that FaBRIZ, a RING-type E3 ligase, functions as a negative regulator of ripening in strawberry fruit. Our findings highlight the critical regulatory roles of protein ubiquitination in fruit ripening. The ubiquitinome data provide a basis for further exploration of the function of ubiquitination on specific proteins.

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

“…Downregulation and knockout of Ripening Inducing Factor (FaRIF) resulted in delayed ripening of both the receptacle and achenes (Martín-Pizarro et al, 2021;Li et al, 2023b). Sucrose Nonfermenting1-Related Protein (FaSnRK2.6) and Brap2 Ring ZnF UBP Domain-Containing Protein (FaBRIZ) were found to promote ripening when silenced (Han et al, 2015;Wang et al, 2023a), while downregulation of Polygalacturonase 1 (FaPG1), a β-galactosidase gene (FaβGAL4), and a pectate lyase gene (Fanjjs25) resulted in increased firmness and reduced postharvest softening (Jiménez-Bermúdez et al, 2002;Garcia-Gago et al, 2009;Quesada et al, 2009;Posé et al, 2013;Paniagua et al, 2016;Paniagua et al, 2020;Paniagua et al, 2022). Knockout of FaPG1 and FvSEP3 resulted in significant increase in firmness and reduced postharvest softening, and delayed ripening, respectively (Pi et al, 2021;López-Casado et al, 2023).…”