Proteome-Wide Identification of Non-histone Lysine Methylation during Grape Berry Ripening

Abstract

To gain a comprehensive understanding of non-histone methylation during berry ripening in grape (Vitis vinifera L.), the methylation of non-histone lysine residues was studied using a 4D label-free quantitative proteomics approach. In total, 822 methylation sites in 416 methylated proteins were identified, with xxExxx_K_xxxxxx as the conserved motif. Functional annotation of non-histone proteins with methylated lysine residues indicated that these proteins were mostly associated with “ripening and senescence”, “energy metabolism”, “oxidation–reduction process”, and “stimulus response”. Most of the genes encoding proteins subjected to methylation during grape berry ripening showed a significant increase in expression during maturation at least at one developmental stage. The correlation of methylated proteins with QTLs, SNPs, and selective regions associated with fruit quality and development was also investigated. This study reports the first proteomic analysis of non-histone lysine methylation in grape berry and indicates that non-histone methylation plays an important role in grape berry ripening.

Investigation of Acid Tolerance Mechanism of Acetobacter pasteurianus under Different Concentrations of Substrate Acetic Acid Based on 4D Label-Free Proteomic Analysis

“…Both the peptide parent ion and its secondary fragments were detected and analyzed using high-resolution TOF. The secondary mass spectrometry scanning range was set to 100-1700 m/z, and the data acquisition used was parallel accumulation serial fragmentation (PASEF) mode [22]. A primary mass spectrum was acquired, followed by 10 PASEF mode acquisitions of secondary spectra with parent ion charges in the range of 0-5, and the dynamic exclusion time of the tandem mass spectral scans was set to 30 s to avoid repeated scans of the parent ions [22].…”

“…with parent ion charges in the range of 0-5, and the dynamic exclusion time of the tandem mass spectral scans was set to 30 s to avoid repeated scans of the parent ions [22].…”

“…In four-dimensional (4D) label-free quantitative proteomics, mass spectrometry identifies and quantifies peptide ions based on the properties of four dimensions: retention time, mass charge ratio, ion intensity, and ion mobility [20]. It is widely used in the proteomics analysis of various biological samples, such as Azotobacter chroococcum [21], Escherichia coli [19], and Grape [22], due to its high sensitivity and wide detection range.…”