Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

Abstract

Background Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening. Results To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively. Conclusions Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

Regulation of Fruit Growth in a Peach Slow Ripening Phenotype

“…These authors, by using a proteomic approach on peach ripening fruit, identified a P. persica homologue of a GUANYLATE-BINDING PROTEIN1 (SlGBP1) (Prupe.4G053400, 70.6% identity), a tomato protein able to maintain endopolyploid cells in a non-proliferative state [56], which was accumulated with the progression of ripening. This result indicates that endopolyploid cells division would be inhibited in the last phase of peach fruit development [55] and is consistent with our cytofluorimetric analysis result on S4 FAN fruits (Figure 1c and Figure S1). Indeed, in S4 FAN fruit the proportion of clearly endoreduplicated cells (sum of 8C-32C populations) account for 39%, a much lower value than that observed in ripening tomato fruit, in which the number of endoreduplicated cells (sum of 8C-256C populations) was more than 85% of total pericarp cells [57].…”

“…For each genotype, the fruit cross diameter of 100 fruits distributed on five trees was monitored on average weekly throughout development over the 2016 growth season, starting measurements 41 days after full bloom (DAFB), up to 132 DAFB to monitor the fruit growth. A total of 13 time points were obtained, i.e., at 41,48,55,62,69,83,90,97,104,111,118,125, and 132 DAFB. On each sampling date, at least 15 fruits were always harvest from the same five trees (for each cultivar), and then the fruits were split in 3 biological replicates, each composed of 5 fruits.…”

“…This analysis also highlights that in SR fruit the number of cells undergoing endoreduplication is lower than in FAN (Figure 1b), in agreement with the smaller size reached by SR fruit (Figure 1a). However, in peach the relationship between endoploidy and final fruit size must be considered in the light of a more recent evidence provided by Nilo-Poyanco et al [55]. These authors, by using a proteomic approach on peach ripening fruit, identified a P. persica homologue of a GUANYLATE-BINDING PROTEIN1 (SlGBP1) (Prupe.4G053400, 70.6% identity), a tomato protein able to maintain endopolyploid cells in a non-proliferative state [56], which was accumulated with the progression of ripening.…”

Molecular Insights into Freezing Stress in Peach Based on Multi-Omics and Biotechnology: An Overview

“…From the list of proteins, it is evident that the majority of the proteins have fundamental roles in sugar synthesis, thus, it is confirmed that peach plants protect themselves from the freezing conditions by synthesizing various sugar compounds, which can also be related to photosynthesis and respiration [ 68 ]. In addition, shotgun proteomics using 1D-gel (PAGE-SDS), combined with LC/MS-MS analysis, revealed 131,435 spectra that can be further matched against available stress tolerance datasets to generate freeze-tolerant datasets [ 69 ]. Furthermore, the PTMs of various proteins involved in stress response can be identified using the combined omics techniques, which will provide more valuable data for investigating stress tolerance [ 70 ].…”

Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species

“…Large-scale proteomics has been providing new information for fundamental biology [1,2], and in several related sciences such as toxicology [3,4], animal physiology and pathology [5], food safety, and aquaculture [6][7][8]. It has been providing insights concerning the mechanisms underlying several diseases [9,10].…”