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iTRAQ-based protein profiling provides insights into the central metabolism changes driving grape berry development and ripening.

Martínez-Esteso MJ, Vilella-Antón MT, Pedreño MÁ, Valero ML, Bru-Martínez R - BMC Plant Biol. (2013)

Bottom Line: These findings lie mainly in metabolism and storage of sugars and malate, energy-related pathways such as respiration, photosynthesis and fermentation, and the synthesis of polyphenolics as major secondary metabolites in grape berry.In conclusion, some proteins not reported to date have been detected to be deregulated in specific tissues and developmental stages, leading to formulate new hypotheses on the metabolic processes underlying grape berry development.These results open up new lines to decipher the processes controlling grape berry development and ripening.

View Article: PubMed Central - HTML - PubMed

Affiliation: Grupo de Proteómica y Genómica Funcional de Plantas, Dept, Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Apartado 99, E-03080 Alicante, Spain. mjose.martinez@ua.es.

ABSTRACT

Background: Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components such as sugars, acids, flavors, anthocyanins, tannins, etc., accumulate in the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance in our understanding of berry development and ripening processes.

Results: We report the developmental analysis of Vitis vinifera cv. Muscat Hamburg berries at the protein level from fruit set to full ripening. An iTRAQ-based bottom-up proteomic approach followed by tandem mass spectrometry led to the identification and quantitation of 411 and 630 proteins in the green and ripening phases, respectively. Two key points in development relating to changes in protein level were detected: end of the first growth period (7 mm-to-15 mm) and onset of ripening (15 mm-to-V100, V100-to-110). A functional analysis was performed using the Blast2GO software based on the enrichment of GO terms during berry growth.

Conclusions: The study of the proteome contributes to decipher the biological processes and metabolic pathways involved in the development and quality traits of fruit and its derived products. These findings lie mainly in metabolism and storage of sugars and malate, energy-related pathways such as respiration, photosynthesis and fermentation, and the synthesis of polyphenolics as major secondary metabolites in grape berry. In addition, some key steps in carbohydrate and malate metabolism have been identified in this study, i.e., PFP-PFK or SuSy-INV switches among others, which may influence the final sugar and acid balance in ripe fruit. In conclusion, some proteins not reported to date have been detected to be deregulated in specific tissues and developmental stages, leading to formulate new hypotheses on the metabolic processes underlying grape berry development. These results open up new lines to decipher the processes controlling grape berry development and ripening.

Show MeSH
Enriched GO terms (Molecular function (F term) (A), Biological process (P term) (B) and Cellular component (C term) (C)) for the sequences annotated in the up- or down-regulated subsets of proteins in each grape berry developmental stage analyzed. Bar diagrams indicate the number of sequences that were up- and down-regulated (X-axis), annotated with each enriched GO term (Y-axis) in the consecutive paired stages. GO terms descriptions are detailed in Additional file 8. Color code for the consecutive pair stages: FS-to-4 mm transitions (dark green bars), 4 mm-to-7 mm transitions (medium intensity green), 15 mm-to-7 mm (light green), V100-to-15 mm transitions (yellow), 110 g/l-to-15 mm transitions (light purple), 140 g/l-to-110 g/l (dark purple).
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Figure 3: Enriched GO terms (Molecular function (F term) (A), Biological process (P term) (B) and Cellular component (C term) (C)) for the sequences annotated in the up- or down-regulated subsets of proteins in each grape berry developmental stage analyzed. Bar diagrams indicate the number of sequences that were up- and down-regulated (X-axis), annotated with each enriched GO term (Y-axis) in the consecutive paired stages. GO terms descriptions are detailed in Additional file 8. Color code for the consecutive pair stages: FS-to-4 mm transitions (dark green bars), 4 mm-to-7 mm transitions (medium intensity green), 15 mm-to-7 mm (light green), V100-to-15 mm transitions (yellow), 110 g/l-to-15 mm transitions (light purple), 140 g/l-to-110 g/l (dark purple).

Mentions: A Fischer’s enrichment analysis [45] was carried out by comparing the frequencies of the annotation terms in the up- and down-regulated protein subsets with those of the whole list of quantified proteins as reference list. As a result, a series of GO terms, which were statistically overrepresented in the subset, was obtained (p<0.005). Figure 3 shows the result of the Fischer’s enrichment analysis for the molecular function (F term) (Figure 3A), biological processes (P term) (Figure 3B) and the cellular components (C term) (Figure 3C) -selected GO terms whose level in most cases was 4 or deeper. Additional file 8 provides a list of the proteins annotated with each enriched GO term.


iTRAQ-based protein profiling provides insights into the central metabolism changes driving grape berry development and ripening.

Martínez-Esteso MJ, Vilella-Antón MT, Pedreño MÁ, Valero ML, Bru-Martínez R - BMC Plant Biol. (2013)

Enriched GO terms (Molecular function (F term) (A), Biological process (P term) (B) and Cellular component (C term) (C)) for the sequences annotated in the up- or down-regulated subsets of proteins in each grape berry developmental stage analyzed. Bar diagrams indicate the number of sequences that were up- and down-regulated (X-axis), annotated with each enriched GO term (Y-axis) in the consecutive paired stages. GO terms descriptions are detailed in Additional file 8. Color code for the consecutive pair stages: FS-to-4 mm transitions (dark green bars), 4 mm-to-7 mm transitions (medium intensity green), 15 mm-to-7 mm (light green), V100-to-15 mm transitions (yellow), 110 g/l-to-15 mm transitions (light purple), 140 g/l-to-110 g/l (dark purple).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016569&req=5

Figure 3: Enriched GO terms (Molecular function (F term) (A), Biological process (P term) (B) and Cellular component (C term) (C)) for the sequences annotated in the up- or down-regulated subsets of proteins in each grape berry developmental stage analyzed. Bar diagrams indicate the number of sequences that were up- and down-regulated (X-axis), annotated with each enriched GO term (Y-axis) in the consecutive paired stages. GO terms descriptions are detailed in Additional file 8. Color code for the consecutive pair stages: FS-to-4 mm transitions (dark green bars), 4 mm-to-7 mm transitions (medium intensity green), 15 mm-to-7 mm (light green), V100-to-15 mm transitions (yellow), 110 g/l-to-15 mm transitions (light purple), 140 g/l-to-110 g/l (dark purple).
Mentions: A Fischer’s enrichment analysis [45] was carried out by comparing the frequencies of the annotation terms in the up- and down-regulated protein subsets with those of the whole list of quantified proteins as reference list. As a result, a series of GO terms, which were statistically overrepresented in the subset, was obtained (p<0.005). Figure 3 shows the result of the Fischer’s enrichment analysis for the molecular function (F term) (Figure 3A), biological processes (P term) (Figure 3B) and the cellular components (C term) (Figure 3C) -selected GO terms whose level in most cases was 4 or deeper. Additional file 8 provides a list of the proteins annotated with each enriched GO term.

Bottom Line: These findings lie mainly in metabolism and storage of sugars and malate, energy-related pathways such as respiration, photosynthesis and fermentation, and the synthesis of polyphenolics as major secondary metabolites in grape berry.In conclusion, some proteins not reported to date have been detected to be deregulated in specific tissues and developmental stages, leading to formulate new hypotheses on the metabolic processes underlying grape berry development.These results open up new lines to decipher the processes controlling grape berry development and ripening.

View Article: PubMed Central - HTML - PubMed

Affiliation: Grupo de Proteómica y Genómica Funcional de Plantas, Dept, Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Apartado 99, E-03080 Alicante, Spain. mjose.martinez@ua.es.

ABSTRACT

Background: Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components such as sugars, acids, flavors, anthocyanins, tannins, etc., accumulate in the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance in our understanding of berry development and ripening processes.

Results: We report the developmental analysis of Vitis vinifera cv. Muscat Hamburg berries at the protein level from fruit set to full ripening. An iTRAQ-based bottom-up proteomic approach followed by tandem mass spectrometry led to the identification and quantitation of 411 and 630 proteins in the green and ripening phases, respectively. Two key points in development relating to changes in protein level were detected: end of the first growth period (7 mm-to-15 mm) and onset of ripening (15 mm-to-V100, V100-to-110). A functional analysis was performed using the Blast2GO software based on the enrichment of GO terms during berry growth.

Conclusions: The study of the proteome contributes to decipher the biological processes and metabolic pathways involved in the development and quality traits of fruit and its derived products. These findings lie mainly in metabolism and storage of sugars and malate, energy-related pathways such as respiration, photosynthesis and fermentation, and the synthesis of polyphenolics as major secondary metabolites in grape berry. In addition, some key steps in carbohydrate and malate metabolism have been identified in this study, i.e., PFP-PFK or SuSy-INV switches among others, which may influence the final sugar and acid balance in ripe fruit. In conclusion, some proteins not reported to date have been detected to be deregulated in specific tissues and developmental stages, leading to formulate new hypotheses on the metabolic processes underlying grape berry development. These results open up new lines to decipher the processes controlling grape berry development and ripening.

Show MeSH