Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Species

Overview

Journal Plants (Basel)

Date 2019 Nov 14

PMID 31717908

Citations 6

Authors

Baiquan Ma

Yuduan Ding

Cuiying Li

Mingjun Li

Fengwang Ma

Yangyang Yuan

Affiliations

Soon will be listed here.

Abstract

Soluble sugars and organic acids are the main determinants of fruit organoleptic quality. To investigate the genes responsible for the soluble sugar and organic acid contents of apple fruits, a label-free proteomic analysis involving liquid chromatography (LC)-mass spectrometry (MS)/MS was conducted with the fruits of two species, and , which exhibit significant differences in soluble sugar and organic acid contents. A total of 13,036 unique peptides and 1,079 differentially-expressed proteins were identified. To verify the LC-MS/MS results, five candidate proteins were further analyzed by parallel reaction monitoring. The results were consistent with the LC-MS/MS data, which confirmed the reliability of the LC-MS/MS analysis. The functional annotation of the differentially-expressed proteins, based on the gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, revealed that they were mainly related to biological processes and cellular components. Additionally, the main enriched KEGG pathways were related to metabolic processes. Moreover, 31 proteins involved in soluble sugar metabolism, organic acid metabolism, and H-transport were identified. The results of this study may be useful for the comprehensive characterization of the complex mechanism regulating apple fruit-soluble sugar and organic acid contents.

Citing Articles

DIA-Based Quantitative Proteomics in the Flower Buds of Two (Ledeb.) M. Roem Subtypes at Different Overwintering Stages.

Li L, Lu X, Dai P, Ma H Int J Mol Sci. 2024; 25(5).

PMID: 38474210 PMC: 10932172. DOI: 10.3390/ijms25052964.

Comparative nutritional and metabolic analysis reveals the taste variations during yellow rambutan fruit maturation.

Deng H, Wu G, Zhang R, Yin Q, Xu B, Zhou L Food Chem X. 2023; 17:100580.

PMID: 36845499 PMC: 9944575. DOI: 10.1016/j.fochx.2023.100580.

Combined nature and human selections reshaped peach fruit metabolome.

Cao K, Wang B, Fang W, Zhu G, Chen C, Wang X Genome Biol. 2022; 23(1):146.

PMID: 35788225 PMC: 9254577. DOI: 10.1186/s13059-022-02719-6.

Identification and verification of key taste components in wampee using widely targeted metabolomics.

Yin Q, Ji J, Zhang R, Duan Z, Xie H, Chen Z Food Chem X. 2022; 13:100261.

PMID: 35499032 PMC: 9040002. DOI: 10.1016/j.fochx.2022.100261.

Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process.

Martinez O, Arce-Rodriguez M, Hernandez-Godinez F, Escoto-Sandoval C, Cervantes-Hernandez F, Hayano-Kanashiro C Plants (Basel). 2021; 10(3).

PMID: 33808668 PMC: 8003350. DOI: 10.3390/plants10030585.

References

Rauniyar N . Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry. Int J Mol Sci. 2015; 16(12):28566-81. PMC: 4691067. DOI: 10.3390/ijms161226120. View

Mintz-Oron S, Mandel T, Rogachev I, Feldberg L, Lotan O, Yativ M . Gene expression and metabolism in tomato fruit surface tissues. Plant Physiol. 2008; 147(2):823-51. PMC: 2409049. DOI: 10.1104/pp.108.116004. View

Ma B, Yuan Y, Gao M, Li C, Ogutu C, Li M . Determination of Predominant Organic Acid Components in Species: Correlation with Apple Domestication. Metabolites. 2018; 8(4). PMC: 6316603. DOI: 10.3390/metabo8040074. View

Chelius D, Bondarenko P . Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res. 2003; 1(4):317-23. DOI: 10.1021/pr025517j. View

Wisniewski J, Zougman A, Mann M . Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res. 2009; 8(12):5674-8. DOI: 10.1021/pr900748n. View

Baerenfaller K, Grossmann J, Grobei M, Hull R, Hirsch-Hoffmann M, Yalovsky S . Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science. 2008; 320(5878):938-41. DOI: 10.1126/science.1157956. View

Terrier N, Glissant D, Grimplet J, Barrieu F, Abbal P, Couture C . Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development. Planta. 2005; 222(5):832-47. DOI: 10.1007/s00425-005-0017-y. View

Washburn M, Ulaszek R, Deciu C, Schieltz D, Yates 3rd J . Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal Chem. 2002; 74(7):1650-7. DOI: 10.1021/ac015704l. View

Zhen Q, Fang T, Peng Q, Liao L, Zhao L, Owiti A . Developing gene-tagged molecular markers for evaluation of genetic association of apple genes with fruit sugar accumulation. Hortic Res. 2018; 5:14. PMC: 5859117. DOI: 10.1038/s41438-018-0024-3. View

10.

Aebersold R, Mann M . Mass spectrometry-based proteomics. Nature. 2003; 422(6928):198-207. DOI: 10.1038/nature01511. View

11.

Mahmood T, Anwar F, Abbas M, Boyce M, Saari N . Compositional variation in sugars and organic acids at different maturity stages in selected small fruits from pakistan. Int J Mol Sci. 2012; 13(2):1380-1392. PMC: 3291965. DOI: 10.3390/ijms13021380. View

12.

He Q, Fang X, Zhu T, Han S, Zhu H, Li S . Differential Proteomics Based on TMT and PRM Reveal the Resistance Response of × Induced by AP-Toxin. Metabolites. 2019; 9(8). PMC: 6724075. DOI: 10.3390/metabo9080166. View

13.

Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M . KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2011; 40(Database issue):D109-14. PMC: 3245020. DOI: 10.1093/nar/gkr988. View

14.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

15.

Cox J, Mann M . MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008; 26(12):1367-72. DOI: 10.1038/nbt.1511. View

16.

Chandramouli K, Qian P . Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Hum Genomics Proteomics. 2010; 2009. PMC: 2950283. DOI: 10.4061/2009/239204. View

17.

Etienne A, Genard M, Lobit P, Mbeguie-A-Mbeguie D, Bugaud C . What controls fleshy fruit acidity? A review of malate and citrate accumulation in fruit cells. J Exp Bot. 2013; 64(6):1451-69. DOI: 10.1093/jxb/ert035. View

18.

Etienne C, Moing A, Dirlewanger E, Raymond P, Monet R, Rothan C . Isolation and characterization of six peach cDNAs encoding key proteins in organic acid metabolism and solute accumulation: involvement in regulating peach fruit acidity. Physiol Plant. 2002; 114(2):259-270. DOI: 10.1034/j.1399-3054.2002.1140212.x. View

19.

Aebersold R, Burlingame A, Bradshaw R . Western blots versus selected reaction monitoring assays: time to turn the tables?. Mol Cell Proteomics. 2013; 12(9):2381-2. PMC: 3769317. DOI: 10.1074/mcp.E113.031658. View

20.

Quadroni M, Ducret A, Stocklin R . Quantify this! Report on a round table discussion on quantitative mass spectrometry in proteomics. Proteomics. 2004; 4(8):2211-5. DOI: 10.1002/pmic.200400868. View