Apple Hypanthium Firmness: New Insights from Comparative Proteomics Claudius Marondedze & Ludivine A. Thomas Received: 22 October 2011 / Accepted: 10 June 2012 / Published online: 26 June 2012 # Springer Science+Business Media, LLC 2012 Abstract Fruit firmness constitutes an important textural property and is one of the key parameters for estimating ripening and shelf life, which has a major impact on commercial- ization. In order to decipher the mechanisms related to firmness of apples (Malus × domestica Borkh.), two-dimensional gel electrophoresis (2-DE) was used to compare the total proteome of high and low firmness phenotypes from apple hypanthia of a ‘Golden Delicious’ × ‘Dietrich’ population. A total of 36 differentially regulated protein spots were positively identified by matrix assisted laser desorption/ionization-time of flight (MALDI- TOF) mass spectrometry (MS) and then validated against the Malus expressed sequence tags (EST) database. The findings of this study indicated a lower expression of ethylene biosynthesis related proteins in the high firmness phenotype, which could be linked to the slowing down of the ripening and softening processes. The reduced accumulation of proteins involved in ethylene biosynthesis juxtaposed to the upregulation of a transposase and a GTP-binding protein in the high firmness phenotype. The results also showed higher expression of cytoskeleton proteins in the high firmness phenotype compared to the low firmness phenotype, which play a role in maintaining cell structure and possibly fruit integrity. Finally, a number of proteins involved in detoxification and defense were expressed in fruit hypanthium. This proteomic study provides a contribution towards a better understanding of regulatory networks involved in fruit hypanthium firmness and/or softening, which could be instrumental in the development of improved fruit quality. Keywords Cytoskeleton . Ethylene biosynthesis . Fruit firmness . Hypanthium . Proteomics . Two-dimensional electrophoresis Appl Biochem Biotechnol (2012) 168:306–326 DOI 10.1007/s12010-012-9774-9 Electronic supplementary material The online version of this article (doi:10.1007/s12010-012-9774-9) contains supplementary material, which is available to authorized users. C. Marondedze Department of Biotechnology, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville 7535( Cape Town, South Africa C. Marondedze (*) : L. A. Thomas Division of Chemical and Life Sciences and Engineering, 4700 King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia e-mail: claudius.marondedze@kaust.edu.sa L. A. Thomas e-mail: ludivine.thomas@kaust.edu.sa