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With proteomic analysis including 2-DE, image analysis, and protein identification with MALDI-TOF/MS, an investigation aiming at a enhanced understanding of the whole fruit proteome and differentially expressed proteins and/or gene products was carried out with total fruit extracts from Bhut Jolokia (Capsicum assamicum) and less pungent Capsicum frutescens. A total of 107 dominant protein spots have been identified here using a 2-DE/MS technique. Among the identified proteins, 14 proteins exhibited qualitative difference with unique expression in Bhut Jolokia and 6 proteins showed quantitative differential expression alterations. Among the 6 differential proteins, one was down-regulated and 5 were up-regulated. Apart from the unique and differential proteins for which a cluster of orthologous groups (COG) could not be assigned (36.84%), most of the dominant unique and differentially expressed proteins were assigned to the COG of energy production and conversion (21.05%) and also carbohydrate transport and metabolism (21.05%). This differential protein expression was further confirmed for selected candidates by semi-quantitative RT PCR and quantitative real time PCR. This is the first proteomic description of world’s hottest chilli ‘Bhut Jolokia’ and a detailed functional analysis of these proteins would provide further information regarding complex cellular processes and mechanism of pungency in this important source of Capsaicinoids.
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