2D-page coupled to mass spectrometry for proteomic analysis of human, microbial and plant samples

The proteome of a cell or an organelle provides information about the ensemble of proteins and protein isoforms expressed in that cell or organelle under specific physiological conditions and at a specific time. Proteomic approaches provide several novel possibilities to address biological questions. In fact, the large-scale screening approach of proteomics enables protein expression studies that are impossible to perform using classical molecular biology and biochemical techniques, in which the expression of only one or a few proteins is studied at a time. Instead, proteomic techniques allow for the analysis of up to thousands of proteins simultaneously, in any tissue or organelle, under any given physiological condition. Thus, proteomic applications are growing in many areas of research and proteomic approaches are nowadays widely exploited for cancer, microbial, and plant investigations. The present work was focused on three proteomics studies: 1) evaluation of the cell response to a novel histone deacetylase inhibitor in colon cancer cell 2) effect of tannic acid on lactobacillus plantarum wine strain during starvation 3) analysis of grapevine leaves after Plasmopara viticola infection The thesis work was conducted at the Proteomics Laboratory of the Biotechnology Department of the University of Verona, in collaboration with other laboratories: concerning the study on colorectal cancer cells, the Laboratory of Oncology of the IRCCS Foundation “Istituto Nazionale dei Tumori”, Milan, provided all the biological samples, whilst the multivariate analysis of protein profiles was possible thanks to the collaboration with the Department of Environmental and Life Sciences of the University of Eastern Piedmont, Alessandria. The biochemical and proteomic analysis of lactobacillus plantarum wine strain was the result of the collaboration with laboratory of Dr. Zapparoli (Department of Biotechnology of the University of Verona). Proteomic investigations on the Grapevine leaves infected by Plasmopara viticola were performed in collaboration with laboratory of Dr. Polverari (Department of Biotechnology of the University of Verona). Finally, the identification of proteins for all the proteomic analyses performed were possible thanks to the collaboration with the Proteomics laboratories of Department of Environmental Sciences, Tuscia University, Viterbo, and of International Centre for Genetic Engineering and Biotechnology, Trieste. The results thus obtained are here discussed and evaluated.