2-DE-based expression proteomics in biological research

Team : Isabel Sá-Correia, Miguel C Teixeira, Nuno P Mira, Sandra C dos Santos, Joana Guerreiro, Ana Moreira.


Expression proteomics, and in particular 2-dimensional electrophoresis (2-DE)-based quantitative proteomics, allows the study of proteome-wide alterations occurring in a cell at the levels of expression, localization and post-translational modifications occurring in response to genomic or environmental changes. It is thus a crucial approach to gain a full understanding of the dynamic and complex behavior of biological systems.

Research Topics

1. Pathoproteomics

Chronic lung infection is the major cause of morbidity and premature mortality in cystic fibrosis (CF) patients. Bacteria of theBurkholderia cepacia complex are the most threatening pathogens in CF. A better understanding of how these bacteria adapt to the CF airway environment while resisting host defense mechanisms and therapeutically administered antibiotics is crucial. Quantitative proteomics approaches are being used to provide molecular insights into these adaptive changes occurring in clinical isolates sequentially harvested at Sta Maria Hospital from persistently colonized CF patients under antibiotic therapy.

2. Toxicoproteomics

Toxicoproteomics is an emerging field that allies proteome-wide approaches to classical toxicology to increase our understanding of mechanisms of toxicity and resistance to xenobiotics, including pharmaceuticals and pesticides. This research area is further expected to increase our ability to predict the toxicological outcome of xenobiotic exposure, a key aspect in the risk assessment of pesticides and other environmental toxicants, and, eventually, be able to establish suitable biomarkers of contamination to be used as hazard indicators.

Toxicogenomics approaches are being applied in the BSRG to pesticides, in particular the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) and the fungicide mancozeb, and to pharmaceuticals, in particular the antimalarial drug quinine   and the anticancer agent imatinib, using S. cerevisiae as an eukaryotic model. In a similar perspective, toxicoproteomics has also been used to unveil the mechanisms of phenol toxicity in Pseudomonas putida. The adaptive response to organic pollutants of plants of thePhragmites genera, widely used in phytoremediation wetlands, is also under analysis, with the objective of optimizing their use and designing more robust plant strains. This study is being carried out in collaboration with ENVERG, IBB/CEBQ, IST.

3. Stem cell Proteomics

Proteomic profiling of human adult stem cells is being used to uncover and further define signaling pathways and molecular mechanisms involved in the maintenance of the undifferentiated state, as well as their multilineage differentiation ability. Since it is known that during time in culture, MSCs partially lose their proliferative potential, quantitative proteomics was applied to get insights into this phenomenon by studying the dynamic and complex behavior of cells throughout several culture passages. The final goal of this research program, carried out in collaboration with the BERG, IBB/CEBQ, IST, is to understand how the ex-vivo culture process affects MSC expansion at the proteome level, with implications in terms of the potential clinical use of the ex-vivo expanded cells in therapeutic procedures.


Selected Publications

- Madeira, A., dos Santos, A.C., Santos, P.M., Coutinho, C.P., Tyrrell, J., McClean, S., Callaghan, M., Sá-Correia, I., Proteomic profiling of Burkholderia cenocepacia clonal isolates with different virulence potential retrieved from a cystic fibrosis patient during chronic lung infection, PLOS ONE 8(12): e83065, 2013.

- dos Santos, S.C., Mira, N.P., Moreira, A.S., Sá-Correia, I., Quantitative- and phospho-proteomic analysis of the yeast response to the tyrosine kinase inhibitor imatinib. OMICS: A Journal of Integrative Biology, 16: 537-51, 2012.

- Guerreiro, J., Mira, N.P., Sá-Correia, I., "Adaptive response to acetic acid in the highly resistant species Zygosaccharomyces bailii revealed by quantitative proteomics", PROTEOMICS, 12: 2303-18, 2012.

- Madeira, A., da Silva, C.L, dos Santos, F., Camafeita, E., Cabral, J.M.S., Sá-Correia, I., "Human Mesenchymal Stem Cell Expression program upon extended ex-vivo cultivation as revealed by 2-DE-Based quantitative proteomics", PLOS One, 7(8), 2012.

- Roma-Rodrigues, C., Santos, P.M., Benndorf, D., Rapp, E., Sá-Correia, I., "Response of Pseudomonas putida KT2440 to phenol at the level of membrane proteome", Journal of Proteomics, 73(8): 1461-1478, 2010.

- Sá-Correia, I., Teixeira, M.C., "Two-dimensional Electrophoresis-based Expression Proteomics: a microbiologist's perspective", Expert Reviews of Proteomics, 7(6), 943-953, 2010.