Plant Proteins ITQB Team - Portugal

Team Members

Margarida Oliveira is Associate Professor with Aggregation at ITQB - Universidade Nova de Lisboa (UNL) since 2008. She is Biologist with PhD in Plant Biotechnology and for 23 years she was Professor at the Fac. Sciences of Univ. Lisboa (FC-UL).Since 1996 she is leading the Genomics of Plant Stress (GPlantS) Lab of ITQB. Since March 2011 she is also Vice-Director of ITQB.

Her main interests are the mechanisms that regulate plant development and adaptation to the environment and the improvement of plants with national interest.She has supervised numerous students (MSc, PhD) working in plant biotechnology and molecular biology. Her research ranges from plant growth manipulation, to the comprehension of the changes occurring as a result of development and response to the environment, in medicinal and aromatic plants, cereals, woody fruit trees, bioenergy plants and forest species.

Since 2003 she is exploring proteomic tools to understand plant adaptation and specialization. She has been involved in EU projects (including a recently approved one on the regulation of C4 photosynthesis metabolism). Margarida Oliveira is the coordinator of the Plant Proteins ITQB Team.

Ana Varela Coelho is Assistant Researcher at ITQB - Universidade Nova de Lisboa (UNL) since 2010. She is Biochemist with PhD in Biochemistry and for 13 years she was Professor at the Univ. of Évora (Portugal).Since 2002 she is leading the Mass Spectrometry (MS) Lab of ITQB as Invited Assistant Professor.

Her main interests are the improvement of mass spectrometry methodologies used for protein identification and characterization, namely in which concerns post-translational modifications and de novo sequencing of proteins. She has supervised several students (MSc, PhD) working in proteomics applications.

The mass spectrometry (MS) Laboratory is a research and service Laboratory. It is included in the ITQB/IBET Analytical Service Unit, which is certified as OCDE Good Laboratory Practice. The MS lab’s main objective is the implementation and development of MS methodologies and its applications to the study of biological systems, in particular with biotechnology and biomedical applications. To date, those methods have been used to support internal and external academic groups, studies contracted mainly with the pharmaceutical industry and research projects.

Carla Pinheiro is Auxiliary Investigator at Instituto de Tecnologia Química e Biológica (ITQB) / Universidade Nova de Lisboa (UNL) since 2008. With a PhD in Biology she has been working in plant biochemistry for more than 10 years.

Her main interests are related with single and combined stress studies and its impact on plant growth, seed development, yield and quality. Plant performance is evaluated through the traditional ecophysiology tools (water status, osmotic potential and carbon assimilation) in combination with new disciplines like proteomics and metabolomics. She has been involved in EU projects (including an ongoing project on sustainable water use securing food production and a recently approved one on the regulation of C4 photosynthesis metabolism).

Isabel Bento is an Auxiliary Researcher at ITQB since 2008. She uses an integrated structural approach to study protein function, which includes expression, purification, dynamic light scattering, fluorescence-based thermal shift assay (thermofluor), surface plasmon resonance (BiaCore), crystallization and crystal structure determination.

The aim of her work is to determine how the protein function correlates with the three-dimensional folding. Ultimately, the objective is to integrate this knowledge in terms of the biological problem addressed and within the organism under study. She has been studying a number of proteins from various organisms including plants.

Nelson Saibo is a Auxiliary researcher at the Genomics of Plant Stress (GPlantS) laboratory at ITQB. In 2003 he was award the PhD in Plant Molecular Biology by the Ghent University, Belgium, and he has over 15 years experience in plant molecular biology, with particular emphasis on signal transduction pathways.

His research interests focus on the transcriptional network regulating plant responses to environmental stimuli. He has been particularly interested on rice responses to abiotic stress, namely cold, high salinity and drought. Using advanced molecular biology techniques, his lab has already identified and characterized a number of new players involved in plant stress adaptation, thus establishing a link between specific environmental cues and developmental patterns. An integrated approach is being used to explain plant stress responses, from the identification of new players in the transcriptional network regulated by stress to the study of post-translational protein modifications (e.g. SUMOylation) and regulation of chromatin structure and epigenetic modifications. He is also involved in a FP7 EU project concerning the characterization of novel proteins involved in the regulation of C4 photosynthesis metabolism.

Isabel Pacheco is a Senior Technician at Universidade Nova de Lisboa (UNL) since 1976. She actively participated in all research projects carried out in the Group of Biochemistry and Biophysics at the Center for Structural Chemistry (1976-1989) and at ITQB (1990-2011), under guidance of Professor António Xavier.

The main objective of the work performed was the purification and physicochemical characterization of metalloproteins of sulfate reducing bacteria and methanogenic bacteria and subsequent physiological characterization. More recently, she worked on the optimization of protocols for clinical diagnosis in pathological situations involving Desulfovibrio spp.

Since 2008 she is responsible for managing high performance liquid chromatography, which is related with the utilization of other techniques, such as gas chromatography, lyophilization, dialysis, ultrafiltration, protein assays, determination of molecular weight and isoelectric point (electrophoresis), UV/visible spectroscopy, EPR spectroscopy, Warburg manometric technique, enzyme assays and amino acid sequencing.

Isabel Abreu is an Invited Researcher at the Genomics of Plant Stress (GPlantS) laboratory at ITQB. In 2002 she was award the PhD in Biochemistry by the Universidade Nova de Lisboa, Portugal, and she completed her training in Biochemistry at Brookhaven National Laboratory, New York, USA. She has joined Dr. Nam-Hai Chua’s Laboratory at Rockefeller University, New York, USA, where she has started her specialization in Plant Biochemistry studying the regulation of the cell proteome by post-translational modifications.
Her research aims at identifying and studying the mechanisms that control rapid plant-response to stress. She has been particularly interested in the regulation of the plant proteome by post-translational modification (e.g. SUMOylation) as a result of imposed water stress. Presently, she uses the model plants arabidopsis and rice to identify targets for protein-SUMOylation in response to drought stress, using proteomics. Additionally, she is characterizing the mechanisms regulating SUMOylation levels and target-discrimination by studying how transcript levels and alternative-splicing isoforms of the rice SUMOylation machinery vary upon stress. She is presently extending this study to Cork Oak by using bioinformatics tools to explore GPlantS previously obtained transcriptome-library collection (under the Portuguese Cork Oak Consortium effort).
Ultimately, Isabel’s aim is to use the obtained information to engineer increased drought-tolerance in plants and thus contribut to new rice varieties better equipped to withstand water stress.

TEAM PUBLICATIONS

Alves, M., Chicau, P., Matias, H., Passarinho, J., Pinheiro, C., and Ricardo, C.P. (2011). Metabolic analysis revealed altered amino acid profiles in Lupinus albus organs as a result of boron deficiency. Physiol Plantarum 142, 224-232.

Farinha, A.P., Irar, S., de Oliveira, E., Oliveira, M.M., and Pages, M. (2011). Novel clues on abiotic stress tolerance emerge from embryo proteome analyses of rice varieties with contrasting stress adaptation. Proteomics 11, 2389-2405.

Franco, C.F., Santos, R., and Coelho, A.V. (2011a). Exploring the proteome of an echinoderm nervous system: 2-DE of the sea star radial nerve cord and the synaptosomal membranes subproteome. Proteomics 11, 1359-1364.

Franco, C.F., Santos, R., and Coelho, A.V. (2011b). Proteome characterization of sea star coelomocytes - The innate immune effector cells of echinoderms. Proteomics. Epub date 14 July 2011.

Pinheiro, C., António, C., Ortuño, M.F., Dobrev, P.I., Hartung, W., Thomas-Oates, J., Ricardo, C.P., Vanková, R., Chaves, M.M., and Wilson, J.C. (2011). Initial water deficit effects on Lupinus albus photosynthetic performance, carbon metabolism and hormonal balance: metabolic reorganisation prior to early stress responses. J Exp Bot. doi:10.1093/jxb/err194

Ricardo, C.P., Martins, I., Francisco, R., Sergeant, K., Pinheiro, C., Campos, A., Renaut, J., and Fevereiro, P. (2011). Proteins associated with cork formation in Quercus suber L. stem tissues. J Proteomics. Epub date 16 February 2011.

Antunes, A.M.M., Godinho, A.L.A., Martins, I.L., Oliveira, M.C., Gomes, R.A., Coelho, A.V., Beland, F.A., and Marques, M.M. (2010). Protein Adducts As Prospective Biomarkers of Nevirapine Toxicity. Chem Res Toxicol 23, 1714-1725.

Batista, A.P., Franco, C., Mendes, M., Coelho, A.V., and Pereira, M.M. (2010). Subunit composition of Rhodothermus marinus respiratory complex I. Anal Biochem 407, 104-110. 

Batista, R., and Oliveira, M. (2010). Plant natural variability may affect safety assessment data. Regul Toxicol Pharm 58, S8-S12.

Campos, A., Carvajal-Vallejos, P.K., Villalobos, E., Franco, C.F., Almeida, A.M., Coelho, A.V., Torne, J.M., and Santos, M. (2010). Characterisation of Zea mays L. plastidial transglutaminase: interactions with thylakoid membrane proteins. Plant Biology 12, 708-716.

Chen, Z., Durao, P., Silva, C.S., Pereira, M.M., Todorovic, S., Hildebrandt, P., Bento, I., Lindley, P.F., and Martins, L.O. (2010). The role of Glu498 in the dioxygen reactivity of CotA-laccase from Bacillus subtilis. Dalton Trans 39, 2875-2882.

de Sanctis, D., Inacio, J.M., Lindley, P.F., de Sa-Nogueira, I., and Bento, I. (2010). New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases. Febs J 277, 4562-4574.

Lamy, E., Graca, G., da Costa, G., Franco, C., Silva, F.C.E., Baptista, E.S., and Coelho, A.V. (2010). Changes in mouse whole saliva soluble proteome induced by tannin-enriched diet. Proteome Sci 8. Epub date 15 December 2010.

Campos, A., da Costa, G., Coelho, A.V., and Fevereiro, P. (2009). Identification of bacterial protein markers and enolase as a plant response protein in the infection of Olea europaea subsp europaea by Pseudomonas savastanoi pv. savastanoi. Eur J Plant Pathol 125, 603-616.

Fonseca, B.M., Saraiva, I.H., Paquete, C.M., Soares, C.M., Pacheco, I., Salgueiro, C.A., and Louro, R.O. (2009). The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes. J Biol Inorg Chem 14, 375-385.

Saibo, N.J.M., Lourenco, T., and Oliveira, M.M. (2009). Transcription factors and regulation of photosynthetic and related metabolism under environmental stresses. Ann Bot-London 103, 609-623.

Sergeant, K., Pinheiro, C., Hausman, J.F., Ricardo, C.P., and Renaut, J. (2009). Taking Advantage of Nonspecific Trypsin Cleavages for the Identification of Seed Storage Proteins in Cereals. J Proteome Res 8, 3182-3190.

Abreu, I.A., An, H., Hearn, A., Nick, H.S., Silverman, D.N., Cabelli, D.E. (2008). The kinetic mechanism of manganese-containing superoxide dismutase from Deinococcus radiodurans: a specialized enzyme for the elimination of high superoxide concentrations. Biochemistry 47,2350-2356.

Batista, R., Saibo, N., Lourenco, T., and Oliveira, M.M. (2008). Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proc Natl Acad Sci USA 105, 3640-3645.

De Lacey, A.L., Gutierrez-Sanchez, C., Fernandez, V.M., Pacheco, I., and Pereira, I.A.C. (2008). FTIR spectroelectrochemical characterization of the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough.J Biol Inorg Chem 13, 1315-1320.

Batista, R., Martins, I., Jenoe, P., Ricardo, C.P., and Oliveira, M.M. (2007). A proteomic study to identify soya allergens - The human response to transgenic versus non-transgenic soya samples. Int Arch Allergy Imm 144, 29-38.

Catala, R., Ouyang, J., Abreu, I.A., Hu, Y., Seo, H., Zhang, X., Chua, N.-H. (2007). The Arabidopsis E3 Sumo ligase Siz1 regulates plant development and drought responses. Plant Cell 19,2952-2966.

Goncalves, S., Cairney, J., Rodriguez, M.P., Canovas, F., Oliveira, M., and Miguel, C. (2007). PpRab1, a Rab GTPase from maritime pine is differentially expressed during embryogenesis. Mol Genet Genomics 278, 273-282.

Saibo, N.J., Vriezen, W.H., De Grauwe, L., Azmi, A., Prinsen, E., and Van der Straeten, D. (2007). A comparative analysis of the Arabidopsis mutant amp1-1 and a novel weak amp1 allele reveals new functions of the AMP1 protein. Planta 225, 831-842.

Guy, J., Abreu, I.A., Moche, M., Lindqvist, Y., Whittle, E., Shanklin, J. (2006). A single mutation in the castor D9-18:0-desaturase changes partitioning between reaction chemistries, from desaturation to oxidase chemistry. Proc. Nat. Acad. Sci. 103,17220-17224.

Valente, F.A.A., Almeida, C.C., Pacheco, I., Carita, J., Saraiva, L.M., and Pereira, I.A.C. (2006). Selenium is involved in regulation of periplasmic hydrogenase gene expression in Desulfovibrio vulgaris Hildenborough. J Bacteriol 188, 3228-3235

Batista, R., Nunes, B., Carmo, M., Cardoso, C., Jose, H.S., de Almeida, A.B., Manique, A., Bento, L., Ricardo, C.P., and Oliveira, M.M. (2005). Lack of detectable allergenicity of transgenic maize and soya samples.J Allergy Clin Immun 116, 403-410.

Bento, I., Martins, L.O., Gato Lopes, G., Armenia Carrondo, M., and Lindley, P.F. (2005). Dioxygen reduction by multi-copper oxidases; a structural perspective. Dalton Trans, 3507-3513.

Pinheiro, C., Rodrigues, A.P., de Carvalho, I.S., Chaves, M.M., and Ricardo, C.P. (2005). Sugar metabolism in developing lupin seeds is affected by a short-term water deficit. J Exp Bot 56, 2705-2712.

Rodriguez, J.A., Abreu, I.A. (2005). Chemical activity of iron in [2Fe-2S]-protein centers and FeS2(100) surfaces. J. Phys. Chem. B. 109,2754-2762.

Price, N.J., Pinheiro, C., Soares, C.M., Ashford, D.A., Ricardo, C.P., and Jackson, P.A. (2003). A biochemical and molecular characterization of LEP1, an extensin peroxidase from lupin. J Biol Chem 278, 41389-41399.

Saibo, N.J.M., Vriezen, W.H., Beemster, G.T.S., and Van der Straeten, D. (2003). Growth and stomata development of Arabidopsis hypocotyls are controlled by gibberellins and modulated by ethylene and auxins. Plant J 33, 989-1000.

Pinheiro, C., Chaves, M.M., and Ricardo, C.P. (2001). Alterations in carbon and nitrogen metabolism induced by water deficit in the stems and leaves of Lupinus albus L. J Exp Bot 52, 1063-1070.

Frazao, C., Bento, I., Costa, J., Soares, C.M., Verissimo, P., Faro, C., Pires, E., Cooper, J., and Carrondo, M.A. (1999). Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp-containing aspartic proteinase from the flowers of Cynara cardunculus L. J Biol Chem 274, 27694-27701.