Bioenergetics and Proteomics group Group leader: Ana Melo Main Interests The group leader is skilled in bacterial biochemistry and bioenergetics, and in molecular biology. Our main goal is the study of bioenergetics pathways in prokaryotes. Special attention is given to the aerobic respiratory chains and the supramolecular organization of its components. In addition we are focused in the characterization of ion and metabolite transporters in the cytosolic membranes, namely Na+/H+ antiporters. In parallel, plant proteomics applied to the study of compartment modifications in response to stress in Coffea sp. and in Casuarina glauca is performed. In ascending order: Sara, Ana, Pedro and Filipe.
Ongoing projects Characterization of supramolecular organization in the respiratory chain of prokaryotes Study of Na+ transport in Neisseria meningitidis Proteomic characterization of Coffea sp. chloroplasts in response to abiotic stresses Role of defense‐related genes during the establishment of root‐nodule symbioses between higher plants and nitrogen‐fixing bacteria Group members: Filipe Santos, Masters student http://www2.iict.pt/index.php?idc=43&idi=15793 Study of Escherichia coli respiratory chain supercomplexes Pedro Sousa, PhD student http://www2.iict.pt/index.php?idc=43&idi=13870 Characterization of supramolecular organization in the respiratory chain of prokaryotes Sara Silva, Research fellowship http://www2.iict.pt/index.php?idc=43&idi=13871 Study of Na+/H+ antiporters in Neisseria meningitidis External Collaborations: Christopher Tang Imperial Colleage of London Deborah Penque Instituto Nacional de Saúde Ricardo Jorge Egbert Boekema University of Groningen James Moir University of York Julia Steuber University of Hohenheim Lígia Saraiva Instituto de Tecnologia Química e Biológica Miguel Teixeira Instituto de Tecnologia Química e Biológica Thomas Conrads University of Pittsburg 1
Internal Collaborations: Ana Ribeiro http://www2.iict.pt/index.php?idc=43&idi=11013 José Ramalho http://www2.iict.pt/index.php?idc=43&idi=11108 Luís Goulão http://www2.iict.pt/index.php?idc=43&idi=15479 Actual appointments 1. Investigadora auxiliar Tropical Research Institute (started at 2008) 2. Professora auxiliar Lusofona University (started at 2001) List of Publications 1. Melo, A. M. P., Tom H. Roberts, and Ian M. Moller (1996) “Evidence for the presence of two rotenone‐insensitive NAD(P)H dehydrogenases on the inner surface of the inner membrane of potato tuber mitochondria”. Biochim. Biophys. Acta 1276, 133‐139. 2. Melo, A. M. P., Margarida Duarte, and Videira Arnaldo Duarte (1999) “Primary structure and characterisation of a 64 kDa NADH dehydrogenase from Neurospora crassa”. Biochim. Biophys. Acta 1412, 282‐287. 3. Fátima Ferreirinha, Margarida Duarte, Ana M. P. Melo, and Arnaldo Videira. (1999) “Effects of disrupting the 21 kDa subunit of complex I from Neurospora crassa”. Biochem. J. 342, 551‐554. 4. Teresa Almeida, Margarida Duarte, Melo, A. M. P., and Arnaldo Videira. (1999) “The 24‐kDa iron‐
sulphur subunit of complex I is required for enzyme activity”. Eur. J. Biochem. 265, 86‐92. 5. Melo, A. M. P., Duarte, M., Moller, I. M., Prokisch, H., Dolan, P., Pinto, L., Nelson, M., and Videira, A. (2001) “The external calcium‐dependent NADPH dehydrogenase from Neurospora crassa mitochondria”. J. Biol. Chem. 276(6): 3947‐51. 6. Pereira, M. M., Jones, K.L., Campos, M. G., Melo, A. M. P., Saraiva, L. M., Louro, R. O., Wittung‐
Stafshede, P. and Teixeira, M. (2002) “A ferredoxin from the thermohalophilic bacterium Rhodothermus marinus”. Biochim. Biophys. Acta 1601 (1) 1‐8 7. Pereira, M. M., Bandeiras, T. M., Fernandes, A. S., Lemos, R. S., Melo, A. M. P. and Teixeira, M. (2004) “Respiratory chains from aerobic thermophilic prokaryotes” J. Bioenerg. Biomembr. 36 (1) 93‐
105 8. Melo, A. M. P., Bandeiras, T. M., Teixeira, M. “New insights into type II NAD(P)H:quinone oxidoreductases”. (2004) Microbiol. Mol. Biol. Rev. 68(4):603‐16 9. Srinivasan, V., Rajendran, C., Sousa, F. L., Melo, A. M. P., Saraiva, L. M., Pereira, M. M., Santana, M., Teixeira, M., Michel, H. “Structure at 1.3 A resolution of Rhodothermus marinus caa3 cytochrome c domain”. (2005) J Mol Biol. 345 (5):1047‐57. 10. Ana M. P. Melo, Susana A. L. Lobo, Filipa L. Sousa, Andreia S. Fernandes, Manuela M. Pereira, Gudmundur O. Hreggvidsson, Jacob K. Kristjansson, Lígia M. Saraiva, and Miguel Teixeira (2005) “A nhaD Na+/H+ antiporter and a pcd homologues are among the Rhodothermus marinus complex I genes”. Biochim. Biophys. Acta, 1709 (1):95‐103. 11. Ana M. P. Melo, Nuno A. M. Felix, João N. Carita, Lígia M. Saraiva, and Miguel Teixeira (2006) “The Na+/H+ antiporter of the thermohalophilic bacterium Rhodothermus marinus ” Biochem. Biophys. Res. Commun. 348: 1011–1017. 12. Susana A. L. Lobo, Ana M. P. Melo, João N. Carita, Miguel Teixeira, and Lígia M. Saraiva (2007) “The anaerobe Desulfovibrio desulfuricans ATCC 27774 grows under atmospheric oxygen levels”. FEBS letters, 581: 433‐436. 13. Andreia F. Veríssimo, Manuela M. Pereira, Ana M. P. Melo, Gudmundur O. Hreggvidsson, Jakop Kr. Kristjansson and Miguel Teixeira “A ba(3) oxygen reductase from the thermohalophilic bacterium Rhodothermus marinus”. FEMS letters 269: 41‐47. 14. Meike Stelter, Ana M. P. Melo, Lígia M. Saraiva, Miguel Teixeira, and Margarida Archer (2007) "Crystallization and X‐ray analysis of Rhodothermus marinus cytochrome c at 1.3 Å resolution" Protein & Peptide Letters 14: 1038‐1040. 15. Tim W. Overton, Marta C. Justino, Ying Li, Joana M. Baptista, Ana MP Melo, Jeffrey A. Cole and Lígia M. Saraiva “Widespread distribution in pathogenic bacteria of di‐iron proteins that repair oxidative and nitrosative damage to iron‐sulfur centers.”(2008) J. Bacteriol. 190(6):2004‐13. 16. Ana MP Melo, Meike Stelter, Manuela M. Pereira, Cláudio M. Gomes, Gudmundur O. Hreggvidsson, Sigridur Hjorleifsdottir, Lígia M. Saraiva, Miguel Teixeira, and Margarida Archer “A novel type of monoheme cytochrome c:biochemical and structural characterization at 1.23 A resolution of Rhodothermus marinus cytochrome c”(2008) Biochemistry, 47 (46):11953‐63. 17. Ana Filipa N. Tavares, Lígia S. Nobre, Ana MP Melo, and Lígia M. Saraiva “A novel nitroreductase ofStaphylococcus aureus with S‐nitrosoglutathione reductase activity.”(2009) J. Bacteriol. 191 (10) 3403‐6. 18. Ana MP Melo, Meike Stelter, Gudmundur O. Hreggvidsson, Sigridur Hjorleifsdottir, Lígia M. Saraiva, Miguel Teixeira, and Margarida Archer “Structure at 1.0 A resolution of a high‐potential iron‐
sulfur protein involved in the aerobic respiratory chain of Rhodothermus marinus.”(2010) J. Biol. Inorg. Chem. 15(3):303‐13. 19. Pedro M. F. Sousa, Sara T. N. Silva, Brian L. Hood, Nuno Charro, João N. Carita, Fátima Vaz, Deborah Penque, Thomas P. Conrads and Ana MP Melo “Supramolecular organizations in the aerobic respiratory chain of Escherichia coli.” (2010) Biochimie DOI: 10.1016/j.biochi.2010.10.014 (in press). 3
CURRICULUM VITAE Name: Ana Margarida Nunes Portugal Carvalho Melo Birthplace and Birthdate: Moçambique, Lourenço Marques, 16th of June, 1972 Nacionality: Portuguese Address: R António Lopes Ribeiro, nº9, 3ºA. 1750‐313 Lisboa Phone number: 919469442 e‐mail: [email protected] ID: 9883904 Academic Degrees: 2001 PhD in Biomedical Sciencies, by Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal. 1995 Applied Plant Biologist, by Faculdade de Ciências, Universidade de Lisboa, Portugal. Scientific activities: 2008 ‐ Auxiliary researcher at Institute for Scientific and Tropical Research (IICT), Ecophysiology, Biochemistry and Plant Biotechnology Center. 2004/2007 – Post‐doctoral fellow at Instituto de Tecnologia Química e Biológica, Grupo de Metaloproteínas e Bioenergética “Study of the aerobic respiratory chain of sulfate reducing bacteria”. Supervisor: Miguel Teixeira. 2001/2004 Post‐doctoral fellow at Instituto de Tecnologia Química e Biológica, Grupo de Metaloproteínas e Bioenergética “New respiratory chain complexes in prokaryotes”. Supervisor: Miguel Teixeira. 1996/2000 PhD student at Instituto de Ciências Biomédicas de Abel Salazar/ Instituto de Biologia Molecular e Celular (Universidade do Porto) “Characterisation of NAD(P)H dehydrogenases from Neurospora crassa mitochondria”. Supervisor: Arnaldo Videira; Co‐Supervisor: Ian Max Moller. 1995 5th year project: “The use of inhibitors to distinguish between different NAD(P)H dehydrogenases on the inner surface of the inner membrane of potato (Solanum tuberosum, L.) tuber mitochondria” na Section of Plant Physiology of Lund University, Sweden; Orientador: Prof. Ian Max Moller; Co‐Orientador: Thomas Hugh Roberts. Classificação “Passed with distinction”. Projects developed in foreign laboratories 2004 “Heterologous expression of the HiPIP:oxygen oxidoreductase (caa3) from the respiratory chain of Rhodothermus marinus in Paracoccus denitrificans” at Free University, Amesterdam, The Netherlands, in collaboration with Rob van Spanning (1 month). 1999 “Topology and import of p64 from Neurospora crassa” at Institut für Physiologische Chemie der Universität München, Germany, in collaboration with Holger Prokisch and Walter Neupert. (3 months). Courses: 2007 EMBO practical course on image processing for cryo‐electron microscopy. 10‐20 September 2007, Birkbeck College, London, United Kingdom. 2007 Masterclass in Systems approaches to membrane proteins, sponsored by EMBN‐Train, MPSi & E‐MeP‐Lab, 2‐9/3, Leeds University, United Kingdom. 2000 FEBS Advanced Course 2000‐03 on “Expression and regulation of mitochondrial oxidative phosphorylation and disorders in human pathology”, Bari, Italy, 5th‐11th of March. 1993 Erasmus Summer course ‐ “Physiological Ecology of Algae”. Laboratoire de Biologie Maritime, Concarneau ‐ Université de Brest, France. Lecturer activities: 2001 – Auxiliary Professor of Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal – Bioenergetics; Enzymology; Histology; Molecular and Cellular Biology. 2003 – 2006 ITQB PhD Program in Chemical and Biological Sciences:“Sedimentation methods” and “Enzymatic manipulation of nucleic acids” Orientation of students 2010‐ Masters thesis. Filipe Santos “Characterization of the supercomplexes from the aerobic respiratory chains of Escherichia coli” 2009‐ PhD Grant. Pedro Miguel Ferreira Assis de Sousa “Identification and characterization of the supercomplexes from the aerobic respiratory chains of Escherichia coli K12 and Bacillus subtilis 168”. 2009‐ Research Grant (BI). Sara Teresa Neves da Silva “Identification and characterization of the supercomplexes from the aerobic respiratory chains of Escherichia coli K12 and Bacillus subtilis 168” 2009‐2010 Research Initiation Grant (BII). Filipe Santos "Characterization of supramolecular organizations in Escherichia coli respiratory chain". 2008‐09 Research Initiation Grant (BII). Levi Redondo Bolacha "In vitro study of supramolecular organizations in Escherichia coli respiratory chain". 2007‐08 5th year project of Biology by Universidade Lusófona de Humanidades e Tecnologias of Pedro Miguel Ferreira Assis de Sousa. “Study of supercomplexes from the Escherichia coli aerobic respiratory chain”. 5th year project of Biology by Universidade Lusófona de Humanidades e Tecnologias of Sara Teresa Neves da Silva. “Study of a Rhodothermus marinus Na+/H+ antiporter”. 5
2005 5th year project of Biotechnological Engineering by Universidade Lusófona de Humanidades e Tecnologias, of Nuno Alexandre Miranda Félix. “Heterologous expression of Rhodothermus marinus proteins”. 2004‐2005 5th year project of Biology by Universidade Lusófona de Humanidades e Tecnologias of Joana Palma Marques. “Oxygen metabolism in Desulfovibrio species”. 2003‐2004 5th year project of Biology by Universidade Lusófona de Humanidades e Tecnologias of Susana André Lima Lobo. “Molecular Biology and Biochemistry of Metalloproteins” Juris 11th of July 2009 – PhD thesis in Biochemistry of Susana André Lima Lobo, by Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa 15th of July, 2008 – PhD thesis in Biochemistry of Nelson Alexandre da Cruz Soares, by Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa 18th of July, 2005 – PhD thesis in Biology of Isabel Margarida Ribeiro Lima e Carmo Pedro, by Faculdade de Ciências da Universidade de Lisboa – Opponent. Participation in projects: PTDC/BIA‐PRO/67105/2006 coordinator PTDC/AGR‐AAM/64078/2006 team member PPCDT/BIA‐PRO/58608/2004 member of team PPCDT/QUI/59824/2004 member of team PBIC/C/BIO/2000/95 member of team Publications: Thesis 2001 PhD thesis “Characterisation of NAD(P)H dehydrogenases from Neurospora crassa mitochondria”. Peer reviewed articles 1. Melo, A. M. P., Tom H. Roberts, and Ian M. Moller (1996) “Evidence for the presence of two rotenone‐insensitive NAD(P)H dehydrogenases on the inner surface of the inner membrane of potato tuber mitochondria”. Biochim. Biophys. Acta 1276, 133‐139. 2. Melo, A. M. P., Margarida Duarte, and Videira Arnaldo Duarte. (1999) “Primary structure and characterisation of a 64 kDa NADH dehydrogenase from Neurospora crassa”. Biochim. Biophys. Acta 1412, 282‐287. 3. Fátima Ferreirinha, Margarida Duarte, Ana M. P. Melo, and Arnaldo Videira. (1999) “Effects of disrupting the 21 kDa subunit of complex I from Neurospora crassa”. Biochem. J. 342, 551‐554. 4. Teresa Almeida, Margarida Duarte, Melo, A. M. P., and Arnaldo Videira. (1999) “The 24‐kDa iron‐
sulphur subunit of complex I is required for enzyme activity”. Eur. J. Biochem. 265, 86‐92. 5. Melo, A. M. P., Duarte, M., Moller, I. M., Prokisch, H., Dolan, P., Pinto, L., Nelson, M., and Videira, A. (2001) “The external calcium‐dependent NADPH dehydrogenase from Neurospora crassa mitochondria”. J. Biol. Chem. 276(6): 3947‐51. 6. Pereira, M. M., Jones, K.L., Campos, M. G., Melo, A. M. P., Saraiva, L. M., Louro, R. O., Wittung‐
Stafshede, P. and Teixeira, M. (2002) “A ferredoxin from the thermohalophilic bacterium Rhodothermus marinus”. Biochim. Biophys. Acta 1601 (1) 1‐8 7. Pereira, M. M., Bandeiras, T. M., Fernandes, A. S., Lemos, R. S., Melo, A. M. P. and Teixeira, M. (2004) “Respiratory chains from aerobic thermophilic prokaryotes” J. Bioenerg. Biomembr. 36 (1) 93‐
105 8. Melo, A. M. P., Bandeiras, T. M., Teixeira, M. “New insights into type II NAD(P)H:quinone oxidoreductases”. (2004) Microbiol. Mol. Biol. Rev. 68(4):603‐16 9. Srinivasan, V., Rajendran, C., Sousa, F. L., Melo, A. M. P., Saraiva, L. M., Pereira, M. M., Santana, M., Teixeira, M., Michel, H. “Structure at 1.3 A resolution of Rhodothermus marinus caa3 cytochrome c domain”. (2005) J Mol Biol. 345 (5):1047‐57. 10. Ana M. P. Melo, Susana A. L. Lobo, Filipa L. Sousa, Andreia S. Fernandes, Manuela M. Pereira, Gudmundur O. Hreggvidsson, Jacob K. Kristjansson, Lígia M. Saraiva, and Miguel Teixeira (2005) “A nhaD Na+/H+ antiporter and a pcd homologues are among the Rhodothermus marinus complex I genes”. Biochim. Biophys. Acta, 1709 (1):95‐103. 11. Ana M. P. Melo, Nuno A. M. Felix, João N. Carita, Lígia M. Saraiva, and Miguel Teixeira (2006) “The Na+/H+ antiporter of the thermohalophilic bacterium Rhodothermus marinus ” Biochem. Biophys. Res. Commun. 348: 1011–1017. 12. Susana A. L. Lobo, Ana M. P. Melo, João N. Carita, Miguel Teixeira, and Lígia M. Saraiva (2007) “The anaerobe Desulfovibrio desulfuricans ATCC 27774 grows under atmospheric oxygen levels”. FEBS letters, 581: 433‐436. 13. Andreia F. Veríssimo, Manuela M. Pereira, Ana M. P. Melo, Gudmundur O. Hreggvidsson, Jakop Kr. Kristjansson and Miguel Teixeira “A ba(3) oxygen reductase from the thermohalophilic bacterium Rhodothermus marinus”. FEMS letters 269: 41‐47. 7
14. Meike Stelter, Ana M. P. Melo, Lígia M. Saraiva, Miguel Teixeira, and Margarida Archer (2007) "Crystallization and X‐ray analysis of Rhodothermus marinus cytochrome c at 1.3 Å resolution" Protein & Peptide Letters 14: 1038‐1040. 15. Tim W. Overton, Marta C. Justino, Ying Li, Joana M. Baptista, Ana M. P. Melo, Jeffrey A. Cole and Lígia M. Saraiva (2008) “Widespread distribution in pathogenic bacteria of di‐iron proteins that repair oxidative and nitrosative damage to iron‐sulfur centers” J. Bacteriol. 190(6):2004‐13. 16. Ana M.P. Melo, Meike Stelter, Manuela M. Pereira, Cláudio M. Gomes, Gudmundur O. Hreggvidsson, Sigridur Hjorleifsdottir, Lígia M. Saraiva, Miguel Teixeira, and Margarida Archer (2008) “A novel type of monoheme cytochrome c: Biochemical and structural characterization at 1.23 Å resolution of Rhodothermus marinus cytochrome c” Biochemistry, 47 (46):11953‐63. 17. Ana Filipa N. Tavares, Lígia S. Nobre, Ana M. P. Melo and Lígia M. Saraiva “A Novel Nitroreductase of Staphylococcus aureus withS‐Nitrosoglutathione Reductase Activity” (2009) J. Bacteriol. 191 (10) 3403‐6 18. Ana MP Melo, Meike Stelter, Gudmundur O. Hreggvidsson, Sigridur Hjorleifsdottir, Lígia M. Saraiva, Miguel Teixeira, and Margarida Archer “Structure at 1.0 A resolution of a high‐potential iron‐
sulfur protein involved in the aerobic respiratory chain of Rhodothermus marinus.”(2010) J. Biol. Inorg. Chem. 15(3):303‐13. 19. Pedro M. F. Sousa, Sara T. N. Silva, Brian L. Hood, Nuno Charro, João N. Carita, Fátima Vaz, Deborah Penque, Thomas P. Conrads and Ana MP Melo “Supramolecular organizations in the aerobic respiratory chain of Escherichia coli.” (2010) Biochimie DOI: 10.1016/j.biochi.2010.10.014 (in press). Oral Communications 2010 “Insights on the supercomplexes of Escherichia coli aerobic respiratory chain” 24th October, Hohenheim University, Germany 2009 "O mosquito: da Biologia ao homem" 3ª Sessão Pública do Grupo Comunitário da Alta de Lisboa. 25th of June at Colégio de S. João de Brito, Lisboa, Portugal. 2008 “Supercomplexes of Escherichia coli aerobic respiratory chain” PathProt I, 8‐10 November, Instituto Gulbenkian de Ciência, Oeiras, Portugal. 2008 "Supercomplexos da Cadeia Respiratória: Ciência Moderna num Instituto com História" 1ªs Jornadas Nacionais de Genética e Biotecnologia, 21‐23 November , University of Trás‐os‐Montes e Alto Douro, Vila Real, Portugal. 2007 EMBO practical course on image processing for cryo‐electron microscopy. 10‐20 September, Birkbeck College, London, United Kingdom. “The NhaE Antiporter of Rhodothermus marinus” 2007 “Unraveling the aerobic respiratory chain of the thermohalophilic bacterium Rhodothermus marinus” 22nd June, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal. Papers in conference proceedings 2008 15th European Bioenergetics Conference (EBEC)19th‐24th July, Dublin, Ireland. Melo, A.M.P., Sara T.N. Silva, Lígia M. Saraiva, and Miguel Teixeira "Evidence for the presence of a Na+/H+ antiporter subunit in Rhodothermus marinus complex I" Biochimica et Biophysica Acta Supplement to BBA Bioenergetics Vol. 1777 (2008) S39 2006 14th European Bioenergetics Conference (EBEC)22th‐27th July, Moscow, Russia. Melo, A.M.P., Andreia S. Fernandes, Susana A. L. Lobo, Manuela M. Pereira, Lígia M. Saraiva, and Miguel Teixeira "The NhaD antiporter from nqoB operon of Rhodothermus marinus complex I" Biochimica et Biophysica Acta EBEC Short reports Vol 14, 210 2004 13th European Bioenergetics Conference (EBEC) 21th‐26th August, Pisa, Italy. Melo, A. M. P., Andreia S. Fernandes, Susana A. L. Lobo, Manuela M. Pereira, Lígia M. Saraiva, and Miguel Teixeira "The rotenone‐sensitive NADH:menaquinone oxidoreductase from the respiratory chain of Rhodothermus marinus" Biochimica et Biophysica Acta EBEC Short reports Vol 13, 139 2004 13th European Bioenergetics Conference (EBEC) 21th‐26th August, Pisa, Italy. C. Rajendran, F.L. Sousa, V. Srinivasan, A.M.P. Melo, L.M. Saraiva, M.M. Pereira, M. Santana, M. Teixeira, H. Michel “Structure at 1.3 A resolution of the cytochrome c domain from Rhodothermus marinus caa3”. Biochimica et Biophysica Acta EBEC Short reports Vol 13, 153. 2002 12th European Bioenergetics Conference (EBEC) 10th to 15th of September, Arcachon, France. Bandeiras, T.M., Gomes, C.M., Melo, A.M.P., Kletzin, A., Teixeira, M. “Covalently‐bound FMN in archaeal type‐II NADH Dehydrogenases” Biochimica et Biophysica Acta EBEC Short reports Vol 12. 1996 9th European Bioenergetics Conference, Louvain‐la‐Neuve, Belgium, 17‐22 of August. Ana M. P. Melo, Thomas H. Roberts, Stephany Agius and Ian M. Moller. “Two rotenone‐insensitive NAD(P)H dehydrogenases on the inner surface of the inner membrane of potato tuber mitochondria”. Biochimica et Biophysica Acta EBEC Short reports Vol 9, 146. Individual grants 9
2010 – Deutscher Akademischer Austauschdienst (DAAD) Research stay fellowship – 2 months at Hohenheim University, hosted by Dr Julia Steuber (Cellular MicrobiologyLaboratory) “Functional characterization of Na+ transporters from the Neisseria meningitidis cytoplasmic membrane”.