Nuno Pereira Mira

POSITION: Assistant Professor

Leader of the Research Theme: Yeast-based synthetic biology

E-mail: nuno.mira@mail.ist.utl.pt

Research Topics

  • Pathway prospecting to implement new-to-nature biochemical pathways for the production of organic acids and relevant derivatives
  • Fostering the utilization of Yeasts (Saccharomyces cerevisiae and other Non-Saccharomyces species) as microbial cell factories by exploring insights gathered from the biology and physiology of these species
  • Implementation and development of computational metabolic modeling approaches to boost the engineering of more robust microbial catalysts
  • Engineering of mixed starter cultures composed of cerevisiae and non-Saccharomyces species to boost biotechnological applications

Research Team

  • Sara Barbosa Salazar, PhD student
  • Ana Vila Santa, PhD student (co-supervised by Frederico Ferreira-IBB and Kristala Prather- MIT)
  • Nuno Pedro, PhD student
  • Maria João Tavares, PhD student
  • Tiago Brito, MsC student
  • Rita Simões, MsC student
  • Fernão Mendes, MsC student
  • Inês Fonseca, MsC student
  • Catarina Lima, MsC student
  • João Lucas, MsC student

Education

  • Ph.D. in Biotechnology, IST, UTL, 2008
  • Graduation in Chemistry-Biochemistry Profile, IST, UTL, Lisbon, Portugal, 2004

Positions

  • Assistant Professor, DBE, IST, University of Lisbon, 2011 – present
  • Post-Doc Researcher, IBB/CEBQ/BSRG, IST, 2008 – 2011

Selected Publications

Seixas I, Barbosa C, Mendes-Faia A, Güldener U, Tenreiro R, Mendes-Ferreira A*and Mira NP*, Genome sequence of the non-conventional wine yeast Hanseniaspora guilliermondiiUTAD222 unveils relevant traits of this species and of the Hanseniaspora genus in the context of wine fermentation, DNA Research, (2018)(in press)

Tavares MJ, Ulrich G, Esteves M, Mendes-Faia A, Mendes-Ferreira A and Mira NP, “Genome sequence of the wine yeast Saccharomycodes ludwigiiUTAD17”, Genome Announcements,(2018) 

Salazar SB, Wang C, Munsterkotter M, Okamoto M, Takahashi-Nakaguchi A, Chibana H, Lopes MM, Guldener U, Butler G and Mira NP, Comparative genomic and transcriptomic analyses unveil novel features of azole resistance and adaptation to the human host in Candida glabrataFEMS Yeast Res, 18(1), (2018)

Cardoso JMS, Guerreiro SI, Lourenço A, Alves MM, Montemor MF, Mira NP*, Leitão JH* and Carvalho MFNN*, Ag(I) camphorimine complexes with antimicrobial activity towards clinically important bacteria and species of the Candida genus, PLoS One, 9;12(5):e0177355, (2017)(*corresponding co-authors)

Cunha D*, Salazar B*, Lopes MM and Mira NP, Mechanistic insights underlying tolerance to acetic acid stress in vaginal Candida glabrata isolates, Frontiers in Microbiology, 8:259 (2017)

Bernardo R, Cunha DV, Wang C, Pereira L, Silva S, Salazar SB, Schroeder MS, Okamoto M, Takahashi-Nakaguchi A, Chibana H, Aoyoama T, Sá-Correia I, Azeredo J, Butler G and Mira NP, The CgHaa1-regulon mediates response and tolerance to acetic acid stress in the human pathogen Candida glabrata, G3: Genes, Genomes and Genetics, 7: 1-18, (2017)

All Papers, Book Chapters and Patents

See all

Thesis

2008: PhD thesis in Biotechnology “Adaptation to weak acid food preservatives in Saccharomyces cerevisiae: the Haa1 and Rim101 signalling pathways"

Edition of books

Sá-Correia, M.C. Teixeira, N.P. Mira, “Book of Abstracts – PYFF6 – 6th Conference on Physiology of Yeasts and Filamentous Fungi", 2016 (ISBN: 978-989-20-6736-0)

Book Chapters

N.P. Mira, M.C. Teixeira, I. Sá-Correia, “Characterization of complex regulatory networks and identification of promoter regulatory elements in yeast: in silico and wet-lab", In: Methods in Molecular Biology – Transcriptional Regulation: Methods and Protocols (Vancura A., Ed), Springer, vol. 809, 27-48, 2012.

Papers in international journals

Marques L, Alves MM, Eugénio S, Salazar SB, Pedro N, Grenho L, Mira NP, Fernandes MH and Montemor MF, Potential anti-cancer and anti-Candidaactivity of Zn-derived foams, Journal of Materials Chemistry B, 6, 2821-2830, (2018)

Alves MM, Marques LM, Nogueira I, Santos CF, Salazar SB, Eugénio S, Mira NP and Montemor F, In silico, in vitro and antifungal activity of the surface layers formed on zinc upon this biomaterial degradation, Applied Surface Science, (2018)(in press)

Alves MM, Cunha DV, Santos CF, Mira NP and Montemor F, Microstructured ZnO-rod like coating prevents biofilm formation prompted by pathogenic Candida spp, Ceramics International, 44(4), 4467-4472, 2018

Salazar SB, Wang C, Munsterkotter M, Okamoto M, Takahashi-Nakaguchi A, Chibana H, Lopes MM, Guldener U, Butler G and Mira NP, Comparative genomic and transcriptomic analyses unveil novel features of azole resistance and adaptation to the human host in Candida glabrata, FEMS Yeast Res, 18(1), (2018)

Guerreiro J*, Mira NP*, Santos AXS, Riezman H and Sá-Correia I, Membrane phosphoproteomics of yeast early response to acetic acid: role of Hrk1 kinase and lipid biosynthetic pathways, in particular sphingolipids, Frontiers in Microbiology, 8:1302, 2017(* co-first authors)

Cardoso JMS, Guerreiro SI, Lourenço A, Alves MM, Montemor MF, Mira NP*, Leitão JH* and Carvalho MFNN*, Ag(I) camphorimine complexes with antimicrobial activity towards clinically important bacteria and species of the Candida genus, PLoS One, 9;12(5):e0177355, (2017) (*corresponding co-authors)

Henriques SF, Mira NP, Sá-Correia I, Genome-wide search for candidate genes for yeast robustness improvement against formic acid reveals novel susceptibility (Trk1 and positive regulators) and resistance (Haa1-regulon) determinants, Biotechnology for Biofuels, 10:96, (2017)

Godinho C, Mira NP, Cabrito TR, Teixeira MC, Alasoo K, Guerreiro JF and Sá-Correia I, Yeast response and tolerance to benzoic acid involves the Gcn4- and Stp1- regulated multidrug/multixenobiotic resistance transporter Tpo1, Applied Microbiology and Biotechnology, 8:259 (2017)

Cunha, D.*, Salazar, B.*, Lopes, M.M., Mira, N.P., Mechanistic insights underlying tolerance to acetic acid stress in vaginal Candida glabrata isolates, Frontiers in Microbiology, 8:259, 2017. (*co-first authors)

Seixas, I., Barbosa, C., Salazar, S.B., Mendes-Faia, A., Wang, Y., Guldener, U., Mendes-Ferreira, A.*, Mira, N.P.*, Genome sequence of the non-conventional yeast Hanseniaspora guilliermondii UTAD222, Genome Announcements, 5(5) e01515-16, 2017. (* co-corresponding authors)

Bernardo, R., Cunha, D.V., Wang, C., Pereira, L., Silva, S., Salazar, S.B., Schroeder, M.S., Okamoto, M., Takahashi-Nakaguchi, A., Chibana, H., Aoyoama, T., Sá-Correia, I., Azeredo, J., Butler, G., Mira, N.P., “The CgHaa1-regulon mediates response and tolerance to acetic acid stress in the human pathogen Candida glabrata"G3: Genes, Genomes and Genetics,7(1):1-18, 2017.

Santos, R., Costa, C., Mil-Homens, D., Romão, D., de Carvalho, C.C.R., Pais, P., Mira, N.P., Fialho, A.M., Teixeira, M.C.,  The multidrug resistance transporters CgTpo1_1 and CgTpo1_2 play a role in virulence and biofilm formation in the human pathogen Candida glabrata“, Cellular Microbiology, doi: 10.1111/cmi.12686, in press.

Alves, M.M., Cunha, D.V., Santos, C.F., Mira, N.P., Montemor, M.F., “In vitro corrosion behaviour and anti-Candida spp. activity of Zn coated with ZnO-nanostructured ‘Anastacia’ flowers", J Mat. Chem. B, 4:4754, 2016.

Palma, P., Roque, F.C., Guerreiro, J., Mira, N.P., Queiroz, L., Sá-Correia, I., “Search for genes responsible for the remarkably high acetic acid tolerance of a Zygosaccharomyces bailii-derived interspecies hybrid strain", BMC Genomics, 16:1070, 2015.

Barbosa, C., Mendes-Faia, A., Lage, P., Mira, N.P., Mendes-Ferreira, A., “Genomic expression program of Saccharomyces cerevisiae along a mixed-culture wine fermentation with Hanseniaspora guilliermondii“. Microb Cell Fact. 14(1):124, 2015.

Trček J, Mira NP, Jarboe LR. Adaptation and tolerance of bacteria against acetic acid. Appl Microbiol Biotechnol. 99(15):6215-29, 2015.

Pereira, F.B., Teixeira, M.C., Mira, N.P., Sá-Correia, I., Domingues, L., “Genome-wide screening of Saccharomyces cerevisiae genes required to foster tolerance towards industrial wheat straw hydrolysates", Journal of Industrial Microbiology & Biotechnology, 41: 1753-61, 2014.

Costa, C., Nunes, J., Henriques, A., Mira, N.P., Nakayama, H., Chibana, H., Teixeira, M.C., The Candida glabrata drug:H+ antiporter CgTpo3 (ORF CAGL0I10384g): role in azole drug resistance and polyamine homeostasis, Journal of Antimicrobial Chemotherapy, 69:1767-76, 2014.

Mira, N.P., Münsterkötter, M., Dias-Valada, F., Santos, J., Palma, M., Roque, F., Guerreiro, J., Rodrigues, F., Sousa, M.J., Leão, C., Guldener, U., Sá-Correia, I., The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant, DNA Research, 21(3):299-313, 2014.

Rodrigues, R.M.M., de Carvalho, J., Henriques, S.F., Mira, N.P., Sá-Correia, I., Ferreira, G.N.M., “Transmission Line Model Analysis of Transcription Factors Binding to Oligoduplexes – Differentiation of the Effect of Single Nucleotide Modifications", Analyst, 139(16):3871-4, 2014.

de Carvalho, J., Rodrigues, R.M.M., Tomé, B., Henriques, S.F., Mira, N.P., Sá-Correia, I., Ferreira, G.N.M., Conformational and Mechanical changes of DNA upon transcription factor binding detected by a QCM and transmission line model, Analyst, 139(8):1847-55, 2014.

Teixeira, M.C., Monteiro, P.T., Guerreiro, J.F., Gonçalves, J.P., Mira, N.P., dos Santos, S.C., Cabrito, T., Palma, M., Costa, C., Francisco, A.P., Madeira, S.C., Oliveira, A.L., Freitas, A.T., Sá-Correia, I., “The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae“, Nucleic Acids Research, 42: D161-D166, 2014.

Mira, N.P., Teixeira, M.C., “Microbial mechanisms of tolerance to weak acid stress", Frontiers in Microbiology (Editorial), 4, 416, 2013.

Teixeira, M.C., Godinho, C.P., Cabrito, T.R., Mira, N.P., Sá-Correia, I., Increased expression of the yeast multidrug resistance ABC transporter Pdr18 leads to increased ethanol tolerance and ethanol production in high gravity alcoholic fermentation, Microbial Cell Factories, 11, 98, 2012.

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.F., 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.

Pereira, F.B., Guimarães, P.M.R., Gomes, D.G., Mira, N.P., Teixeira, M.C., Sá-Correia, I., Domingues, L., Identification of candidate genes for yeast engineering to improve bioethanol production in Very-High-Gravity and lignocellulosic biomass industrial fermentations. Biotechnology for Biofuels, 4, 57, 2011.

Mira, N.P., Madeira, A., Moreira, A.S., Coutinho, A.P., Sá-Correia, I., Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to the airways of cystic fibrosis patients and antimicrobial therapy . PLOS One, 6, e28831, 2011.

Coutinho, C.P., dos Santos, S.C., Madeira, A., Mira, N.P., Moreira, A.S., Sá-Correia, I., Long-term colonization of the cystic fibrosis lung by Burkholderia cepacia complex bacteria: epidemiology, clonal variation and genome-wide expression alterations. Frontiers in Cellular and Infection Microbiology, 1, article12, 2011.

Gonçalves, J.P., Francisco, A.P., Mira, N.P., Teixeira, M.C., Sá-Correia, I., Oliveira, A.L., Madeira, S.C., TFRank: Network-based prioritization of regulatory associations underlying transcriptional responses. Bioinformatics, 27, 3149-57, 2011.

Mira, N.P., Henriques, S., Keller, G., Teixeira, M.C., Matos, R., Arraiano, C., Winge, D.R., Sá-Correia, I., Identification of a DNA binding site for the transcription factor Haa1p, required forSaccharomyces cerevisiae response to acetic acid stress. Nucleic Acids Research, 16, 6898-907, 2011.

Teixeira M.C., Mira N.P., Sá-Correia I., A genome-wide perspective on the response and tolerance to food-relevant stresses in Saccharomyces cerevisiaeCurrent Opinion in Biotechnology, 22, 150-156, 2011 (abstract).

Mira, N.P., Palma, M., Guerreiro, J., Sá-Correia I., Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid. Microbial Cell Factories, 9:79, 2011 (abstract)

Abdulrehman D., Monteiro P.T., Teixeira M.C., Mira N.P., Lourenço A.B., dos Santos S.C., Cabrito T.R., Francisco A., Madeira S.C., Santos R., Oliveira, A.L., Sá-Correia I., Freitas A. T., “YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.” Nucleic Acids Research39, D136-140, 2011

Mira N.P., Becker J.D., Sá-Correia I., Genomic expression program involving the Haa1p-regulon in Saccharomyces cerevisiae response to acetic acid. OMICS: a Journal of Integrative Biology, 14(5), 587-601, 2010 (abstract)

Mira N.P., Teixeira M.C., Sá-Correia I., Adaptive response and tolerance to weak acids in Saccharomyces cerevisiae : a genome-wide view. OMICS: a Journal of Integrative Biology, 14(5), 525-540, 2010 (abstract)

Teixeira M.C., Raposo L.R., Mira N.P., Lourenço A.B., and Sá-Correia I., “Genome-wide identification of genes required for maximal tolerance to ethanol in yeast: important role of FPS1Applied Environmental Microbiology, 75: 5761-5772, 2009

Mira N.P., Lourenço A.,  Fernandes A., Becker J., Sa-Correia I., The RIM101 pathway has a role in Saccharomyces cerevisiae adaptive response and resistance to propionic acid and other weak acids, FEMS Yeast Research,  9, 202-216, 2009 (abstract)

Sá-Correia I., dos Santos S.C., Teixeira M.C., Cabrito T.R., Mira N.P., “Drug:H+ antiporters in chemical stress response in yeast". Trends in Microbiology, 17, 22-31, 2009 (abstract)

Monteiro P., Mendes N., Teixeira M.C., d'Orey S., Tenreiro S., Mira N.P., Pais H., Francisco A., Carvalho A., Lourenço A.R., Sá-Correia I., Oliveira A.L., Freitas A.T. “YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae“. Nucleic Acids Res. Database Issue 36: D132-D136, 2008 (abstract)

Simões T., Mira N.P., Fernandes A.R., Sá-Correia I., “The SPI1 gene, encoding a glycosylphosphatidylinositol (GPI)-anchored cell wall protein, plays a prominent role in the development of yeast resistance to lipophilic weak acids food preservatives", Applied and Environmental Microbiology, 72, 7168-7175, 2006 (abstract)

Teixeira M.C., Fernandes A.R., Mira N.P., Becker J.D., Sá-Correia I., “Early transcriptional response of Saccharomyces cerevisiae to stress imposed by the herbicide 2,4-dichlorophenoxyacetic acid", FEMS Yeast Research, 6, 230–248, 2006 (abstract)

Teixeira M.C., Monteiro P., Jain P., Tenreiro S., Fernandes A.R., Mira N.P., Alenquer M., Freitas A.T., Oliveira A.L., Sá-Correia I., “The YEASTRACT database: a tool for the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae“, Nucleic Acids Research, Database Issue, 34, D446-D451, 2006 (abstract)

Fernandes A.R., Mira N.P., Vargas R.C., Canelhas I., Sá-Correia I., “Saccharomyces cerevisiae adaptation to weak acids involves the transcription factor Haa1p and of Haa1p-regulated genes”, Biochemical and Biophysical Research Communications, 337, 95-103, 2005 (abstract)

Papers in national journals with referees:

Teixeira M. C., Monteiro P., Jain P., Tenreiro S., Fernandes A. R., Mira N. P., Alenquer M., Freitas A. T., Oliveira  A.L., Sá-Correia I., “A Bioinformática e as Bases de Dados: o exemplo de uma Base de Dados para Análise de Mecanismos de Regulação em Levedura", Boletim de Biotecnologia, 81, 23-31,  2005.

Alternative Webpages