Theme Leader: Isabel Sá-Correia

Microbial Physiological Genomics allows a holistic understanding of the complex adaptive responses and determinants of tolerance or susceptibility to environmental challenges, at a genome-wide scale. Understanding microbial responses to environmental insults or other alterations, at a systems level, has a paramount importance in Biotechnology, Health and Environmental sectors.

Our current projects within this subject include

  • Yeast Toxicogenomics and Bacterial Pathogenomics approaches
  • Studies on the mechanisms of response and tolerance to multiple stresses of biotechnological and clinical relevance in yeasts and Gram-negative bacteria
  • Transcriptional regulation of gene and genomic expression in yeast
  • Multidrug/multixenobiotic resistance (MDR/MXR) membrane transporters: biological function, regulation and evolution
  • Understanding and manipulating tolerance to multiple stresses in the cell factory Saccharomyces cerevisiae and the food spoilage yeast Zygosaccharomyces bailii
  • The study of Burkholderia cepacia complex bacteria as contaminants of medicines and medical devices and in cystic fibrosis respiratory infections
  • Development of superior yeast strains and process conditions for improved robustness towards a Circular Bio-based economy

Major Areas of Research Focus:

Response and tolerance to multiple stresses in yeasts for Biotechnology and Food Industries

The improvement of the capacity of industrially relevant yeast strains to tolerate toxic substrates or products combined with operating conditions that do not allow maximum stress tolerance, is an important challenge of modern Biotechnology [1]. This knowledge is instrumental to guide synthetic pathway engineering for increased cell robustness manipulation either for the sustainable production of fuels and chemicals or for the control of growth and activity of food and beverage spoilage yeasts. Chemogenomic, transcriptomic, (quantitative- and phospho-) proteomic, lipidomic and genome sequence analyses, complemented by the use and development of the required bioinformatics tools and molecular and cell biology studies, are being explored to unveil genome-wide adaptive response programs and tolerance/susceptibility determinants to single and multiple relevant stresses in the cell factory Saccharomyces cerevisiae and the food spoilage yeast Zygosaccharomyces bailii [2-12]. These physiological genomics studies are identifying candidate molecular targets for genetic manipulations to endure/sensitize yeast cells against multiple stresses expected to occur during biotechnological and food industry processes.

Publications

[1] dos Santos, S.C., Sá-Correia, I., “Yeast toxicogenomics: lessons from a eukaryotic cell model and cell factory", Current Opinion in Biotechnology 33:183–191, 2015

[2] dos Santos, S.C., Teixeira, M.C., Cabrito, T.R., Sá-Correia, I., “Yeast Toxicogenomics: genome-wide responses to chemical stresses with impact in Environmental Health, Pharmacology and Biotechnology", Frontiers in Genetics, 3, 63, 2012

[3] Guerreiro, J. F.*, Mira, N. P.*, Santos, A.X.S., Riezman, H., 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, DOI:10.3389/fmicb.2017.01302  

[4] Henriques, S.F., Mira, N.P., 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, DOI:10.1186/s13068-017-0781-5

[5] Palma, M., Dias, P.J., Roque, F.C., Luzia, L., Guerreiro, J.F., Sá-Correia, I., “The Zygosaccharomyces bailii transcription factor Haa1 is required for acetic acid and copper stress responses suggesting subfunctionalization of the ancestral bifunctional protein Haa1/Cup2", BMC Genomics, 18: 75, 2017 doi: 10.1186/s12864-016-3443-2

[6] 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

[7] Guerreiro, J.F., Sampaio-Marques, B., Soares, R., Coelho, A.V., Leão, C., Ludovico, P., Sá-Correia, I., “Mitochondrial proteomics of the acetic acid–induced programmed cell death response in a highly tolerant Zygosaccharomyces bailii–derived hybrid strain”, Microbial Cell, 3 65-78, 2016. doi: 10.15698/mic2016.02.477

[8] Swinnen, S.*, Henriques, S.C.F.*, Shrestha, R., Ho, P.W., Sá-Correia, I.**, Nevoigt, E.**, “Improvement of yeast tolerance to acetic acid through Haa1 transcription factor engineering: towards the underlying mechanisms", Microbial Cell Factories, 16:7, 2017. (*co-first;**co-correspondent) 

[9] Guerreiro, J., Muir, A., Ramachandran, S., Thorner, J., Sá-Correia, I., “Sphingolipid biosynthesis upregulation by TOR Complex 2-Ypk1 signaling during yeast adaptive response to acetic acid stress", Biochemical Journal 473(23): 4311-4325, 2016. (*co-first;**co-correspondent

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

[11] Palma, M., Münsterkötter, M., Peça, J., Güldener, U., Sá-Correia, I., “Genome sequence of the highly weak-acid-tolerant Zygosaccharomyces bailii IST302, amenable to genetic manipulations and physiological studie", FEMS Yeast Research. 17(4), 2017

[12] Palma, M., Guerreiro, J.F., Sá-Correia, I., “Adaptive response and tolerance to acetic acid in Saccharomyces cerevisiae and Zygosaccharomyces bailii: a physiological genomics perspective", Frontiers in Microbiology, 9:274, 2018

Projects

ERA-NET Industrial Biotechnology project ERA-IB-16-013-YEASTPEC – Engineering of the yeast Saccharomyces cerevisiae for bioconversion of pectin-containing agro-industrial side-streams, 1-01-2017-1-01 2020

ERA-NET Industrial Biotechnology Project ERA-IB/0002/2010, INTACT – Integral engineering of acetic acid tolerance in yeast (2011-2014)

PTDC/AGR-ALI/102608/2008- ZygoSacAR-Mechanistic insights into acetic acid resistance in food spoilage yeasts: from the experimental model Saccharomyces cerevisiae to Zygosaccharomyces spp (2010-2013)

Transcription regulation of Gene and Genomic expression in Yeasts

The rapid and adequate reprogramming of yeast genomic expression in response to environmental alterations, in particular to stress, is essential to cell survival or metabolic efficiency. We have been examining and defining yeast regulons dependent on specific transcription factors (TF) based on transcriptomic analysis and identifying the corresponding DNA-binding sites. The most important example is the TF Haa1 required for Saccharomyces cerevisiae response to acetic acid stress [1-3].

In collaboration with a research team affiliated to INESC-ID, we also developed and are regularly upgrading and updating the YEASTRACT database (www.yeastract.com) [4], a bioinformatics tool, used worldwide in the fields of Yeast Molecular and Systems Biology, for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in the model eukaryote and cell factory Saccharomyces cerevisiae. Bioinformatics tools that enable the user to exploit the existing information to predict the TFs involved in the regulation of a gene or genome-wide transcriptional response and promoter analysis tools and interactive visualization tools for the representation of TF regulatory networks are also provided. We plan to extend Yeastract to the pathogenic yeasts Candida albicans and C. glabrata and the food spoilage yeast Zygosaccharomyces bailii in the frame of the Portuguese distributed infrastructure for biological data BioData.pt, included in FCT’s Infrastructure Road Map of 2013. The resulting YEASTRACT+-platform for gene and genomic transcription regulation in yeasts will be a service of the Portuguese Node of ESFRI-ELIXIR (European Distributed Infrastructure for Life Science Information).

Publications

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

[2] Mira, N.P., Henriques, S.F., Keller, G., Matos, R., Arraiano, C., Teixeira, M.C., Winge, D.R. and Sá-Correia, I., “Identification of a DNA-binding site for the transcription factor Haa1, required for Saccharomyces cerevisiae response to acetic acid stress", Nucleic Acids Research, 16, 6896-907, 2011

[3] Swinnen, S.*, Henriques, S.C.F.*, Shrestha, R., Ho, P.W., Sá-Correia, I.**, Nevoigt, E.**, “Improvement of yeast tolerance to acetic acid through Haa1 transcription factor engineering: towards the underlying mechanisms", Microbial Cell Factories, 16:7, 2017. (*co-first;**co-correspondent) 

[4] 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, Database Issue, 42: D161-D166, 2014

Projects

PTDC/BBB-BEP/0385/2014 Structural and functional analysis of the Haa1 transcription factor required for yeast response and resistance to acetic acid (2016-2019)

01/SAICT/2016: BioData.pt -Projeto de Desenvolvimento e Implementação de Infraestruturas de Investigação, inserido no Roteiro Nacional de Infraestruturas de Investigação-RNIE (Project for the Development and Implementation of Research Infrastructures) (2017-2020)

MDR/MXR transporters: biological function, regulation and evolution

Multidrug/Multixenobiotic resistance (MDR/MXR) is a widespread phenomenon with clinical, agricultural and biotechnological implications, where MDR/MXR transporters (of the major facilitator superfamily -MFS and the ATP-cassette Superfamily-ABC) play a key role in the acquisition of resistance [1], [2]. Although these proteins have been traditionally considered drug exporters, their physiological function and involvement in resistance to cytotoxic compounds are still open to debate [1], [2]. We have been contributing to the field by examining the biological function, regulation and evolution of yeast MDR/MXR transporters [3-6]. Heterologous expression of yeast MDR/MXR transporters encoding genes in the plant model and vice-versa is also being explored to enlighten the biological role of poorly characterized proteins [7].

Publications

[1]. 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

[2]. dos Santos, S.C., Teixeira, M.C., Dias, P.J., Sá-Correia, I., “MFS transporters required for multidrug/multixenobiotic (MD/MX) resistance in the model yeast: understanding their physiological function through post-genomic approaches", Frontiers in Physiology, 5:180, 2014

[3]. Godinho, C.P., Mira, N.P., Cabrito, T.R., Teixeira, M.C., Alasoo, K., Guerreiro, J.F., 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, 2017 Apr 13. doi: 10.1007/s00253-017-8277-6. [Epub ahead of print]

[4]. 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

[5]. Cabrito, T.R., Teixeira, M.C., Singh, A., Prasad, R., Sá-Correia, I., “The yeast ABC transporter Pdr18 (ORF YNR070w) controls plasma membrane sterol composition, playing a role in multidrug resistance", Biochemical Journal, 440, 195-202, 2011

[6]. Dias, P.J., Sá-Correia, I., “Phylogenetic and syntenic analyses of the 12-spanner drug:H+ antiporter family 1 (DHA1) in pathogenic Candida species: evolution of MDR1 and FLU1 genes", Genomics, 104(1): 45-57, 2014.

[7]. Remy, E., Niño-González, M., Godinho, C., Cabrito, T.R., Teixeira, M.C., Sá-Correia, I., Duque, P., “Heterologous expression of the yeast Tpo1p or Pdr5p membrane transporters in Arabidopsis confers plant xenobiotic tolerance", Scientific Reports, 7(1): 4529, 2017, doi: 10.1038/s41598-017-04534-7.

Projects

EXPL/AGR-PRO/1013/2013-Major Facilitator Superfamily transporters in the context of modern agriculture constraints: exploratory studies (2014-2015)

PTDC/AGR-AAM/102967/2008Resistance to pesticides and other chemical stresses of agricultural interest: role of plant Major Facilitator Superfamily transporters (2010-2013)

Burkholderia cepacia complex bacteria in cystic fibrosis respiratory infections and as as contaminants of medicines and medical devices

Burkholderia cepacia complex (Bcc) bacteria are feared contaminants of medicines and medical devices, causing nosocomial outbreaks and posing a health threat for susceptible individuals, in particular cystic fibrosis (CF) patients. Our studies aim at increasing the understanding of the molecular mechanisms underlying Bcc success as health products´ contaminants and in causing persistent and devastating respiratory infections in CF patients. Based on a 2-decade long collaboration with Hospital Sta Maria CF Centre, retrospective studies are focused on: i) adaptive evolution of Bcc species in CF lungs ii) B. cepacia and B. contaminans outbreak related with contaminated nasal solutions iii) the clinically important small colony variants, exploring an integrated molecular systems microbiology strategy. In collaboration, with INFARMED-National Authority of Medicines and Health Products, the implementation of molecular methods for direct and rapid Bcc detection in health products is envisaged.

Publications

Hassan, A.A. Maldonado, R.F., Sandra Costa dos Santos, S.C., Di Lorenzo, F., Silipo, A.C., Coutinho, Cooper, V.S., Molinaro, A., Valvano, M.A., Sá-Correia, I., “Structure of O-antigen and hybrid biosynthetic locus in Burkholderia cenocepacia clonal variants recovered from a cystic fibrosis patient", Frontiers in Microbiology, 2017, doi: 10.3389/fmicb.2017.01027

Moreira, A.S., Mil-Homens, D.*, Sousa, S.A.*, Coutinho, C.P.*, Pinto-de-Oliveira, A., Ramos, C.G., dos Santos, S.C., Fialho, A.M., Leitão, J.H., Sá-Correia, I., “Variation of Burkholderia cenocepacia virulence potential during cystic fibrosis chronic lung infection", Virulence, 21:1-15, 2016, doi: 10.1080/21505594.2016.1237334

Moreira, A.S., Lourenço, A.B., Sá-Correia, I., “1H-NMR-based endometabolome profiles of Burkholderia cenocepacia clonal variants retrieved from a cystic fibrosis patient during chronic infection", Frontiers in Microbiology, 7:2024, 2016.

Maldonado, R., Sá-Correia, I., Valvano, M., “Lipopolysaccharide modification in Gram-negative bacteria during chronic infection", FEMS Microbiology Reviews, 40(4): 480-493, 2016.

Coutinho, C.P., Barreto, C., Pereira, L., Lito, L., Melo Cristino, J., Sá-Correia, I., “Incidence of Burkholderia contaminans at a cystic fibrosis centre with an unusually high representation of Burkholderia cepacia during 15 years of epidemiological surveillance", Journal of Medical Microbiology. 64(8):927-35, 2015

Madeira, A., Dos Santos, S.C., Santos, P.M., Coutinho, C.P., Tyrrell, J., McClean, S., Callaghan, M., Sá-Correia, I. (2013) “Proteomic profiling of Burkholderia cenocepacia clonal isolates with different virulence potential retrieved from a cystic fibrosis patient during chronic lung infection", PLoS One. 8:e83065,v 2014

Projects

COST Action BM1003, “Microbial cell surface determinants of virulence as targets for new therapeutics in Cystic Fibrosis”, supported by the EU RTD Framework Programme in the field Biomedicine and Molecular Biosciences (20 EU countries involved) (2010-2014)

PTDC/FIS-NAN/6101/2014 Molecular and Mechanical Forces in Biology measured with Force Feedback Microscopy (2016-2019)

ERA-NET PathoGenomics ERA-PTG/SAU/0001/2008 -ADHRES – Signature Project: Expression profiling of adhesive (ADH) and resistance (RES) genes in biofilm lifestyle in P. aeruginosa, P. putida and B. cenocepacia (2009-2012)