Centro de Biologia Molecular e Ambiental

Centre of Molecular and Environmental Biology


Functional Genomics andNanobiotechnologyfor SustainableLiving Group

The group INNOVATION FOR LIFE - Functional Genomics and Nanobiotechnology for Sustainable Living uses molecular biotechnology and applied microbiology, omics and bioinformatics tools in synthetic biology approaches to re-design natural biological systems (or parts of) and to promote a knowledge-based society.

Our scientific expertise is focused on:

1) optimization of high throughput methods to exploit microbial resources for industrial applications;

2) genetic engineering for bioprocess optimization;

3) development of bio inspired nanostructured materials.

High-throughput methodologies have been developed and implemented to characterize biological collections for posterior prediction of biotechnologically useful traits. Microorganism with unique metabolic features with industrial interest (e.g. for production of chemical building blocks) have been identified.

Several biotechnology R&D topics with application potential have also been explored. Efficient, biosustainable metabolic engineering of yeast has also been a focus of our work, creating the possibility of using these modified microorganisms to transform biowaste or industrial bioproducts in added value materials for biodiesel or bioethanol industries, for example.

A lot of effort has been put in the design and scaled up production of protein-based polymers, with varying features in terms of physical-chemical properties. Bioactive peptides and growth factors (BMPs, antimicrobial peptides) have similarly been efficiently produced. Protein polymers were validated per se or processed into nanostructured materials by self-assembly, electrospinning and solvent-cast technologies. These polymers and derived structures have an immense potential for application in biomedicine and will continue to be a strong area of work in 2015-2020.

Main achievements


The team has been working intensively on characterizing and exploring bacteria and yeast biodiversity, in order to harness natural genetic and phenotypic variability.

High-throughput, non-invasive methods were established for phenometabolomic characterization of S. cerevisiae strains collected in the wild and from the other collections [Schuller et al., 2012]. This methodology allowed the creation of a relational database describing the pheno-metabolomic landscape of this species. This data can be used for predicting biotechnologically useful traits [Oliveira et al., 2008; Eiriz et al., 2008; Mendes et al., 2013].

The strain Pseudomonas sp. M1 is able to biotransform an unusually high range of organic compounds (e.g. recalcitrant solvents, terpenoids and PAHs) with biotechnological potential [Santos PM & Sá-Correia I]. We identified a genomic island involved in sensing and biotransformation of terpenoids using high throughput methods. Terpenoids of natural origin are important as fragrances and flavors due to their organoleptic properties but may also be converted into chemical building-blocks.

Pseudomonas aeruginosa is a known opportunistic pathogen and with reported increasing resistance to antibiotics. A library of clinical isolates of P. aeruginosa was created and the mobilome component of the genome was characterized, providing new insights into the understanding of persistence and virulence during human infection [Soares-Castro et al., 2011].


Development of tools for efficient, biosustainable metabolic engineering of yeast have also been a focus of our work.

An assortment of protein-based polymers, with varying features in terms of physical-chemical properties, were produced at levels of grams per liter. Using the same set up, bioactive human growth factors was also efficiently produced [Bessa et al., 2010a; Bessa et al., 2010b; Bessa et al., 2008; Machado et al., 2013a]. Production of silk-elastin copolymers was scaled up to industrial level in a 500L fermentor anticipating its translation into industry [Collins et al., 2013]. Protein polymers were processed into new structured materials by self-assembly, electrospinning and solvent-cast technologies [Machado et al., 2013b] for regenerative medicine.

Several of the group’s main achievements relate to technology or tools that are being transferred to the economic domain in the form of services, patent applications and spin-off companies [Schuller et al., 2008; Oliveira et al., 2008; Bessa et al., 2008; Machado et al., 2013; Collins et al., 2013; Machado et al., 2013b; Vasconcelos et al., 2012; Silva et al., 2011; Araújo et al., 2009; Amaral et al., 2008]. Enzymes were enhanced by genetically engineering, with direct application in wool fibre modification (WO 2010/001356). Furthermore, the development of lipidic nanovehicles composed of DODAB and monoolein [Silva et al., 2011] was recognized for its potential application in human gene therapy, which led to the genesis of spin-off Nanodelivery, supported by national and international patents (PN 104158, W0/2010/029035 A2).

Key publications (last 5 years)

Amaral C, Lucas M, Coutinho J, Crespí AL, Anjos MR, Pais C. (2008). Microbiological and Physicochemical Characterization of Olive Mill Wastewaters from a Continuous Olive Mill in Northeastern Portugal. Bioresource Technology, 99: 7215- 7223.   DOI: 10.1016/j.biortech.2007.12.058 

Araújo R, Silva C, Machado R, Casal M, Cunha AM, Rodriguez-Cabello C, Cavaco-Paulo A. (2009). Proteolytic enzyme engineering: a tool for wool. Biomacromolecules, 10: 1655-1661. DOI: 10.1002/term.245

Bessa P, Machado R, Nürnberger S, Dopler D, Banerjee A, Cunha AM, Rodríguez-Cabello C, Redl H, van Griensven M, Reis RL, Casal M. (2010)a. Thermoresponsive self-assembled elastin-based nanoparticles for delivery of BMPs. Journal of Controlled Release, 142: 312–318. DOI: 10.1016/j.jconrel.2009.11.003

Bessa PC, Balmayor ER, Azevedo HS, Nürnberger S, Casal M, van Griensven M, Reis RL, Redl H. (2010)b. Silk fibroin microparticles as carriers for delivery of human recombinant BMPs. Physical characterization and drug release. Journal of Tissue Engineering and Regenerative Medicine, 4: 349-355. DOI: 10.1002/term.245

Bessa PC, Casal M, Reis RL. (2008). Bone morphogenetic proteins in tissue engineering: the road from laboratory to the clinic, part II (BMP delivery). Journal of Tissue Engineering and Regenerative Medicine, 2: 81-96.    DOI: 10.1002/term.74

Collins T, Azevedo-Silva J, da Costa A, Branca F, Machado R, Casal M (2013). Batch production of a silk-elastin-like protein in E. coli BL21(DE3): key parameters for optimisation. Microb Cell Fact, 12:21. doi:10.1186/1475-2859-12-21

Eiriz MF, Carreto L, Gomes AC, Pereira PM, Schuller D, Santos MAS . (2008). Comparative genomics of yeast strains isolated from diverse ecological niches unveils important genome diversity. BMC Genomics, 9: 524. DOI: 10.1186/1471-2164-9-524

Machado R, Azevedo-Silva J, Correia C, Collins T, Arias FJ, Rodríguez-Cabello JC, Casal M. (2013)a. High level expression and facile purification of recombinant silk-elastin-like polymers in auto induction shake flask cultures. AMB Express, 3(1), 1-15. doi:10.1186/2191-0855-3-11

Machado R, da Costa A, Sencadas V, Garcia-Arevalo C, Costa CM, Padrão J,

Gomes A, Lanceros-Méndez S, Rodríguez-Cabello JC, Casal M (2013)b. Electrospun silk-elastin-like fibre mats for tissue engineering applications. Biomed. Mater. 8 065009 (13pp). doi:10.1088/1748-6041/8/6/065009

Mendes I, Franco-Duarte R, Umek L, Fonseca E, Drumonde-Neves J, Dequin S, Zupan B, Schuller D. (2013). Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles. PLOSone 8(7): e66523. doi: 10.1371/journal.pone.0066523.

Oliveira VA, Vicente MA, Fietto LG, Castro IM, Coutrim MX, Schuller D, Casal M, Santos JO, Araújo LD, Silva PHA, Brandão RL. (2008). Biochemical and molecular characterization of Saccharomyces cerevisiae strains obtained from sugar-cane juice fermentations and their impact in cachaça production. Applied and Environmental Microbiology, 74: 693-701.  DOI: 10.1128/AEM.01729-07 

Santos PM & Sá-Correia I. (2009). Adaptation to ?-myrcene catabolism in Pseudomonas sp. M1: An expression proteomics analysis. Proteomics, 9: 5101-5111. DOI: 10.1002/pmic.200900325

Schuller D, Cardoso F, Sousa S, Gomes P, Gomes AC, Santos MAS, Casal M. (2012). Genetic Diversity and Population Structure of Saccharomyces cerevisiae Strains Isolated from Different Grape Varieties and Winemaking Regions. PLoS One, 7: e32507. DOI: 10.1371/journal.pone.0032507

Silva JPN, Oliveira ACN, Casal MPPA, Gomes AC, Coutinho PJG, Coutinho OP, Oliveira MECDR. (2011). DODAB:monoolein-based lipoplexes as non-viral vectors for transfection of mammalian cells. Biochimica et Biophysica Acta - Biomembranes, 1808: 2440-9. DOI: 10.1016/j.bbamem.2011.07.002

Soares-Castro P, Marques D, Demyanchuk S, Faustino A, Santos PM. (2011). Draft genome sequences of two Pseudomonas aeruginosa clinical isolates with different antibiotic susceptibilities. J Bacteriol,193: 5573. doi: 10.1128/JB.05446-11

Vasconcelos A, Gomes AC, Cavaco-Paulo A. (2012). Novel silk fibroin/elastin wound dressings. Acta biomaterialia, 8: 3049-60. DOI: 10.1016/j.actbio.2012.04.035 

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