iBB

Responding to the recent interest of the yeast research community in non-Saccharomyces cerevisiae species of biotechnological relevance, the N.C.Yeastract was associated to YEASTRACT+, a curated repository of known regulatory associations between transcription factors (TFs) and target genes in yeasts. A recent Minireview published in FEMS Yeast Research aims to advertise the update of the existing information since the release of N.C.Yeastract in 2019, and to raise awareness in the community about its potential to help the day-to-day work on non-Saccharomyces species, exploring all the information and bioinformatics tools available in YEASTRACT +. Using simple and widely used examples, a guided exploitation is offered. The usage potentialities of the new CommunityYeastract platform by the yeast community are also discussed. The Minireview is coauthored by a BSRG-iBB team coordinated by Isabel Sá-Correia and including Cláudia P. Godinho, Margarida Palma, Miguel C. Teixeira and the PhD students Miguel Antunes and Marta N. Mota, in collaboration with INESC-ID colleagues.

The role of the cell wall in yeast response and tolerance to stress is frequently neglected. A BSRG-iBB research paper just published in Scientific Reports, provides, for the first time, a comprehensive view of the alterations occurring at the cell wall in a yeast population adapting to sub-lethal stress induced by acetic acid. The results reveal changes to the cell wall polysaccharide composition and nanomechanical properties, as well as alterations in the transcript levels of key cell wall biosynthetic genes. This paper reinforces the notion that the adaptive yeast response to acetic acid involves coordinated alterations of the cell wall at the biophysical and molecular levels. The gathered knowledge is important for the design of superior industrial strains and for the efficient control of the deleterious activity of spoilage yeasts, particularly in the Food Industry. This research work is first-authored by the PhD student of the PhD programme in Biotechnology and Biosciences Ricardo Ribeiro (FCT_DP AEM fellowship), performed under the supervision of Isabel Sá-Correia. This collaborative study with Fábio Fernandes (BSIRG-iBB) and Mário S. Rodrigues and his team (BioISI, Faculty of Sciences, ULisboa), is also coauthored by Cláudia Godinho (posdoc researcher) and the PhD student Nuno Bourbon-Melo (FCT_DP BIOTECnico) from the BSRG-iBB team.

A new paper by researchers from iBB-BSRG describes, for the first time, the involvement of a plasma membrane multidrug/multixenobiotic resistance (MDR/MXR) ABC transporter in yeast thermotolerance. The expression of the ABC transporter Pdr18, required for pleotropic drug resistance and involved in ergosterol transport at the plasma membrane level, is related with decreased plasma membrane permeabilization induced by a supraoptimal growth temperature. Ergosterol biosynthesis and plasma membrane ergosterol content were implicated in yeast response and capacity to overcome stress induced by supraoptimal growth temperatures. These results support the notion that MDR/MXR transporters perform biological activities other than their accepted role as drug/xenobiotic exporters. Cláudia Godinho is the first author of this research work, coordinated by Isabel Sá-Correia and published in the journal Environmental Microbiology.

Knowledge of the function and regulation of the yeast multidrug/multixenobiotic resistance (MDR/MXR) transporters can be explored to guide the design of robust yeast strains for industrial biotechnology and to overcome and control the deleterious activities of spoiling yeasts in the food industry. In a recent book chapter, Cláudia Godinho and Isabel Sá-Correia from BSRG-iBB provide an overview of the toxicity and tolerance to relevant stresses in the model yeast and cell factory Saccharomyces cerevisiae. The publication also explores how yeast models can be used to uncover the function of novel MDR/MXR transporters in the plant model Arabidopsis thaliana, and to develop efficient strategies to improve crop productivity in agricultural biotechnology. The chapter is part of the book “Yeasts in Biotechnology and Human Health - Physiological Genomic Approaches” edited by Prof. Isabel Sá-Correia within the book series “Progress in Molecular and Subcellular Biology” published by Springer.

Cláudia P. Godinho, a PhD researcher at BSRG-iBB, presented the work "The N.C.Yeastract and CommunityYeastract databases and tools: studying transcriptional regulation in non-conventional yeasts" during the Synthetic & Systems biology Symposium. Cláudia provided a guided exploration of the tools of the N.C.Yeastract database, which gathers all published regulatory associations and TF-binding sites for five yeast species of biotechnological potential. The potential of the database was also explained. The presentation was based in a recent MiniReview published this year in FEMS Yeast Research, resulting from collaborative work between the BSRG-iBB team coordinated by Isabel Sá-Correia and INESC-ID colleagues. Cláudia P. Godinho was also selected for presenting the International Microorganism Day initiative in the Teaching and Communicating in Science symposium. The purpose of the presentation, co-authored by Cláudia and Isabel Sá-Correia, was to report the results from IMD 2021 campaign and event, to promote IMD, and to provide an idea of the power of social media in Microbiology dissemination.

Cláudia P. Godinho, PhD researcher at Sá-Correia’s lab in BSRG-iBB, participated in the clarification of a well-known myth for the TVI news section “A Hora da Verdade”. The participation can be watched here. The 5-second rule states a time window of 5 seconds where it is safe to pick up food after it has been dropped to the floor. The experimental setup organized at the iBB Biological Sciences Research Group Laboratories contributed to demonstrate that the transfer of bacteria from a contaminated floor to food takes less than 5 seconds to happen and that the “rule” is in fact false.

Cláudia P. Godinho, PhD researcher at iBB-BSRG, was awarded 1st place in the “GENERAL” category of the competition “Science Communication in Microbiology”, promoted by the Portuguese Society of Microbiology (SPM) to commemorate the International Microorganism Day 2020. The competition aims to encourage and facilitate communication of relevant topics and research fields in ​​microbiology to the general public in a concise, clear and attractive way, through the presentation of an image and respective explanatory summary. The winning entry, entitled “Contribution of microbial diversity to a circular Bioeconomy”, draws attention to the role that yeast biodiversity can play in the production of a wide range of bioproducts, from agro-industrial residues.

The Burkholderia cepacia complex (Bcc) bacteria are feared contaminants in pharmaceutical industries and cause nosocomial outbreaks, posing health threats to immunocompromised individuals and cystic fibrosis (CF) patients. In this study, the adaptation and survival of B. cepacia and B. contaminans isolates was investigated after long-term incubation in nutrient depleted saline solutions supplemented with increasing concentrations of the biocidal preservative benzalkonium chloride (BZK), recreating the storage conditions of pharmaceutical products. This study just published in the section Biosafety and Biosecurity of Frontiers in Bioengineering and Biotechnology is co-authored by several members of Isabel Sá-Correia team from iBB/BSRG. This study reveals mechanisms underlying the prevalence of Bcc bacteria as contaminants of aqueous pharmaceutical products containing BZK, which often lead to false-negative results during quality control and routine testing.

Several membrane transporters from the ATP-binding cassette (ABC) superfamily present in yeast genomes are implicated in multidrug/multixenobiotic resistance (MDR/MXR). This is the case of Pdr18, that confers tolerance to ethanol and acetic acid and several other toxicants in yeast and has a biological role attributed in ergosterol transport at the plasma membrane. A recently iBB-BSRG paper published in Frontiers in Genetics, Evolutionary and Genomic Microbiology section, reconstructs the evolutionary history of the encoding gene PDR18 and the paralogue gene SNQ2. This publication results from the PhD thesis in Biotechnology and Biosciences of Cláudia P. Godinho advised by Prof. Isabel Sá-Correia with collaboration of Paulo J. Dias and Elise Ponçot. By combining phylogenetic gene neighborhood analysis for 117 yeast genomes belonging to 29 species across the Saccharomycetaceae family, the gene duplication event was traced to the last common ancestor of the Saccharomyces genus yeasts. The fact that Snq2 and Pdr18 confer resistance to different sets of chemical compounds with little overlapping is consistent with the subfunctionalization and neofunctionalization of these gene copies. Remarkably, PDR18 is only found in Saccharomyces genus genomes. 

The ability of Saccharomyces cerevisiae to overcome the stress induced by cytotoxic compounds depends on the activity of plasma membrane transporters of the ABC superfamily, presumably through the questionable unspecific efflux of multiple drugs and xenobiotic compounds. A recent paper by iBB researchers provides new insights into the biological role of the ABC transporter of the pleiotropic drug resistance family of putative drug efflux pumps Pdr18, proposed to mediate ergosterol incorporation in plasma membrane. Pdr18 expression was found to help cells to counteract acetic acid-induced decrease of plasma membrane lipid order, increase the non-specific membrane permeability and decrease the transmembrane electrochemical potential. Results support the notion that Pdr18-mediated multistress resistance is linked to the status of plasma membrane lipid environment related with ergosterol content and the associated plasma membrane properties. The paper, published in Scientific Reports, results from the PhD project of Cláudia Godinho, advised by Prof. Isabel Sá-Correia from BSRG-iBB in collaboration with Fábio Fernandes and Sandra Pinto from BSIRG-iBB).