Danilo Porro

Università degli Studi di Milano-Bicocca | UNIMIB

The design of alternative biodegradable polymers has the potential of severely reducing the environmental impact, cost and production time currently associated with the petrochemical industry. In fact, growing demand for renewable feedstock has recently brought to the fore synthetic biology and metabolic engineering. These two interdependent resear...

Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amoun...

The industrial relevance of organic acids is high; because of their chemical properties, they can be used as building blocks as well as single-molecule agents with a huge annual market. Organic acid chemical platforms can derive from fossil sources by petrochemical refining processes, but most of them also represent natural metabolites produced by...

Background Omega-3 fatty acids (FAs) are relevant commodities in the market since their important role in human wellbeing. As the worldwide demand is increasing, alternative sources and sustainable processes are needed to face the limited supply of the omega-3 FAs of fish origin. Microalgae provide a portfolio of biodiversity able to satisfy the qu...

Microorganisms offer a tremendous potential as cell factories, and they are indeed been used by humans since the previous centuries for biotransformations. Among them, yeasts combine the advantage of a unicellular state with a eukaryotic organization. Moreover, in the era of biorefineries, their biodiversity can offer solutions to specific process...

Several compounds on the market derive from petrochemical synthesis, and carotenoids are no exception. Nonetheless, since their applications in the food, feed and cosmetic sectors, and because of sustainability issues, carotenoids of natural origin are desirable. Carotenoids can be extracted from several plants but also from carotenogenic microorga...

Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amoun...

Using a circular economy concept, the present study investigated the use of crude glycerol, a primary by-product of biodiesel production, as a low-priced nutrient source for heterotrophic cultivation of the fungus-like protist Schizochytrium limacinum SR21 strain. The whole biomass of this oleaginous microorganism, rich in docosahexaenoic acid (DHA...

Background Petrochemical synthetic dominates several markets, and carotenoids are not an exception. Since their applications in the food, feed and cosmetic sectors, carotenoids of natural origin are increasingly requested, but the production needs to be sustainable also in terms of initial feedstock. For these reasons we deployed the carotenogenic...

Background Lipids from oleaginous yeasts emerged as a sustainable alternative to vegetable oils and animal fat to produce biodiesel, the biodegradable and environmentally friendly counterpart of petro-diesel fuel. To develop economically viable microbial processes, the use of residual feedstocks as growth and production substrates is required. Res...

Background: As the circular economy advocates a near total waste reduction, the industry has shown an increased interest toward the exploitation of various residual biomasses. The origin and availability of biomass used as feedstock strongly affect the sustainability of biorefineries, where it is converted in energy and chemicals. Here, we explore...

Background: As the circular economy advocates a near total waste reduction, the industry has shown an increased interest towards the exploitation of various residual biomasses. The origin and availability of biomass used as feedstock strongly affects the sustainability of biorefineries, where it is converted in energy and chemicals. Here, we explor...

Background: Lipids from oleaginous yeasts emerged as sustainable alternative to vegetable oils and animal fat to produce biodiesel, the biodegradable and environmentally friendly counterpart of diesel fuel. To develop economically viable microbial processes, the use of residual feedstocks as growth substrates is required. Results: In this work, we...

Background: Lipids from oleaginous yeasts emerged as a sustainable alternative to vegetable oils and animal fat to produce biodiesel, the biodegradable and environmentally friendly counterpart of petro-diesel fuel. To develop economically viable microbial processes, the use of residual feedstocks as growth and production substrates is required. Res...

Background Lipids from oleaginous yeasts emerged as a sustainable alternative to vegetable oils and animal fat to produce biodiesel, the biodegradable and environmentally friendly counterpart of petro-diesel fuel. To develop economically viable microbial processes, the use of residual feedstocks as growth and production substrates is required. Resu...

Background: The sustainability of biorefineries is strongly related to the origin, the availability and the market of the biomass used as feedstock. Moreover, one of the pillars of circular economy aims at reducing waste, ideally to zero. These considerations well justify the increasing industrial interest in exploiting many and diverse residual bi...

This study focused on the characterization of microbial communities during the desulfurization of ground tire rubber (GTR) by two bacterial strains i) Gordonia desulfuricans DSM 44462T, and ii) Rhodococcus sp. AF21875. Automated ribosomal inter-genic spacer analysis (ARISA), and high throughput sequencing of 16S rRNA gene amplicons were used to ana...

Genome-scale metabolic models are powerful tools to understand and engineer cellular systems facilitating their use as cell factories. This is especially true for microorganisms with known genome sequences from which nearly complete sets of enzymes and metabolic pathways are determined, or can be inferred. Yeasts are highly diverse eukaryotes whose...

The yeast Saccharomyces cerevisiae is widely used as a cell factory for the biotechnological production of various industrial products. During these processes, yeasts meet different kinds of stressors that often cause oxidative stress and thus impair cell growth. Therefore, the development of robust strains is indispensable to improve production, y...

Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH a...

White-rot fungi are the main natural producers of lignin modifying enzymes, i.e. laccases and peroxidases, whose secretion and activity allows the depolymerization of lignin and the release of polysaccharides contained in lignocellulose. These enzymes are able to oxidize, in addition to lignin, a wide spectrum of natural and synthetic substrates, m...

Organic acids are broadly distributed in nature, and humans used them in their natural sources since the early ages, essentially for food and drink preparations. Organic acids are low-molecular-weight organic compounds with one or more acidic groups such as carboxyl, sulfonic, alcohol and thiol groups. These functional groups make organic acids key...

Zygosaccharomyces bailii is a non-Saccharomyces budding yeast known as one of the most aggressive food spoilage microorganism, often isolated as contaminant during wine fermentation, as well as from many acidic, high sugar and canned foods. The spoilage ability relies on the yeast's unique feature to tolerate the most common preservatives such as s...

Many interspecies hybrids have been discovered in yeasts, but most of these hybrids are asexual and can replicate only mitotically. Whole-genome duplication has been proposed as a mechanism by which interspecies hybrids can regain fertility, restoring their ability to perform meiosis and sporulate. Here, we show that this process occurred naturally...

Sequence alignment of the VPS1-MET14 intergenic regions from Z. rouxii and Z. parabailii. The Z. parabailii regions contain CEN4 and CEN11 whereas the Z. rouxii region is not a centromere. Putative CDE I and CDE III motifs are boxed. (TIF)

Homeolog pairs in which one gene is damaged and the other is intact, in ATCC60483. (XLSX)

PCR primer sequences used for MAT locus genotyping. (DOC)

Phylogenetic tree of internal transcribed spacer (ITS) regions of rDNA. Chr4 and Chr11 are the ITS sequences from the chromosome 4 and 11 rDNA units in the Z. parabailii ATCC60483 genome. All other sequences are from Suh et al. [28] for strains of Z. parabailii(Zpar), Z. bailii(Zbai), and Z. pseudobailii (Zpse). Letters a-n are ITS variant designat...

Z. parabailii orthologs of S. cerevisiae genes involved in mating or meiosis. (XLSX)

Excel spreadsheet containing, in separate sheets, the underlying numerical data for Fig panels 2A, 2B and 2C. (XLSX)

Background The big challenge in any anti-tumor therapeutic approach is represented by the development of drugs selectively acting on the target with limited side effects, that exploit the unique characteristics of malignant cells. The urokinase (urokinase-type plasminogen activator, uPA) and its receptor uPAR have been identified as preferential ta...

The ability of Zygosacchromyces bailii to grow at low pH and in the presence of considerable amounts of weak organic acids, lethal condition for Saccharomyces cerevisiae, increased the interest in the biotechnological potential of the yeast. To understand the mechanism of tolerance and growth effect of weak acids on Z. bailii, we evaluated the phys...

Background Microbial lipids can represent a valuable alternative feedstock for biodiesel production in the context of a viable bio-based economy. This production can be driven by cultivating some oleaginous microorganisms on crude-glycerol, a 10 % (w/w) by-product produced during the transesterification process from oils into biodiesel. Despite att...

The economic upturn of the past 200 years would not have been conceivable without fossil resources such as coal and oil. However, the fossil-based economy increasingly reaches its limits and displays contradictions. Bioeconomy, strategically combining economy and ecology willing to make biobased and sustainable growth possible, is promising to make...

Lactic acid is a versatile chemical platform with many different industrial applications. Yeasts have been demonstrated as attractive alternative to natural lactic acid producers since they can grow at low pH, allowing the direct purification of the product in the desired acidic form. However, when very high concentrations of organic acids are reac...

When exploited as cell factories, Saccharomyces cerevisiae cells are exposed to harsh environmental stresses impairing titer, yield and productivity of the fermentative processes. The development of robust strains therefore represents a pivotal challenge for the implementation of cost-effective bioprocesses. Altering master regulators of general ce...

Saccharomyces cerevisiae is one of the most employed cell factories for the production of bioproducts. While monomeric hexose sugars constitute the preferential carbon source, this yeast can grow on a wide variety of nitrogen sources, which are catabolised through the Central Nitrogen Metabolism (CNM). To evaluate the effects of internal perturbati...

Background The great interest in the production of highly pure lactic acid enantiomers comes from the application of polylactic acid (PLA) for the production of biodegradable plastics. Yeasts can be considered as alternative cell factories to lactic acid bacteria for lactic acid production, despite not being natural producers, since they can better...

Development of robust yeast strains that can efficiently ferment lignocellulose-based feedstocks is one of the requirements for achieving economically feasible bioethanol production processes. With this goal, several genes have been identified as promising candidates to confer improved tolerance to S. cerevisiae. In most of the cases, however, the...

Microorganisms appear as ideal catalysts for chemical conversions. Diverse metabolic routes seem to open doors to the whole range of chemistry. Indeed, a vast amount of scientific papers suggesting new microbial cell factories for old and new products is published every year. However, only very few of them reached industrial relevance. Chemical bal...

Microorganisms offer a tremendous potential as cell factories, and they are indeed used by humans for centuries for biotransformations. Among them, yeasts combine the advantage of unicellular state with a eukaryotic organization, and, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomy...

The yeast Kluyveromyces marxianus features specific traits that render it attractive for industrial applications. These include production of ethanol which, together with thermotolerance and the ability to grow with a high specific growth rate on a wide range of substrates, could make it an alternative to Saccharomyces cerevisiae as an ethanol prod...

Yeasts play a significant role in biotechnology. They are important production hosts for chemicals, enzymes and biopharmaceutical ingredients. This chapter outlines our current knowledge about the interrelation of the central carbon metabolism and various microbial production processes. It is obvious that every production process is inevitably conn...

Oleaginous microorganisms, such as different yeast and algal species, can represent a sustainable alternative to plant oil for the production of biodiesel. They can accumulate fatty acids (FA) up to 70% of their dry weight with a predominance of (mono)unsaturated species, similarly to what plants do, but differently from animals. In addition, their...

In the context of the global objective of shifting from petroleum to a biomass-based economy, the research on fermentative strategies to produce alternative biofuels and chemicals has become a predominant field of study. Microorganisms, because of their substrate versatility and metabolic efficiency, are promising to partially support our increasin...

Biotechnological processes are of increasing significance for industrial production of fine and bulk chemicals, including biofuels. Unfortunately, under operative conditions microorganisms meet multiple stresses such as non-optimal pH, temperature, oxygenation and osmotic stress. Moreover, they have to face inhibitory compounds released during the...

Background The sustainable production of biofuels remains one of the major issues of the upcoming years. Among the number of most desirable molecules to be produced, butanol and isobutanol deserve a prominent place. They have superior liquid-fuel features in respect to ethanol. Particularly, butanol has similar properties to gasoline and thus it ha...

• To date, S. cerevisiae and E. coli are the two microbial workhorses for commercialization of recombinant heterologous proteins. This is a direct reflection of the familiarity of molecular biologists with these two hosts, combined with the deep knowledge about their genetics, biochemistry, physiology, and fermentation technologies. Despite the sig...

Recombinant protein production is a multibillion-dollar market. The development of a new product begins with the choice of a production host. While one single perfect host for every protein does not exist, several expression systems ranging from bacterial hosts to mammalian cells have been established. Among them, yeast cell factories combine the a...

The demand for recombinant proteins both for biopharmaceutical and technical applications is rapidly growing, and therefore the need to establish highly productive expression systems is steadily increasing. Yeasts, such as Pichia pastoris, are among the widely used production platforms with a strong emphasis on secreted proteins. Protein secretion...

Saccharomyces cerevisiae and Pichia pastoris are two of the most relevant microbial eukaryotic platforms for the production of recombinant proteins. Their known genome sequences enabled several transcriptomic profiling studies under many different environmental conditions, thus mimicking not only perturbations and adaptations which occur in their n...

Microorganisms employed in industrial fermentation processes are often subjected to a variety of stresses that negatively affect growth, production and productivity. Therefore, stress robustness is an important property for their application. Reactive Oxygen Species (ROS) accumulation is a common denominator to a lot of these stress factors. Ascorb...

Recombinant DNA (rDNA) technologies allow the production of a wide range of peptides, proteins and metabolites from naturally non-producing cells. Since human insulin was the first heterologous compound produced in a laboratory in 1977, rDNA technology has become one of the most important technologies developed in the 20th century. Recombinant prot...

The modification of enzyme cofactor concentrations can be used as a method for both studying and engineering metabolism. We varied Saccharomyces cerevisiae mitochondrial NAD levels by altering expression of its specific mitochondrial carriers. Changes in mitochondrial NAD levels affected the overall cellular concentration of this coenzyme and the c...

Microorganisms encounter diverse stress conditions in their native habitats but also during fermentation processes, which have an impact on industrial process performance. These environmental stresses and the physiological reactions they trigger, including changes in the protein folding/secretion machinery, are highly interrelated. Thus, the invest...

Microorganismsemployedinindustrialfermentationprocessesareoftensubjectedtoavarietyof stressesthatnegativelyaffectgrowth,productionandproductivity.Therefore,stressrobustnessisan importantpropertyfortheirapplication.ReactiveOxygenSpecies(ROS)accumulationisacommon denominatortoalotofthesestressfactors.Ascorbicacid(L-AA) actsasROSscavenger,thuspotentia...

The nonconventional yeast Zygosaccharomyces bailii has been proposed as a new host for biotechnological processes due to convenient properties such as its resistance to high sugar concentrations, relatively high temperatures and especially to acidic environments. We describe a series of new expression vectors specific for Z. bailii and the resultin...

CK2 is a highly conserved protein kinase controlling different cellular processes. It shows a higher activity in proliferating mammalian cells, in various types of cancer cell lines and tumors. The findings presented herein provide the first evidence of an in vivo modulation of CK2 activity, dependent on growth rate, in Saccharomyces cerevisiae. In...

Since about three decades, Saccharomyces cerevisiae can be engineered to efficiently produce proteins and metabolites. Even recognizing that in baker's yeast one determining step for the glucose consumption rate is the sugar uptake, this fact has never been conceived to improve the metabolite(s) productivity.In this work we compared the ethanol and...

Zygosaccharomyces bailii is a diploid budding yeast still poorly characterized, but widely recognised as tolerant to several stresses, most of which related to industrial processes of production. Because of that, it would be very interesting to develop its ability as a cell factory. Gas1p is a beta-1,3-glucanosyltransglycosylase which plays an impo...

Clustalw_ntd. Nucleotidic sequence of the ZbGAS1 gene and alignment with the homologue ScGAS1 (entry: YMR307W). Grey coloring represent nucleotidic identity. Alignment was performed with ClustalW software http://www.ebi.ac.uk/clustalw and graphical editing was made using Jalview software [31].

The use of plastic produced from non-renewable resources constitutes a major environmental problem of the modern society. Polylactide polymers (PLA) have recently gained enormous attention as one possible substitution of petroleum derived polymers. A prerequisite for high quality PLA production is the provision of optically pure lactic acid, which...