Characterization ofDhKHA1, a gene coding for a putative Na+transporter fromDebaryomyces hansenii

Utilization of salt-rich by-products from the dairy industry as feedstock for recombinant protein production by Debaryomyces hansenii

The dairy industry processes vast amounts of milk and generates high amounts of secondary by-products, which are still rich in nutrients (high Chemical Oxygen Demand (COD) and Biochemical Oxygen Demand (BOD) levels) but contain high concentrations of salt. The current European legislation only allows disposing of these effluents directly into the waterways with previous treatment, which is laborious and expensive. Therefore, as much as possible, these by-products are reutilized as animal feed material and, if not applicable, used as fertilizers adding phosphorus, potassium, nitrogen, and other nutrients to the soil. Finding biological alternatives to revalue dairy by-products is of crucial interest in order to improve the utilization of dry dairy matter and reduce the environmental impact of every litre of milk produced. Debaryomyces hansenii is a halotolerant non-conventional yeast with high potential for this purpose. It presents some beneficial traits - capacity to metabolize a variety of sugars, tolerance to high osmotic environments, resistance to extreme temperatures and pHs - that make this yeast a well-suited option to grow using complex feedstock, such as industrial waste, instead of the traditional commercial media. In this work, we study for the first time D. hansenii's ability to grow and produce a recombinant protein (YFP) from dairy saline whey by-products. Cultivations at different scales (1.5, 100 and 500 ml) were performed without neither sterilizing the medium nor using pure water. Our results conclude that D. hansenii is able to perform well and produce YFP in the aforementioned salty substrate. Interestingly, it is able to outcompete other microorganisms present in the waste without altering its cell performance or protein production capacity.

Debaryomyces hansenii: an old acquaintance for a fresh start in the era of the green biotechnology

The halophilic yeast Debaryomyces hansenii has been studied for several decades, serving as eukaryotic model for understanding salt and osmotic tolerance. Nevertheless, lack of consensus among different studies is found and, sometimes, contradictory information derived from studies performed in very diverse conditions. These two factors hampered its establishment as the key biotechnological player that was called to be in the past decade. On top of that, very limited (often deficient) engineering tools are available for this yeast. Fortunately Debaryomyces is again gaining momentum and recent advances using highly instrumented lab scale bioreactors, together with advanced –omics and HT-robotics, have revealed a new set of interesting results. Those forecast a very promising future for D. hansenii in the era of the so-called green biotechnology. Moreover, novel genetic tools enabling precise gene editing on this yeast are now available. In this review, we highlight the most recent developments, which include the identification of a novel gene implicated in salt tolerance, a newly proposed survival mechanism for D. hansenii at very high salt and limiting nutrient concentrations, and its utilization as production host in biotechnological processes.

DebaryOmics: an integrative -omics study to understand the halophilic behaviour of Debaryomyces hansenii

Debaryomyces hansenii is a non-conventional yeast considered to be a well-suited option for a number of different industrial bioprocesses. It exhibits a set of beneficial traits (halotolerant, oleaginous, xerotolerant, inhibitory compounds resistant) which translates to a number of advantages for industrial fermentation setups when compared to traditional hosts. Although D. hansenii has been highly studied during the last three decades, especially in regards to its salt-tolerant character, the molecular mechanisms underlying this natural tolerance should be further investigated in order to broadly use this yeast in biotechnological processes. In this work, we performed a series of chemostat cultivations in controlled bioreactors where D. hansenii (CBS 767) was grown in the presence of either 1M NaCl or KCl and studied the transcriptomic and (phospho)proteomic profiles. Our results show that sodium and potassium trigger different responses at both expression and regulation of protein activity levels and also complemented previous reports pointing to specific cellular processes as key players in halotolerance, moreover providing novel information about the specific genes involved in each process. The phosphoproteomic analysis, the first of this kind ever reported in D. hansenii, also implicated a novel and yet uncharacterized cation transporter in the response to high sodium concentrations.

A physiological characterization in controlled bioreactors reveals a novel survival strategy for Debaryomyces hansenii at high salinity

Debaryomyces hansenii is traditionally described as a halotolerant non-conventional yeast and has served as a model organism for the study of osmotolerance and salt tolerance mechanisms in eukaryotic systems for the past 30 years. However, unraveling of D. hansenii's biotechnological potential has always been difficult due to the persistent limitations in the availability of efficient molecular tools described for this yeast. Additionally, there is a lack of consensus and contradictory information along the recent years that limits a comprehensive understanding of its central carbon metabolism, mainly due to a lack of physiological studies in controlled and monitored environments. Moreover, there is little consistency in the culture conditions (media composition, temperature, and pH among others) used by different groups, which makes it complicated when trying to get prevalent conclusions on behavioral patterns. In this work, we present for the first time a characterization of D. hansenii in batch cultivations using highly controlled lab-scale bioreactors. Our findings contribute to a more complete picture of the central carbon metabolism and the external pH influence on the yeast's ability to tolerate high Na⁺ and K⁺ concentrations, pointing to a differential effect of both salts, as well as a positive effect in cell performance when low environmental pH values are combined with a high sodium concentration in the media. Finally, a novel survival strategy at very high salinity (2 M) is proposed for this yeast, as well as potential outcomes for its use in industrial biotechnology applications. TAKE AWAY: High salt concentrations stimulate respiration in Debaryomyces hansenii. Sodium exerts a stronger positive impact on cell performance than potassium. μ_max is higher at a combination of low pH, high salt, and high temperature. Concentrations of 2 M salt result in slower growth but increased biomass yield. The positive effect of salts is enhanced at low glucose concentration.

Cell Factories for Industrial Production Processes: Current Issues and Emerging Solutions

Despite all the progresses made by metabolic engineering, still only a few biotechnological processes are running at an industrial level. In order to boost the biotechnological sector, integration strategies as well as long-term views are needed. The aim of the present review is to identify the main drawbacks in biotechnological processes, and to propose possible solutions to overcome the issues in question. Novel cell factories and bioreactor design are discussed as possible solutions. In particular, the following microorganisms: Yarrowia lipolytica, Trichosporon oleaginosus, Ustilago cynodontis, Debaryomyces hansenii along with sequential bioreactor configurations are presented as possible cell factories and bioreactor design solutions, respectively.

Overlapping responses between salt and oxidative stress in Debaryomyces hansenii

Debaryomyces hansenii is a halotolerant yeast of importance in basic and applied research. Previous reports hinted about possible links between saline and oxidative stress responses in this yeast. The aim of this work was to study that hypothesis at different molecular levels, investigating after oxidative and saline stress: (i) transcription of seven genes related to oxidative and/or saline responses, (ii) activity of two main anti-oxidative enzymes, (iii) existence of common metabolic intermediates, and (iv) generation of damages to biomolecules as lipids and proteins. Our results showed how expression of genes related to oxidative stress was induced by exposure to NaCl and KCl, and, vice versa, transcription of some genes related to osmotic/salt stress responses was regulated by H₂O₂. Moreover, and contrary to S. cerevisiae, in D. hansenii HOG1 and MSN2 genes were modulated by stress at their transcriptional level. At the enzymatic level, saline stress also induced antioxidative enzymatic defenses as catalase and glutathione reductase. Furthermore, we demonstrated that both stresses are connected by the generation of intracellular ROS, and that hydrogen peroxide can affect the accumulation of in-cell sodium. On the other hand, no significant alterations in lipid oxidation or total glutathione content were observed upon exposure to both stresses tested. The results described in this work could help to understand the responses to both stressors, and to improve the biotechnological potential of D. hansenni.

Vacuolar control of subcellular cation distribution is a key parameter in the adaptation of Debaryomyces hansenii to high salt concentrations

Debaryomyces hansenii is a halotolerant and Na⁺-includer yeast that can be isolated from different food and low-water activity products. It has also been defined as a marine-occurring yeast but key aspects for this salt tolerant behavior are far from being understood. Here, we searched for clues helping to elucidate the basis of this ability. Our results on growth, Rb⁺ transport, total K⁺ and Na⁺ content and vacuolar fragmentation are compatible with a yeast species adapted to cope with salt stress. On the other hand, we confirmed the existence of D. hansenii strategies that are generally observed in sensitive organisms, such as the production of glycerol as a compatible solute and the efficient vacuolar sequestration of Na⁺. We propose a striking role of D. hansenii vacuoles in the maintenance of constant cytosolic K⁺ values, even in the presence of extracellular Na⁺ concentration values more than two orders of magnitude higher than extracellular K⁺. Finally, the ability to deal with cytosolic Na⁺ levels significantly higher than those found in S. cerevisiae, shows the existence of important and specific salt tolerance mechanisms and determinants in D. hansenii.

The halotolerant Debaryomyces hansenii, the Cinderella of non-conventional yeasts

Debaryomyces hansenii is a halotolerant yeast with a high biotechnological potential, particularly in the food industry. However, research in this yeast is limited by its molecular peculiarities. In this review we summarize the state of the art of research in this microorganisms, describing both pros and cons. We discuss (i) its halotolerance, (ii) the molecular factors involved in saline and osmotic stress, (iii) its high gene density and ambiguous CUG decoding, and (iv) its biotechnological and medical interests. We trust that all the bottlenecks in its study will soon be overcome and D. hansenii will become a fundamental organism for food biotechnological processes. Copyright © 2016 John Wiley & Sons, Ltd.

Alkali metal cation transport and homeostasis in yeasts

The maintenance of appropriate intracellular concentrations of alkali metal cations, principally K(+) and Na(+), is of utmost importance for living cells, since they determine cell volume, intracellular pH, and potential across the plasma membrane, among other important cellular parameters. Yeasts have developed a number of strategies to adapt to large variations in the concentrations of these cations in the environment, basically by controlling transport processes. Plasma membrane high-affinity K(+) transporters allow intracellular accumulation of this cation even when it is scarce in the environment. Exposure to high concentrations of Na(+) can be tolerated due to the existence of an Na(+), K(+)-ATPase and an Na(+), K(+)/H(+)-antiporter, which contribute to the potassium balance as well. Cations can also be sequestered through various antiporters into intracellular organelles, such as the vacuole. Although some uncertainties still persist, the nature of the major structural components responsible for alkali metal cation fluxes across yeast membranes has been defined within the last 20 years. In contrast, the regulatory components and their interactions are, in many cases, still unclear. Conserved signaling pathways (e.g., calcineurin and HOG) are known to participate in the regulation of influx and efflux processes at the plasma membrane level, even though the molecular details are obscure. Similarly, very little is known about the regulation of organellar transport and homeostasis of alkali metal cations. The aim of this review is to provide a comprehensive and up-to-date vision of the mechanisms responsible for alkali metal cation transport and their regulation in the model yeast Saccharomyces cerevisiae and to establish, when possible, comparisons with other yeasts and higher plants.

Characterization of a salt-induced DhAHP, a gene coding for alkyl hydroperoxide reductase, from the extremely halophilic yeast Debaryomyces hansenii

BACKGROUND

Debaryomyces hansenii is one of the most salt tolerant species of yeast and has become a model organism for the study of tolerance mechanisms against salinity. The goal of this study was to identify key upregulated genes that are involved in its adaptation to high salinity.

RESULTS

By using forward subtractive hybridization we have cloned and sequenced DhAHP from D. hansenii that is significantly upregulated during salinity stress. DhAHP is orthologous to the alkly hydroperoxide reductase of the peroxiredoxin gene family, which catalyzes the reduction of peroxides at the expense of thiol compounds. The full-lengthed cDNA of DhAHP has 674 bp of nucleotide and contains a 516 bp open reading frame (ORF) encoding a deduced protein of 172 amino acid residues (18.3 kDa). D. hansenii Ahp is a cytosolic protein that belongs to the Ahp of the 1-Cys type peroxiredoxins. Phylogentically, the DhAhp and Candida albicans Ahp11 (Swiss-Prot: Q5AF44) share a common ancestry but show divergent evolution. Silence of its expression in D. hansenii by RNAi resulted in decreased tolerance to salt whereas overexpression of DhAHP in D. hansenii and the salt-sensitive yeasts Saccharomyces cereviasiae and Pichia methanolica conferred a higher tolerance with a reduced level of reactive oxygen species.

CONCLUSION

In conclusion, for the first time our study has identified alkly hydroperoxide reductase as a key protein involved in the salt tolerance of the extremely halophilic D. hansenii. Apparently, this enzyme plays a multi-functional role in the yeast's adaptation to salinity; it serves as a peroxidase in scavenging reactive oxygen species, as a molecular chaperone in protecting essential proteins from denaturation, and as a redox sensor in regulating H2O2-mediated cell defense signaling.