A cadmium-transporting P1B-type ATPase in yeast Saccharomyces cerevisiae

Cryo-EM structure of cadmium-bound human ABCB6

ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy structures of human ABCB6 bound to a cadmium Cd(II) ion in the presence of antioxidant thiol peptides glutathione (GSH) and phytochelatin 2 (PC2) at resolutions of 3.2 and 3.1 Å, respectively. The overall folding of the two structures resembles the inward-facing apo state but with less separation between the two halves of the transporter. Two GSH molecules are symmetrically bound to the Cd(II) ion in a bent conformation, with the central cysteine protruding towards the metal. The N-terminal glutamate and C-terminal glycine of GSH do not directly interact with Cd(II) but contribute to neutralizing positive charges of the binding cavity by forming hydrogen bonds and van der Waals interactions with nearby residues. In the presence of PC2, Cd(II) binding to ABCB6 is similar to that observed with GSH, except that two cysteine residues of each PC2 molecule participate in Cd(II) coordination to form a tetrathiolate. Structural comparison of human ABCB6 and its homologous Atm-type transporters indicate that their distinct substrate specificity might be attributed to variations in the capping residues situated at the top of the substrate-binding cavity.

Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast

In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.

The cadmium tolerance enhancement through regulating glutathione conferred by vacuolar compartmentalization in Aspergillus sydowii

Aspergillus was found to be a vital hyperaccumulation species for heavy metal removal with admirable tolerance capacity. But the potential tolerance mechanism has not been completely studied. This study quantified the amounts of total cadmium (Cd), Cd2+, glutathione (GSH), and reactive oxygen species (ROS) in the protoplasts and vacuoles of mycelium. We modulated GSH synthesis using buthionine sulfoximine (BSO) and 2-oxothiazolidine-4-carboxylic acid (OTC) to investigate the subcellular regulatory mechanisms of GSH in the accumulation of Cd. The results confirmed that GSH plays a crucial role in vacuolar compartmentalization under Cd stress. GSH and GSSG as a redox buffer to keep the cellular redox state in balance and GSH as a metal chelating agent to reduce toxicity. When regulating the decreased GSH content with BSO, and increased GSH content with OTC, the system of Cd-GSH-ROS can change accordingly, this also supported that vacuolar compartmentalization is a detoxification strategy that can modulate the transport and storage of substances inside and outside the vacuole reasonably. Interestingly, GSH tended to be distributed in the cytoplasm, the battleground of redox takes place in the cytoplasm but not in the vacuole. These finding potentially has implications for the understanding of tolerance behavior and detoxification mechanisms of cells. In the future bioremediation of Cd in soil, the efficiency of soil remediation can be improved by developing organisms with high GSH production capacity.

The arbuscular mycorrhizal fungus Rhizophagus irregularis uses the copper exporting ATPase RiCRD1 as a major strategy for copper detoxification

Arbuscular mycorrhizal (AM) fungi establish a mutualistic symbiosis with most land plants. AM fungi regulate plant copper (Cu) acquisition both in Cu deficient and polluted soils. Here, we report characterization of RiCRD1, a Rhizophagus irregularis gene putatively encoding a Cu transporting ATPase. Based on its sequence analysis, RiCRD1 was identified as a plasma membrane Cu + efflux protein of the P1B1-ATPase subfamily. As revealed by heterologous complementation assays in yeast, RiCRD1 encodes a functional protein capable of conferring increased tolerance against Cu. In the extraradical mycelium, RiCRD1 expression was highly up-regulated in response to high concentrations of Cu in the medium. Comparison of the expression patterns of different players of metal tolerance in R. irregularis under high Cu levels suggests that this fungus could mainly use a metal efflux based-strategy to cope with Cu toxicity. RiCRD1 was also expressed in the intraradical fungal structures and, more specifically, in the arbuscules, which suggests a role for RiCRD1 in Cu release from the fungus to the symbiotic interface. Overall, our results show that RiCRD1 encodes a protein which could have a pivotal dual role in Cu homeostasis in R. irregularis, playing a role in Cu detoxification in the extraradical mycelium and in Cu transfer to the apoplast of the symbiotic interface in the arbuscules.

Functional characterization of genes encoding cadmium pumping P1B-type ATPases in Aspergillus fumigatus and Aspergillus nidulans

Several P1B-type ATPases are important Cd2+/Cu2+ pumps in Aspergillus species, and they are tightly associated with the heavy metal stress tolerance of these ascomycetous fungi. To better understand the roles of the two P1B-type ATPases, Aspergillus nidulans CrpA Cd2+/Cu2+ pump (orthologue of the Candida albicans Crp1 Cd2+/Cu2+ pump) and Aspergillus fumigatus PcaA Cd2+ pump (orthologue of the Saccharomyces cerevisiae Pca1 Cd2+ pump), we have generated individual mutants and characterized their heavy metal susceptibilities. The deletion of CrpA in A. nidulans has led to the increased sensitivity of the fungus to stresses induced by Zn2+, Fe2+, or the combination of oxidative-stress-inducing menadione sodium bisulfite and Fe3+. Heterologous expression of A. fumigatus PcaA in the S. cerevisiae pca1 deletion mutant has resulted in enhanced tolerance of the yeast to stresses elicited by Cd2+or Zn2+ but not by Fe2+/Fe3+ or Cu2+. Mammalian host immune defense can attack microbes by secreting Zn2+ or Cu2+, and the oxidative stress induced by host immune systems can also disturb metal (Cu2+, Fe2+, and Zn2+) homeostasis in microbes. In summary, PcaA and CrpA can protect fungal cells from these complex stresses that contribute to the virulence of the pathogenic Aspergillus species. Moreover, due to their presence on the fungal cell surface, these P1B-type ATPases may serve as a novel drug target in the future. IMPORTANCE Mammalian host immune defense disrupts heavy metal homeostasis of fungal pathogens. P1B-type ATPase of Aspergillus fumigatus and Aspergillus nidulans may help to cope with this stress and serve as virulence traits. In our experiments, both A. nidulans Cd2+/Cu2+ pump CrpA and A. fumigatus Cd2+ pump PcaA protected fungal cells from toxic Zn2+, and CrpA also decreased Fe2+ susceptibility most likely indirectly. In addition, CrpA protected cells against the combined stress induced by the oxidative stressor menadione and Fe3+. Since P1B-type ATPases are present on the fungal cell surface, these proteins may serve as a novel drug target in the future.

A novel method of rapid detection for heavy metal copper ion via a specific copper chelator bathocuproinedisulfonic acid disodium salt

The extensive usage and production of copper may lead to toxic effects in organisms due to its accumulation in the environment. Traditional methods for copper detection are time consuming and infeasible for field usage. It is necessary to discover a real-time, rapid and economical method for detecting copper to ensure human health and environmental safety. Here we developed a colorimetric paper strip method and optimized spectrum method for rapid detection of copper ion based on the specific copper chelator bathocuproinedisulfonic acid disodium salt (BCS). Both biological assays and chemical methods verified the specificity of BCS for copper. The optimized reaction conditions were 50 mM Tris-HCl pH 7.4, 200 µM BCS, 1 mM ascorbate and less than 50 µM copper. The detection limit of the copper paper strip test was 0.5 mg/L by direct visual observation and the detection time was less than 1 min. The detection results of grape, peach, apple, spinach and cabbage by the optimized spectrum method were 0.91 μg/g, 0.87 μg/g, 0.19 μg/g, 1.37 μg/g and 0.39 μg/g, respectively. The paper strip assays showed that the copper contents of grape, peach, apple, spinach and cabbage were 0.8 mg/L, 0.9 mg/L, 0.2 mg/L, 1.3 mg/L and 0.5 mg/L, respectively. These results correlated well with those determined by inductively coupled plasma-mass spectrometry (ICP-MS). The visual detection limit of the paper strip based on Cu-BCS-AgNPs was 0.06 mg/L. Our study demonstrates the potential for on-site, rapid and cost-effective copper monitoring of foods and the environment.

A contrast of Pb(II), Cd(II), and Cu(II) toxicities to Aspergillus niger through biochemical, morphological, and genetic investigations

The toxicity of metals to microorganisms is highly correlated with the type of metal used. However, the differences in the resistance mechanisms of filamentous fungi to multiple metals remain unclear. In this study, we investigated the responses of Aspergillus niger to three toxic metals, i.e., Pb²⁺, Cd²⁺, and Cu²⁺. Fungal growth and metabolism indices showed that A. niger had a higher tolerance to Pb²⁺ (>1000 mg L^-1) than to Cu²⁺ (300 mg L^-1) and Cd²⁺ (50 mg L^-1). An appropriate Pb²⁺ concentration (<500 mg L^-1) stimulated fungal growth and metabolic activity, whereas Cd²⁺ and Cu²⁺ stress showed continuously negative influences on fungal physiological parameters, such as biomass and secretion of oxalic acid. A. niger responded to Pb stress by constructing a new border layer around its cell wall. This pathway was also confirmed using RNA-seq analysis, i.e., the gene encoding cell wall α-1,3-glucan synthase was upregulated. This upregulation subsequently promoted the production of polysaccharides, which are the main components that support fungal cell walls. In contrast, the expression of genes encoding both AAA family ATPase and efflux pump antibiotic resistance proteins for Cd²⁺ and Cu²⁺ was significantly downregulated. Therefore, these findings elucidated the relatively complete fungal responses to different metal stresses.

Longitudinal physiological and transcriptomic analyses reveal the short term and long term response of Synechocystis sp. PCC6803 to cadmium stress

Due to the bioaccumulation and non-biodegradability of cadmium, Cd can pose a serious threat to ecosystem even at low concentration. Microalgae is widely distributed photosynthetic organisms in nature, which is a promising heavy metal remover and an effective industrial sewage cleaner. However, there are few detailed reports on the short-term and long-term molecular mechanisms of microalgae under Cd stress. In this study, the adsorption behavior (growth curve, Cd removal efficiency, scanning electron microscope, Fourier transform infrared spectroscopy, and dynamic change of extracellular polymeric substances), cytotoxicity (photosynthetic pigment, MDA, GSH, H₂O₂, O₂^-) and stress response mechanism of microalgae were discussed under EC50. RNA-seq detected 1413 DEGs in 4 treatment groups. These genes were related to ribosome, nitrogen metabolism, sulfur transporter, and photosynthesis, and which been proved to be Cd-responsive DEGs. WGCNA (weighted gene co-expression network analysis) revealed two main gene expression patterns, short-term stress (381 genes) and long-term stress (364 genes). The enrichment analysis of DEGs showed that the expression of genes involved in N metabolism, sulfur transporter, and aminoacyl-tRNA biosynthesis were significantly up-regulated. This provided raw material for the synthesis of the important component (cysteine) of metal chelate protein, resistant metalloprotein and transporter (ABC transporter) in the initial stage, which was also the short-term response mechanism. Cd adsorption of the first 15 min was primary dependent on membrane transporter and beforehand accumulated EPS. Simultaneously, the up-regulated glutathione S-transferase (GSTs) family proteins played a role in the initial resistance to exogenous Cd. The damaged photosynthetic system was repaired at the later stage, the expressions of glycolysis and gluconeogenesis were up-regulated, to meet the energy and substances of physiological metabolic activities. The study is the first to provide detailed short-term and long-term genomic information on microalgae responding to Cd stress. Meanwhile, the key genes in this study can be used as potential targets for algae-mediated genetic engineering.

Accumulation and Enrichment of Trace Elements by Yeast Cells and Their Applications: A Critical Review

Maintaining the homeostasis balance of trace elements is crucial for the health of organisms. Human health is threatened by diseases caused by a lack of trace elements. Saccharomyces cerevisiae has a wide and close relationship with human daily life and industrial applications. It can not only be used as fermentation products and single-cell proteins, but also as a trace elements supplement that is widely used in food, feed, and medicine. Trace-element-enriched yeast, viz., chromium-, iron-, zinc-, and selenium-enriched yeast, as an impactful microelements supplement, is more efficient, more environmentally friendly, and safer than its inorganic and organic counterparts. Over the last few decades, genetic engineering has been developing large-scaled genetic re-design and reconstruction in yeast. It is hoped that engineered yeast will include a higher concentration of trace elements. In this review, we compare the common supplement forms of several key trace elements. The mechanisms of detoxification and transport of trace elements in yeast are also reviewed thoroughly. Moreover, genes involved in the transport and detoxification of trace elements are summarized. A feasible way of metabolic engineering transformation of S. cerevisiae to produce trace-element-enriched yeast is examined. In addition, the economy, safety, and environmental protection of the engineered yeast are explored, and the future research direction of yeast enriched in trace elements is discussed.

Microbial silver resistance mechanisms: recent developments

In this mini-review, after a brief introduction into the widespread antimicrobial use of silver ions and nanoparticles against bacteria, fungi and viruses, the toxicity of silver compounds and the molecular mechanisms of microbial silver resistance are discussed, including recent studies on bacteria and fungi. The similarities and differences between silver ions and silver nanoparticles as antimicrobial agents are also mentioned. Regarding bacterial ionic silver resistance, the roles of the sil operon, silver cation efflux proteins, and copper-silver efflux systems are explained. The importance of bacterially produced exopolysaccharides as a physiological (biofilm) defense mechanism against silver nanoparticles is also emphasized. Regarding fungal silver resistance, the roles of metallothioneins, copper-transporting P-type ATPases and cell wall are discussed. Recent evolutionary engineering (adaptive laboratory evolution) studies are also discussed which revealed that silver resistance can evolve rapidly in bacteria and fungi. The cross-resistance observed between silver resistance and resistance to other heavy metals and antibiotics in bacteria and fungi is also explained as a clinically and environmentally important issue. The use of silver against bacterial and fungal biofilm formation is also discussed. Finally, the antiviral effects of silver and the use of silver nanoparticles against SARS-CoV-2 and other viruses are mentioned. To conclude, silver compounds are becoming increasingly important as antimicrobial agents, and their widespread use necessitates detailed understanding of microbial silver response and resistance mechanisms, as well as the ecological effects of silver compounds. Figure created with BioRender.com.

Comparative Copper Resistance Strategies of Rhodonia placenta and Phanerochaete chrysosporium in a Copper/Azole-Treated Wood Microcosm

Copper-based formulations of wood preservatives are widely used in industry to protect wood materials from degradation caused by fungi. Wood treated with preservatives generate toxic waste that currently cannot be properly recycled. Despite copper being very efficient as an antifungal agent against most fungi, some species are able to cope with these high metal concentrations. This is the case for the brown-rot fungus Rhodonia placenta and the white-rot fungus Phanerochaete chrysosporium, which are able to grow efficiently in pine wood treated with Tanalith E3474. Here, we aimed to test the abilities of the two fungi to cope with copper in this toxic environment and to decontaminate Tanalith E-treated wood. A microcosm allowing the growth of the fungi on industrially treated pine wood was designed, and the distribution of copper between mycelium and wood was analysed within the embedded hyphae and wood particles using coupled X-ray fluorescence spectroscopy and Scanning Electron Microscopy (SEM)/Electron Dispersive Spectroscopy (EDS). The results demonstrate the copper biosorption capacities of P. chrysosporium and the production of copper-oxalate crystals by R. placenta. These data coupled to genomic analysis suggest the involvement of additional mechanisms for copper tolerance in these rot fungi that are likely related to copper transport (import, export, or vacuolar sequestration).

Insight Into the Molecular Mechanisms Underpinning the Mycoremediation of Multiple Metals by Proteomic Technique

We investigated the fungus Aspergillus fumigatus PD-18 responses when subjected to the multimetal combination (Total Cr, Cd2+, Cu2+, Ni2+, Pb2+, and Zn2+) in synthetic composite media. To understand how multimetal stress impacts fungal cells at the molecular level, the cellular response of A. fumigatus PD-18 to 30 mg/L multimetal stress (5 mg/L of each heavy metal) was determined by proteomics. The comparative fungal proteomics displayed the remarkable inherent intracellular and extracellular mechanism of metal resistance and tolerance potential of A. fumigatus PD-18. This study reported 2,238 proteins of which 434 proteins were exclusively expressed in multimetal extracts. The most predominant functional class expressed was for cellular processing and signaling. The type of proteins and the number of proteins that were upregulated due to various stress tolerance mechanisms were post-translational modification, protein turnover, and chaperones (42); translation, ribosomal structure, and biogenesis (60); and intracellular trafficking, secretion, and vesicular transport (18). In addition, free radical scavenging antioxidant proteins, such as superoxide dismutase, were upregulated upto 3.45-fold and transporter systems, such as protein transport (SEC31), upto 3.31-fold to combat the oxidative stress caused by the multiple metals. Also, protein–protein interaction network analysis revealed that cytochrome c oxidase and 60S ribosomal protein played key roles to detoxify the multimetal. To the best of our knowledge, this study of A. fumigatus PD-18 provides valuable insights toward the growing research in comprehending the metal microbe interactions in the presence of multimetal. This will facilitate in development of novel molecular markers for contaminant bioremediation.

Nonsense-mediated mRNA decay and metal ion homeostasis and detoxification in Saccharomyces cerevisiae

The highly conserved Nonsense-mediated mRNA decay (NMD) pathway is a translation dependent mRNA degradation pathway. Although NMD is best known for its role in degrading mRNAs with premature termination codons (PTCs) generated during transcription, splicing, or damage to the mRNAs, NMD is now also recognized as a pathway with additional important functions. Notably, NMD precisely regulates protein coding natural mRNAs, hence controlling gene expression within several physiologically significant pathways. Such pathways affected by NMD include nutritional bio-metal homeostasis and metal ion detoxification, as well as crosstalk between these pathways. Here, we focus on the relationships between NMD and various metal homeostasis and detoxification pathways. We review the described role that the NMD pathway plays in magnesium, zinc, iron, and copper homeostasis, as well as cadmium detoxification.

Novel Latex Microsphere Immunochromatographic Assay for Rapid Detection of Cadmium Ion in Asparagus

Recently, concerns about heavy metal cadmium ion (Cd²⁺) residue in asparagus have been frequently reported, and there is an urgent need to develop an effective, sensitive, and rapid detection method for Cd²⁺. In this study, we innovatively combined molecular microbiology to carry out the comparative screening of Cd²⁺ chelators in a green, efficient, and specific way. The knock-out putative copper-transporter gene (pca1Δ) yeast strain with high sensitivity to Cd²⁺ was first used to screen the Cd²⁺ chelator, and the optimum chelator 1-(4-Isothiocyanatobenzyl)ethylenediamine-N,N,N,N′-tetraacetic acid (ITCBE) was obtained. Additionally, a rapid latex microsphere immunochromatographic assay (LMIA) was developed, based on the obtained monoclonal antibody (mAb) with high specificity and high affinity (affinity constant Ka = 1.83 × 10¹⁰ L/mol), to detect Cd²⁺ in asparagus. The 50% inhibitive concentration (IC₅₀) of test strip was measured to be 0.2 ng/mL, and the limit of detection (IC₁₀) for qualitative (LOD, for visual observation) and quantitative detection (LOQ, for data simulation) of the test strip was 2 ng/mL and 0.054 ng/mL, respectively. In all, the developed mAb-based LMIA shows a great potential for monitoring Cd²⁺ in asparagus, even in vegetable samples.

Molecular Biology of Cadmium Toxicity in Saccharomyces cerevisiae

Cadmium (Cd) is a toxic heavy metal mainly originating from industrial activities and causes environmental pollution. To better understand its toxicity and pollution remediation, we must understand the effects of Cd on living beings. Saccharomyces cerevisiae (budding yeast) is an eukaryotic unicellular model organism. It has provided much scientific knowledge about cellular and molecular biology in addition to its economic benefits. Effects associated with copper and zinc, sulfur and selenium metabolism, calcium (Ca²⁺) balance/signaling, and structure of phospholipids as a result of exposure to cadmium have been evaluated. In yeast as a result of cadmium stress, "mitogen-activated protein kinase," "high osmolarity glycerol," and "cell wall integrity" pathways have been reported to activate different signaling pathways. In addition, abnormalities and changes in protein structure, ribosomes, cell cycle disruption, and reactive oxygen species (ROS) following cadmium cytotoxicity have also been detailed. Moreover, the key OLE1 gene that encodes for delta-9 FA desaturase in relation to cadmium toxicity has been discussed in more detail. Keeping all these studies in mind, an attempt has been made to evaluate published cellular and molecular toxicity data related to Cd stress, and specifically published on S. cerevisiae.

Genetic system underlying responses of Cryptococcus neoformans to cadmium

Cryptococcus neoformans, basidiomycetous pathogenic yeast, is basically an environmental fungus and, therefore, challenged by ever changing environments. In this study, we focused on how C. neoformans responds to stress caused by cadmium that is one of high-risk pollutants. By tracking phenotypes of the resistance or sensitivity to cadmium, we undertook forward and reverse genetic studies to identify genes involved in cadmium metabolism in C. neoformans. We found that the main route of Cd²⁺ influx is through Mn²⁺ ion transporter, Smf1, which is an ortholog of Nramp (natural resistance-associated macrophage protein 1) of mouse. We found that serotype A strains are generally more resistant to cadmium than serotype D strains and that cadmium resistance of H99, a representative of serotype A strains, was found to be due to a partial defect in SMF1. We found that calcium channel has a subsidiary role for cadmium uptake. We also showed that Pca1 (P-type-ATPase) functions as an extrusion pump for cadmium. We examined the effects of some metals on cadmium toxicity and suggested (i) that Ca²⁺ and Zn²⁺ could exert their protective function against Cd²⁺ via restoring cadmium-inhibited cellular processes and (ii) that Mg²⁺ and Mn²⁺ could have antagonistic roles in an unknown Smf1-independent Cd²⁺ uptake system. We proposed a model for Cd2⁺-response of C. neoformans, which will serve as a platform for understanding how this organism copes with the toxic metal.

Genome-Scale Screening and Combinatorial Optimization of Gene Overexpression Targets to Improve Cadmium Tolerance in Saccharomyces cerevisiae

Heavy metal contamination is an environmental issue on a global scale. Particularly, cadmium poses substantial threats to crop and human health. Saccharomyces cerevisiae is one of the model organisms to study cadmium toxicity and was recently engineered as a cadmium hyperaccumulator. Therefore, it is desirable to overcome the cadmium sensitivity of S. cerevisiae via genetic engineering for bioremediation applications. Here we performed genome-scale overexpression screening for gene targets conferring cadmium resistance in CEN.PK2-1c, an industrial S. cerevisiae strain. Seven targets were identified, including CAD1 and CUP1 that are known to improve cadmium tolerance, as well as CRS5, NRG1, PPH21, BMH1, and QCR6 that are less studied. In the wild-type strain, cadmium exposure activated gene transcription of CAD1, CRS5, CUP1, and NRG1 and repressed PPH21, as revealed by real-time quantitative PCR analyses. Furthermore, yeast strains that contained two overexpression mutations out of the seven gene targets were constructed. Synergistic improvement in cadmium tolerance was observed with episomal co-expression of CRS5 and CUP1. In the presence of 200 μM cadmium, the most resistant strain overexpressing both CAD1 and NRG1 exhibited a 3.6-fold improvement in biomass accumulation relative to wild type. This work provided a new approach to discover and optimize genetic engineering targets for increasing cadmium resistance in yeast.

Variation of the response to metal ions and nonsense-mediated mRNA decay across different Saccharomyces cerevisiae genetic backgrounds

Regulation of mRNA steady-state levels is important in controlling gene expression particularly in response to environmental stimuli. This allows cells to rapidly respond to environment changes. The highly conserved nonsense-mediated mRNA decay (NMD) pathway was initially identified as a pathway that degrades aberrant mRNAs. NMD is now recognized as a pathway with additional functions including precisely regulating the expression of select natural mRNAs. Majority of these natural mRNAs encode fully functional proteins. Regulation of natural mRNAs by NMD is activated by NMD targeting features and environmental cues. Here, we show that Saccharomyces cerevisiae strains from three genetic backgrounds respond differentially to NMD depending on the environmental stimuli. We found that wild type and NMD mutant W303a, BY4741, and RM11-1a yeast strains respond similarly to copper in the environment but respond differentially to toxic cadmium. Furthermore, the PCA1 alleles encoding different mRNAs from W303a and RM11-1a strains are regulated similarly by NMD in response to the bio-metal copper but differentially in response to toxic cadmium.

Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice

Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a small number of other Aureobasidium species have been reported, that in contrast to A. pullulans, appear far more constrained to specific habitats. It is unknown whether grape juice is a reservoir of novel Aureobasidium species, overlooked in the course of conventional morphological and meta-barcoding analyses. In this study, eight isolates from grape juice taxonomically classified as Aureobasidium through ITS sequencing were subjected to whole-genome phylogenetic, synteny and nucleotide identity analyses, which revealed three isolates to likely represent newly discovered Aureobasidium species. Analyses of ITS and metagenomic sequencing datasets show that these species can be present in grape juice samples from different locations and vintages. Functional annotation revealed the Aureobasidium isolates possess the genetic potential to support growth on the surface of plants and grapes. However, the loss of several genes associated with tolerance to diverse environmental stresses suggest a more constrained ecological range than A. pullulans.

Aneuploidy-induced proteotoxic stress can be effectively tolerated without dosage compensation, genetic mutations, or stress responses

BACKGROUND

The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport, and degradation within a cell. Failure to maintain proteostasis is associated with aging and disease, leading to concerted efforts to study how the network responds to various proteotoxic stresses. This is often accomplished using ectopic overexpression of well-characterized, model misfolded protein substrates. However, how cells tolerate large-scale, diverse burden to the proteostasis network is not understood. Aneuploidy, the state of imbalanced chromosome content, adversely affects the proteostasis network by dysregulating the expression of hundreds of proteins simultaneously. Using aneuploid haploid yeast cells as a model, we address whether cells can tolerate large-scale, diverse challenges to the proteostasis network.

RESULTS

Here we characterize several aneuploid Saccharomyces cerevisiae strains isolated from a collection of stable, randomly generated yeast aneuploid cells. These strains exhibit robust growth and resistance to multiple drugs which induce various forms of proteotoxic stress. Whole genome re-sequencing of the strains revealed this was not the result of genetic mutations, and transcriptome profiling combined with ribosome footprinting showed that genes are expressed and translated in accordance to chromosome copy number. In some strains, various facets of the proteostasis network are mildly upregulated without chronic activation of environmental stress response or heat shock response pathways. No severe defects were observed in the degradation of misfolded proteins, using model misfolded substrates of endoplasmic reticulum-associated degradation or cytosolic quality control pathways, and protein biosynthesis capacity was not impaired.

CONCLUSIONS

We show that yeast strains of some karyotypes in the genetic background studied here can tolerate the large aneuploidy-associated burden to the proteostasis machinery without genetic changes, dosage compensation, or activation of canonical stress response pathways. We suggest that proteotoxic stress, while common, is not always an obligate consequence of aneuploidy, but rather certain karyotypes and genetic backgrounds may be able to tolerate the excess protein burden placed on the protein homeostasis machinery. This may help clarify how cancer cells are paradoxically both highly aneuploid and highly proliferative at the same time.

Effect of cadmium on essential metals and their impact on lipid metabolism in Saccharomyces cerevisiae

Cadmium (Cd) is a toxic heavy metal that induces irregularity in numerous lipid metabolic pathways. Saccharomyces cerevisiae, a model to study lipid metabolism, has been used to establish the molecular basis of cellular responses to Cd toxicity in relation to essential minerals and lipid homeostasis. Multiple pathways sense these environmental stresses and trigger the mineral imbalances specifically calcium (Ca) and zinc (Zn). This review is aimed to elucidate the role of Cd toxicity in yeast, in three different perspectives: (1) elucidate stress response and its adaptation to Cd, (2) understand the physiological role of a macromolecule such as lipids, and (3) study the stress rescue mechanism. Here, we explored the impact of Cd interference on the essential minerals such as Zn and Ca and their influence on endoplasmic reticulum stress and lipid metabolism. Cd toxicity contributes to lipid droplet synthesis by activating OLE1 that is essential to alleviate lipotoxicity. In this review, we expanded our current findings about the effect of Cd on lipid metabolism of budding yeast.

Fungal Endophytes of Alnus incana ssp. rugosa and Alnus alnobetula ssp. crispa and Their Potential to Tolerate Heavy Metals and to Promote Plant Growth

Soil contamination by metals is of particular interest, given that their retention times within the profile can be indefinite. Thus, phytostabilization can be viewed as a means of limiting metal toxicity in soils. Due to their ability to grow on contaminated soils, alders have repeatedly been used as key species in phytostabilization efforts. Alder ability to grow on contaminated sites stems, in part, from its association with microbial endophytes. This work emphasizes the fungal endophytes populations associated with Alnus incana ssp. rugosa and Alnus alnobetula ssp. crispa (previously A. viridis ssp. crispa) under a phytostabilization angle. Fungal endophytes were isolated from alder trees that were growing on or near disturbed environments; their tolerances to Cu, Ni, Zn, and As, and acidic pH (4.3, 3, and 2) were subsequently assessed. Cryptosporiopsis spp. and Rhizoscyphus spp. were identified as fungal endophytes of Alnus for the first time. When used as inoculants for alder, some isolates promoted plant growth, while others apparently presented antagonistic relationships with the host plant. This study reports the first step in finding the right fungal endophytic partners for two species of alder used in phytostabilization of metal-contaminated mining sites.

Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance

The contribution of stress protein duplication and deletion events to the evolution of the Aspergilli was studied. We performed a large-scale homology analysis of stress proteins and generated and analysed three stress defence system models based on Saccharomyces cerevisiae, Schizosaccharomyces pombe and Aspergillus nidulans. Although both yeast-based and A. nidulans-based models were suitable to trace evolutionary changes, the A. nidulans-based model performed better in mapping stress protein radiations. The strong Mantel correlation found between the positions of species in the phylogenetic tree on the one hand and either in the A. nidulans-based or S. cerevisiae-based models on the other hand demonstrated that stress protein expansions and reductions contributed significantly to the evolution of the Aspergilli. Interestingly, stress tolerance attributes correlated well with the number of orthologs only for a few stress proteins. Notable examples are Ftr1 iron permease and Fet3 ferro-O2-oxidoreductase, elements of the reductive iron assimilation pathway, in the S. cerevisiae-based model, as well as MpkC, a HogA-like mitogen activated protein kinase in the A. nidulans-based model. In the case of the iron assimilation proteins, the number of orthologs showed a positive correlation with H2O2-induced stress tolerance while the number of MpkC orthologs correlated positively with Congo Red induced cell wall stress, sorbitol induced osmotic stress and H2O2 induced oxidative stress tolerances. For most stress proteins, changes in the number of orthologs did not correlate well with any stress tolerance attributes. As a consequence, stress tolerance patterns of the studied Aspergilli did not correlate with either the sets of stress response proteins in general or with the phylogeny of the species studied. These observations suggest that stress protein duplication and deletion events significantly contributed to the evolution of stress tolerance attributes of Aspergilli. In contrast, there are other processes, which may counterbalance the effects of stress gene duplications or deletions including (i) alterations in the structures of stress proteins leading to changes in their biological activities, (ii) varying biosynthesis of stress proteins, (iii) rewiring stress response regulatory networks or even (iv) acquiring new stress response genes by horizontal gene transfer. All these multilevel changes are indispensable for the successful adaptation of filamentous fungi to altering environmental conditions, especially when these organisms are entering new ecological niches.

Physiological background of the remarkably high Cd2+ tolerance of the Aspergillus fumigatus Af293 strain

The physiological background of the unusually high cadmium tolerance (MIC₅₀  > 2 mM) of Aspergillus fumigatus Af293 was investigated. The cadmium tolerance of the tested environmental and clinical A. fumigatus strains varied over a wide range (0.25 mM < MIC₅₀  < 1 mM). Only the Af293 strain showed a MIC₅₀ value of >2 mM, and this phenotype was accompanied by increased in vivo virulence in mice. A strong correlation was found between the cadmium tolerance and the transcription of the pcaA gene, which encodes a putative cadmium efflux pump. The cadmium tolerance also correlated with the iron tolerance and the extracellular siderophore production of the strains. In addition to these findings, Af293 did not show the synergism between iron toxicity and cadmium toxicity that was detected in the other strains. Based on these results, we suggest that the primary function of PcaA should be acting as a ferrous iron pump and protecting cells from iron overload. Nevertheless, the heterologous expression of pcaA may represent an attractive strain improvement strategy to construct fungal strains for use in biosorption or biomining processes or to prevent accumulation of this toxic metal in crops.

Two P1B-1-ATPases of Amanita strobiliformis With Distinct Properties in Cu/Ag Transport

As we have shown previously, the Cu and Ag concentrations in the sporocarps of Ag-hyperaccumulating Amanita strobiliformis are correlated, and both metals share the same uptake system and are sequestered by the same metallothioneins intracellularly. To further improve our knowledge of the Cu and Ag handling in A. strobiliformis cells, we searched its transcriptome for the P_1B-1-ATPases, recognizing Cu⁺ and Ag⁺ for transport. We identified transcripts encoding 1097-amino acid (AA) AsCRD1 and 978-AA AsCCC2, which were further subjected to functional studies in metal sensitive Saccharomyces cerevisiae. The expression of AsCRD1 conferred highly increased Cu and Ag tolerance to metal sensitive yeasts in which the functional AsCRD1:GFP (green fluorescent protein) fusion localized exclusively to the tonoplast, indicating that the AsCRD1-mediated Cu and Ag tolerance was a result of vacuolar sequestration of the metals. Increased accumulation of AsCRD1 transcripts observed in A. strobiliformis mycelium upon the treatments with Cu and Ag (8.7- and 4.5-fold in the presence of 5 μM metal, respectively) supported the notion that AsCRD1 can be involved in protection of the A. strobiliformis cells against the toxicity of both metals. Neither Cu nor Ag affected the levels of AsCCC2 transcripts. Heterologous expression of AsCCC2 in mutant yeasts did not contribute to Cu tolerance, but complemented the mutant genotype of the S. cerevisiae ccc2Δ strain. Consistent with the role of the yeast Ccc2 in the trafficking of Cu from cytoplasm to nascent proteins via post-Golgi, the GFP fluorescence in AsCCC2-expressing ccc2Δ yeasts localized among Golgi-like punctate foci within the cells. The AsCRD1- and AsCCC2-associated phenotypes were lost in yeasts expressing mutant transporter variants in which a conserved phosphorylation/dephosphorylation site was altered. Altogether, the data support the roles of AsCRD1 and AsCCC2 as genuine P_1B-1-ATPases, and indicate their important functions in the removal of toxic excess of Cu and Ag from the cytoplasm and charging the endomembrane system with Cu, respectively.

Heavy Metal-Induced Expression of PcaA Provides Cadmium Tolerance to Aspergillus fumigatus and Supports Its Virulence in the Galleria mellonella Model

Most of the metal transporters in Aspergillus fumigatus are yet uncharacterized. Their role in fungal metabolism and virulence remains unclear. This paper describes the novel PIB-type cation ATPase PcaA, which links metal homeostasis and heavy metal tolerance in the opportunistic human pathogen A. fumigatus. The protein possesses conserved ATPase motif and shares 51% amino acid sequence identity with the Saccharomyces cerevisiae cadmium exporter Pca1p. A pcaA deletion, an overexpression and a gfp-pcaA complementation strain of A. fumigatus were constructed and their heavy metal susceptibilities were studied. The pcaA knock out strain showed drastically decreased cadmium tolerance, however, its growth was not affected by the exposure to high concentrations of copper, iron, zinc, or silver ions. Although the lack of PcaA had no effect on copper adaption, we demonstrated that not only cadmium but also copper ions are able to induce the transcription of pcaA in A. fumigatus wild type Af293. Similarly, cadmium and copper ions could induce the copper exporting ATPase crpA. These data imply a general response on the transcriptomic level to heavy metals in A. fumigatus through the induction of detoxification systems. Confocal microscopy of the gfp-pcaA complementation strain expressing functional GFP-PcaA supports the predicted membrane localization of PcaA. The GFP-PcaA fusion protein is located in the plasma membrane of A. fumigatus in the presence of cadmium ions. Virulence assays support a function of PcaA for virulence of A. fumigatus in the Galleria mellonella wax moth larvae model, which might be linked to the elimination of reactive oxygen species.

Surface display of synthetic phytochelatins on Saccharomyces cerevisiae for enhanced ethanol production in heavy metal-contaminated substrates

The aim of this work was to study the feasibility of surface displaying synthetic phytochelatin (EC) on Saccharomyces cerevisiae to overcome the inhibitory effect of heavy metals on ethanol production. Via the fusion of a gene encoding EC to an α-agglutinin gene, the engineered S. cerevisiae was able to successfully display EC on its surface. This surface engineered yeast strain exhibited an efficient cadmium adsorption capability and a remarkably enhanced cadmium tolerance. Moreover, its ethanol production efficiency was significantly improved as compared to a control strain in the presence of cadmium. Similar results could also be observed in the presence of other metals, such as nickel, lead and copper. Overall, this method allows simultaneous biorefinery and heavy metal removal when using heavy metal-contaminated biomass as raw materials.

Zinc protects against cadmium-induced toxicity by regulating oxidative stress, ions homeostasis and protein synthesis

The widespread environmental toxin cadmium (Cd) is associated with numerous human diseases. The essential trace element zinc (Zn) strongly counteracts Cd-induced toxicity; however, the mechanism is incompletely understood. Here, we conducted RNA sequencing and bioinformatics analyses to determine the global gene expression profiles of yeast cells exposed to Cd or Cd plus Zn. We identified 912 Cd-induced and 627 Cd plus Zn-induced differentially expressed genes (DEGs). Adding Zn during Cd exposure efficiently reversed the expression of 92.1% of Cd-induced DEGs; that of 48.7% was entirely reversed. Gene Ontology, Cluster of Orthologous Group and KEGG Ontology analyses revealed that the response of yeasts to Cd or Cd plus Zn was mainly involved in metal-specific oxidative stress; energy production and conversion; ion homeostasis and ribosome biogenesis and translation. Exposure of yeasts to Cd plus Zn protected them from oxidative stress by efficiently inhibiting the expression of genes associated with Cd-triggered oxidative stress and preventing the disruption of Fe- and Zn-ion homeostasis and reduced glutathione and partially restored mitochondrial membrane potential. Moreover, Zn reduced the intracellular level of Cd to prevent the replacement by Cd of elements required for antioxidant enzyme activity and to protect protein sulphydryl groups against oxidation by free radicals. Further, Zn inhibited the synthesis alterations of Cd-induced ribosomal proteins, S-containing amino acids, S-rich proteins and antioxidant enzymes. Conversely, the investigation results of our study on the yeast model revealed that the Cd-treated protective effects of Zn on Cd-induced toxicity might be partially protective.

Genomics of Adaptation Depends on the Rate of Environmental Change in Experimental Yeast Populations

The rate of directional environmental change may have profound consequences for evolutionary dynamics and outcomes. Yet, most evolution experiments impose a sudden large change in the environment, after which the environment is kept constant. We previously cultured replicate Saccharomyces cerevisiae populations for 500 generations in the presence of either gradually increasing or constant high concentrations of the heavy metals cadmium, nickel, and zinc. Here, we investigate how each of these treatments affected genomic evolution. Whole-genome sequencing of evolved clones revealed that adaptation occurred via a combination of SNPs, small indels, and whole-genome duplications and other large-scale structural changes. In contrast to some theoretical predictions, gradual and abrupt environmental change caused similar numbers of genomic changes. For cadmium, which is toxic already at comparatively low concentrations, mutations in the same genes were used for adaptation to both gradual and abrupt increase in concentration. Conversely, for nickel and zinc, which are toxic at high concentrations only, mutations in different genes were used for adaptation depending on the rate of change. Moreover, evolution was more repeatable following a sudden change in the environment, particularly for nickel and zinc. Our results show that the rate of environmental change and the nature of the selection pressure are important drivers of evolutionary dynamics and outcomes, which has implications for a better understanding of societal problems such as climate change and pollution.

Transcriptomic Profiles Reveal the Interactions of Cd/Zn in Dwarf Polish Wheat (Triticum polonicum L.) Roots

Different intra- or interspecific wheat show different interactions of Cd/Zn. Normally, Zn has been/being widely utilized to reduce the Cd toxicity. In the present study, the DPW seedlings exhibited strong Cd tolerance. Zn and Cd mutually inhibited their uptake in the roots, showed antagonistic Cd/Zn interactions. However, Zn promoted the Cd transport from the roots to shoots, showed synergistic. In order to discover the interactive molecular responses, a transcriptome, including 123,300 unigenes, was constructed using RNA-Sequencing (RNA-Seq). Compared with CK, the expression of 1,269, 820, and 1,254 unigenes was significantly affected by Cd, Zn, and Cd+Zn, respectively. Only 381 unigenes were co-induced by these three treatments. Several metal transporters, such as cadmium-transporting ATPase and plant cadmium resistance 4, were specifically regulated by Cd+Zn. Other metal-related unigenes, such as ABC transporters, metal chelator, nicotianamine synthase (NAS), vacuolar iron transporters (VIT), metal-nicotianamine transporter YSL (YSL), and nitrate transporter (NRT), were regulated by Cd, but were not regulated by Cd+Zn. These results indicated that these transporters participated in the mutual inhibition of the Cd/Zn uptake in the roots, and also participated in the Cd transport, accumulation and detoxification. Meanwhile, some unigenes involved in other processes, such as oxidation-reduction, auxin metabolism, glutathione (GSH) metabolism nitrate transport, played different and important roles in the detoxification of these heavy metals.

Cadmium and Secondary Structure-dependent Function of a Degron in the Pca1p Cadmium Exporter

Protein turnover is a critical cellular process regulating biochemical pathways and destroying terminally misfolded or damaged proteins. Pca1p, a cadmium exporter in the yeast Saccharomyces cerevisiae, is rapidly degraded by the endoplasmic reticulum-associated degradation (ERAD) system via a cis-acting degron that exists at the 250-350 amino acid region of Pca1p and is transferable to other proteins to serve as a degradation signal. Cadmium stabilizes Pca1p in a manner dependent on the degron. This suggested that cadmium-mediated masking of the degron impedes its interaction with the molecular factors involved in the ERAD. The characteristics and mechanisms of action of the degron in Pca1p and most of those in other proteins however remain to be determined. The results presented here indicate that specific cysteine residues in a degron of Pca1p sense cadmium. An unbiased approach selecting non-functional degrons indicated a critical role of hydrophobic amino acids in the degron for its function. A secondary structure modeling predicted the formation of an amphipathic helix. Site-directed mutagenesis confirmed the functional significance of the hydrophobic patch. Last, hydrophobic amino acids in the degron- and cadmium-binding region affected the interaction of Pca1p with the Ssa1p molecular chaperone, which is involved in ERAD. These results reveal the mechanism of action of the degron, which might be useful for the identification and characterization of other degrons.

Yeast Fex1p Is a Constitutively Expressed Fluoride Channel with Functional Asymmetry of Its Two Homologous Domains

Fluoride is a ubiquitous environmental toxin with which all biological species must cope. A recently discovered family of fluoride export (FEX) proteins protects organisms from fluoride toxicity by removing it from the cell. We show here that FEX proteins in Saccharomyces cerevisiae function as ion channels that are selective for fluoride over chloride and that these proteins are constitutively expressed at the yeast plasma membrane. Continuous expression is in contrast to many other toxin exporters in yeast, and this, along with the fact that two nearly duplicate proteins are encoded in the yeast genome, suggests that the threat posed by fluoride ions is frequent and detrimental. Structurally, eukaryotic FEX proteins consist of two homologous four-transmembrane helix domains folded into an antiparallel dimer, where the orientation of the two domains is fixed by a single transmembrane linker helix. Using phylogenetic sequence conservation as a guide, we have identified several functionally important residues. There is substantial functional asymmetry in the effect of mutation at corresponding sites in the two domains. Specifically, mutations to residues in the C-terminal domain proved significantly more detrimental to function than did similar mutations in the N-terminal domain. Our data suggest particular residues that may be important to anion specificity, most notably the necessity of a positive charge near the end of TMH1 in the C-terminal domain. It is possible that a cationic charge at this location may create an electrostatic well for fluoride ions entering the channel from the cytoplasm.

KlGcr1 controls glucose-6-phosphate dehydrogenase activity and responses to H2O2, cadmium and arsenate in Kluyveromyces lactis

It has been previously reported that Gcr1 differentially controls growth and sugar utilization in Saccharomyces cerevisiae and Kluyveromyces lactis, although the regulatory mechanisms causing activation of glycolytic genes are conserved (Neil et al., 2004). We have found that KlGCR1 deletion diminishes glucose consumption and ethanol production, but increases resistance to oxidative stress caused by H2O2, cadmium and arsenate, glucose 6P dehydrogenase activity, and the NADPH/NADP(+) and GSH/GSSG ratios in K. lactis. The gene KlZWF1 that encodes for glucose 6P dehydrogenase, the first enzyme in the pentose phosphate pathway, is transcriptionally regulated by KlGcr1. The high resistance to oxidative stress observed in the ΔKlgcr1 mutant strain, could be explained as a consequence of an increased flux of glucose through the pentose phosphate pathway. Since mitochondrial respiration decreases in the ΔKlgcr1 mutant (García-Leiro et al., 2010), the reoxidation of the NADPH, produced through the pentose phosphate pathway, has to be achieved by the reduction of other molecules implied in the defense against oxidative stress, like GSSG. The higher GSH/GSSG ratio in the mutant would explain its phenotype of increased resistance to oxidative stress.

Repression of the Low Affinity Iron Transporter Gene FET4: A NOVEL MECHANISM AGAINST CADMIUM TOXICITY ORCHESTRATED BY YAP1 VIA ROX1

Cadmium is a well known mutagenic metal that can enter cells via nonspecific metal transporters, causing several cellular damages and eventually leading to death. In the yeast Saccharomyces cerevisiae, the transcription factor Yap1 plays a key role in the regulation of several genes involved in metal stress response. We have previously shown that Yap1 represses the expression of FET4, a gene encoding a low affinity iron transporter able to transport metals other than iron. Here, we have studied the relevance of this repression in cell tolerance to cadmium. Our results indicate that genomic deletion of Yap1 increases FET4 transcript and protein levels. In addition, the cadmium toxicity exhibited by this strain is completely reversed by co-deletion of FET4 gene. These data correlate well with the increased intracellular levels of cadmium observed in the mutant yap1. Rox1, a well known aerobic repressor of hypoxic genes, conveys the Yap1-mediated repression of FET4. We further show that, in a scenario where the activity of Yap1 or Rox1 is compromised, cells activate post-transcriptional mechanisms, involving the exoribonuclease Xrn1, to compensate the derepression of FET4. Our data thus reveal a novel protection mechanism against cadmium toxicity mediated by Yap1 that relies on the aerobic repression of FET4 and results in the impairment of cadmium uptake.

Human regulatory T cells lack the cyclophosphamide-extruding transporter ABCB1 and are more susceptible to cyclophosphamide-induced apoptosis

ATP-binding cassette (ABC) transporters, including ABC-transporter B1 (ABCB1), extrude drugs, metabolites, and other compounds (such as mitotracker green (MTG)) from cells. Susceptibility of CD4(+) regulatory T (Treg) cells to the ABCB1-substrate cyclophosphamide (CPA) has been reported. Here, we characterized ABCB1 expression and function in human CD4(+) T-cell subsets. Naïve, central memory, and effector-memory CD4(+) T cells, but not Treg cells, effluxed MTG in an ABCB1-dependent manner. In line with this, ABCB1 mRNA and protein was expressed by nonregulatory CD4(+) T-cell subsets, but not Treg cells. In vitro, the ABCB1-substrate CPA was cytotoxic for Treg cells at a 100-fold lower dose than for nonregulatory counterparts, and, inversely, verapamil, an inhibitor of ABC transporters, increased CPA-toxicity in nonregulatory CD4(+) T cells but not Treg cells. Thus, Treg cells lack expression of ABCB1, rendering them selectively susceptible to CPA. Our findings provide mechanistic support for therapeutic strategies using CPA to boost anti-tumor immunity by selectively depleting Treg cells.

YCF1-mediated cadmium resistance in yeast is dependent on copper metabolism and antioxidant enzymes

AIMS

Acquisition and detoxification of metal ions are vital biological processes. Given the requirement of metallochaperones in cellular copper distribution and metallation of cuproproteins, this study investigates whether the metallochaperones also deliver metal ions for transporters functioning in metal detoxification.

RESULTS

Resistance to excess cadmium and copper of the yeast Saccharomyces cerevisiae, which is conferred by PCA1 and CaCRP1 metal efflux P-type ATPases, respectively, does not rely on known metallochaperones, Atx1p, Ccs1p, and Cox17p. Copper deficiency induced by the expression of CaCRP1 encoding a copper exporter occurs in the absence of Atx1p. Intriguingly, CCS1 encoding the copper chaperone for superoxide dismutase 1 (Sod1p) is necessary for cadmium resistance that is mediated by Ycf1p, a vacuolar cadmium sequestration transporter. This is attributed to Ccs1p's role in the maturation of Sod1p rather than its direct interaction with Ycf1p for cadmium transfer. Functional defect in Ycf1p associated with the absence of Sod1p as well as another antioxidant enzyme Glr1p is rescued by anaerobic growth or substitutions of specific cysteine residues of Ycf1p to alanine or serine. This further supports oxidative inactivation of Ycf1p in the absence of Ccs1p, Sod1p, or Glr1p.

INNOVATION

These results provide new insights into the mechanisms of metal metabolism, interaction among metal ions, and the roles for antioxidant systems in metal detoxification.

CONCLUSION

Copper metabolism and antioxidant enzymes maintain the function of Ycf1p for cadmium defense.

Characterization of the HMA7 gene and transcriptomic analysis of candidate genes for copper tolerance in two Silene vulgaris ecotypes

Silene vulgaris possesses ecotype-specific tolerance to high levels of copper in the soil. Although this was reported a few decades ago, little is known about this trait on a molecular level. The aim of this study was to analyze the transcription response to elevated copper concentrations in two S. vulgaris ecotypes originating from copper-contrasting soil types - copper-tolerant Lubietova and copper-sensitive Stranska skala. To reveal if plants are transcriptionally affected, we first analyzed the HMA7 gene, a known key player in copper metabolism. Based on BAC library screening, we identified a BAC clone containing a SvHMA7 sequence with all the structural properties specific for plant copper-transporting ATPases. The functionality of the gene was tested using heterologous complementation in yeast mutants. Analyses of SvHMA7 transcription patterns showed that both ecotypes studied up-regulated SvHMA7 transcription after the copper treatment. Our data are supported by analysis of appropriate reference genes based on RNA-Seq databases. To identify genes specifically involved in copper response in the studied ecotypes, we analyzed transcription profiles of genes coding Cu-transporting proteins and genes involved in the prevention of copper-induced oxidative stress in both ecotypes. Our data show that three genes (APx, POD and COPT5) differ in their transcription pattern between the ecotypes with constitutively increased transcription in Lubietova. Taken together, we have identified transcription differences between metallifferous and non-metalliferous ecotypes of S. vulgaris, and we have suggested candidate genes participating in metal tolerance in this species.

Cadmium

Cadmium is not an essential element for life. It is geologically marginal but anthropogenic activities have contributed significantly to its dispersion in the environment and to cadmium exposure of living species. The natural speciation of the divalent cation Cd2+ is dominated by its high propensity to bind to sulfur ligands, but Cd2+ may also occupy sites providing imidazole and carboxylate ligands. It binds to cell walls by passive adsorption (bio-sorption) and it may interact with surface receptors. Cellular uptake can occur by ion mimicry through a variety of transporters of essential divalent cations, but not always. Once inside cells, Cd2+ preferentially binds to thiol-rich molecules. It can accumulate in intracellular vesicles. It may also be transported over long distances within multicellular organisms and be trapped in locations devoid of efficient excretion systems. These locations include the renal cortex of animals and the leaves of hyper-accumulating plants. No specific regulatory mechanism monitors Cd2+ cellular concentrations. Thiol recruitment by cadmium is a major interference mechanism with many signalling pathways that rely on thiolate-disulfide equilibria and other redox-related processes. Cadmium thus compromises the antioxidant intracellular response that relies heavily on molecules with reactive thiolates. These biochemical features dominate cadmium toxicity, which is complex because of the diversity of the biological targets and the consequent pleiotropic effects. This chapter compares the cadmium-handling systems known throughout phylogeny and highlights the basic principles underlying the impact of cadmium in biology.

Zinc export results in adaptive zinc tolerance in the ectomycorrhizal basidiomycete Suillus bovinus

On Zn-polluted soils, populations of the ectomycorrhizal basidiomycete Suillus bovinus exhibit an elevated Zn tolerance when compared to populations on non-polluted sites. To elucidate the mechanism of Zn tolerance, the time-course of Zn uptake was studied in isolates with contrasting Zn tolerance. Unidirectional fluxes and subcellular compartmentation of Zn were investigated through radiotracer flux analyses. Fluorescence imaging was used to support the subcellular Zn compartmentation. After 2 h of exposure to 200 μM Zn, significantly more Zn was accumulated in Zn-sensitive isolates compared to tolerant isolates, despite similar short-term uptake kinetics and similar extracellular Zn sequestration in cell walls. In Zn-sensitive isolates twice as much Zn accumulated in the cytoplasm and 12 times more Zn in the vacuole. (65)Zn efflux analyses revealed a considerably faster Zn export in the Zn-tolerant isolate. The adaptive Zn tolerance in S. bovinus is therefore achieved by a preferential removal of Zn out of the cytoplasm, back into the apoplast, instead of the usual transfer of Zn into the vacuole. Zn exclusion in the fungal symbiont eventually contributes to a lower Zn influx in host plants.

Role of the yeast multidrug transporter Qdr2 in cation homeostasis and the oxidative stress response

We have identified QDR2 in a screening for genes able to confer tolerance to sodium and/or lithium stress upon overexpression. Qdr2 is a multidrug transporter of the major facilitator superfamily, originally described for its ability to transport the antimalarial drug quinidine and the herbicide barban. To identify its physiological substrate, we have screened for phenotypes dependent on QDR2 and found that Qdr2 is able to transport monovalent and divalent cations with poor selectivity, as shown by growth tests and the determination of internal cation content. Moreover, strains overexpressing or lacking QDR2 also exhibit phenotypes when reactive oxygen species- producing agents, such as hydrogen peroxide or menadione were added to the growth medium. We have also found that the presence of copper and hydrogen peroxide repress the expression of QDR2. In addition, the copper uptake of a qdr2 mutant strain is similar to a wild type, but the extrusion is clearly impaired. Based on our results, we propose that free divalent copper is the main physiological substrate of Qdr2. As copper is a substrate for several redox reactions that occur within the cytoplasm, its function in copper homeostasis explains its role in the oxidative stress response.

Bacterial transition metal P(1B)-ATPases: transport mechanism and roles in virulence

P(1B)-type ATPases are polytopic membrane proteins that couple the hydrolysis of ATP to the efflux of cytoplasmic transition metals. This paper reviews recent progress in our understanding of the structure and function of these proteins in bacteria. These are members of the P-type superfamily of transport ATPases. Cu(+)-ATPases are the most frequently observed and best-characterized members of this group of transporters. However, bacterial genomes show diverse arrays of P(1B)-type ATPases with a range of substrates (Cu(+), Zn(2+), Co(2+)). Furthermore, because of the structural similarities among transitions metals, these proteins can also transport nonphysiological substrates (Cd(2+), Pb(2+), Au(+), Ag(+)). P(1B)-type ATPases have six or eight transmembrane segments (TM) with metal coordinating amino acids in three core TMs flanking the cytoplasmic domain responsible for ATP binding and hydrolysis. In addition, regulatory cytoplasmic metal binding domains are present in most P(1B)-type ATPases. Central to the transport mechanism is the binding of the uncomplexed metal to these proteins when cytoplasmic substrates are bound to chaperone and chelating molecules. Metal binding to regulatory sites is through a reversible metal exchange among chaperones and cytoplasmic metal binding domains. In contrast, the chaperone-mediated metal delivery to transport sites appears as a largely irreversible event. P(1B)-ATPases have two overarching physiological functions: to maintain cytoplasmic metal levels and to provide metals for the periplasmic assembly of metalloproteins. Recent studies have shown that both roles are critical for bacterial virulence, since P(1B)-ATPases appear key to overcome high phagosomal metal levels and are required for the assembly of periplasmic and secreted metalloproteins that are essential for survival in extreme oxidant environments.

Comparative study of the active cadmium efflux systems operating at the plasma membrane and tonoplast of cucumber root cells

The strategies developed by plants to avoid the toxicity of cadmium (Cd) and other heavy metals involve active sequestration of metals into the apoplast and vacuoles. The protein systems excluding heavy metals from the cell cytosol localize to the plasma membrane and tonoplast and are energized either by ATP or by the electrochemical gradient generated by H(+)-ATPase or by V-ATPase and pyrophosphatase (PPase), respectively. In this work, a comparative study on the contribution of both the plasma membrane and tonoplast in the active detoxification of plant cells after treatment with Cd was performed. The studies using plants treated and untreated with Cd reveal that both, H(+)-coupled and MgATP-driven efflux of Cd across plasma membranes and tonoplast is markedly stimulated in the presence of Cd in the environment. Previous studies on plasma-membrane localized H(+)-coupled Cd efflux together with the present data demonstrating tonoplast H(+)/Cd(2+) antiport activity suggest that H(+)-coupled secondary transport of Cd displays a lower affinity for Cd when compared with Cd primary pumps driven by MgATP. In addition, it is shown that MgATP-energized Cd efflux across both membranes is significantly enhanced by cysteine, dithiothreitol, and glutathione. These results suggest that Cd is excluded from the cytosol through an energy-dependent system as a free ion as well as a complexed form. Although both membranes contribute in the active exclusion of ionized and complexed Cd from the cytosol, the overall calculation of Cd accumulation in the everted plasma membranes and vacuolar vesicles suggests that the tonoplast and vacuole have a major function in Cd efflux from the cytosol in the roots of cucumber subjected to Cd stress.

New insights into the Ca2+-ATPases that contribute to cadmium tolerance in yeast

Cadmium (Cd(2+)) is a toxic heavy metal which triggers several toxic effects in eukaryotes, including neurotoxicity and impaired calcium metabolism. In the model organism Saccharomyces cerevisiae, the best characterized pathway for Cd(2+) detoxification involves conjugation with glutathione (GSH) and subsequent transport to vacuoles by Ycf1p, an ATPase homologous to human MRP1 (Multidrug resistance associated protein 1). However, Cd(2+) tolerance also can be mediated by Pmr1p, a Ca(2+) pump located in the Golgi membrane, possibly through to the secretory pathway. Herein, we showed that inactivation of the PMR1 gene, alone or simultaneously with YCF1, delayed initial Cd(2+) capture compared to wild-type (WT) cells. In addition, Cd(2+) treatment altered the expression profile of yeast internal Ca(2+) transporters; specifically, PMC1 gene expression is induced substantially by the metal in WT cells, and this induction is stronger in mutants lacking YCF1. Taken together, these results indicate that, in addition to Pmr1p, the vacuolar Ca(2+)-ATPase Pmc1p also helps yeast cells cope with Cd(2+) toxicity. We propose a model where Pmc1p and Pmr1p Ca(2+)-ATPase function in cooperation with Ycf1p to promote Cd(2+) detoxification.

A tradeoff drives the evolution of reduced metal resistance in natural populations of yeast

Various types of genetic modification and selective forces have been implicated in the process of adaptation to novel or adverse environments. However, the underlying molecular mechanisms are not well understood in most natural populations. Here we report that a set of yeast strains collected from Evolution Canyon (EC), Israel, exhibit an extremely high tolerance to the heavy metal cadmium. We found that cadmium resistance is primarily caused by an enhanced function of a metal efflux pump, PCA1. Molecular analyses demonstrate that this enhancement can be largely attributed to mutations in the promoter sequence, while mutations in the coding region have a minor effect. Reconstruction experiments show that three single nucleotide substitutions in the PCA1 promoter quantitatively increase its activity and thus enhance the cells' cadmium resistance. Comparison among different yeast species shows that the critical nucleotides found in EC strains are conserved and functionally important for cadmium resistance in other species, suggesting that they represent an ancestral type. However, these nucleotides had diverged in most Saccharomyces cerevisiae populations, which gave cells growth advantages under conditions where cadmium is low or absent. Our results provide a rare example of a selective sweep in yeast populations driven by a tradeoff in metal resistance.

Understanding the genetic and molecular bases of adaptive mutations allows us to gain insight into how new biological functions evolve. In natural populations, examples in which adaptive mutations are characterized at the molecular level are still rare. We studied wild yeast strains isolated from Evolution Canyon (EC), Israel, that exhibit an extremely high tolerance to the heavy metal cadmium. We found that high cadmium resistance was mainly caused by DNA sequence changes in the promoter of a metal transport gene, PCA1.These mutations increase PCA1 gene expression, thus leading to a more efficient cadmium pump-out. Comparison among different yeast species shows that the critical nucleotides found in EC strains are conserved and functionally important for cadmium resistance in other species, suggesting that they represent an ancestral type. When the PCA1 sequence and the cadmium resistance in different S. cerevisiae populations collected globally were compared, we found that most populations carried weak PCA1 alleles and had a low cadmium tolerance. Since cells carrying the strong PCA1 allele grow slowly under low-cadmium conditions, it is likely that the tradeoff between cadmium resistance and growth rate drives the evolution of reduced cadmium tolerance in most S. cerevisiae populations.

How Saccharomyces cerevisiae copes with toxic metals and metalloids

Toxic metals and metalloids are widespread in nature and can locally reach fairly high concentrations. To ensure cellular protection and survival in such environments, all organisms possess systems to evade toxicity and acquire tolerance. This review provides an overview of the molecular mechanisms that contribute to metal toxicity, detoxification and tolerance acquisition in budding yeast Saccharomyces cerevisiae. We mainly focus on the metals/metalloids arsenic, cadmium, antimony, mercury, chromium and selenium, and emphasize recent findings on sensing and signalling mechanisms and on the regulation of tolerance and detoxification systems that safeguard cellular and genetic integrity.

Mechanisms of contact-mediated killing of yeast cells on dry metallic copper surfaces

Surfaces made of copper or its alloys have strong antimicrobial properties against a wide variety of microorganisms. However, the molecular mode of action responsible for the antimicrobial efficacy of metallic copper is not known. Here, we show that dry copper surfaces inactivate Candida albicans and Saccharomyces cerevisiae within minutes in a process called contact-mediated killing. Cellular copper ion homeostasis systems influenced the kinetics of contact-mediated killing in both organisms. Deregulated copper ion uptake through a hyperactive S. cerevisiae Ctr1p (ScCtr1p) copper uptake transporter in Saccharomyces resulted in faster inactivation of mutant cells than of wild-type cells. Similarly, lack of the C. albicans Crp1p (CaCrp1p) copper-efflux P-type ATPase or the metallothionein CaCup1p caused more-rapid killing of Candida mutant cells than of wild-type cells. Candida and Saccharomyces took up large quantities of copper ions as soon as they were in contact with copper surfaces, as indicated by inductively coupled plasma mass spectroscopy (ICP-MS) analysis and by the intracellular copper ion-reporting dye coppersensor-1. Exposure to metallic copper did not cause lethality through genotoxicity, deleterious action on a cell's genetic material, as indicated by a mutation assay with Saccharomyces. Instead, toxicity mediated by metallic copper surfaces targeted membranes in both yeast species. With the use of Live/Dead staining, onset of rapid and extensive cytoplasmic membrane damage was observed in cells from copper surfaces. Fluorescence microscopy using the indicator dye DiSBaC(2)(3) indicated that cell membranes were depolarized. Also, during contact-mediated killing, vacuoles first became enlarged and then disappeared from the cells. Lastly, in metallic copper-stressed yeasts, oxidative stress in the cytoplasm and in mitochondria was elevated.