ACE1 transcription factor produced in Escherichia coli binds multiple regions within yeast metallothionein upstream activation sequences

Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress

Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.

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.

Activation of Haa1 and War1 transcription factors by differential binding of weak acid anions in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, Haa1 and War1 transcription factors are involved in cellular adaptation against hydrophilic weak acids and lipophilic weak acids, respectively. However, it is unclear how these transcription factors are differentially activated depending on the identity of the weak acid. Using a field-effect transistor (FET)-type biosensor based on carbon nanofibers, in the present study we demonstrate that Haa1 and War1 directly bind to various weak acid anions with different affinities. Haa1 is most sensitive to acetate, followed by lactate, whereas War1 is most sensitive to benzoate, followed by sorbate, reflecting their differential activation during weak acid stresses. We show that DNA binding by Haa1 is induced in the presence of acetic acid and that the N-terminal Zn-binding domain is essential for this activity. Acetate binds to the N-terminal 150-residue region, and the transcriptional activation domain is located between amino acid residues 230 and 483. Our data suggest that acetate binding converts an inactive Haa1 to the active form, which is capable of DNA binding and transcriptional activation.

The Role of Copper Homeostasis at the Host-Pathogen Axis: From Bacteria to Fungi

Copper is an essential trace element participating in many vital biological processes, however it becomes a toxic agent when in excess. Thus, precise and tight regulation of copper homeostasis processes, including transport, delivery, storage, detoxification, and efflux machineries, is important, ensuring that only the amount needed to sustain basic biological functions and simultaneously prevent copper toxicity in the cell is maintained. Numerous exciting studies have revealed that copper plays an indispensable role at the microbial pathogen-host axis for entities ranging from pathogenic bacteria to deadly fungal species. Analyses of copper homeostases in bacteria and fungi extensively demonstrate that copper is utilized by the host immune system as an anti-microbial agent. The expression of copper efflux and detoxification from microbial pathogens is induced to counteract the host's copper bombardment, which in turn disrupts these machineries, resulting in the attenuation of microbial survival in host tissue. We hereby review the latest work in copper homeostases in pathogenic bacteria and fungi and focus on the maintenance of a copper balance at the pathogen-host interaction axis.

Genome-wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans

The ability of the human fungal pathogen Cryptococcus neoformans to adapt to variable copper (Cu) environments within the host is key for successful dissemination and colonization. During pulmonary infection, host alveolar macrophages compartmentalize Cu into the phagosome and C. neoformans Cu-detoxifying metallothioneins, MT1 and MT2, are required for survival of the pathogen. In contrast, during brain colonization the C. neoformans Cu+ importers Ctr1 and Ctr4 are required for virulence. Central for the regulation and expression of both the Cu detoxifying MT1/2 and the Cu acquisition Ctr1/4 proteins is the Cu-metalloregulatory transcription factor Cuf1, an established C. neoformans virulence factor. Due to the importance of the distinct C. neoformans Cu homeostasis mechanisms during host colonization and virulence, and to the central role of Cuf1 in regulating Cu homeostasis, we performed a combination of RNA-Seq and ChIP-Seq experiments to identify differentially transcribed genes between conditions of high and low Cu. We demonstrate that the transcriptional regulation exerted by Cuf1 is intrinsically complex and that Cuf1 also functions as a transcriptional repressor. The Cu- and Cuf1-dependent regulon in C. neoformans reveals new adaptive mechanisms for Cu homeostasis in this pathogenic fungus and identifies potential new pathogen-specific targets for therapeutic intervention in fungal infections.

Copper Acquisition and Utilization in Fungi

Fungal cells colonize and proliferate in distinct niches, from soil and plants to diverse tissues in human hosts. Consequently, fungi are challenged with the goal of obtaining nutrients while simultaneously elaborating robust regulatory mechanisms to cope with a range of availability of nutrients, from scarcity to excess. Copper is essential for life but also potentially toxic. In this review we describe the sophisticated homeostatic mechanisms by which fungi acquire, utilize, and control this biochemically versatile trace element. Fungal pathogens, which can occupy distinct host tissues that have their own intrinsic requirements for copper homeostasis, have evolved mechanisms to acquire copper to successfully colonize the host, disseminate to other tissues, and combat host copper bombardment mechanisms that would otherwise mitigate virulence.

The Zygosaccharomyces bailii transcription factor Haa1 is required for acetic acid and copper stress responses suggesting subfunctionalization of the ancestral bifunctional protein Haa1/Cup2

Background

The food spoilage yeast species Zygosaccharomyces bailii exhibits an extraordinary capacity to tolerate weak acids, in particular acetic acid. In Saccharomyces cerevisiae, the transcription factor Haa1 (ScHaa1) is considered the main player in genomic expression reprogramming in response to acetic acid stress, but the role of its homologue in Z. bailii (ZbHaa1) is unknown.

Results

In this study it is demonstrated that ZbHaa1 is a ScHaa1 functional homologue by rescuing the acetic acid susceptibility phenotype of S. cerevisiae haa1Δ. The disruption of ZbHAA1 in Z. bailii IST302 and the expression of an extra ZbHAA1 copy confirmed ZbHAA1 as a determinant of acetic acid tolerance. ZbHaa1 was found to be required for acetic acid stress-induced transcriptional activation of Z. bailii genes homologous to ScHaa1-target genes. An evolutionary analysis of the Haa1 homologues identified in 28 Saccharomycetaceae species genome sequences, including Z bailii, was carried out using phylogenetic and gene neighbourhood approaches. Consistent with previous studies, this analysis revealed a group containing pre-whole genome duplication species Haa1/Cup2 single orthologues, including ZbHaa1, and two groups containing either Haa1 or Cup2 orthologues from post-whole genome duplication species. S. cerevisiae Cup2 (alias Ace1) is a transcription factor involved in response and tolerance to copper stress. Taken together, these observations led us to hypothesize and demonstrate that ZbHaa1 is also involved in copper-induced transcriptional regulation and copper tolerance.

Conclusions

The transcription factor ZbHaa1 is required for adaptive response and tolerance to both acetic acid and copper stresses. The subfunctionalization of the single ancestral Haa1/Cup2 orthologue that originated Haa1 and Cup2 paralogues after whole genome duplication is proposed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3443-2) contains supplementary material, which is available to authorized users.

Effective induction of pblac1 laccase by copper ion in Polyporus brumalis ibrc05015

Polyporus brumalis ibrc05015 is a strain capable of high laccase (Lac) production. Among several inducers, 0.25 mM copper was most effective for Lac production. One of the Lacs induced by copper was PbLac1, and its transcription was induced within 60 min after copper addition. The promoter region of pblac1 contained six putative metal response elements and one Ace1 consensus cis-element. We cloned the P. brumalis PbAce1 transcription factor, a homologue of Saccharomyces cerevisiae transcription factor Ace1, which regulates metallothionein genes in response to excess copper. PbAce1 complemented the function of Ace1 in an S. cerevisiae Δace strain. The conserved N-terminal copper-fist DNA binding domain of PbAce1 was required for complementation. In the PbAce1 complemented Δace1 strain, the pblac1 promoter was constitutively expressed at a high level, independent of copper concentration. PbAce1 has two Cys-rich repeat motifs (PbC1 and PbC2), which are similar to the Cys-rich repeat domain in metallothionein proteins, and are uniquely conserved in the C-terminal domain of basidiomycetous Ace1 sequences. These C-terminal domains could be involved in copper sensing and concentration-dependent Lac production in basidiomycetous fungi.

Identification of negative cis-acting elements in response to copper in the chloroplastic iron superoxide dismutase gene of the moss Barbula unguiculata

Superoxide dismutases (SODs) are ubiquitous metalloenzymes that catalyze the dismutation of superoxide radicals. Chloroplasts have two isozymes, copper/zinc SOD (Cu/ZnSOD) and iron SOD (FeSOD), encoded by nuclear genes. Because bryophytes are considered as the earliest land plants, they are one of the most interesting plant models for adaptation against oxidative stress. In a previous study, we found that the FeSOD gene was expressed under Cu-deficient conditions and repressed under high-Cu-supply conditions; on the other hand, the Cu/ZnSOD gene was induced by Cu in a moss, Barbula unguiculata. The expression of Cu/ZnSOD and FeSOD is coordinately regulated at the transcriptional level depending on metal bioavailability. Here, using transgenic moss plants, we determined that the GTACT motif is a negative cis-acting element of the moss FeSOD gene in response to Cu. Furthermore, we found that a plant-specific transcription factor, PpSBP2 (for SQUAMOSA promoter-binding protein), and its related proteins bound to the GTACT motif repressed the expression of the FeSOD gene. The moss FeSOD gene was negatively regulated by Cu in transgenic Nicotiana tabacum plants, and the Arabidopsis thaliana FeSOD gene promoter containing the GTACT motif was repressed by Cu. Our results suggested that molecular mechanisms of GTACT motif-dependent transcriptional suppression by Cu are conserved in land plants.

A copper-responsive transcription factor, CRF1, mediates copper and cadmium resistance in Yarrowia lipolytica

The dimorphic yeast Yarrowia lipolytica is more resistant to high copper concentrations than Saccharomyces cerevisiae. This differential tolerance to copper ions has been observed in several strains arising from non-related isolates. To investigate the molecular basis of this resistance, we obtained several copper-sensitive mutants. By complementation of one of them, we isolated the YlCRF1 gene encoding for a copper-binding transcription factor of 411 amino acids homologous to ScAce1p, CgAmt1p, and ScMac1p. Naturally occurring copper-sensitive strains lack the CRF1 allele. The YlCRF1 transcript is not induced by the addition of copper to the medium. Gene disruption demonstrated that YlCRF1 is responsible for a 4- to 5-fold increase in Y. lipolytica copper tolerance. We further show that strain Deltacrf1 is more sensitive to cadmium but not to other metals. The role of YlCrf1p as a copper-sensitive transcription factor is supported by the finding that the protein is immunolocalized in the nucleus during growth in copper-supplemented but not in copper-free medium. However, in contrast to the S. cerevisiae strain mutated in the metallothionein transcription activator ACE1, Y. lipolytica strain Deltacrf1 is still able to increase metallothionein (MTP) mRNA levels in response to copper addition. CRF1 deletion does not affect superoxide dismutase (SOD) activity either. Our data suggest the existence of one or more different target genes for Crf1p, other than MTP or SOD1, and support its role as a novel copper-responsive transcription factor involved in metal detoxification.

Phosphorylation and Cu+ coordination-dependent DNA binding of the transcription factor Mac1p in the regulation of copper transport

Copper ions are essential at a proper level yet toxic when present in excess. To maintain a proper intracellular level, cells must be able to sense the changes in copper ion concentrations. The yeast transcription factor Mac1p plays a critical role in the transcriptional regulation of CTR1 and CTR3, both encoding high affinity copper ion transporters. Here we report that the Mac1p binding of the copper ion-responsive elements (CuREs) in the promoters of CTR1 and CTR3 is affected by copper ions. On one hand, the Mac1p DNA binding is Cu(+) coordination-dependent, and on the other hand, exogenous Cu(+) and isoelectronic Ag(+) ions disrupt the DNA binding of Mac1p. These results suggest that the Mac1p is able to sense two different levels of copper ions. These two levels are probably the physiological and toxic copper levels in yeast cells. Furthermore, we found that Mac1p undergoes posttranslational phosphorylation modification in yeast and that the phosphorylation is required for the Mac1p to become DNA-binding active. Nonphosphorylated Mac1p is unable to bind the CTR1 promoter DNA. The data support the model of intradomain interactions and indicate further that the phosphorylation probably prevents the inhibition of DNA-binding domain activity by the activation domain of Mac1p. Taken together, these findings demonstrate that Mac1p functions critically in maintaining a proper intracellular concentration of copper ions.

yTAFII61 has a general role in RNA polymerase II transcription and is required by Gcn4p to recruit the SAGA coactivator complex

We obtained a recessive insertion mutation in the gene encoding yeast TBP-associated factor yTAFII61/68 that impairs Gcn4p-independent and Gcn4p-activated HIS3 transcription. This mutation also reduces transcription of seven other class II genes, thus indicating a broad role for this yTAFII in RNA polymerase II transcription. The Gcn4p activation domain interacts with multiple components of the SAGA complex in cell extracts, including the yTAFII proteins associated with SAGA, but not with two yTAFIIs restricted to TFIID. The taf61-1 mutation impairs binding of Gcn4p to SAGA/yTAFII subunits but not to components of holoenzyme mediator. Our results provide strong evidence that recruitment of SAGA, in addition to holoenzyme, is crucial for activation by Gcn4p in vivo and that yTAFII61 plays a key role in this process.

Yeast metallothionein gene expression in response to metals and oxidative stress

Metals and oxygen are chemically linked in biological systems. Metals and oxygen play important roles in enzymatic reactions, metabolism, and signal transduction; however, metals and oxygen react to form highly toxic oxygen-derived free radical species. In this review we focus on the use of yeast cells, as unicellular eukaryotic model systems, to conduct studies aimed at understanding fundamental mechanisms for the sensation and protective responses to toxic metals and oxygen-derived radicals via the activation of yeast metallothionein gene expression.

Toxic metal-responsive gene transcription

Metals play a dual role in biological systems, serving as essential co-factors for a wide range of biochemical reactions yet these same metals may be extremely toxic to cells. To cope with the stress of increases in environmental metal concentrations, eukaryotic cells have developed sophisticated toxic metal sensing proteins which respond to elevations in metal concentrations. This signal is transmitted to stimulate the cellular transcriptional machinery to activate expression of metal detoxification and homeostasis genes. This review summarizes our current understanding of the biochemical and genetic mechanisms which underlie cellular responses to toxic metals via metalloregulatory transcription factors.

Metal ion resistance in fungi: molecular mechanisms and their regulated expression

One stress response in cells is the ability to survive in an environment containing excessive concentrations of metal ions. This paper reviews current knowledge about cellular and molecular mechanisms involved in the response and adaptation of various fungal species to metal stress. Most cells contain a repertoire of mechanisms to maintain metal homeostasis and prevent metal toxicity. Roles played by glutathione, related (gamma-EC)nG peptides, metallothionein-like polypeptides, and sulfide ions are discussed. In response to cellular metal stress, the biosynthesis of some of these molecules are metalloregulated via intracellular metal sensors. The identify of the metal sensors and the role of metal ions in the regulation of biosynthesis of metallothionein and (gamma-EC)nG peptides are subjects of much current attention and are discussed herein.