A proteome analysis of the cadmium response in Saccharomyces cerevisiae

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.

Genome-scale integrative data analysis and modeling of dynamic processes in yeast

Building a dynamic model of a complete biological cell is one of the great challenges of the 21st century. While this objective could appear unrealistic until recently, considerable improvements in high-throughput data collection techniques, computational performance, data integration, and modeling approaches now allow us to consider it within reach in the near future. In this chapter, we review recent developments that pave the way toward the construction of genome-scale dynamic models. We first describe methodologies for the integration of heterogeneous "omics" datasets, which enable the interpretation of cellular activity at the genome scale and in fluctuating conditions, providing the necessary input to models. We subsequently discuss principles of such models and describe a series of approaches that open perspectives toward the construction of genome-scale dynamic models.

Peptide biomarkers as evidence of perchlorate biodegradation

Perchlorate is a known health hazard for humans, fish, and other species. Therefore, it is important to assess the response of an ecosystem exposed to perchlorate contamination. The data reported here show that a liquid chromatography-mass spectrometry-based proteomics approach for the detection of perchlorate-reducing enzymes can be used to measure the ability of microorganisms to degrade perchlorate, including determining the current perchlorate degradation status. Signature peptides derived from chlorite dismutase (CD) and perchlorate reductase can be used as biomarkers of perchlorate presence and biodegradation. Four peptides each derived from CD and perchlorate reductase subunit A (PcrA) and seven peptides derived from perchlorate reductase subunit B (PcrB) were identified as signature biomarkers for perchlorate degradation, as these sequences are conserved in the majority of the pure and mixed perchlorate-degrading microbial cultures examined. However, chlorite dismutase signature biomarker peptides from Dechloromonas agitata CKB were found to be different from those in other cultures used and should also be included with selected CD biomarkers. The combination of these peptides derived from the two enzymes represents a promising perchlorate presence/biodegradation biomarker system. The biomarker peptides were detected at perchlorate concentrations as low as 0.1 mM and at different time points both in pure cultures and within perchlorate-reducing environmental enrichment consortia. The peptide biomarkers were also detected in the simultaneous presence of perchlorate and an alternate electron acceptor, nitrate. We believe that this technique can be useful for monitoring bioremediation processes for other anthropogenic environmental contaminants with known metabolic pathways.

Corynebacterium glutamicum as an indicator for environmental cobalt and silver stress--a proteome analysis

Cobalt and silver are toxic for cells, but mechanisms of this toxicity are largely unknown. Analysis of Corynebacterium glutamicum proteome from cells grown in control and cobalt or silver enriched media was performed by two dimensional gel electrophoresis (2DE) followed by mass spectrometry. Our results indicate that the cell adapted to cobalt stress by inducing five defense mechanisms: Scavenging of free radicals, promotion of the generation of energy, reparation of DNA, reparation and biogenesis of Fe-S cluster proteins and supporting and reparation of cell wall. In response to the detoxification of Ag+ many proteins were up-regulated, which involved reparation of damaged DNA, minimizing the toxic effect of reactive oxygen species (ROS) and energy generation. Overexpression of proteins involved in cell wall biosynthesis (1,4-alpha-glucan branching enzyme and nucleoside-diphosphate-sugar epimerase) upon cobalt stress and induction of proteins involved in energy metabolism (2-methylcitrate dehydratase and 1, 2-methylcitrate synthase) upon silver demonstrate the potential of these enzymes as biomarkers of sub-lethal Ag+ and Co toxicity.

Oxidative stress in yeast

The mechanisms of production and elimination of reactive oxygen species in the cells of the budding yeast Saccharomyces cerevisiae are analyzed. Coordinative role of special regulatory proteins including Yap1p, Msn2/4p, and Skn7p (Pos9p) in regulation of defense mechanisms in S. cerevisiae is described. A special section is devoted to two other well-studied species from the point of view of oxidative stress -- Schizosaccharomyces pombe and Candida albicans. Some examples demonstrating the use of yeast for investigation of apoptosis, aging, and some human diseases are given in the conclusion part.

Crystallization and preliminary crystallographic analysis of Gre2p, an NADP(+)-dependent alcohol dehydrogenase from Saccharomyces cerevisiae

Gre2p [Genes de respuesta a estres (stress-response gene)] from Saccharomyces cerevisiae is a monomeric enzyme of 342 amino acids with a molecular weight of 38.1 kDa. The enzyme catalyses both the stereospecific reduction of keto compounds and the oxidation of various hydroxy compounds and alcohols by the simultaneous consumption of the cofactor NADPH and formation of NADP(+). Crystals of a Gre2p complex with NADP(+) were grown using PEG 8000 as a precipitant. They belong to the monoclinic space group P2(1). The current diffraction resolution is 3.2 A. In spite of the monomeric nature of Gre2p in solution, packing and self-rotation calculations revealed the existence of two Gre2p protomers per asymmetric unit related by a twofold noncrystallographic axis.

Comparative transcriptomic and proteomic profiling of industrial wine yeast strains

The geno- and phenotypic diversity of commercial Saccharomyces cerevisiae wine yeast strains provides an opportunity to apply the system-wide approaches that are reasonably well established for laboratory strains to generate insight into the functioning of complex cellular networks in industrial environments. We have previously analyzed the transcriptomes of five industrial wine yeast strains at three time points during alcoholic fermentation. Here, we extend the comparative approach to include an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis of two of the previously analyzed wine yeast strains at the same three time points during fermentation in synthetic wine must. The data show that differences in the transcriptomes of the two strains at a given time point rather accurately reflect differences in the corresponding proteomes independently of the gene ontology (GO) category, providing strong support for the biological relevance of comparative transcriptomic data sets in yeast. In line with previous observations, the alignment proves to be less accurate when assessing intrastrain changes at different time points. In this case, differences between the transcriptome and proteome appear to be strongly dependent on the GO category of the corresponding genes. The data in particular suggest that metabolic enzymes and the corresponding genes appear to be strongly correlated over time and between strains, suggesting a strong transcriptional control of such enzymes. The data also allow the generation of hypotheses regarding the molecular origin of significant differences in phenotypic traits between the two strains.

The gld1+ gene encoding glycerol dehydrogenase is required for glycerol metabolism in Schizosaccharomyces pombe

The budding yeast Saccharomyces cerevisiae is able to utilize glycerol as the sole carbon source via two pathways (glycerol 3-phosphate pathway and dihydroxyacetone [DHA] pathway). In contrast, the fission yeast Schizosaccharomyces pombe does not grow on media containing glycerol as the sole carbon source. However, in the presence of other carbon sources such as galactose and ethanol, S. pombe could assimilate glycerol and glycerol was preferentially utilized over ethanol and galactose. No equivalent of S. cerevisiae Gcy1/glycerol dehydrogenase has been identified in S. pombe. However, we identified a gene in S. pombe, SPAC13F5.03c (gld1 (+)), that is homologous to bacterial glycerol dehydrogenase. Deletion of gld1 caused a reduction in glycerol dehydrogenase activity and prevented glycerol assimilation. The gld1 Delta cells grew on 50 mM DHA as the sole carbon source, indicating that the glycerol dehydrogenase encoded by gld1 (+) is essential for glycerol assimilation in S. pombe. Strains of S. pombe deleted for dak1 (+) and dak2 (+) encoding DHA kinases could not grow on glycerol and showed sensitivity to a higher concentration of DHA. The dak1 Delta strain showed a more severe reduction of growth on glycerol and DHA than the dak2 Delta strain because the expression of dak1 (+) mRNA was higher than that of dak2 (+). In wild-type S. pombe, expression of the gld1 (+), dak1 (+), and dak2 (+) genes was repressed at a high concentration of glucose and was derepressed during glucose starvation. We found that gld1 (+) was regulated by glucose repression and that it was derepressed in scr1 Delta and tup12 Delta strains.

Cr-(III)-organic compounds treatment causes genotoxicity and changes in DNA and protein level in Saccharomyces cerevisiae

Natural Cr-(III)-organic species are being known as the part of natural biogeochemical cycle of chromium, but unfortunately, their mechanism of toxicity as well as genotoxic potentiality is still unknown. To evaluate the characteristic toxic effect exerted by natural Cr-(III)-organic species on the cellular macromolecules, changes in DNA and protein level was observed. Besides, Comet assay was applied to measure genotoxic potentiality of Cr-(III)-organic species in the target organism Saccharomyces cerevisiae exposed to Cr-(III)-citrate and Cr-(III)-histidine. It has been observed that both of the Cr-(III)-organic compounds are responsible for diminution in macromolecules concentration. Cr-(III)-citrate showed ladder pattern of DNA fragmentation in support of apoptosis. Two new protein bands appeared in protein profile of the Saccharomyces cerevisiae treated with Cr-(III)-organic compounds. Thus it supports the possibility of the synthesis of stress proteins. Comet assay proved positive correlation between Cr-(III)-organic compounds' concentration and DNA damage. The Cr-(III)-citrate causes DNA damage at the concentrations ranging from 50 to 150 mg L(-1), whereas the DNA damaging capacity of Cr-(III)-histidine was found insignificant, except at highest concentration (150 mg L(-1)). These results can throw light on the mechanism of the toxic effect as well as genotoxicity exerted by natural Cr-(III)-organic species.

A proteomic analysis of the salt, cadmium and peroxide stress responses in Candida albicans and the role of the Hog1 stress-activated MAPK in regulating the stress-induced proteome

Stress responses are important for the virulence of the major fungal pathogen of humans, Candida albicans. In this study we employed a 2-DE approach to examine the impact of exposure to peroxide (5 mM H(2)O(2)), salt (300 mM NaCl) or cadmium stress (0.5 mM Cd(2+)) upon the C. albicans proteome. Highly reproducible changes in the C. albicans proteome were observed in response to each stress condition. Significantly more proteins were up-regulated in response to cadmium (77) than to the salt (35) or peroxide stresses (35). These proteomic changes displayed minimal overlap with those observed in the transcriptome under equivalent conditions and, importantly, revealed functional categories that respond to stress at the protein level but not the transcript level. Six proteins were up-regulated by all three conditions: Adh1, Atp2, Cip1, Eft2, Ssa1 and Ssb1, which is consistent with the concept that a core stress response exists in C. albicans. This is the first time that a fungal core stress response has been defined at the proteomic level. We have also shown that the Hog1 stress-activated mitogen-activated protein kinase, which is activated in response to the stresses examined in this study, makes a major contribution to the C. albicans stress proteome.

Ssz1 restores endoplasmic reticulum-associated protein degradation in cells expressing defective cdc48-ufd1-npl4 complex by upregulating cdc48

The endoplasmic reticulum (ER)-associated protein degradation (ERAD) pathway eliminates aberrant proteins from the ER. The key role of Cdc48p-Ufd1p-Npl4p is indicated by impaired ERAD in Saccharomyces cerevisiae with mutations in any of this complex's genes. We identified SSZ1 in genetic screens for cdc48-10 suppressors and show that it upregulates Cdc48p via the pleiotropic drug resistance (PDR) network. A pSSZ1 plasmid restored impaired ERAD-M of 6myc-Hmg2 in cdc48-10, ufd1-2, and npl4-1, while SSZ1 deletion had no effect. Ssz1p activates Pdr1p, the PDR master regulator. Indeed, plasmids of PDR1 or its target gene RPN4 increased cdc48-10p levels and restored ERAD-M in cdc48-10. Rpn4p regulates transcription of proteasome subunits and CDC48, thus RPN4 deletion abolished ERAD. However, the diminished proteasome level in Deltarpn4 was sufficient for degrading a cytosolic substrate, whereas the impaired ERAD-M was the result of diminished Cdc48p and was restored by expression of pCDC48. The corrected ERAD-M in the hypomorphic strains of the Cdc48 partners ufd1-2 and npl4-1 by the pCDC48 plasmid, and in cdc48-10 cells by the pcdc48-10 plasmid, combined with the finding that neither pSSZ1 nor pcdc48-10 restored ERAD-L of CPY*-HA, support our conclusion that Ssz1p suppressing effects is brought about by upregulating Cdc48p.

Structure and function of yeast glutaredoxin 2 depend on postranslational processing and are related to subcellular distribution

We have previously shown that glutaredoxin 2 (Grx2) from Saccharomyces cerevisiae localizes at 3 different subcellular compartments, cytosol, mitochondrial matrix and outer membrane, as the result of different postranslational processing of one single gene. Having set the mechanism responsible for this remarkable phenomenon, we have now aimed at defining whether this diversity of subcellular localizations correlates with differences in structure and function of the Grx2 isoforms. We have determined the N-terminal sequence of the soluble mitochondrial matrix Grx2 by mass spectrometry and have determined the exact cleavage site by Mitochondrial Processing Peptidase (MPP). As a consequence of this cleavage, the mitochondrial matrix Grx2 isoform possesses a basic tetrapeptide extension at the N-terminus compared to the cytosolic form. A functional relationship to this structural difference is that mitochondrial Grx2 displays a markedly higher activity in the catalysis of GSSG reduction by the mitochondrial dithiol dihydrolipoamide. We have prepared Grx2 mutants affected on key residues inside the presequence to direct the protein to one single cellular compartment; either the cytosol, the mitochondrial membrane or the matrix and have analyzed their functional phenotypes. Strains expressing Grx2 only in the cytosol are equally sensitive to H(2)O(2) as strains lacking the gene, whereas those expressing Grx2 exclusively in the mitochondrial matrix are more resistant. Mutations on key basic residues drastically affect the cellular fate of the protein, showing that evolutionary diversification of Grx2 structural and functional properties are strictly dependent on the sequence of the targeting signal peptide.

Cadmium(II) complex formation with glutathione

Complex formation between heavy metal ions and glutathione (GSH) is considered as the initial step in many detoxification processes in living organisms. In this study the structure and coordination between the cadmium(II) ion and GSH were investigated in aqueous solutions (pH 7.5 and 11.0) and in the solid state, using a combination of spectroscopic techniques. The similarity of the Cd K-edge and L(3)-edge X-ray absorption spectra of the solid compound [Cd(GS)(GSH)]ClO(4).3H(2)O, precipitating at pH 3.0, with the previously studied cysteine compound {Cd(HCys)(2).H(2)O}(2).H(3)O(+).ClO(4) (-) corresponds to Cd(S-GS)(3)O (dominating) and Cd(S-GS)(4) four-coordination within oligomeric complexes with mean bond distances of 2.51 +/- 0.02 A for Cd-S and 2.24 +/- 0.04 A for Cd-O. For cadmium(II) solutions (C (Cd(II)) approximately 0.05 M) at pH 7.5 with moderate excess of GSH (C (GSH)/C (Cd(II)) = 3.0-5.0), a mix of Cd(S-GS)(3)O (dominating) and Cd(S-GS)(4) species is consistent with the broad (113)Cd NMR resonances in the range 632-658 ppm. In alkaline solutions (pH 11.0 and C (GSH)/C (Cd(II)) = 2.0 or 3.0), two distinct peaks at 322 and 674 ppm are obtained. The first peak indicates six-coordinated mononuclear and dinuclear complexes with CdS(2)N(2)(N/O)(2) and CdSN(3)O(2) coordination in fast exchange, whereas the second corresponds to Cd(S-GS)(4) sites. At high ligand excess the tetrathiolate complex, Cd(S-GS)(4), characterized by a sharp delta((113)Cd) NMR signal at 677 ppm, predominates. The average Cd-S distance, obtained from the X-ray absorption spectra, varied within a narrow range, 2.49-2.53 A, for all solutions (pH 7.5 and 11.0) regardless of the coordination geometry.

Mechanism of cadmium-mediated inhibition of Msh2-Msh6 function in DNA mismatch repair

The observation that Cadmium (Cd(2+)) inhibits Msh2-Msh6, which is responsible for identifying base pair mismatches and other discrepancies in DNA, has led to the proposal that selective targeting of this protein and consequent suppression of DNA repair or apoptosis promote the carcinogenic effects of the heavy metal toxin. It has been suggested that Cd(2+) binding to specific sites on Msh2-Msh6 blocks its DNA binding and ATPase activities. To investigate the mechanism of inhibition, we measured Cd(2+) binding to Msh2-Msh6, directly and by monitoring changes in protein structure and enzymatic activity. Global fitting of the data to a multiligand binding model revealed that binding of about 100 Cd(2+) ions per Msh2-Msh6 results in its inactivation. This finding indicates that the inhibitory effect of Cd(2+) occurs via a nonspecific mechanism. Cd(2+) and Msh2-Msh6 interactions involve cysteine sulfhydryl groups, and the high Cd(2+):Msh2-Msh6 ratio implicates other ligands such as histidine, aspartate, glutamate, and the peptide backbone as well. Our study also shows that cadmium inactivates several unrelated enzymes similarly, consistent with a nonspecific mechanism of inhibition. Targeting of a variety of proteins, including Msh2-Msh6, in this generic manner would explain the marked broad-spectrum impact of Cd(2+) on biological processes. We propose that the presence of multiple nonspecific Cd(2+) binding sites on proteins and their propensity to change conformation on interaction with Cd(2+) are critical determinants of the susceptibility of corresponding biological systems to cadmium toxicity.

Orthologs of the class A4 heat shock transcription factor HsfA4a confer cadmium tolerance in wheat and rice

Cadmium (Cd) is a widespread soil pollutant; thus, the underlying molecular controls of plant Cd tolerance are of substantial interest. A screen for wheat (Triticum aestivum) genes that confer Cd tolerance to a Cd hypersensitive yeast strain identified Heat shock transcription factor A4a (HsfA4a). Ta HsfA4a is most similar to the class A4 Hsfs from monocots. The most closely related rice (Oryza sativa) homolog, Os HsfA4a, conferred Cd tolerance in yeast, as did Ta HsfA4a, but the second most closely related rice homolog, Os HsfA4d, did not. Cd tolerance was enhanced in rice plants expressing Ta HsfA4a and decreased in rice plants with knocked-down expression of Os HsfA4a. An analysis of the functional domain using chimeric proteins constructed from Ta HsfA4a and Os HsfA4d revealed that the DNA binding domain (DBD) of HsfA4a is critical for Cd tolerance, and within the DBD, Ala-31 and Leu-42 are important for Cd tolerance. Moreover, Ta HsfA4a-mediated Cd resistance in yeast requires metallothionein (MT). In the roots of wheat and rice, Cd stress caused increases in HsfA4a expression, together the MT genes. Our findings thus suggest that HsfA4a of wheat and rice confers Cd tolerance by upregulating MT gene expression in planta.

Sulfur metabolism actively promotes initiation of cell division in yeast

BACKGROUND

Sulfur metabolism is required for initiation of cell division, but whether or not it can actively promote cell division remains unknown.

METHODOLOGY/PRINCIPAL FINDINGS

Here we show that yeast cells with more mtDNA have an expanded reductive phase of their metabolic cycle and an increased sulfur metabolic flux. We also show that in wild type cells manipulations of sulfur metabolic flux phenocopy the enhanced growth rate of cells with more mtDNA. Furthermore, introduction of a hyperactive cystathionine-beta-synthase (CBS) allele in wild type cells accelerates initiation of DNA replication.

CONCLUSIONS/SIGNIFICANCE

Our results reveal a novel connection between a key sulfur metabolic enzyme, CBS, and the cell cycle. Since the analogous hyperactive CBS allele in human CBS suppresses other disease-causing CBS mutations, our findings may be relevant for human pathology. Taken together, our results demonstrate the importance of sulfur metabolism in actively promoting initiation of cell division.

Molecular cloning and characterization of an ATP-binding cassette (ABC) transmembrane transporter from the white shrimp Litopenaeusvannamei

ATP-binding cassette transmembrane transporters (ABC transporters) have a potential role in drug and xenobiotic resistance. Here, we report for the first time the cloning of an ABC transporter from white shrimp Litopenaeusvannamei (designated LvABCG), along with a study of its phylogenetic relationships, and measurements of its expression in different shrimp tissues exposed to cadmium and pH stress (acidic and alkaline conditions). Sequence analysis showed that LvABCG shares many similarities with the white/ABC transmembrane transporter, including two conserved regions: a highly conserved ATP-binding cassette (ABC) and transmembrane domain (TMD). Spatial analyses of transcript levels for ABCG in shrimp tissues, using reverse transcript PCR, revealed the highest transcript level in the hepatopancreas, less in the intestine and stomach, and none in the other tissues examined. The ABC transporter mRNA transcript in the hepatopancreas of L.vannamei was significantly up-regulated after 1.5 h and 24 h of exposure to alkaline and acidic conditions, respectively. LvABCG was also induced in intestine, but was downregulated in the stomach under the alkaline treatment. Upon exposure to cadmium (4.25 micromol L(-1) and 8.5 micromol L(-1)) for 48 h, the mRNA expression of LvABCG was up-regulated 4.79-fold (at 6 h) and 2.09-fold (at 12 h) in the hepatopancreas. LvABCG was also induced in the stomach after exposure to 4.25 micromol L(-1) cadmium, but downregulated in the stomach and intestine after exposure to 8.5 micromol L(-1) cadmium. These findings indicate that LvABCG might play an important role in the physiological changes related to metabolism and cell detoxification that occur when Pacific white shrimp are exposed to cadmium and pH stress.

Environmental stresses inhibit splicing in the aquatic fungus Blastocladiella emersonii

Background

Exposure of cells to environmental stress conditions can lead to the interruption of several intracellular processes, in particular those performed by macromolecular complexes such as the spliceosome.

Results

During nucleotide sequencing of cDNA libraries constructed using RNA isolated from B. emersonii cells submitted to heat shock and cadmium stress, a large number of ESTs with retained introns was observed. Among the 6,350 ESTs obtained through sequencing of stress cDNA libraries, 181 ESTs presented putative introns (2.9%), while sequencing of cDNA libraries from unstressed B. emersonii cells revealed only 0.2% of ESTs containing introns. These data indicate an enrichment of ESTs with introns in B. emersonii stress cDNA libraries. Among the 85 genes corresponding to the ESTs that retained introns, 19 showed more than one intron and three showed three introns, with intron length ranging from 55 to 333 nucleotides. Canonical splicing junctions were observed in most of these introns, junction sequences being very similar to those found in introns from genes previously characterized in B. emersonii, suggesting that inhibition of splicing during stress is apparently a random process. Confirming our observations, analyses of gpx3 and hsp70 mRNAs by Northern blot and S1 protection assays revealed a strong inhibition of intron splicing in cells submitted to cadmium stress.

Conclusion

In conclusion, data indicate that environmental stresses, particularly cadmium treatment, inhibit intron processing in B. emersonii, revealing a new adaptive response to cellular exposure to this heavy metal.

Tolerance and stress response of Macrolepiota procera to nickel

Nickel (Ni) is an essential element for many organisms; however, it is very toxic at high concentrations and also depending on the species. In macrofungi the mechanisms underlying their Ni tolerance are poorly documented. This study examines, for the first time, the participation of the antioxidative system in Macrolepiota procera exposed to different Ni2+ concentrations and their relation with Ni tolerance. The effect of the pH on Ni tolerance was also evaluated. The fungus was cultivated on solid medium with different NiCl2 concentrations (0.05, 0.2, 0.8 mM) at pH 4, 6, and 8, and fungi growth and Ni uptake were determined. The antioxidative enzymes catalase (CAT) and superoxide dismutase (SOD) and the production of hydrogen peroxide H2O2 were evaluated on fungal submerged cultures within the first hours of Ni2+ exposure. Results showed that M. procera growth decreased when Ni2+ concentrations increased, reaching a maximum growth inhibition (>80%) up to 0.2 mM of NiCl2. Ni uptake increased proportionally to Ni increase in the medium. Both Ni tolerance and Ni accumulation were affected by medium pH. Microscope observations showed differences in the size of spores produced by fungi at different Ni concentrations. Ni exposure induced oxidative stress, as indicated by the production of H2O2, the levels of which seem to be regulated by the antioxidant enzymes SOD and CAT. The time variation pattern of SOD and CAT activities indicated that the former has a greater role in alleviating the stress. The results obtained suggested that tolerance of M. procera to Ni2+ is associated with the ability of this macrofungus to initiate an efficient antioxidant defense system.

On the mechanisms of cadmium stress alleviation in Medicago truncatula by arbuscular mycorrhizal symbiosis: a root proteomic study

The arbuscular mycorrhizal (AM) symbiosis belongs to the strategies plants have developed to cope with adverse environmental conditions including contamination by heavy metals such as cadmium (Cd). In the present work, we report on the protective effect conferred by AM symbiosis to the model legume Medicago truncatula grown in presence of Cd, and on the 2-D-based proteomic approach further used to compare the proteomes of M. truncatula roots either colonised or not with the AM fungus Glomus intraradices in Cd-free and Cd-contaminated substrates. The results indicated that at the proteome level, 9 out of the 15 cadmium-induced changes in nonmycorrhizal roots were absent or inverse in those Cd-treated and colonized by G. intraradices, including the G. intraradices-dependent down-accumulation of Cd stress-responsive proteins. Out of the twenty-six mycorrhiza-related proteins that were identified, only six displayed changes in abundance upon Cd exposure, suggesting that part of the symbiotic program, which displays low sensitivity to Cd, may be recruited to counteract Cd toxicity through the mycorrhiza-dependent synthesis of proteins having functions putatively involved in alleviating oxidative damages, including a cyclophilin, a guanine nucleotide-binding protein, an ubiquitin carboxyl-terminal hydrolase, a thiazole biosynthetic enzyme, an annexin, a glutathione S-transferase (GST)-like protein, and a S-adenosylmethionine (SAM) synthase.

Intracellular oxidative stress and cadmium ions release induce cytotoxicity of unmodified cadmium sulfide quantum dots

OBJECTIVE

To fully understand the cytotoxicity of after-degradation QDs, we synthesized CdS QDs and investigated its toxicity mechanism.

METHODS

Biomimetic method was proposed to synthesize cadmium sulfide (CdS) QDs. Thereafter MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide) assay was conducted to evaluate their cytotoxicity. To investigate the toxicity mechanism, we subsequently conducted intracellular reactive oxygen species (ROS) measurement with DCFH-DA, glutathione (GSH) measurement with DTNB, and cellular cadmium assay using atomic absorption spectrometer. Microsized CdS were simultaneously tested as a comparison.

RESULTS

MTT assay results indicated that CdS QDs are more toxic than microsized CdS especially at concentrations below 40 microg/ml. While microsized CdS did not trigger ROS elevation, CdS QDs increase ROS by 20-30% over control levels. However, they both deplete cellular GSH significantly at the medium concentration of 20 microg/ml. In the presence of NAC, cells are partially protected from CdS QDs, but not from microsized particles. Additionally, nearly 20% of cadmium was released from CdS nanoparticles within 24h, which also accounts for QDs' toxicity.

CONCLUSION

Intracellular ROS production, GSH depletion, and cadmium ions (Cd(2+)) release are possible mechanisms for CdS QDs' cytotoxicity. We also suggested that with QD concentration increasing, the principal toxicity mechanism changes from intracellular oxidative stress to Cd(2+) release.

Activation of the oxidative stress regulator PpYap1 through conserved cysteine residues during methanol metabolism in the yeast Pichia pastoris

The methylotrophic yeast Pichia pastoris can grow on methanol as sole source of carbon and energy. The first reaction in yeast methanol metabolism, catalyzed by an abundant peroxisomal enzyme, alcohol oxidase, generates high levels of H(2)O(2), but the oxidative stress response during methanol metabolism has not been elucidated. In this study, we isolated the Yap1 homolog of P. pastoris (PpYap1) and analyzed the properties of a PpYAP1-disruption strain. The PpYap1 transcription factor is activated after exposure to various reactive agents, and therefore functions as a regulator of the redox system in P. pastoris. We have also identified PpGPX1, the unique glutathione peroxidase-encoding gene in P. pastoris whose expression is induced by PpYap1. PpGpx1, but not the ScTsa1 or SpTpx1 homolog PpTsa1, functions as a H(2)O(2) sensor and activates PpYap1. This study is the first demonstration of a yeast Yap1 family protein activated during conventional metabolism.

Hydrogen peroxide-induced response in E. coli and S. cerevisiae: different stages of the flow of the genetic information

Adaptation to oxidative stress is a major topic in basic and applied research. Cell response to stressful changes is realized through coordinated reorganization of gene expression. E. coli and S. cerevisiae are extremely amenable to genetic or molecular biological and biochemical approaches, which make these microorganisms suitable models to study stress response at a molecular level in prokaryotes and eukaryotes, respectively. The main focus of this review is (i) to discuss transcriptional control of global response to hydrogen peroxide in E. coli and S. cerevisiae, (ii) to summarize recent literature data on E. coli and S. cerevisiae adaptive response to oxidative stress at different stages of the flow of the genetic information: from transcription and translation to functionally active proteins and (iii) to discuss possible reasons for a lack of correlation between the expression of certain antioxidant genes at different levels of cellular organization.

Genetic basis of arsenite and cadmium tolerance in Saccharomyces cerevisiae

Background

Arsenic and cadmium are widely distributed in nature and pose serious threats to the environment and human health. Exposure to these nonessential toxic metals may result in a variety of human diseases including cancer. However, arsenic and cadmium toxicity targets and the cellular systems contributing to tolerance acquisition are not fully known.

Results

To gain insight into metal action and cellular tolerance mechanisms, we carried out genome-wide screening of the Saccharomyces cerevisiae haploid and homozygous diploid deletion mutant collections and scored for reduced growth in the presence of arsenite or cadmium. Processes found to be required for tolerance to both metals included sulphur and glutathione biosynthesis, environmental sensing, mRNA synthesis and transcription, and vacuolar/endosomal transport and sorting. We also identified metal-specific defence processes. Arsenite-specific defence functions were related to cell cycle regulation, lipid and fatty acid metabolism, mitochondrial biogenesis, and the cytoskeleton whereas cadmium-specific defence functions were mainly related to sugar/carbohydrate metabolism, and metal-ion homeostasis and transport. Molecular evidence indicated that the cytoskeleton is targeted by arsenite and that phosphorylation of the Snf1p kinase is required for cadmium tolerance.

Conclusion

This study has pin-pointed core functions that protect cells from arsenite and cadmium toxicity. It also emphasizes the existence of both common and specific defence systems. Since many of the yeast genes that confer tolerance to these agents have homologues in humans, similar biological processes may act in yeast and humans to prevent metal toxicity and carcinogenesis.

Proteomic changes in response to acute cadmium toxicity in gill tissue of Paralichthys olivaceus

In the present study, we developed a two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) technique for examining the response of the proteome from gill tissue of Paralichthys olivaceus (POGT) to acute cadmium (AC) toxicity. Approximately 700 protein spots were detected from the gill sample when applying a 600μg protein 2D-PAGE gel in the pH range 5.0-8.0, and approximately 400 of these were identified by peptide mass fingerprinting (PMF) and database search. Compared to a control sample, significant changes were visualized in 18 protein spots exposed to seawater cadmium acute toxicity at 10.0ppm for 24h. Among these spots, two were up-regulated, one was down-regulated, seven showed low expression, and eight showed high expression. The collected spots were further identified by PMF and database search. Ten of the 18 proteins identified on the 2D-PAGE gel, including heat shock protein 70 and calcium-binding protein, demonstrated a synchronous response to AC, and we suggest that the variable levels and trends of these spots on the gel might be utilized as biomarker profiles to investigate cadmium contamination levels in seawater and to evaluate the degree of risk of human fatalities. The experimental results emphasize that the application of multiple biomarkers has an advantage over single biomarkers for monitoring levels of heavy metal contamination in seawater.

The catalytic subunit of Drosophila glutamate-cysteine ligase is a nucleocytoplasmic shuttling protein

GSH concentration is considerably lower in the nucleus than in the cytoplasm; however, it is significantly elevated during active cell proliferation. The main purpose of this study was to understand the mechanism underlying these variations in nuclear/cytoplasmic distribution of GSH. The rate-limiting step in the de novo GSH biosynthesis pathway is catalyzed by glutamate cysteine ligase (GCL), a heterodimer, composed of a catalytic subunit (GCLc) and a modulatory subunit (GCLm). In Drosophila, GCLc, but not GCLm, contains a nuclear localization signal (NLS). Drosophila S2 cells, constitutively expressing regular GCLc protein or expressing GCLc protein with a mutated NLS motif, were generated by transfection. In quiescent S2 cells, GCLc is aggregated in the perinuclear cytosol and the nucleus, whereas GLCm resides solely in the cytosol. In actively proliferating S2 cells, expressing the normal NLS motif, GCLc migrates from the perinuclear cytoplasm into the nucleus, and the nuclear GSH level becomes elevated; in contrast, in proliferating cells, expressing the mutated NLS motif, neither does the GCLc migrate into the nucleus nor does the nuclear GSH amount rise. In S2 cells expressing wild type GCLc, perturbation of cellular redox state by exposure to cadmium resulted in the migration of GCLc into the nucleus but not in cells expressing GCLc with the mutated NLS motif. Overall, results indicated that GSH biosynthesis in the nucleus is associated with migration of only the GCLc subunit from the cytoplasm into the nucleus, and this migration requires the presence of an intact NLS.

Analysis of environmental stress response on the proteome level

Thousands of man-made chemicals are annually released into the environment by agriculture, transport, industries, and other human activities. In general, chemical analysis of environmental samples used to assess the pollution status of a specific ecosystem is complicated by the complexity of the mixture, and in some cases by the very low toxicity thresholds of chemicals present. In that sense, a proteomics approach, capable of detecting subtle changes in the level and structure of individual proteins within the whole proteome in response to the altered surroundings, has obvious applications in the field of ecotoxicology. In addition to identifying new protein biomarkers, it can also help to provide an insight into underlying mechanisms of toxicity. Despite being a comparatively new field with a number of caveats, proteomics applications have spread from microorganisms and plants to invertebrates and vertebrates, gradually becoming an established technology used in environmental research. This review article highlights recent advances in the field of environmental proteomics, mainly focusing on experimental approaches with a potential to understand toxic modes of action and to identify novel ecotoxicological biomarkers.

Heat shock and oxygen radicals stimulate ubiquitin-dependent degradation mainly of newly synthesized proteins

Accumulation of misfolded oxidant-damaged proteins is characteristic of many diseases and aging. To understand how cells handle postsynthetically damaged proteins, we studied in Saccharomyces cerevisiae the effects on overall protein degradation of shifting from 30 to 38°C, exposure to reactive oxygen species generators (paraquat or cadmium), or lack of superoxide dismutases. Degradation rates of long-lived proteins (i.e., most cell proteins) were not affected by these insults, even when there was widespread oxidative damage to proteins. However, exposure to 38°C, paraquat, cadmium, or deletion of SOD1 enhanced two- to threefold the degradation of newly synthesized proteins. By 1 h after synthesis, their degradation was not affected by these treatments. Degradation of these damaged cytosolic proteins requires the ubiquitin–proteasome pathway, including the E2s UBC4/UBC5, proteasomal subunit RPN10, and the CDC48–UfD1–NPL4 complex. In yeast lacking these components, the nondegraded polypeptides accumulate as aggregates. Thus, many cytosolic proteins proceed through a prolonged “fragile period” during which they are sensitive to degradation induced by superoxide radicals or increased temperatures.

Chromate causes sulfur starvation in yeast

Chromate is a widespread pollutant as a waste of human activities. However, the mechanisms underlying its high toxicity are not clearly understood. In this work, we used the yeast Saccharomyces cerevisiae to analyse the physiological effects of chromate exposure in a eukaryote cell model. We show that chromate causes a strong decrease of sulfate assimilation and sulfur metabolite pools suggesting that cells experience sulfur starvation. As a consequence, nearly all enzymes of the sulfur pathway are highly induced as well as enzymes of the sulfur-sparing response such as Pdc6, the sulfur-poor pyruvate decarboxylase. The induction of Pdc6 was regulated at the mRNA level and dependent upon Met32, a coactivator of Met4, the transcriptional activator of the sulfur pathway. Finally, we found that chromate enters the cells mainly through sulfate transporters and competitively inhibits sulfate uptake. Also consistent with a competition between the two substrates, sulfate supplementation relieves chromate toxicity. However, the data suggest that the chromate-mediated sulfur depletion is not simply due to this competitive uptake but would also be the consequence of competitive metabolism between the two compounds presumably at another step of the sulfur assimilation pathway.

Molecular responses of Campylobacter jejuni to cadmium stress

Cadmium ions are a potent carcinogen in animals, and cadmium is a toxic metal of significant environmental importance for humans. Response curves were used to investigate the effects of cadmium chloride on the growth of Camplyobacter jejuni. In vitro, the bacterium showed reduced growth in the presence of 0.1 mm cadmium chloride, and the metal ions were lethal at 1 mm concentration. Two-dimensional gel electrophoresis combined with tandem mass spectrometry analysis enabled identification of 67 proteins differentially expressed in cells grown without and with 0.1 mm cadmium chloride. Cellular processes and pathways regulated under cadmium stress included fatty acid biosynthesis, protein biosynthesis, chemotaxis and mobility, the tricarboxylic acid cycle, protein modification, redox processes and the heat-shock response. Disulfide reductases and their substrates play many roles in cellular processes, including protection against reactive oxygen species and detoxification of xenobiotics, such as cadmium. The effects of cadmium on thioredoxin reductase and disulfide reductases using glutathione as a substrate were studied in bacterial lysates by spectrophotometry and nuclear magnetic resonance spectroscopy, respectively. The presence of 0.1 mm cadmium ions modulated the activities of both enzymes. The interactions of cadmium ions with oxidized glutathione and reduced glutathione were investigated using nuclear magnetic resonance spectroscopy. The data suggested that, unlike other organisms, C. jejuni downregulates thioredoxin reductase and upregulates other disulfide reductases involved in metal detoxification in the presence of cadmium.

Expressional control of a cadmium-transporting P1B-type ATPase by a metal sensing degradation signal

Cadmium is a highly toxic environmental contaminant implicated in various diseases. Our previous data demonstrated that Pca1, a P1B-type ATPase, plays a critical role in cadmium resistance in yeast S. cerevisiae by extruding intracellular cadmium. This illustrates the first cadmium-specific efflux pump in eukaryotes. In response to cadmium, yeast cells rapidly enhance expression of Pca1 by a post-transcriptional mechanism. To gain mechanistic insights into the cadmium-dependent control of Pca1 expression, we have characterized the pathway for Pca1 turnover and the mechanism of cadmium sensing that leads to up-regulation of Pca1. Pca1 is a short-lived protein (t1/2 < 5 min) and is subject to ubiquitination when cells are growing in media lacking cadmium. Distinct from many plasma membrane transporters targeted to the vacuole for degradation via endocytosis, cells defective in this pathway did not stabilize Pca1. Rather, Pca1 turnover was dependent on the proteasome. These data suggest that, in the absence of cadmium, Pca1 is targeted for degradation before reaching the plasma membrane. Mapping of the N terminus of Pca1 identified a metal-responding degradation signal encompassing amino acids 250-350. Fusion of this domain to a stable protein demonstrated that it functions autonomously in a metal-responsive manner. Cadmium sensing by cysteine residues within this domain circumvents ubiquitination and degradation of Pca1. These data reveal a new mechanism for substrate-mediated control of P1B-type ATPase expression. Cells have likely evolved this mode of regulation for a rapid and specific cellular response to cadmium.

Application of comparative proteome analysis to reveal influence of cultivation conditions on asymmetric bioreduction of beta-keto ester by Saccharomyces cerevisiae

Industrial bakers' yeast strain Saccharomyces cerevisiae LH1 was selected for asymmetric reduction of ethyl benzoylacetate to (S)-ethyl 3-hydroxy-3-phenylpropionate. Higher reductive efficiency and higher cofactor availability were obtained with the alternation of cultivation condition (mainly growth medium). Compared to the bioreduction by yeast cells grown in malt extract (ME) medium, the concentration of substrate was increased 25-fold (up to 15.6 g/l) in the yeast peptone dextrose (YPD)-grown cells mediated bioreduction with 97.5% of enantioselective excess of (S)-product. The proteomic responses of S. cerevisiae LH1 cells to growth in aerobic batch cultures fed with either YPD or ME medium were examined and compared. Among the relative quantities of 550 protein spots in each gel, changes were shown in the expression level of 102 intracellular proteins when comparing YPD gel to ME gel. Most of the identified proteins were involved in energy metabolism and several cellular molecular biosynthetic pathway and catabolism. For YPD-grown yeast cells, not only enzymes involved in nicotinamide adenine dinucleotide phosphate regeneration, especially 6-phosphogluconate dehydrogenase, but also alcohol dehydrogenase 1 and D: -arabinose 1-dehydrogenase which had been demonstrated activity toward ethyl benzoylacetate to (S)-hydroxy ester were significantly upregulated. These changes provided us insight in the way the yeast cells adapted to a change in cultivation medium and regulated its catalytic efficiency in the bioreduction.

Response of antioxidant enzymes, ascorbate and glutathione metabolism towards cadmium in hyperaccumulator and nonhyperaccumulator ecotypes of Sedum alfredii H

Hydroponics studies were conducted to investigate the antioxidant adaptations, ascorbate and glutathione metabolism in hyperaccumulating ecotype of Sedum alfredii (HE) exposed to high Cd environment, when compared with its nonhyperaccumulating ecotype (NHE). Exposure to Cd induced a burst of oxidative stress in both ecotypes which was evident by the sharp increase in hydrogen peroxide (H(2)O(2)) contents and lipid peroxidation. Buthionine sulfoximine (BSO), an inhibitor of glutathione (GSH) synthesis, did not affect H(2)O(2) concentrations as well as growth of both ecotypes in the absence of Cd. However, compared with Cd application alone, BSO combined with Cd treatment caused a substantial augmentation of H(2)O(2) accumulation accompanied by a reduction in Cd concentrations in roots and leaves of HE at the end of treatment, which may rule out the possibility that GSH biosynthesis may play an important role as a signal of the stress regulation. No efficient and superior enzymatic antioxidant defense mechanisms against Cd-imposed oxidative stress existed in both NHE and HE, but the essential nonenzymatic components like ascorbic acid (AsA) and GSH played a prominent role in tolerance against Cd. Cadmium stimulated a notable rise in AsA concentration in both ecotypes soon after the application of treatment. A preferential Cd-stress response in HE was suggested to changes in the GSH pool, where acclimation was marked by increased GSH concentrations.

Engineering expression of polyphosphate confers cadmium resistance in tobacco

The feasibility of transgenic tobacco, genetically engineered to express bacterial polyphosphate (polyP) for phytoremediation of cadmium pollution was examined. The transgenic tobacco showed more resistance to Cd2+ and accumulated more Cd2+ than its wild-type progenitors. These results suggest that polyP has abilities to reduce Cd2+ toxicity, probably via a chelation mechanism, and to accumulate cadmium in the transgenic tobacco. Based on the results obtained in this study, polyP-mediated Cd2+ accumulation may serve as a useful strategy for Cd2+ phytoremediation.

The emerging regulatory potential of SCFMet30 -mediated polyubiquitination and proteolysis of the Met4 transcriptional activator

The yeast SCF^Met30 ubiquitin ligase plays a critical role in cell division by regulating the Met4 transcriptional activator of genes that control the uptake and assimilation of sulfur into methionine and S-adenosyl-methionine. The initial view on how SCF^Met30 performs its function has been driven by the assumption that SCF^Met30 acts exclusively as Met4 inhibitor when high levels of methionine drive an accumulation of cysteine. We revisit this model in light of the growing evidence that SCF^Met30 can also activate Met4. The notion that Met4 can be inhibited or activated depending on the sulfur metabolite context is not new, but for the first time both aspects have been linked to SCF^Met30, creating an interesting regulatory paradigm in which polyubiquitination and proteolysis of a single transcriptional activator can play different roles depending on context. We discuss the emerging molecular basis and the implications of this new regulatory phenomenon.

Cadmium induces a heterogeneous and caspase-dependent apoptotic response in Saccharomyces cerevisiae

The toxic metal cadmium is linked to a series of degenerative disorders in humans, in which Cd-induced programmed cell death (apoptosis) may play a role. The yeast, Saccharomyces cerevisiae, provides a valuable model for elucidating apoptosis mechanisms, and this study extends that capability to Cd-induced apoptosis. We demonstrate that S. cerevisiae undergoes a glucose-dependent, programmed cell death in response to low cadmium concentrations, which is initiated within the first hour of Cd exposure. The response was associated with induction of the yeast caspase, Yca1p, and was abolished in a yca1Delta mutant. Cadmium-dependent apoptosis was also suppressed in a gsh1Delta mutant, indicating a requirement for glutathione. Other apoptotic markers, including sub-G(1) DNA fragmentation and hyper-polarization of mitochondrial membranes, were also evident among Cd-exposed cells. These responses were not distributed uniformly throughout the cell population, but were restricted to a subset of cells. This apoptotic subpopulation also exhibited markedly elevated levels of intracellular reactive oxygen species (ROS). The heightened ROS levels alone were not sufficient to induce apoptosis. These findings highlight several new perspectives to the mechanism of Cd-dependent apoptosis and its phenotypic heterogeneity, while opening up future analyses to the power of the yeast model system.

Quantitative proteomics as a new piece of the systems biology puzzle

The definition of the role of each gene product in its cellular context is of outstanding importance in the post-genomics era. Recent technological innovations have driven research in proteomics from single protein characterization to global approaches, aiming to achieve a comprehensive qualitative and quantitative description of complex molecular mechanisms. In this review, we discuss the methodology of quantitative proteomics as it applies to the analysis of complex biological model systems. A special attention will be given to model systems that are suitable for functional genomic studies, where the potential of quantitative proteomics can be effectively demonstrated.

Enhancing phytoremediation through the use of transgenics and endophytes

In the last decade, there has been an increase in research on improving the ability of plants to remove environmental pollution. Genes from microbes, plants, and animals are being used successfully to enhance the ability of plants to tolerate, remove, and degrade pollutants. Through expression of specific bacterial genes in transgenic plants, the phytotoxic effects of nitroaromatic pollutants were overcome, resulting in increased removal of these chemicals. Overexpression of mammalian genes encoding cytochrome P450s led to increased metabolism and removal of a variety of organic pollutants and herbicides. Genes involved in the uptake or detoxification of metal pollutants were used to enhance phytoremediation of this important class of pollutants. Transgenic plants containing specific bacterial genes converted mercury and selenium to less toxic forms. In addition to these transgenic approaches, the use of microbes that live within plants, termed endophytes, also led to improved tolerance to normally phytotoxic chemicals and increased removal of the pollutants. Bacteria that degraded a herbicide imparted resistance to the herbicide when inoculated into plants. In another study, plants harboring bacteria capable of degrading toluene were more tolerant to normally phytotoxic concentrations of the chemical, and transpired less of it into the atmosphere. This review examines the recent advances in enhancing phytoremediation through transgenic plant research and through the use of symbiotic endophytic microorganisms within plant tissues.

Cadmium toxicity in glutathione mutants of Escherichia coli

The higher affinity of Cd(2+) for sulfur compounds than for nitrogen and oxygen led to the theoretical consideration that cadmium toxicity should result mainly from the binding of Cd(2+) to sulfide, thiol groups, and sulfur-rich complex compounds rather than from Cd(2+) replacement of transition-metal cations from nitrogen- or oxygen-rich biological compounds. This hypothesis was tested by using Escherichia coli for a global transcriptome analysis of cells synthesizing glutathione (GSH; wild type), gamma-glutamylcysteine (DeltagshB mutant), or neither of the two cellular thiols (DeltagshA mutant). The resulting data, some of which were validated by quantitative reverse transcription-PCR, were sorted using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system, which groups genes hierarchically with respect to the cellular functions of their respective products. The main difference among the three strains concerned tryptophan biosynthesis, which was up-regulated in wild-type cells upon cadmium shock and strongly up-regulated in DeltagshA cells but repressed in DeltagshB cells containing gamma-glutamylcysteine instead of GSH. Overall, however, all three E. coli strains responded to cadmium shock similarly, with the up-regulation of genes involved in protein, disulfide bond, and oxidative damage repair; cysteine and iron-sulfur cluster biosynthesis; the production of proteins containing sensitive iron-sulfur clusters; the storage of iron; and the detoxification of Cd(2+) by efflux. General energy conservation pathways and iron uptake were down-regulated. These findings indicated that the toxic action of Cd(2+) indeed results from the binding of the metal cation to sulfur, lending support to the hypothesis tested.

Environmental proteomics and metallomics

Monitoring environmental pollution using biomarkers requires detailed knowledge about the markers, and many only allow a partial assessment of pollution. New proteomic methods (environmental proteomics) can identify proteins that, after validation, might be useful as alternative biomarkers, although this approach also has its limitations, derived mainly from their application to non-model organisms. Initial studies using environmental proteomics were carried out in animals exposed to model pollutants, and led to the concept of protein expression signatures. Experiments have been carried out in model organisms (yeast, Arabidopsis, rat cells, or mice) exposed to model contaminants. Over the last few years, proteomics has been applied to organisms from ecosystems with different pollution levels, forming the basis of an environmental branch in proteomics. Another focus is connected with the presence of metals bound to biomolecules, which adds an additional dimension to metal-biomolecule and metalloprotein characterization - the field of metallomics. The metallomic approach considers the metallome: a whole individual metal or metalloid species within a cell or tissue. A metallomic analytical approach (MAA) is proposed as a new tool to study and identify metalloproteins.

Yeast genes involved in cadmium tolerance: Identification of DNA replication as a target of cadmium toxicity

Cadmium (Cd(2+)) is a ubiquitous environmental pollutant and human carcinogen. The molecular basis of its toxicity remains unclear. Here, to identify the landscape of genes and cell functions involved in cadmium resistance, we have screened the Saccharomyces cerevisiae deletion collection for mutants sensitive to cadmium exposure. Among the 4866 ORFs tested, we identified 73 genes whose inactivation confers increased sensitivity to Cd(2+). Most were previously unknown to play a role in cadmium tolerance and we observed little correlation between the cadmium sensitivity of a gene deletant and the variation in the transcriptional activity of that gene in response to cadmium. These genes encode proteins involved in various functions: intracellular transport, stress response and gene expression. Analysis of the sensitive phenotype of our "Cd(2+)-sensitive mutant collection" to arsenite, cobalt, mercury and H(2)O(2) revealed 17 genes specifically involved in cadmium-induced response. Among them we found RAD27 and subsequently DNA2 which encode for proteins involved in DNA repair and replication. Analysis of the Cd(2+)-sensitivity of RAD27 (rad27-G67S) and DNA2 (dna2-1) separation of function alleles revealed that their activities necessary for Okazaki fragment processing are essential in conditions of cadmium exposure. Consistently, we observed that wild-type cells exposed to cadmium display an enhanced frequency of forward mutations to canavanine resistance and minisatellite destabilisation. Taken together these results provide a global picture of the genetic requirement for cadmium tolerance in yeast and strongly suggest that DNA replication, through the step of Okazaki fragment processing, is a target of cadmium toxicity.