Tandem quadruplication of HMA4 in the zinc (Zn) and cadmium (Cd) hyperaccumulator Noccaea caerulescens

Zinc (Zn) and cadmium (Cd) hyperaccumulation may have evolved twice in the Brassicaceae, in Arabidopsis halleri and in the Noccaea genus. Tandem gene duplication and deregulated expression of the Zn transporter, HMA4, has previously been linked to Zn/Cd hyperaccumulation in A. halleri. Here, we tested the hypothesis that tandem duplication and deregulation of HMA4 expression also occurs in Noccaea.A Noccaea caerulescens genomic library was generated, containing 36,864 fosmid pCC1FOS™ clones with insert sizes ∼20–40 kbp, and screened with a PCR-generated HMA4 genomic probe. Gene copy number within the genome was estimated through DNA fingerprinting and pooled fosmid pyrosequencing. Gene copy numbers within individual clones was determined by PCR analyses with novel locus specific primers. Entire fosmids were then sequenced individually and reads equivalent to 20-fold coverage were assembled to generate complete whole contigs.Four tandem HMA4 repeats were identified in a contiguous sequence of 101,480 bp based on sequence overlap identities. These were flanked by regions syntenous with up and downstream regions of AtHMA4 in Arabidopsis thaliana. Promoter-reporter β-glucuronidase (GUS) fusion analysis of a NcHMA4 in A. thaliana revealed deregulated expression in roots and shoots, analogous to AhHMA4 promoters, but distinct from AtHMA4 expression which localised to the root vascular tissue.This remarkable consistency in tandem duplication and deregulated expression of metal transport genes between N. caerulescens and A. halleri, which last shared a common ancestor >40 mya, provides intriguing evidence that parallel evolutionary pathways may underlie Zn/Cd hyperaccumulation in Brassicaceae.     

Variation of trace metal accumulation,major nutrient uptake and growth parameters and their correlations in 22 populations of Noccaea caerulescens

Background and aims

Noccaea caerulescens is a model plant for the understanding of trace metal accumulation and a source of cultivars for phytoextraction. The aim of this study was to investigate natural variation for trace metal accumulation, major nutrient uptake and growth parameters in 22 populations. The correlations among these traits were particularly examined to better understand the eco-physiology and the phytoextraction potential of the species.

Methods

Populations from three edaphic groups, i.e. calamine (CAL), serpentine (SERP) and non metalliferous (NMET) sites were grown in hydroponics for seven weeks at moderate trace metal exposure. Growth indicators, element contents and correlations between these variables were compared.

Results

All the phenotypic characteristics showed a wide variability among groups and populations. The SERP populations showed a smaller plant size, higher cation contents and strong correlations between all element concentrations. NMET populations did not differ in plant size from the CAL ones, but had higher Zn and Ni contents. The CAL populations showed higher Cd and Mn accumulations and lower Ca contents. The trade-off between biomass production and Cd, Ni and Zn accumulation was high in SERP populations and low in the CAL and NMET ones.

Conclusions

N. caerulescens is a genetically diverse species, showing specific features depending on the group and the population. These features may reflect the wide adaptive capacities of the species, and also reveal promising potential for phytoextraction of Cd, Ni and Zn.     

Variation in tissue-specific gene expression among natural populations

Background  

Variation in gene expression is extensive among tissues, individuals, strains, populations and species. The interactions among these sources of variation are relevant for physiological studies such as disease or toxic stress; for example, it is common for pathologies such as cancer, heart failure and metabolic disease to be associated with changes in tissue-specific gene expression or changes in metabolic gene expression. But how conserved these differences are among outbred individuals and among populations has not been well documented. To address this we examined the expression of a selected suite of 192 metabolic genes in brain, heart and liver in three populations of the teleost fish Fundulus heteroclitus using a highly replicated experimental design.     

Variation in tissue-specific gene expression among natural populations

Background

Variation in gene expression is extensive among tissues, individuals, strains, populations and species. The interactions among these sources of variation are relevant for physiological studies such as disease or toxic stress; for example, it is common for pathologies such as cancer, heart failure and metabolic disease to be associated with changes in tissue-specific gene expression or changes in metabolic gene expression. But how conserved these differences are among outbred individuals and among populations has not been well documented. To address this we examined the expression of a selected suite of 192 metabolic genes in brain, heart and liver in three populations of the teleost fish Fundulus heteroclitus using a highly replicated experimental design.

Results

Half of the genes (48%) were differentially expressed among individuals within a population-tissue group and 76% were differentially expressed among tissues. Differences among tissues reflected well established tissue-specific metabolic requirements, suggesting that these measures of gene expression accurately reflect changes in proteins and their phenotypic effects. Remarkably, only a small subset (31%) of tissue-specific differences was consistent in all three populations.

Conclusions

These data indicate that many tissue-specific differences in gene expression are unique to one population and thus are unlikely to contribute to fundamental differences between tissue types. We suggest that those subsets of treatment-specific gene expression patterns that are conserved between taxa are most likely to be functionally related to the physiological state in question.     

Nickel and zinc accumulation capacities and tolerance to these metals in the excluder Thlaspi arvense and the hyperaccumulator Noccaea caerulescens

Representatives of Brassicaceae species—the hyperaccumulator Noccaea caerulescens F.K. Mey and the metal excluder Thlaspi arvense L.—were compared in terms of their ability to accumulate nickel (Ni) and zinc (Zn) and their tolerance to these metals. Four ecotypes of N. caerulescens were used: the ecotypes La Calamine (LC, Belgium) and Saint Felix de Palliéres (SF, France) grow naturally on calamine soils rich in Zn, Cd, and Pb; the ecotype Monte Prinzera (MP, Italy) originates from serpentine soils rich in Ni, Co, and Cr; and the ecotype Lellingen (LE, Luxembourg) inhabits non-metalliferous soils. The plants of N. caerulescens were grown for 8 weeks in a half-strength Hoagland solution supplemented with 25, 100, 200, 300, and 400 μM Ni(NO₃)₂ (ecotypes LC, SF, MP, LE) or 100, 200, 400, 800, and 1000 μM Zn(NO₃)₂ (ecotypes LC, SF, LE); the plants of T. arvense were grown in the presence of 10, 20, 25, and 30 μM Ni(NO₃)₂ or 40, 50, 60, 70, 80 μM Zn(NO₃)₂. The toxic effect of Ni and Zn was assessed from changes in dry matter of roots and shoots of treated plants compared to untreated. The content of metals in roots and shoots was determined by means of atomic absorption spectrophotometry. The Ni-accumulating capacity of N. caerulescens ecotypes increased in the order: LC < SF < LE < MP, and the Zn-accumulating capacity increased in the row: LC < SF < LE. In the hyperaccumulating plant N. caerulescens, the increments of biomass started to decrease at a lower metal content in roots than in shoots, whereas the opposite pattern was observed in the metal excluder T. arvense. Since T. arvense plants accumulated Ni and Zn in roots, whereas N. caerulescens accumulated these metals in shoots, one may assume that the greater sensitivity of root growth compared with shoots in N. caerulescens was determined by more effective mechanisms of metal detoxification in shoots. Conversely, the higher sensitivity of shoot growth compared to root growth in T. arvense was determined by more effective mechanisms of metal detoxification in roots. Being more tolerant to Ni and Zn than T. arvense plants, the N. caerulescens ecotypes differed substantially in terms of metal-accumulating capacity and their tolerance to heavy metals. The ecotype originating from non-metalliferous soils (LE) accumulated larger amounts of Zn, but was less tolerant compared with ecotypes growing naturally on calamine soils (SF and LC), whereas the ecotype occurring on serpentine soils (MP) exhibited a markedly greater tolerance to Ni, compared with other ecotypes examined, as well as the largest accumulation of this metal. The results indicate the existence of different mechanisms responsible for plant tolerance to Ni and Zn; the study of these mechanisms is a promising direction for future research.     

Metal concentration and metal mass of metallicolous, non metallicolous and serpentine Noccaea caerulescens populations, cultivated in different growth media

Aims

Evaluate the genetic and environmental variability of metal concentration and metal mass of Noccaea caerulescens, from metalliferous (MET), non metalliferous (NMET) and serpentine (SERP) soils.

Methods

18 populations were cultivated in 18 different growth conditions, such as a soil mine tailing, soils amended with zinc (Zn), cadmium (Cd) and nickel (Ni) salts (in mixtures or in monometallic salts) and a hydroponic solution with two Zn concentrations.

Results

MET populations had Zn concentrations lower than NMET and SERP in the different soils but higher Cd mass (the product of aerial biomass and foliar metal concentration). SERP had the highest Ni concentration and Ni mass values. The addition of Cd or Ni to a Zn-contaminated soil significantly decreases Zn concentration. In hydroponics, MET and NMET had equivalent Zn concentrations but these were three times higher than those obtained in soil experiments. Zn mass of NMET was significantly lower than MET with the latter having Zn mass values largely above those obtained in mine soil.

Conclusions

Results showed a large heterogeneity of responses among populations depending on the substrate used, and it was not possible to correctly assign a single population to its accurate origin with only one experiment. Finally, data on metal concentration obtained in culture soils are closer to those in field soils than those from hydroponics so that they could give a more accurate information on the accumulating capacity of Noccaea caerulescens and its use in phytoextraction of metals in field conditions.     

Heavy metal tolerance and accumulation in metallicolous and non-metallicolous populations of Thlaspi caerulescens from continental Europe

In continental Europe, the heavy metal hyperaccumulator Thlaspi caerulescens occurs both on heavy-metal polluted soils (subsp. calaminare) and on soils with normal heavy metal content (subsp. caerulescens). In order to assess the extent and partitioning of variation in heavy metal tolerance and foliar mineral composition, twelve families from two populations of each subspecies were grown in pots in four soil treatments differing in heavy metal (Zn, Pb) and macronutrient concentrations. The two subspecies differed systematically in many respects. Subsp. calaminare had a higher survival at high levels of heavy metals and a higher tolerance index in all treatments. It also had three times lower foliar zinc and lead concentrations when grown at moderate levels of heavy metals. This, together with a negative correlation of foliar Pb concentration with growth in subsp. caerulescens, suggests that heavy metal accumulation per se is not a mechanism of tolerance in this species. Variation among families within populations accounted for a larger proportion of total variance in growth and mineral composition than variation between populations. Additionally, within population variation in heavy metal tolerance and accumulation was significantly lower in subsp. calaminare. This suggests that, adding to a background constitutive tolerance at the species level, natural selection has increased heavy metal tolerance in metallicolous populations of Thlaspi caerulescens.     

Cadmium accumulation in populations of Thlaspi caerulescens and Thlaspi goesingense

The capacity to accumulate cadmium (Cd) and zinc (Zn) was compared in Thlaspi goesingense and four populations of Thlaspi caerulescens . Two populations of T. caerulescens were grown in hydroponics at five concentrations of Cd. In addition, plants were grown in pots containing compost in which three different concentrations of Cd and two concentrations of Zn were added. A field trial was conducted to compare Zn and Cd uptake by three populations of T. caerulescens on nine selected plots of the Woburn Market Garden Experiment (UK) which had been contaminated to different degrees with heavy metals owing to past applications of sewage sludge. Results show that the four populations of T. caerulescens had the same ability to hyperaccumulate Zn but were significantly different in terms of Cd accumulation. Two populations of T. caerulescens from Southern France accumulated much more Cd than the populations from Prayon (Belgium) and Whitesike (UK). Generally, uptake of Cd was not decreased by increased concentrations of Zn in the substrate. These results indicate that the mechanisms of Cd and Zn hyperaccumulation are not identical in this species. This is the first report of hyperaccumulation of Cd by T. goesingense , but the growth of this species was markedly reduced by the large concentrations of Zn in the substrate. Future work should focus on the differences between Cd and Zn uptake in hyperaccumulator plants at the species and population level.     

Variation among alfalfa somaclones in copy number of repeated DNA sequences.

Repeated DNA sequences of alfalfa (Medicago sativa L.) somaclonal variants were analyzed to determine if changes in copy number had occurred during tissue culture. DNA clones containing highly repeated nuclear sequences from the diploid line HG2 (2x = 16) were slot blotted and probed with labeled DNAs from HG2 and several somaclones of HG2. Two DNA clones that differed visually in hybridization intensity among the plant DNAs and one clone that had constant hybridization intensity were selected and used as probes on Southern blots and slot blots containing equal quantities of DNAs from HG2 and 15 régénérants. Statistically significant differences were detected in the copy number of two anonymous DNA sequences initially selected as variable and in the copy number of sequences homologous to pea ribosomal DNA. Based on Southern blot analysis, these sequences appeared to be arranged as tandem repeats. The cloned sequence initially selected as stable did not vary significantly in copy number and it appeared to be arranged as a dispersed repeat. Both increases and decreases in copy number of repeated sequences were observed in plants from successive regeneration cycles. Results from this study indicate that specific repeated nuclear DNA sequences have changed copy number in plants regenerated from tissue culture.     

Variation in selenium tolerance and accumulation among 19 Arabidopsis thaliana accessions

Selenium (Se) is an essential element for many organisms but also toxic at higher levels. The objective of this study was to identify accessions from the model species Arabidopsis thaliana that differ in Se tolerance and accumulation. Nineteen Arabidopsis accessions were grown from seed on agar medium with or without selenate (50 microM) or selenite (20 microM), followed by analysis of Se tolerance and accumulation. Tissue sulfur levels were also compared. The Se Tolerance Index (root length+Se/root length control) varied among the accessions from 0.11 to 0.44 for selenite and from 0.05 to 0.24 for selenate. When treated with selenite, the accessions differed by two-fold in shoot Se concentration (up to 250 mgkg(-1)) and three-fold in root Se concentration (up to 1000 mgkg(-1)). Selenium accumulation from selenate varied 1.7-fold in shoot (up to 1000 mgkg(-1)) and two-fold in root (up to 650 mgkg(-1)). Across all accessions, a strong correlation was observed between Se and S concentration in both shoot and root under selenate treatment, and in roots of selenite-treated plants. Shoot Se accumulation from selenate and selenite were also correlated. There was no correlation between Se tolerance and accumulation, either for selenate or selenite. The F(1) offspring from a cross between the extreme selenate-sensitive Dijon G and the extreme selenate-tolerant Estland accessions showed intermediate selenate tolerance. In contrast, the F(1) offspring from a cross between selenite-sensitive and -tolerant accessions (Dijon GxCol-PRL) were selenite tolerant. The results from this study give new insight into the mechanisms of plant selenium (Se) tolerance and accumulation, which may help develop better plants for selenium phytoremediation or as fortified foods.     

Relative argininosuccinate synthetase mRNA levels and gene copy number in canavanine-resistant lymphoblasts

Mutants resistant to the arginine analogue, canavanine, have been isolated from two normal lymphoblast lines, MGL8B2 and MGL33. These mutants constitutively express up to 200-fold higher amounts of structurally normal argininosuccinate synthetase, the urea cycle enzyme that converts citrulline to argininosuccinate. Relative levels of argininosuccinate synthetase mRNA were compared among normal and canavanine-resistant lines using in vitro translation of poly(adenylic acid) RNA and blot hybridization of total cytoplasmic RNA to an argininosuccinate synthetase cDNA. Both of these approaches indicated that the canavanine-resistant lines contain increased steady-state levels of synthetase-specifc mRNA relative to their sensitive parents and that these were roughly correlated with levels of enzyme activity. Blot hybridization of Eco RI-digested genomic DNA preparations revealed no detectable differences in argininosuccinate synthetase structural gene copy number between normal and canavanine-resistant lymphoblasts, demonstrating that the canavanine-resistant phenotype is not caused by gene amplification.     

Integrated analyses of copy number variations and gene expression in lung adenocarcinoma

Numerous efforts have been made to elucidate the etiology and improve the treatment of lung cancer, but the overall five-year survival rate is still only 15%. Identification of prognostic biomarkers for lung cancer using gene expression microarrays poses a major challenge in that very few overlapping genes have been reported among different studies. To address this issue, we have performed concurrent genome-wide analyses of copy number variation and gene expression to identify genes reproducibly associated with tumorigenesis and survival in non-smoking female lung adenocarcinoma. The genomic landscape of frequent copy number variable regions (CNVRs) in at least 30% of samples was revealed, and their aberration patterns were highly similar to several studies reported previously. Further statistical analysis for genes located in the CNVRs identified 475 genes differentially expressed between tumor and normal tissues (p<10⁻⁵). We demonstrated the reproducibility of these genes in another lung cancer study (p = 0.0034, Fisher''s exact test), and showed the concordance between copy number variations and gene expression changes by elevated Pearson correlation coefficients. Pathway analysis revealed two major dysregulated functions in lung tumorigenesis: survival regulation via AKT signaling and cytoskeleton reorganization. Further validation of these enriched pathways using three independent cohorts demonstrated effective prediction of survival. In conclusion, by integrating gene expression profiles and copy number variations, we identified genes/pathways that may serve as prognostic biomarkers for lung tumorigenesis.     

Functional profiling and gene expression analysis of chromosomal copy number alterations

Contrarily to the traditional view in which only one or a few key genes were supposed to be the causative factors of diseases, we discuss the importance of considering groups of functionally related genes in the study of pathologies characterised by chromosomal copy number alterations. Recent observations have reported the existence of regions in higher eukaryotic chromosomes (including humans) containing genes of related function that show a high degree of coregulation. Copy number alterations will consequently affect to clusters of functionally related genes, which will be the final causative agents of the diseased phenotype, in many cases. Therefore, we propose that the functional profiling of the regions affected by copy number alterations must be an important aspect to take into account in the understanding of this type of pathologies. To illustrate this, we present an integrated study of DNA copy number variations, gene expression along with the functional profiling of chromosomal regions in a case of multiple myeloma.     

Integrated analysis of DNA copy number and gene expression microarray data using gene sets

Background  

Genes that play an important role in tumorigenesis are expected to show association between DNA copy number and RNA expression. Optimal power to find such associations can only be achieved if analysing copy number and gene expression jointly. Furthermore, some copy number changes extend over larger chromosomal regions affecting the expression levels of multiple resident genes.     

Determination of beta-defensin genomic copy number in different populations: a comparison of three methods

Background

There have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and β-defensins and Crohn''s disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with disease. At present, real-time quantitative PCR (QPCR) is the most commonly used method to determine gene copy number, however the Paralogue Ratio Test (PRT) is being used in more and more laboratories.

Findings

In this study we compare a Pyrosequencing-based Paralogue Ratio Test (PPRT) for determining beta-defensin gene copy number with two currently used methods for gene copy number determination, QPCR and triplex PRT by typing five different cohorts (UK, Danish, Portuguese, Ghanaian and Czech) of DNA from a total of 576 healthy individuals. We found a systematic measurement bias between DNA cohorts revealed by QPCR, but not by the PRT-based methods. Using PRT, copy number ranged from 2 to 9 copies, with a modal copy number of 4 in all populations.

Conclusions

QPCR is very sensitive to quality of the template DNA, generating systematic biases that could produce false-positive or negative disease associations. Both triplex PRT and PPRT do not show this systematic bias, and type copy number within the correct range, although triplex PRT appears to be a more precise and accurate method to type beta-defensin copy number.     

Variation in gene copy number and polymorphism of the human salivary amylase isoenzyme system in Caucasians

Summary The polymorphic patterns of human salivary amylase of a large number of individuals of Caucasian origin were determined by using isoelectric focusing and polyacrylamide gel electrophoresis. Nine different salivary amylase protein variants were found; three of them are recorded for the first time and their heredity is shown. Some of the variants are encoded by haplotypes expressing three allozymes. Most variants display low frequencies. Analysis of the relative intensities of variant-specific isozyme bands, combined with segregation analysis, show that extensive quantitative variation is present in the population. The numbers of salivary amylase genes in some families showing quantitative variation at the protein level have been estimated by the polymerase chain reaction. We present evidence that quantitative variations in amylase protein patterns do not always reflect variations in gene copy number but that other mechanisms are also involved.