Characterisation and quantification of earthworm cyclophilins: identification of invariant and heavy metal responsive isoforms

Mechanistic evaluation of chromium bioremediation in Acinetobacter junii strain b2w: A proteomic approach

Growing industrialization and unchecked release of industrial waste, including heavy metals have resulted in disastrous effects on environment. Considering the problem of heavy metal pollution, the present research was designed to study the bioremediation of chromium, a highly toxic and prominent heavy metal pollutant by Acinetobacter junii strain b2w isolated from the Mithi river, Mumbai, India. The bacterial isolate could grow without affecting its growth kinetics up to a concentration of 200 ppm of chromium and showed resistance towards 400 ppm of chromium. It was able to bioremediate 83.06% of total chromium and reduces 98.24% of Cr⁶⁺ to C³⁺ at a concentration of 10 ppm of chromium. The bacterial isolate could grow well at a wide pH range from 5 to 9, salinity of up to 3.5% and could also tolerate heavy metals such as Cd, Zn, As, Hg, Pb and Cu. Thus, indicating its possible on-ground applicability for bioremediation of chromium. Acinetobacter junii bioaccumulate chromium without disrupting the cell integrity and biosorption. However, chromium alters the functional groups on bacterial cell surface and led to decrease in sulfate-containing molecules. Further, the protein expression study has revealed that Cr significantly up-regulates proteins broadly classified under envelope stress responses, oxidative stress responses, energy metabolism and quorum sensing and growth regulator. The possible mechanisms of Cr detoxification in Acinetobacter junii strain b2w could be reduction, bioaccumulation and efflux along with neutralization of oxidative stress generated by Cr. Thus, based on bacterial bioremediation potential and its molecular response, it can be proposed that the isolated Acinetobacter junii has potential applicability for chromium bioremediation.

Inhibition of Cyclophilin A on the replication of red spotted grouper nervous necrosis virus associates with multiple pro-inflammatory factors

Cyclophilin A (CypA) is a ubiquitously expressed cellular protein and involves in diverse pathological conditions, including infection and inflammation. CypA acts as a key factor in the replication of several viruses. However, little is known about the role of CypA in the replication of the red-spotted grouper nervous necrosis virus (RGNNV). In the present report, grouper CypA (GF-CypA) was cloned from the grouper fin cell line (GF-1) derived from orange-spotted grouper (Epinephelus coioides). Sequence analysis found that GF-CypA open reading frame (ORF) of 495 bp encodes a polypeptide of 164 amino acids residues with a molecular weight of 17.4 kDa. The deduced amino acid sequence shared highly conserved regions with CypA of other animal species, showing that GF-CypA is a new member of Cyclophilin A family. We observed that GF-CypA was up-regulated in the GF-1 cells infected with RGNNV. Additionally, overexpression of CypA could significantly inhibit the replication of RGNNV in GF-1 cells. By contrast, when the GF-CypA was knock-downed by siRNA in GF-1 cells, the replication of RGNNV was enhanced. Furthermore, the expressions of pro-inflammatory factors, such as TNF-2, TNF-α, IL-1b, and ISG-15, were increased in GF-CypA transfected GF-1 cells challenged with RGNNV, indicating that GF-CypA might be involved in the regulation of the host pro-inflammatory factors. Altogether, we conclude that GF-CypA plays a vital role in the inhibitory effect of RGNNV replication that might be modulating the cytokines secretion in GF-1 cells during RGNNV infection. These results will shed new light on the function of CypA in the replication of RGNNV and will pave a new way for the prevention of the infection of RGNNV in fish.

Earthworms produce phytochelatins in response to arsenic

Phytochelatins are small cysteine-rich non-ribosomal peptides that chelate soft metal and metalloid ions, such as cadmium and arsenic. They are widely produced by plants and microbes; phytochelatin synthase genes are also present in animal species from several different phyla, but there is still little known about whether these genes are functional in animals, and if so, whether they are metal-responsive. We analysed phytochelatin production by direct chemical analysis in Lumbricus rubellus earthworms exposed to arsenic for a 28 day period, and found that arsenic clearly induced phytochelatin production in a dose-dependent manner. It was necessary to measure the phytochelatin metabolite concentrations directly, as there was no upregulation of phytochelatin synthase gene expression after 28 days: phytochelatin synthesis appears not to be transcriptionally regulated in animals. A further untargetted metabolomic analysis also found changes in metabolites associated with the transsulfuration pathway, which channels sulfur flux from methionine for phytochelatin synthesis. There was no evidence of biological transformation of arsenic (e.g. into methylated species) as a result of laboratory arsenic exposure. Finally, we compared wild populations of earthworms sampled from the field, and found that both arsenic-contaminated and cadmium-contaminated mine site worms had elevated phytochelatin concentrations.

The strong induction of metallothionein gene following cadmium exposure transiently affects the expression of many genes in Eisenia fetida: a trade-off mechanism?

Metal pollution causes disturbances at various levels of biological organization in most species. Important physiological functions could be affected in the exposed individuals and among the main physiological functions, immunity may provide one (or more) effector(s) whose expression can be directly affected by a metal exposure in various macroinvertebrates. Protein expressions were studied in order to test them as molecular biomarkers of metal exposure in Eisenia fetida. Selected effectors were calmodulin, heat shock proteins, superoxide dismutase, catalase, metallothionein, beta-adrenergic receptor kinase, pyruvate carboxylase, transcriptionally controlled tumor protein, protein kinase C, ubiquitin and cyclophilin-A. The level of expression of each gene was analysed in whole organism following exposures to cadmium in soil using real-time PCR. Metallothionein, transcriptionally controlled tumor protein and cyclophilin-A expression were also measured following copper exposures in soil because these genes seemed to be sensitive to copper. This work enabled to distinguish metallothionein and cyclophilin-A among the 15 selected effectors. A strong decrease of the number of transcripts was also detected for most effectors soon after the exposure to cadmium suggesting that a trade-off mechanism occurs.

Gene transcription profiling in pollutant exposed mussels (Mytilus spp.) using a new low-density oligonucleotide microarray

In this study we describe the design and implementation of a novel low-density oligonucleotide microarray (the "Mytox-chip"). It consists of 24 mussel genes involving both normalizing elements and stress response related genes, each represented on the array with one or two different 50 mer oligonucleotide-probe reporters spotted in replicated samples on glass-activated slides. Target genes were selected on the basis of their potential involvement in mechanisms of pollutant and xenobiotic response. They are implicated in both basic and stress related cellular processes such as shock response, biotransformation and excretion, cell-cycle regulation, immune defense, drug metabolism, etc. The microarray was tested on mussels exposed to sublethal concentrations of mercury or a crude North Sea oil mixture. RNA samples were extracted from digestive glands of control and treated mussels for the synthesis of fluorescence labeled cDNAs to be used in dual color hybridizations. Transcription rates of two metallothionein iso-genes (mt10 and mt20), a p53-like gene and actin were quantitatively estimated also by real-time PCR to confirm microarray data. Significant alterations in the gene transcription patterns were seen in response to both treatments.

Toxicological, cellular and gene expression responses in earthworms exposed to copper and cadmium

This study correlates sub-organismal changes with toxicological effects in earthworms (Lumbricus rubellus) exposed to copper and cadmium. Both metals reduced survival and reproduction at the highest concentration (LC50 5.11 microM Cu g(-1) and 4.04 microM Cd g(-1); cocoon production EC50s 5.17 microM Cu g(-1) and 1.86 microM Cd g(-1), all values as dry mass soil). Cadmium significantly reduced lysosomal membrane stability (at 1.86 microM Cd g(-1) and higher), upregulated metallothionein gene expression (at least sevenfold in all treatments) and reduced lysosome-associated-glycoprotein gene expression. Copper did not lower lysosomal membrane stability, but did upregulate metallothionein gene expression (at 2.5 microM Cu g(-1)), reduce lysosome-associated-glycoprotein gene expression and gave a nonlinear pattern for mitochondrial ribosomal subunit transcript expression (reduced at 0.35 and 0.811 microM Cu g(-1); higher at 2.5 microM Cu g(-1)). Correlation of metal body residue concentrations and cellular and molecular genetic responses with juvenile production rate confirmed a relationship for metallothionein expression, lysosomal membrane stability and cadmium tissue concentration in cadmium-exposed worms. Relationships between responses were also found for both metals. These suggested mechanisms for the interaction of cadmium and copper with specific gene products and with organelle (mitochondrial, lysosomal) functioning.

A cyclophilin gene marker confirming geographical differentiation of Norway spruce populations and indicating viability response on excess soil-born salinity

A newly identified cyclophilin-encoding cDNA clone was used to design a codominant inherited EST-PCR marker in Norway spruce. The study of the current minor polymorphism revealed a geographically structured differentiation pattern across 17 test populations, showing a slight clinal variation south-north through Europe. Based on the frequency of alleles, isolation-by-distance analysis and the Ewens-Watterson test, we conclude that a selectively neutral random-drift mutation recently occurred within the Alpine population group, thus being responsible for the genetic variation detected. Analysis of tolerant and susceptible subsets of two adjacent Bavarian spruce populations affected by soil-born NaCl pollution, revealed that the cyclophilin marker locus also confirms biased genotype frequencies. Considering an unlinked PCR marker of a ribosomal protein-encoding EST clone, deviations between pooled tolerant subsets and pooled sensitive subsets were proven to be more significant for two-locus homozygous genotypes than for each locus alone. We suggest that both loci are linked to adaptive genomic regions. Their potential to test the feasibility of marker-assisted selection of both NaCl-tolerant and drought resistant tree populations is discussed.

Developing a new method for soil pollution monitoring using molecular genetic biomarkers

Physiological responses to environmental stressors may induce changes in gene expression as part of an organism's homeostatic mechanisms. Thus molecular genetic biomarkers have the potential to be used for monitoring sublethal chemical exposure in ecosystems. This paper describes a methodological assessment of the suitability of a protocol to monitor selected biomarkers. The TaqMan real-time quantitative polymerase chain reaction was used to measure gene transcription in earthworms (Lumbricus rubellus) maintained on control or cadmium- or copper-spiked soil. Changes in the expression of two target genes, that encoding metallothionein isoform 2 (MT-2) and that encoding the mitochondrial large ribosomal subunit (MLRS), were quantified against the internal control gene beta-actin. The protocol used produced reliable and reproducible results. Transcript levels displayed qualitative and quantitative differences in the responses to the two metal ions. MLRS gene levels were unaffected by exposure to cadmium but displayed a response to high levels of copper. Conversely, cadmium greatly induced MT-2 gene expression, but copper only altered transcription of this gene at high exposure concentrations. This study demonstrates that it is now technically feasible to use gene expression as an index of pollution exposure in environmentally relevant organisms.

Control genes in quantitative molecular biological techniques: the variability of invariance

The measurement of transcript levels constitutes the foundation of today's molecular genetics. Independent of the techniques used, quantifications are generally normalised using invariant control genes to account for sample handling, loading and experimental variation. All of the widely used control genes are evaluated, dissecting different methodological approaches and issues regarding the experimental context (e.g. development and tissue type). Furthermore, the major sources of error are highlighted when applying these techniques. Finally, different approaches undertaken to assess the invariance of control genes are critically analysed to generate a procedure that will help to discern the best control for novel experiments.