Roko Žaja

Distribution of protein poly(ADP-ribosyl)ation systems across all domains of life

Highlights • PARPs are present in representatives from all six major eukaryotic supergroups.• Reversible PAR metabolism was established early in eukaryotic evolution.• The last common ancestor of all eukaryotes possessed five types of PARP proteins.• PARPs are associated to a large variety of different pathways.

Hepatic biomarker responses to organic contaminants in feral chub (Leuciscus cephalus)—laboratory characterization and field study in the Sava River, Croatia

As a widely spread cyprinid fish species, the European chub (Leuciscus cephalus) has been used extensively in biomonitoring programs. However, no laboratory dose-response and/or time course studies related to applied biomarkers have been reported on chub yet. In order to address this issue, specimens of juvenile chub caught in September 2005 in the Sava River, Croatia, were laboratory exposed to various (0.25-50 mg/kg) doses of either model polycyclic aromatic hydrocarbons (PAH) premutagen benzo[a]pyrene (BaP), or beta-naphthoflavone (beta-NF), a well-known model cytochrome 1A (CYP1A) inducer, for 3 (BaP) or 5 d (beta-NF). The responses of several hepatic biomarkers were determined in the exposed fish: The hepatic 7-ethoxyresorufin-O-deethylase activity, CYP1A content, glutathione S-transferase (GST) activity, liver bioactivation potential, and the amount of hydroxylated polycyclic aromatic hydrocarbon bile metabolites determined by the fixed wavelength fluorescence and the high-performance liquid chromatography technique. The relevance of determined biomarker responses has been analyzed further and crosscorrelated with the same set of biomarkers, as well as with tissue concentrations of polycyclic aromatic hydrocarbons and polychlorinated biphenyls, determined in chub specimens collected in September 2005 at five different polluted locations along the Sava River. The species-specific upper and lower limits in responses of studied biomarkers were determined and the obtained ranges successfully evaluated in real field situation. With the exception of the GST activity, all other biomarkers determined in chub proved to be valuable indicators of environmental pollution. Finally, the results of the present study demonstrated that the same strategy of laboratory characterization in combination with field evaluation should be used regularly in the selection of optimal biomarkers and indicator species.

CYP1A induction potential and the concentration of priority pollutants in marine sediment samples – In vitro evaluation using the PLHC-1 fish hepatoma cell line

The use of in vitro biotests in combination with chemical determination of priority pollutants is considered a promising approach in environmental risk assessment. The main goal of this study was to evaluate the relationship between the CYP1A induction potential and the concentration of priority pollutants (PAHs, PCBs and heavy metals) in contaminated marine sediments. Six sediment samples characterized by different types of pollution were collected from the Bay of Kvarner, Croatia. CYP1A induction potency was determined in vitro by the measurement of ethoxyresorufin-O-deethylase (EROD) activity in PLHC-1 fish hepatoma cells. The results were compared to the potency of the model CYP1A inducer 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and expressed in 2,3,7,8-TCDD equivalents. All of the tested sediment samples were able to induce CYP1A activity in a dose-dependent manner. On a general scale, there was a good correlation between CYP1A induction and the concentration of priority pollutants in the tested samples. However, some samples, which had relatively low levels of priority pollutants, exhibited a strong CYP1A induction response. Therefore, apart from the confirmed usability and sensitivity of the EROD determination in the PLHC-1 cells as a suitable in vitro model in ecotoxicology, the results of this study indicate that the list of priority pollutants usually determined in the attempt to evaluate the risk of adverse effects to marine wildlife should be reconsidered.

Prioritisation of organic contaminants in a river basin using chemical analyses and bioassays

Region-specific contaminant prioritisation is an important prerequisite for sustainable and cost-effective monitoring due to the high number of different contaminants that may be present. Surface water and sediment samples from the Sava River, Croatia, were collected at four locations covering a 150-km-long river section characterised by well-defined pollution gradients. Analysis of contaminant profiles along the pollution gradients was performed by combining toxicity screening using a battery of small-scale or in vitro bioassays, which covered different modes of action, with detailed chemical characterisation based on gas chromatography/mass spectrometry (GC/MS) and liquid chromatography/quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). A large number of contaminants, belonging to different toxicant classes, were identified in both analysed matrices. Analyses of water samples showed that contaminants having polar character occurred in the highest concentrations, while in sediments, contributions from both non-polar and amphiphilic contaminants should be taken into account. Estimated contributions of individual contaminant classes to the overall toxicity indicated that, besides the classical pollutants, a number of emerging contaminants, including surfactants, pharmaceuticals, personal care products and plasticizers, should be taken into consideration in future monitoring activities. This work demonstrates the importance of the integrated chemical and bioanalytical approach for a systematic region-specific pollutant prioritisation. Finally, the results presented in this study confirm that hazard assessment in complex environmental matrices should be directed towards identification of key pollutants, rather than focusing on a priori selected contaminants alone.

Molecular Insights into Poly(ADP-ribose) Recognition and Processing

Poly(ADP-ribosyl)ation is a post-translational protein modification involved in the regulation of important cellular functions including DNA repair, transcription, mitosis and apoptosis. The amount of poly(ADP-ribosyl)ation (PAR) in cells reflects the balance of synthesis, mediated by the PARP protein family, and degradation, which is catalyzed by a glycohydrolase, PARG. Many of the proteins mediating PAR metabolism possess specialised high affinity PAR-binding modules that allow the efficient sensing or processing of the PAR signal. The identification of four such PAR-binding modules and the characterization of a number of proteins utilising these elements during the last decade has provided important insights into how PAR regulates different cellular activities. The macrodomain represents a unique PAR-binding module which is, in some instances, known to possess enzymatic activity on ADP-ribose derivatives (in addition to PAR-binding). The most recently discovered example for this is the PARG protein, and several available PARG structures have provided an understanding into how the PARG macrodomain evolved into a major enzyme that maintains PAR homeostasis in living cells.

Cloning and mRNA expression analysis of an ABCG2 (BCRP) efflux transporter in rainbow trout (Oncorhynchus mykiss) liver and primary hepatocytes.

As has been recently demonstrated in mammals, apart from the P-glycoprotein (Pgp, ABCB) and the MRP-like proteins (MRPs, ABCC), another efflux transporter - the BCRP (ABCG2) - expressed in polarized epithelial cells of different tissues, is involved in regulation of intestinal absorption and biliary excretion of potentially toxic xenobiotics. However, no study has been directed towards identification of BCRP (ABCG2) in fish species. In the present study we have cloned the full ABCG2 transcript from rainbow trout (Oncorhynchus mykiss) liver, showing a high sequence identity (60%) to human ABCG2 gene. Using Real-Time PCR we measured relative expression of ABCG2 in trout liver and primary hepatocytes and compared these expression levels to the expression of other ABC transporters expressed in apical membrane of hepatocytes (ABCB1, ABCB11 and ABCC2). ABCG2 expression was 6-fold higher than ABCC2 and almost 42 fold higher than ABCB1, indicating that the ABCG2 probably plays a significant role in the overall disposition and excretion of xenobiotics in fish.

Presence of Ecotoxicologically Relevant Pgp and MRP Transcripts and Proteins in Cyprinid Fish

Presence of Ecotoxicologically Relevant Pgp and MRP Transcripts and Proteins in Cyprinid Fish One of the most intriguing defence strategies which aquatic organisms developed through evolution is multixenobiotic resistance (MXR). The key mediators of MXR activity are ATP-binding cassette (ABC) transport proteins. They provide resistance of aquatic organisms by binding xenobiotics and extruding them from cells in an energy-dependent manner. Since Cyprinid fish species are common target in freshwater biomonitoring programs, we have studied the presence of two main MDR/MXR efflux transporters P-glycoprotein (Pgp, Abcb1) and MRP-like protein(s) (Abcc) in the liver of five Cyprinid species: common carp, European chub, sneep, barbel, and silver prussian carp. Their presence was evaluated on the mRNA and protein level. Various pairs of primers were designed to clone homologous fragments of MXR-related genes. At the protein level, we used Western blotting with specific monoclonal antibodies against human Pgp (Abcb1, Ab C219), MRP1 (Abcc1; Ab MRPm6) or MRP2 (Abcc2; Ab M2I-4). Transcripts of both key types of MXR transporters were identified in all species examined and here we provide the phylogenetic analysis of new partial sequences. Immunochemical determinations with mammalian antibodies failed to identify the presence of MRP(s), but Pgp expression was found in all five Cyprinid species. These results support that MXR is a defence system mediated by both Pgp and MRP types of ABC transport proteins. Određivanje prisutnosti ekotoksikološki važnih Pgp i MRP-proteina u šarankama na genskoj i proteinskoj razini Mehanizam multiksenobiotičke otpornosti (MXR) stanični je obrambeni sustav odgovoran za svojstvo istovremene otpornosti na različite ksenobiotike, koje se očituje smanjenjem akumulacije, odnosno povećanjem izbacivanja potencijalno toksičnih tvari iz stanica vodenih organizama. MXR-mehanizam pokazuje odlike analogne fenomenu istovremene otpornosti na različite lijekove (engl. multidrug resistance, MDR) prvi put dokazanom u tumorskim stanicama. Posredovan je istim ABC transportnim proteinima kao i MDR. Istraživanja vezana uz MXR vodenih životinja uglavnom su imala težište na određivanju prisutnosti i funkcije P-glikoproteina (Pgp). Budući da se ribe iz reda šaranki često rabe u biomonitoringu slatkovodnih voda, cilj ovog istraživanja bilo je određivanje prisutnosti dvaju glavnih MDR/MXR-tipova proteina - Pgp i MRP-tip proteina - u jetri iz pet vrsta šaranki; šarana (Cyprinus carpio), klena (Sqalius cephalus), mrene (Barbus barbus), babuške (Carassius auratus gibelio) i podusta (Chondrostoma nasus). Njihova prisutnost utvrđena je na razini mRNA te na proteinskoj razini. Različiti parovi početnica dizajnirani su kako bi se identificirali homologni fragmenti gena sličnih MXR-u. Detekcija na razini proteina napravljena je putem Western blot analize s pomoću specifičnih monoklonskih protutijela proizvedenih da prepoznaju konzervirane epitope; Pgp (C219), MRP1 (MRPm6) ili MRP2 (M2I-4) u sisavaca. Transkripti obaju ključnih MXR-transportera identificirani su u svim jedinkama, a napravljena je i filogenetska analiza dobivenih sekvenci. Imunokemijskom detekcijom s protutijelima sisavaca nismo uspjeli detektirati prisutnost MRP-proteina, dok je Pgp-ekspresija potvrđena u svih pet vrsta šaranki. Nove spoznaje da je za MXR-mehanizam zaslužno više transportnih proteina zasigurno će pridonijeti potpunijoj karakterizaciji MXR-a kao integralnog dijela detoksikacijskog, odnosno temeljnog obrambenog sustava vodenih organizama te njegovoj znanstvenoj afirmaciji kao vjerodostojnog pokazatelja kvalitete okoliša.

Disruption of macrodomain protein SCO6735 increases antibiotic production in Streptomyces coelicolor

ADP-ribosylation is a post-translational modification that can alter the physical and chemical properties of target proteins and that controls many important cellular processes. Macrodomains are evolutionarily conserved structural domains that bind ADP-ribose derivatives and are found in proteins with diverse cellular functions. Some proteins from the macrodomain family can hydrolyze ADP-ribosylated substrates and therefore reverse this post-translational modification. Bacteria and Streptomyces, in particular, are known to utilize protein ADP-ribosylation, yet very little is known about their enzymes that synthesize and remove this modification. We have determined the crystal structure and characterized, both biochemically and functionally, the macrodomain protein SCO6735 from Streptomyces coelicolor. This protein is a member of an uncharacterized subfamily of macrodomain proteins. Its crystal structure revealed a highly conserved macrodomain fold. We showed that SCO6735 possesses the ability to hydrolyze PARP-dependent protein ADP-ribosylation. Furthermore, we showed that expression of this protein is induced upon DNA damage and that deletion of this protein in S. coelicolor increases antibiotic production. Our results provide the first insights into the molecular basis of its action and impact on Streptomyces metabolism.

Interaction between the zebrafish (Danio rerio) organic cation transporter 1 (Oct1) and endo- and xenobiotics

Organic cation transporters (OCTs) serve as uptake transporters of numerous endo- and xenobiotics. They have been in the focus of medical toxicological research for more than a decade due to their key role in absorption, distribution, metabolism and excretion due to their expression on basolateral membranes of various barrier tissues. OCTs belong to the SLC22A family within the SLC (Solute carrier) protein superfamily, with three co-orthologs identified in humans (OCT1, 2 and 3), and two Oct orthologs in zebrafish (Oct1 and Oct2). The structural and functional properties of zebrafish Octs, along with their toxicological relevance, have still not been explored. In this study, we performed a functional characterization of zebrafish Oct1 using transient and stable heterologous expression systems and model fluorescent substrates as the basis for interaction studies with a wide range of endo- and xenobiotics. We also conducted a basic topology analysis and homology modeling to determine the structure and membrane localization of Oct1. Finally, we performed an MTT assay to evaluate the toxic effects of the seven interactors identified - oxaliplatin, cisplatin, berberine, MPP+, prazosin, paraquat and mitoxantrone - in human embryonic kidney cells (HEK293T) stably expressing zebrafish Oct1 (HEK293T-drOct1 cells). Our results show that the zebrafish Oct1 structure consists of 12 transmembrane alpha helices, which form the active region with more than one active site. Five new fluorescent substrates of Oct1 were identified: ASP+ (Km=26μM), rhodamine 123 (Km=103.7nM), berberine (Km=3.96μM), DAPI (Km=780nM), and ethidium bromide (Km=97nM). Interaction studies revealed numerous interactors that inhibited the Oct1-dependent uptake of fluorescent substrates. The identified interactors ranged from physiological compounds (mainly steroid hormones) to different classes of xenobiotics, with IC50 values in nanomolar (e.g., pyrimethamine and prazosin) to millimolar range (e.g., cimetidine). Cytotoxicity experiments with HEK293T-drOct1 cells enabled us to identify berberine, oxaliplatin and MPP+ as substrates of Oct1. The data presented in this study provide the first insights into the functional properties of zebrafish Oct1 and offer an important basis for more detailed molecular and ecotoxicological characterizations of this transporter.