Evolutionary, comparative, and functional analyses of STATs and regulation of the JAK-STAT pathway in lumpfish upon bacterial and poly(I:C) exposure.

Background: The Janus kinase/signal transducers and activators of transcription (JAK-STAT) system regulates several biological processes by affecting transcription of genes as a response to cytokines and growth factors. In the present study, we have characterized the STAT genes in lumpfish (Cyclopterus lumpus L.), belonging to the order Perciformes, and investigated regulation of the JAK-STAT signaling pathway upon exposure to bacteria (Vibrio anguillarum) and poly(I:C), the latter mimicking antiviral responses. Methods: Characterization and evolutionary analyses of the STATs were performed by phylogeny, protein domain, homology similarity and synteny analyses. Antibacterial and antiviral responses were investigated by performing KEGG pathway analysis. Results: We observed that lumpfish have stat1a, 2, 3, 4, 5a, 5b, and 6. Transcriptome-wide analyses showed that most components of the JAK-STAT pathway were present in lumpfish. il-6, il-10, il-21, iκBα and stat3 were upregulated 6 hours post exposure (hpe) against bacteria while type I interferons (IFNs), irf1, irf3, irf10, stat1 and 2 were upregulated 24 hpe against poly(I:C). Conclusions: Our findings shed light on the diversity and evolution of the STATs and the data show that the STAT genes are highly conserved among fish, including lumpfish. The transcriptome-wide analyses lay the groundwork for future research into the functional significance of these genes in regulating critical biological processes and make an important basis for development of prophylactic measure such as vaccination, which is highly needed for lumpfish since it is vulnerable for both bacterial and viral diseases.

Transcriptome-wide analyses of early immune responses in lumpfish leukocytes upon stimulation with poly(I:C).

Background: Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed. Methods: To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs). Results: Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species. Conclusions: Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.).

Antibacterial treatment of lumpfish (Cyclopterus lumpus) experimentally challenged with Vibrio anguillarum, atypical Aeromonas salmonicida and Pasteurella atlantica.

Lumpfish is a novel farmed species used as cleaner fish for the removal of lice from farmed salmon. As often with new, farmed species, there are challenges with bacterial infections. The frequency of prescription of antibiotic agents to lumpfish is increasing, despite the lack of knowledge about appropriate doses, duration of treatment and application protocols for the various antibacterial agents. In the current study, we have tested the effect of medicated feed with florfenicol (FFC), oxolinic acid (OA) and flumequine (FLU) on lumpfish experimentally challenged with Vibrio anguillarum, atypical Aeromonas salmonicida and Pasteurella atlantica. We found that all three antibacterial agents efficiently treated lumpfish with vibriosis using 10 and 20 mg kg-1  day-1 of FFC, 25 mg kg-1  day-1 of OA and 25 mg kg-1  day-1 FLU, whereas only FFC (20 mg kg-1  day-1 ) had good effect on lumpfish with pasteurellosis. None of the antibacterial agents were efficient to treat lumpfish with atypical furunculosis. FFC 20 mg kg-1  day-1 showed promising results in the beginning of the experiment, but the mortality increased rapidly 14 days post-medication. Efficient treatment is important for the welfare of lumpfish and for reducing the risk of development of antibiotic-resistant bacteria. To our knowledge, this is the first study to establish protocols for antibacterial treatment of lumpfish.

Interleukin-1 Ligands and Receptors in Lumpfish (Cyclopterus lumpus L.): Molecular Characterization, Phylogeny, Gene Expression, and Transcriptome Analyses.

The interleukin (IL)-1 family play a fundamental role as immune system modulators. Our previous transcriptome-analyses of leukocytes from lumpfish (Cyclopterus lumpus L.) showed that IL-1ß was among the most highly upregulated genes following bacterial exposure. In the present study, we characterized IL-1 signaling pathways, identified and characterized four ligands of the IL-1 family in lumpfish; IL-1ß type I and type II, IL-18, and the novel IL-1 family members (nIL-1F), both at mRNA and gene levels. The two IL-1ß in lumpfish is termed IL-1ß1 (type II) and IL-1ß2 (type I). Furthermore, a comprehensive phylogenetic analysis of 277 IL-1 ligands showed that nIL-1F, in common with IL-1ß, likely represents an ancestral gene, as representatives for nIL-1F were found in cartilaginous and lobe-finned fish, in addition to teleosts. This shows that nIL-1F is not exclusively present in teleosts as previously suggested. Our analyses of exon-intron structures, intron phases, phylogeny and synteny clearly show the separation of IL-1ß into groups; type I and type II, which likely is a result of the third whole genome duplication (3R WGD). The phylogenetic analysis shows that most teleosts have both type I and type II. Furthermore, we have determined transcription levels of the IL-1 ligands in leukocytes and 16 different tissues, and their responses upon in vitro stimulation with seven different ligands. In addition, we have identified the IL-1 receptors IL-1R1, IL-1R2, IL-1R4 (ST2/IL-33 receptor/IL-1RL), IL-1R5 (IL-18R1), and partial sequences of DIGIRR and IL-1R3 (IL-RAcP). Identification of immune molecules and description of innate responses in lumpfish is interesting for comparative and evolutionary studies and our study constitutes a solid basis for further functional analyses of IL-1 ligands and receptors in lumpfish. Furthermore, since lumpfish are now farmed in large numbers to be used as cleaner fish for removal of sea lice on farmed salmon, in-depth knowledge of key immune molecules, signaling pathways and innate immune responses is needed, as the basis for design of efficient immune prophylactic measures such as vaccination.

Pharmacokinetic Data Show That Oxolinic Acid and Flumequine Are Absorbed and Excreted Rapidly From Plasma and Tissues of Lumpfish.

This study examined the uptake, tissue distribution and elimination of the antibacterial agents oxolinic acid and flumequine in lumpfish (Cyclopterus lumpus L.) by use of LC-MS/MS following a single oral administration of 25 mg/kg fish given in feed. Lumpfish are increasingly used as cleaner fish for removal of sea lice on commercially farmed salmon. The production of lumpfish is successful, but there are challenges with bacterial infections and the number of antibacterial treatments has increased in recent years. As the lumpfish is a novel species to farming, there is a need for pharmacokinetic data and establishment of protocols for efficient antibacterial treatment. The current study describes the pharmacokinetic properties of oxolinic acid and flumequine in lumpfish. Absorption of oxolinic acid was moderate and was characterized by a calculated peak plasma concentration (Cmax) of 2.12 µg/ml after 10.3 h (Tmax) and an elimination half-life (t1/2ß) of 21 h. Area under curve (AUC) and AUC from 0 to 24 h (AUC0-24h) were calculated to be 60.9 and 34.0 h µg/ml, respectively. For flumequine, plasma Cmax was found to be 2.77 µg/ml after 7.7 h (Tmax) with t1/2ß of 22 h. The area under the curve (AUC) and AUC from 0 to 24 h (AUC0-24) were calculated as 104.3 and 50.3 h µg/ml, respectively. Corresponding Cmax values in muscle, liver, and head-kidney for oxolinic acid were 4.01, 3.04, and, 4.68 µg/g, respectively and Tmax of 11.1, 9.2, and 10.0 h, respectively. For flumequine, Cmax values of 4.16, 4.01, and 7.48 µg/g were obtained in muscle, liver, and head kidney, respectively, with corresponding Tmax values of 10.2, 10.3, and 6.0 h. Antimicrobial susceptibility values as determined by minimum inhibitory concentration (MIC) analyses against 28 isolates of Aeromonas salmonicida isolated from diseased lumpfish ranged from 0.06 to 15 µg/ml for oxolinic acid and 0.024 to 6.25 µg/ml for flumequine. Bimodal distributions in susceptibility to both oxolinic acid and flumequine were observed. The combination of pharmacokinetic properties and MIC data make possible calculation of efficient treatment doses, which are needed to improve the welfare of lumpfish and minimize development of antibiotic resistant bacteria.

Transcriptome-wide mapping of signaling pathways and early immune responses in lumpfish leukocytes upon in vitro bacterial exposure.

We performed RNA sequencing, identified components of the immune system and mapped early immune responses of lumpfish (Cyclopterus lumpus) leukocytes following in vitro exposure to the pathogenic bacterium Vibrio anguillarum O1. This is the first characterization of immune molecules in lumpfish at the gene level. In silico analyses revealed that genes encoding proteins involved in pathogen recognition, cell signaling and cytokines in mammals and teleosts are conserved in lumpfish. Unique molecules were also identified. Pathogen recognition components include 13 TLRs, several NLRs and complement factors. Transcriptome-wide analyses of immune responses 6 and 24 hours post bacterial exposure revealed differential expression of 9033 and 15225 genes, respectively. These included TLR5S, IL-1ß, IL-8, IL-6, TNFα, IL-17A/F3, IL-17C and several components of the complement system. The data generated will be valuable for comparative studies and make an important basis for further functional analyses of immune and pathogenicity mechanisms. Such knowledge is also important for design of immunoprophylactic measures in lumpfish, a species of fish now farmed intensively for use as cleaner-fish in Atlantic salmon (Salmo salar) aquaculture.

Development of anaesthetic protocols for lumpfish (Cyclopterus lumpus L.): Effect of anaesthetic concentrations, sea water temperature and body weight.

In recent years, use of lumpfish (Cyclopterus lumpus L.) as cleaner-fish to remove sea-lice have been chosen by many salmon farmers in Europe and Canada as an alternative to medical treatment, which has led to large scale production of lumpfish. At present, there is limited knowledge of how lumpfish respond upon anaesthesia, which anaesthetics and concentrations that are efficient and conditions for euthanasia. We have therefore tested and developed protocols for bath immersion for three commonly used anaesthetics metacaine (Finquel, buffered tricaine methanesulfonate, MS-222 and Tricaine Pharmaq), benzocaine (Benzoak vet) and isoeugenol (Aqui-S), determined concentration for normal and fast anaesthesia and evaluated safety margin for each condition. Also, a behavioral matrix has been developed. We have examined the effect of fish size (10-20 g, 200-400 g and 600-1300 g) and sea water temperature (6°C and 12°C). We found that 200 mg L-1 metacaine is an efficient dose for deep narcosis independently for fish size and temperature due to good safety margins with regards to both exposure times and doses. However, for many tasks lighter anaesthesia is sufficient, and then 100 mg L-1 metacaine can be used. Benzocaine is less efficient than metacaine, but can be used as anaesthetic of fish < 400 g. The optimal doses of benzocaine were 100-200 mg L-1 for small fish (10-20 g) and 200 mg L-1 for medium sized fish (200-400 g). For larger fish (> 600 g), benzocaine is not suitable. Isoeugenol cannot be recommended for full anesthesia of lumpfish. The conditions for lethal doses varied with chosen anaesthetic, fish size and temperature. For small fish (10-20 g), exposure to 1600 mgL-1 of metacaine in 10 minutes it lethal. Guided protocols for non-lethal anaesthesia will contribute to ensure safe treatment of lumpfish according to an ethical standard for good fish welfare.

Protection and antibody reactivity following vaccination of lumpfish (Cyclopterus lumpus L.) against atypical Aeromonas salmonicida.

Atypical Aeromonas salmonicida is frequently associated with disease and mortality in farmed lumpfish (Cyclopterus lumpus L). Challenge experiments using different modes of exposure identified both high and low pathogenic isolates. Intraperitoneal vaccination induced production of high levels of specific antibodies particularly in fish given multiple injections. The immune sera contained antibodies cross reactive with both high and low pathogenic isolates. SDS-PAGE and LC/MSMS analyses showed that the highly virulent isolate expressed the virulence array protein (A-layer) while the less virulent isolate did not. Vaccines, containing the highly virulent isolate, formulated as a monovalent or as a trivalent vaccine, provided 73 and 60 relative percent survival (RPS) respectively, following intraperitoneal challenge. The detection of high levels of specific antibodies in immune sera and the protection provided by the test vaccines strongly indicate that it is possible to vaccinate lumpfish against atypical A. salmonicida and most probably also against other infectious bacterial diseases.

Functional characterization of IgM+ B cells and adaptive immunity in lumpfish (Cyclopterus lumpus L.).

The innate immune responses in lumpfish (Cyclopterus lumpus L.) have been shown to be functional, but little is currently known about the B cells, immunoglobulins or adaptive immune responses in this species. We have used anti-IgM antiserum to isolate B cells and compared them morphologically and functionally with other cell types. The fraction of IgM(+) cells among isolated peripheral blood leukocytes (PBL), head kidney leukocytes (HKL) and spleen leukocytes (SL) was in the range of 40%, 12% and 34%, respectively. The IgM(+) B cells had high phagocytic ability and were the predominant phagocytes in blood with higher capacity than IgM(+) B cells in HKL. Interestingly, among PBL, the most potent phagocytes were, in addition to monocytes, some small agranular uncharacterized IgM(-) cells. The IgM(+) B cells were positive for acid phosphatases (AcP), but negative for myeloperoxidase (MPO). Neutrophils were positive for MPO, while monocytes/macrophages and dendritic-like cells stained negatively. Monocytes/macrophages and the small, agranular IgM(-) cells stained most strongly positive for AcP corresponding to their high phagocytic capacity. Further, the ability to produce specific antibodies upon immunization verified adaptive immunity in the species. The high proportion of phagocytic IgM(+) B cells and their phagocytic ability indicate a significant role of phagocytic B cells in lumpfish innate immunity. The present analyses also give strong indications that vaccination and immunostimulation of farmed lumpfish can be used to prevent disease and mortality caused by pathogenic organisms.

Flow cytometry analyses of phagocytic and respiratory burst activities and cytochemical characterization of leucocytes isolated from wrasse (Labrus bergylta A.).

We have isolated leucocytes from peripheral blood (PBL), head kidney (HKL) and spleen (SL) of wrasse (Labrus bergylta A.) and studied the innate immune responses phagocytosis and respiratory burst using flow cytometry. Further, we have characterized the phenotypic properties of the leucocytes by cytochemical staining. We could differentiate between several subsets of leucocytes; lymphocytes, monocytes/macrophages, neutrophils, eosinophils, basophils and small leucocytes that might be precursor or immature cells. One striking observation was the eosinophils which were present among HKL, PBL and SL. The neutrophils had rounded, bean shaped or bi-lobed nuclei and resembled neutrophils in Atlantic cod (Gadus morhua L.) and lumpsucker (Cyclopterus lumpus L.), but were different from the polymorphonucleated neutrophils in Atlantic salmon (Salmo salar L.) and humans. Basophils were observed, but they were rare. Phagocytosis and respiratory burst activities were detected among different cell types. Highest phagocytic activity was observed among monocytes/macrophages and small leucocytes. Several different subtypes had ability to perform an oxygen-dependent degradation of microbes, measured as respiratory burst activity. Knowledge of the basic properties of wrasse's leucocytes and innate immunology can benefit further studies on its adaptive immune responses.

Antibiotic uptake by cultured Atlantic cod leucocytes and effect on intracellular Francisella noatunensis subsp. noatunensis replication.

The granuloma disease caused by Francisella noatunensis subsp. noatunensis in farmed Atlantic cod has not been successfully treated by use of antibacterials, even when antibacterial resistance testing indicates a sufficient effect. The reason for this treatment failure may be the intracellular existence of the bacteria within immune cells, mainly macrophages. To investigate the effect of antibacterials on intracellular Francisella replication, we established a protocol for the detection of drugs within Atlantic cod immune cells using high-performance liquid chromatography (HPLC). When the uptake and intracellular concentrations of oxolinic acid and flumequine were analysed in isolated adherent head kidney leucocytes (HKLs) by HPLC, we found that uptake was rapid and the intracellular concentrations reflected the extracellular exposure concentrations. To investigate the effect of the antibacterial compounds on intracellular bacterial replication, adherent HKLs experimentally infected with the bacteria were analysed using flow cytometry and intracellular labelling of bacteria by specific antibodies. We found that flumequine did not inhibit intracellular bacterial replication. Unexpectedly, the results indicated that the intracellularly effiacy of the drug was reduced. The HPLC method used proved to be highly applicable for accurate determination of intracellular drug concentrations. When combined with sensitive and specific flow cytometry analyses for identification and measurement of intracellular bacterial replication, we suggest that this approach can be very valuable for the design of antibacterial treatments of intracellular pathogens.

Francisella noatunensis subsp. noatunensis replicates within Atlantic cod (Gadus morhua L.) leucocytes and inhibits respiratory burst activity.

Francisella noatunensis subsp. noatunensis, causing granulomatosis in cod, has been shown to reside within cod immune cells, mainly within monocytes and macrophages. In the present study, we analysed the ability of the bacterium to replicate within adherent cells isolated from head kidney by in vitro infection of leucocytes. Two different technical approaches for flow cytometry analyses were performed for detection of intracellular bacteria. The presence of the wild type was assessed after identification by intracellular binding of specific antibodies to the pathogen. The other way was to use green fluorescent protein (GFP) transformed bacterium for infection studies allowing direct measurements of fluorescence from infected cells. By both methods we found an increase in fluorescence in infected cells, verifying bacterial replication, both after 4 and 28 h post infection in leucocytes isolated from head kidney (HKL). The GFP transformed bacterium was similar to the wild type in growth and infectivity pattern, showing that it can be a valuable tool for further studies of infection routes and pathology. Further, F. noatunensis subsp. noatunensis was found to inhibit respiratory burst activity, a potent pathogen killing mechanism, in cod leucocytes, but not in such cells from salmon. Our findings may indicate that inhibition of respiratory burst during Francisella infection is a key to its intracellular existence. This strategy seems to be conserved through evolution as it is also observed during infections in higher vertebrates caused by bacteria within the Francisella genus. The results presented here, showing the intracellular existence of Francisella, its replication within leucocytes and the inhibitory effect on respiratory burst, strongly support that these factors contribute to disease and pathology in infected cod. The intracellular replication shown in the present study might contribute to explain the problems of obtaining protective vaccines against Francisella and effective antibiotic treatment of infected fish.

Characterization of small, mononuclear blood cells from salmon having high phagocytic capacity and ability to differentiate into dendritic like cells.

Phagocytes are the principal component of the innate immune system, playing a key role in the clearance of foreign particles that include potential pathogens. In vertebrates, both neutrophils and mononuclear cells like monocytes, macrophages and dendritic cells are all professional phagocytes. In teleosts, B-lymphocytes also have potent phagocytic ability. We have isolated a population of small (<5 µm), mononuclear blood cells from Atlantic salmon (Salmo salar L.) not previously characterized. In order to identify them, we have performed morphological, gene expression, flow cytometry, cytochemical, ultrastructural and functional analyses. Interestingly, they highly express the gene encoding CD83, the most characteristic cell surface marker for dendritic cells in mammals, and MHC class II limited to professional antigen presenting cells. They did not express genes nor did they have cell markers for B-cells, T-cells, monocytes/macrophages or neutrophils as shown by qRT-PCR, flow cytometry and immunoblotting. A remarkable feature of these cells is their potent phagocytic capacity. Their oxygen-independent killing mechanism, as shown by intense acid phosphatase staining, is supported by lack of respiratory burst and myeloperoxidase activity and the acid phosphatase's sensitivity to tartrate. They show a high level of morphological plasticity, as, upon stimulation with mitogens, they change morphology and obtain branching protrusions similarly to dendritic cells. We suggest, based on our findings, that the small, round cells described here are progenitor cells with potential to differentiate into dendritic like cells, although we can not exclude the possibility that they represent a novel cell type.

Phagocytosis and respiratory burst activity in lumpsucker (Cyclopterus lumpus L.) leucocytes analysed by flow cytometry.

In the present study, we have isolated leucocytes from peripheral blood, head kidney and spleen from lumpsucker (Cyclopterus lumpus L.), and performed functional studies like phagocytosis and respiratory burst, as well as morphological and cytochemical analyses. Different leucocytes were identified, such as lymphocytes, monocytes/macrophages and polymorphonuclear cells with bean shaped or bilobed nuclei. In addition, cells with similar morphology as described for dendritic cells in trout were abundant among the isolated leucocytes. Flow cytometry was successfully used for measuring phagocytosis and respiratory burst activity. The phagocytic capacity and ability were very high, and cells with different morphology in all three leucocyte preparations phagocytised beads rapidly. Due to lack of available cell markers, the identity of the phagocytic cells could not be determined. The potent non-specific phagocytosis was in accordance with a high number of cells positive for myeloperoxidase, an enzyme involved in oxygen-dependent killing mechanism present in phagocytic cells. Further, high respiratory burst activity was present in the leucocytes samples, verifying a potent oxygen- dependent degradation. At present, the specific antibody immune response could not be measured, as immunoglobulin or B-cells have not yet been isolated. Therefore, analyses of the specific immune response in this fish species await further clarification. The present study presents the first analyses of lumpsucker immunity and also the first within the order Scopaeniformes.

The effect of triploidy and vaccination on neutrophils and B-cells in the peripheral blood and head kidney of 0+ and 1+ Atlantic salmon (Salmo salar L.) post-smolts.

Sterile triploid fish are being used in aquaculture to prevent early unwanted sexual maturation and the genetic interaction between wild and cultured fish; however, triploid fish are typically considered to be more susceptible to disease than diploid counterparts. Proportions of leucocytes from the head kidney and peripheral blood were identified using monoclonal antibodies and flow cytometry in triploid and diploid, vaccinated and unvaccinated, out-of-season (0+) and 1+ Atlantic salmon (Salmo salar L.) three weeks post seawater transfer. Triploid 1+ fish were significantly (P<0.05) heavier than diploid fish at the time of sampling, whereas triploid 0+ had a significantly lower condition factor than diploids. Ploidy had a significant effect on the proportion of B-cells in the blood of both 0+ and 1+ fish, and the head kidney of 1+ fish, with triploids having lower proportions of B-cells to diploids in both smolt groups. In addition, a significant ploidy×vaccination interaction effect was observed in the response of neutrophils in the blood (vaccinated diploids had a higher mean proportion than diploid unvaccinated) and B-cells in the head kidney (in vaccinated fish, triploids had a lower mean proportion than diploids) in 0+ smolts. Vaccination was found to significantly increase the proportion of B-cells in the head kidney of 1+ smolts in both ploidy. Size (fish weight) was positively correlated with neutrophil proportions in 1+ fish. Our findings are discussed in relation to the physiological differences related to ploidy. The results suggest that ploidy as well as smelting regime influences the immune system of Atlantic salmon post-smolts.

Uracil-DNA glycosylase of Thermoplasma acidophilum directs long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and ATP/ADP, into short-patch repair.

Hydrolytic deamination of cytosine to uracil in DNA is increased in organisms adapted to high temperatures. Hitherto, the uracil base excision repair (BER) pathway has only been described in two archaeons, the crenarchaeon Pyrobaculum aerophilum and the euryarchaeon Archaeoglobus fulgidus, which are hyperthermophiles and use single-nucleotide replacement. In the former the apurinic/apyrimidinic (AP) site intermediate is removed by the sequential action of a 5'-acting AP endonuclease and a 5'-deoxyribose phosphate lyase, whereas in the latter the AP site is primarily removed by a 3'-acting AP lyase, followed by a 3'-phosphodiesterase. We describe here uracil BER by a cell extract of the thermoacidophilic euryarchaeon Thermoplasma acidophilum, which prefers a similar short-patch repair mode as A. fulgidus. Importantly, T. acidophilumcell extract also efficiently executes ATP/ADP-stimulated long-patch BER in the presence of deoxynucleoside triphosphates, with a repair track of ∼15 nucleotides. Supplementation of recombinant uracil-DNA glycosylase (rTaUDG; ORF Ta0477) increased the formation of short-patch at the expense of long-patch repair intermediates, and additional supplementation of recombinant DNA ligase (rTalig; Ta1148) greatly enhanced repair product formation. TaUDG seems to recruit AP-incising and -excising functions to prepare for rapid single-nucleotide insertion and ligation, thus excluding slower and energy-costly long-patch BER.

The hyperthermophilic euryarchaeon Archaeoglobus fulgidus repairs uracil by single-nucleotide replacement.

Hydrolytic deamination of cytosine to uracil in cellular DNA is a major source of C-to-T transition mutations if uracil is not repaired by the DNA base excision repair (BER) pathway. Since deamination increases rapidly with temperature, hyperthermophiles, in particular, are expected to succumb to such damage. There has been only one report of crenarchaeotic BER showing strong similarities to that in most eukaryotes and bacteria for hyperthermophilic Archaea. Here we report a different type of BER performed by extract prepared from cells of the euryarchaeon Archaeoglobus fulgidus. Although immunodepletion showed that the monofunctional family 4 type of uracil-DNA glycosylase (UDG) is the principal and probably only UDG in this organism, a ß-elimination mechanism rather than a hydrolytic mechanism is employed for incision of the abasic site following uracil removal. The resulting 3' remnant is removed by efficient 3'-phosphodiesterase activity followed by single-nucleotide insertion and ligation. The finding that repair product formation is stimulated similarly by ATP and ADP in vitro raises the question of whether ADP is more important in vivo because of its higher heat stability.

Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA.

N(1)-methyladenine (m(1)A) and N(3)-methylcytosine (m(3)C) are major toxic and mutagenic lesions induced by alkylation in single-stranded DNA. In bacteria and mammals, m(1)A and m(3)C were recently shown to be repaired by AlkB-mediated oxidative demethylation, a direct DNA damage reversal mechanism. No AlkB gene homologues have been identified in Archaea. We report that m(1)A and m(3)C are repaired by the AfAlkA base excision repair glycosylase of Archaeoglobus fulgidus, suggesting a different repair mechanism for these lesions in the third domain of life. In addition, AfAlkA was found to effect a robust excision of 1,N(6)-ethenoadenine. We present a high-resolution crystal structure of AfAlkA, which, together with the characterization of several site-directed mutants, forms a molecular rationalization for the newly discovered base excision activity.