Antigen presentation genes in gadoid species (haddock: Melanogrammus aeglefinus and Atlantic cod: Gadus morhua) raise questions about cross-presentation pathways and glycosylated beta-2-microglobulin.

The Atlantic cod immune system deviates from antigen presentation processes seen in other vertebrates in that it lacks the necessary genes for exogenous antigen presentation (i.e., MHC-II and li) and a key MHC-II interacting molecule necessary for T-helper cell function (i.e., CD4), while possessing an expanded repertoire of MHC-I genes that facilitate endogenous antigen presentation. These observations, combined with the identification of putative endosomal sorting signals in MHC-I cytoplasmic tails, have led to speculation that cod rely on cross-presentation of exogenous antigens to elicit cytotoxic T-lymphocyte responses against extracellular threats. In light of this suggestion, we investigated MHC-I transcriptional profiles and endosomal sorting signals in a closely related gadoid species, the haddock. Analysis of transcripts from one individual identified 13 unique MHC-I molecules, including two non-classical molecules as determined by the level of conservation at their peptide anchoring sites. This suggests that like the cod, the haddock has an expanded MHC-I repertoire. Analysis of haddock MHC-I cytoplasmic tail sequences revealed that the dileucine- and tyrosine-based endosomal signaling motifs, that are suggested to facilitate cross-presentation in cod, were absent. Closer examination of the cod signaling motifs, including their relative position in the cytoplasmic tail region, indicates that these motifs might be non-functional, further supporting the need for functional studies to assess cross-presentation. Finally, in silico analysis and in vitro N-type de-glycosylation experiments demonstrate that haddock and cod beta-2-microglobulin (ß2M) are glycosylated at the same NQT sequon. Interestingly, whole genome tBLASTn searches also revealed that putative ß2 M glycosylation sites appear frequently within the Gadiformes lineage, as the predictive NQT and other N-X-S/T sequons were located in ß2M orthologues from 19 of the 25 additional gadoid genomes analyzed. Though the exact significance of ß2M glycosylation has yet to be elucidated, phylogenetic comparisons predict that the same NQT glycosylation sequence occurs in 13 additional species comprising four different orders of Actinopterygii (Gymnotiformes, Esociformes, Beryciformes and Perciformes). This suggests either that this feature has arisen independently in multiple lineages or that it comes from a common ancestor and has been lost or modified in many species. Together, the analysis of gadoid MHC-I genes and ß2M molecules highlights the challenges in generalizing immune system paradigms across the most diverse vertebrate lineage (i.e., fish) and between fish and more well-studied mammals.

Characterization of cDNA clones encoding major histocompatibility class II receptors from walleye (Sander vitreus).

The teleost major histocompatibility (MH) class II receptor presents peptides from exogenous sources to CD4+ T cells, leading to the initiation of the adaptive immune response. The genes encoding MH class II have been identified in a number of teleost species, but not in walleye, an important recreational fish and commercial fishery in North America. In this study, we cloned and characterized the sequences encoding walleye MH class II α and ß chains. These sequences contained all of the domains typical for functional MH class II α and ß chain proteins, and aligned with other teleost sequences of MH class II. The walleye MH class II α amino acid sequence, along with other members of the Supraorder Percomorpharia, contains a high concentration of methionine residues in the beginning of the leader peptide. Southern blotting indicated that there is more than one gene copy for both MH class II α and ß, while northern blotting analysis of both genes showed that expression of these genes is greatest in lymphoid tissues and at potential entry points for pathogens. These results help to further the understanding of MH class II receptors in teleosts, and could prove useful in the study of disease issues in walleye such as dermal sarcoma virus.

CK-2 of rainbow trout (Oncorhynchus mykiss) has two differentially regulated alleles that encode a functional chemokine.

Rainbow trout chemokine 2 (CK-2) is currently the only known CC chemokine to have a mucin stalk. Further analysis of the mucin stalk region revealed a second, related CC chemokine sequence, denoted here as CK-2.1. This second sequence was determined to be an allele of CK-2 following genomic PCR analysis on several outbred individuals. Furthermore, in both in vivo and in vitro trials, CK-2 and CK-2.1 were both present, but appeared to have differential tissue expression in both control and PHA stimulated samples. Upon the development of a polyclonal antibody to rCK-2, CK-2 was only observed in the brain, liver and head kidney of PHA stimulated rainbow trout tissues. In comparison, when using the rainbow trout monocyte/macrophage-like cell line, RTS-11, CK-2 protein was observed in both control and PHA stimulated conditions. When studying the function of CK-2, a chemotaxis assay revealed that both peripheral blood leukocytes and RTS-11 cells migrated towards rCK-2 significantly at all concentrations studied when compared to truncated ß2m. Interestingly, this migration was lowest at both the highest concentration and the lowest concentrations of CK-2. Thus, teleostean chemokine receptors may become desensitized when overstimulated as has been observed in mammalian models. The observed chemotactic function was indeed due to rCK-2 as cell migration was inhibited through pre-treatment of both the cells and the polyclonal antibody with rCK-2. As has been observed thus far with all other chemokines, CK-2 does appear to function through binding to a G-coupled protein receptor as chemotaxis could be inhibited through pre-treatment with pertussis toxin. Overall, the results of this study indicate that CK-2 is a functional chemokine that is encoded by two differentially expressed alleles in rainbow trout, CK-2 and CK-2.1.

A comparison of rainbow trout cell lines for their expression of the major histocompatibility complex genes and the induction of beta-2-microglobulin by dsRNA.

Western blotting with polyclonal antisera to polypeptides of the rainbow trout major histocompatibility (MH) genes and reverse transcriptase-polymerase chain reaction (RT-PCR) were used to compare expression of MH genes in rainbow trout cell lines. One line was the spleen monocyte/macrophage-like RTS11, which grew loosely on plastic surfaces. Adherent cell lines were fibroblast-like RTG-2 from gonads and four epithelial-like cell lines from gill, intestine, liver and hepatoma: RTgill-W1, RTgutGC, RTL-W1, and RTH-149 respectively. All cell lines expressed a 45 kDa MHC class I alpha chain. All cell lines expressed beta-2-microglobulin (beta2m), which was at 11 kDa, but detection was abrogated following trypsinization prior to cell collection. All cell lines expressed transcripts for MH class II alpha and MH class II beta genes; however, MH class II polypeptides were expressed only in RTS11, the only cell line from a lineage of antigen-presenting cells. We report here that double stranded RNA up regulates beta2m and that these cell lines and antisera can be employed for studying MH regulation.

Characterization of rainbow trout CHK2 and its potential as a genotoxicity biomarker.

Checkpoint kinase 2 (CHK2) plays a central and conserved role in the eukaryotic DNA damage response. Few cell cycle checkpoint proteins have been examined in aquatic organisms, and this study is the first to characterize CHK2 expression in a fish species. CHK2 was cloned from Oncorhynchus mykiss, the rainbow trout. The coding region extends over 5741 nucleotides in the genome, including 13 introns, and specifies a predicted 533 amino acid protein. Southern blot analysis revealed that CHK2 exists as a single copy in the rainbow trout genome. Recombinant protein representing the FHA domain was used to generate polyclonal anti-CHK2 antibodies. While CHK2 transcript levels were relatively low in gill and high in brain, the opposite was true for protein levels. Both gill and brain cell cultures were treated with bleomycin, which induces double-strand DNA breaks. There was no effect on levels of CHK2 in gill cells, suggesting that the protein is constitutively active in this tissue. In contrast, brain cells upregulated CHK2 in a dose-dependent manner. The tissue specific expression of CHK2 and its ability to respond to bleomycin treatment suggests that some checkpoint proteins may serve as suitable biomarkers for DNA damage in rainbow trout and other fish species.

Cloning and characterization of a cDNA encoding walleye (Sander vitreum) beta-2 microglobulin.

Beta(2)-microglobulin (beta(2)m) is an essential component of the MHC class I antigen presentation pathway, necessary for heavy chain folding and peptide binding. In this study a beta(2)m cDNA isolated from a walleye head kidney library was sequenced and found to be similar to other known beta(2)m sequences. The clone encodes a predicted protein sequence of 116 residues, with a mature peptide 100 amino acids in length. This represents an inconsistency with other predicted beta(2)m protein sequences as walleye contains an additional 3 residues at the N terminus of the mature protein. Southern blot analysis showed that beta(2)m is present in one copy in the walleye genome and northern blot analysis showed expression of a 1.2Kb transcript, with high expression in kidney, spleen, gills and intestine. Characterization of this gene will enable further studies of immune function in walleye, which comprises both an important fishery and an emerging aquaculture species in Canada.

A cell line (HEW) from embryos of haddock (Melanogrammus aeglefinius) and its capacity to tolerate environmental extremes.

Cell lines can be useful experimental tools for studying marine fish, which are often difficult to routinely obtain and maintain in the laboratory. As few cell lines are available from coldwater marine fish, cultures were initiated from late gastrula embryos of haddock (Melanogrammus aeglefinus) in Leibovitz's L-15 with fetal bovine serum (FBS). From one culture, a cell line (HEW) emerged that has been grown for close to 100 population doublings, was heteroploid, and expressed telomerase activity, all of which suggest HEW is immortal. Growth occurred only if FBS was present and was optimal at 12 to 18 degrees C. Usually most cells had an epithelial-like morphology, but under some conditions, cells drew up into round central bodies from which radiated cytoplasmic extensions with multiple branches. These neural-like cells appeared within a few hours of cultures being placed at 28 degrees C or being switch to a simple salt solution (SSS). At 28 degrees C, cells died within 24 h. In SSS, HEW cells survived as a monolayer for at least 7 days. The sensitivity of HEW cells to morphological change and their capacity to withstand starvation should make them useful for investigating cellular responses to environmental stresses.

Major histocompatibility class II genes in rainbow trout (Oncorhynchus mykiss) exhibit temperature dependent downregulation.

Major histocompatibility (MH) class II receptors are expressed on the surface of specialized antigen-presenting cells in vertebrate immune systems. Their function is to present peptides derived from exogenous pathogens to CD4+ T cells. Variation in the level of expression of these genes has been linked to pathogenesis in various diseases. Very little has been published on the function of MH class II receptors in teleost fish to date. In this study, we have produced polyclonal antibodies recognizing MH class II alpha and beta proteins of rainbow trout and employed them to characterize the expression pattern of these genes. Deglycosylation using N-glycosidase F and endoglycosidase H showed that MH class II alpha is glycosylated in rainbow trout. MH class II beta was also found to be glycosylated as reported previously. Results from Northern blotting revealed that the expression of these genes was not affected by exposure of rainbow trout to temperature of 5 degrees C. However, at 2 degrees C, downregulation of MH class II alpha and beta genes was evident at both the mRNA and protein levels as assessed by Northern and Western blotting, respectively. Because MH class II antigens play an important role in generating an immune response to bacterial and fungal pathogens, downregulation of these genes at low temperature could account for the susceptibility of fish to low temperature-related diseases such as bacterial cold-water disease and winter saprolegniosis.

Lens and retina formation require expression of Pitx3 in Xenopus pre-lens ectoderm.

Pitx3 is expressed in tissues fated to contribute to eye development, namely, neurula stage ectoderm and pre-chordal mesoderm, then presumptive lens ectoderm, placode, and finally lens. Pitx3 overexpression alters lens, optic cup, optic nerve, and diencephalon development. Many of the induced anomalies are attributable to midline deficits; however, as assessed by molecular markers, ectopic Pitx3 appears to temporarily enlarge the lens field. These changes are usually insufficient to generate either ectopic lenses to enlarge the eye that eventually differentiates. Conversely, use of a repressor chimera or of antisense morpholinos alters early expression of marker genes, and later inhibits lens development, thereby abrogating retinal induction. Reciprocal grafting experiments using wild-type and morpholino-treated tissues demonstrate that Pitx3 expression in the presumptive lens ectoderm is required for lens formation. Contradictory to recent assertions that retina can form in the absence of a lens, the expression of Pitx3 in the presumptive lens ectoderm is critical for retina development.

Analysis of genomic and expressed major histocompatibility class Ia and class II genes in a hexaploid Lake Tana African 'large' barb individual (Barbus intermedius).

Expression of too many co-dominant major histocompatibility complex (MHC) alleles is thought to be detrimental to proper functioning of the immune system. Polyploidy of the genome will increase the number of expressed MHC genes unless they are prone to a silencing mechanism. In polyploid Xenopus species, the number of MHC class I and II genes has been physically reduced, as it does not increase with higher ploidy genomes. In the zebrafish some class II B loci have been silenced, as only two genomically bona fide loci, DAA/DAB and DEA/DEB, have been described. Earlier studies indicated a reduction in the number of genomic and expressed class II MHC genes in a hexaploid African 'large' barb. This prompted us to study the number of MHC genes present in the genome of an African 'large' barb individual (Barbus intermedius) in relation to those expressed, adopting the following strategy. Full-length cDNA sequences were generated from mRNA and compared with partial genomic class Ia and II sequences generated by PCR using the same primer set. In addition, we performed Southern hybridizations to obtain a verification of the number of class I and II B genes. Our study revealed three beta2-microglobulin, five class Ia, four class II A, and four class II B genes at the genomic level, which were shown to be expressed in the hexaploid barb individual. The class Ia and class II data indicate that the ploidy status does not correlate with the presence and expression of these MHC genes.

Molecular cloning and characterization of calreticulin from rainbow trout ( Oncorhynchus mykiss).

Calreticulin (CRT) is a highly conserved, high-capacity, calcium-binding protein shared among vertebrates, invertebrates and higher plants. Its biological importance, highlighted by its highly conserved nature, is supported by its crucial physiological and immunological functions. Within the endoplasmic reticulum, CRT serves as a calcium modulator and a lectin-like chaperone for glycoproteins, especially class I major histocompatibility receptors. To date, CRT cDNA clones have been isolated from a wide range of phyla, yet little is known about this gene in fish species, the largest and most diverse group of jawed vertebrates. This report describes the cloning of a cDNA from a rainbow trout pronephros library that encodes a deduced 419-amino acid protein, which includes a predicted 20-amino acid signal peptide and has a 69% amino acid identity to both murine and human CRT. Like its mammalian counterparts, this cDNA contains conserved cysteine residues believed to form a disulphide bond, a proline-rich region which includes a potential N-glycosylation site, and a highly acidic C-terminal domain terminating with the endoplasmic reticulum retrieval sequence, KDEL. Reverse transcription tissue-distribution assays indicate it is ubiquitously expressed in all tissues tested with highest expression in liver, while Southern blotting indicates it is a single copy gene.

Molecular cloning and characterization of rainbow trout (Oncorhynchus mykiss) C5a anaphylatoxin receptor.

In the course of suppression subtractive hybridization between the cDNA of phytohemagglutinin-stimulated and non-stimulated head kidney cells in rainbow trout (Oncorhynchus mykiss), a cDNA clone was obtained that showed most similarity to mammalian receptor for the anaphylatoxin of the fifth complement component (C5aR). The rainbow trout C5aR cDNA contains a 1,679-bp nucleotide sequence that encodes a 350-amino-acid putative protein with 29.0-31.5% identity to mammalian C5aR. Rainbow trout C5aR has seven putative transmembrane domains that are common to mammalian C5aR. A cysteine residue in the second cytoplasmic domain in mammalian C5aR, required for formation of disulfide-linked dimers, is seen in trout C5aR but not in other similar rhodopsin-like receptors. An arginine residue in the fifth transmembrane domain, which is critical for activation of the C5aR by C5a, is also conserved in rainbow trout C5aR. The rainbow trout C5aR gene has a 1.9-kb intron in the position 12 bp upstream of the start codon, which is similar to that seen right after the start codon in human C5aR gene. These results indicate that the clone is a rainbow trout homologue of mammalian C5aR. Southern blot hybridization suggested that C5aR is a single-copy gene. Northern blotting and RT-PCR analyses detected higher amounts of the transcript in head kidney and posterior kidney, but much lower levels in peripheral blood leukocytes and spleen, faint expression in brain and gills, heart, intestine and very faint expression in liver and muscle.

Molecular cloning and characterization of rainbow trout (Oncorhynchus mykiss) CCAAT/enhancer binding protein beta.

A full-length cDNA encoding CCAAT/enhancer-binding protein beta (C/EBPbeta) was cloned from rainbow trout by anchored PCR. The putative 291 amino acid protein has 53% and 32% identity to the zebrafish and Japanese flounder sequences, respectively, and 30-34% identity to tetrapod homologues. This clone contains most conserved C/EBPbeta domains except the second transactivation domain just like the zebrafish homologue. Also similar to zebrafish, rainbow trout produces only shorter C/EBPbeta isoforms (LAP and LIP) but not the longer isoform (LAP*). However, unlike the zebrafish and Japanese flounder homologues, trout C/EBPbeta has the short open reading frame (uORF) upstream of the start codon for LAP but in an alternate reading frame, a feature of tetrapod C/EBPbeta genes. In normal rainbow trout, C/EBPbeta mRNA was detected in peripheral blood leukocytes, head kidney, posterior kidney, liver, spleen, gills, intestine and muscle. RT-PCR revealed that transcript levels of trout C/EBPbeta are clearly higher in sodium alginate-induced peritoneal cells than in head kidney and peritoneal cells of saline-injected fish or head kidney cells of alginate-injected fish. Together with expression in immunologically important tissues, this indicates that C/EBPbeta is likely to be involved in the immune response just as in mammals. Southern hybridization suggested that C/EBPbeta is a single copy gene. There are no introns in this C/EBPbeta gene, just like the mammalian homologues. These data suggest that we have obtained the trout ortholog of C/EBPbeta.

Genomic cloning of novel isotypes of the rainbow trout interleukin-8.

A cDNA clone, designated IL-8nL, was obtained by suppression subtractive hybridisation between lipopolysaccharide-stimulated and non-stimulated populations of the rainbow trout macrophage-like cell line, RTS11. IL-8nL was similar but not identical to a recently published sequence of the gene encoding rainbow trout interleukin-8 (IL-8). Amplification of genomic DNA by the polymerase chain reaction (genomic PCR) using a single outbred trout with common primers in the 5' and 3' untranslated regions gave six distinct genomic sequences, including one ( IL-8A) almost identical to that of the published IL-8 gene and another identical to IL-8nL. The other four clones were termed IL-8B, IL-8C, IL-8D and IL-8E. The deduced amino acid sequences of IL-8A through IL-8E are all identical to the published IL-8, while the IL-8nL protein has a substitution of Arg87 to Lys. Analysis of ten outbred trout by genomic PCR of a repeat region in exon 4, which has three different sizes in the above alleles, revealed a shorter, fourth fragment termed IL-8X and another of the same size as IL-8nL, but with a different single nucleotide replacement, called IL-8nL2. These results, together with a Southern blot of the same ten individuals showing up to five bands, indicate that rainbow trout has at least four copies of the IL-8 gene. Like IL-8nL, IL-8X lacks the repeat sequence in exon 4 and encodes a protein identical to IL-8nL protein. Polymerase chain reaction of the repeat region was useful for typing rainbow trout into four categories, and the type III and IV fish have a new allele, IL-8F, which lacks one repeat unit compared with IL-8A.

Alternate forms of MHC class II-associated invariant chain are not produced by alternative splicing in rainbow trout (Oncorhynchus mykiss) but are encoded by separate genes.

A major limiting factor in understanding teleost major histocompatibility receptor function is the lack of knowledge about antigen presentation accessory molecules. We report here two cDNA clones encoding teleost versions of invariant chain and one encoding a related protein that may play a protease inhibition role in antigen presentation. The two invariant chain equivalents are similar to each other where they overlap, but differ in the presence or absence of a thyroglobulin domain. This domain is added to tetrapod invariant chain protein by alternative splicing but there was no evidence of alternative splicing of the two trout genes. Southern blotting confirmed that all three trout cDNAs are derived from single copy genes and Northern blotting indicated that they are expressed in antigen tissues. Thus the encoded proteins are probably involved in antigen presentation, but their expression is probably regulated in a manner different from tetrapods.

Molecular cloning and characterisation of a carp (Cyprinus carpio) cytokine-like cDNA that shares sequence similarity with IL-6 subfamily cytokines CNTF, OSM and LIF.

In the course of suppression subtractive hybridisation between sodium alginate-induced peritoneal cells (SA-PC) and normal head kidney cDNAs in common carp (Cyprinus carpio), a cytokine-like cDNA clone was found. The clone, named M17, contains a 1600bp nucleotide sequence that encodes a 215 amino acid putative protein that would have a pI of 9.01 and would include a 33 amino acid signal peptide. The 3' untranslated region has seven ATTTA mRNA destabilising motifs that are common in cytokines and oncogenes. In a BLASTP search, M17 was most similar to chicken ciliary neurotrophic factor (CNTF) with 25% amino acid identity, followed by mammalian CNTF, cardiotrophin-1 and leukemia inhibitory factor (LIF) all of which belong to the IL-6 subfamily. However, M17 has some differences with CNTF in that CNTF has no signal sequence, the gene organisation of M17 is three exons and two introns, whereas that of CNTF is two exons and one intron, M17 has seven cysteines while CNTF has one cysteine, and M17 mRNA is detected in peripheral blood leukocytes as well as brain, whereas CNTF is expressed only in the nervous system. Compared to other members in the IL-6 subfamily cytokines, M17's cysteine positions and gene organisation are similar to those of oncostatin M and LIF, although amino acid identities are only 15-17%. Southern hybridisation suggested that M17 is a single copy gene. SA-PC showed significantly higher M17 mRNA levels than normal head kidney cells, which are considered to be a source of the SA-PC, indicating that M17 is inducible by inflammatory stimulation.

Cloning and characterization of cDNA clones encoding CD9 from Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss).

In comparison to mammals, relatively few of the molecules involved in teleost immune responses have been isolated and characterized. A rapid method of isolating molecules important for immune function is subtractive hybridization. One such experiment using infectious hematopoietic necrosis virus-infected Atlantic salmon produced several cDNA clones with similarity to mammalian immune-specific genes, including granzyme M (accession no. AF434669) and CD9. After cloning the rainbow trout version of CD9, sequence analysis showed that both salmonid sequences contained many features of the tetraspanin receptor family to which CD9 belongs. Phylogenetic analysis revealed a close association of the trout and salmon sequences to known CD9 and CD81 receptors. Southern blotting demonstrated that the rainbow trout gene is single copy. Reverse transcriptase PCR showed strong expression of this clone in many tissues, but liver expression was very low - an observation consistent with the clone being a CD9, not a CD81, equivalent. The evidence suggests that the sequences reported here are bona fide teleost CD9 homologues and we are currently producing recombinant proteins and polyclonal antisera for use in functional studies.

Diversity of complement factor B/C2 in the common carp (Cyprinus carpio): three isotypes of B/C2-A expressed in different tissues.

Complement factor B and C2 are two critical proteases for complement activation. Some bony fish have been reported to possess duplicated genes for B/C2, but there is no direct evidence regarding possible functional divergence. Here, we report the isolation of the second and third isotypes of carp B/C2-A, a close relative of other bony fish B reported to date, and designated B/C2-A2 and B/C2-A3. B/C2-A1 (previously reported B/C2-A) and B/C2-A2 share 78% amino acid identity and are synthesized mainly in hepatopancreas. On the other hand, B/C2-A3 showed less (approximately 60%) sequence identity with the other two isotypes. It was expressed mainly in kidney and spleen, and was up-regulated after injection of carp with scleroglucan or sodium alginate, known immunostimulants for fish. Phylogenetic analysis suggests that B/C2-A3 diverged before separation of carp and zebrafish. B/C2-A3 represent a novel B/C2-lineage functioning as an acute phase reactant in cyprinid fish.

The immune responses of common carp, Cyprinus carpio L., injected with carp interleukin-1beta gene.

The function of the common carp, Cyprinus carpio L., interleukin-1beta (IL-1beta) gene was studied by DNA injection. To investigate the immune responses to IL-1beta, a plasmid construct of cytomegalovirus (CMV)-driven carp IL-1beta was injected into the epaxial muscle of carp. IL-1beta protein expressed in serum on 1, 3, and 5 days after plasmid injection was quantified by ELISA and immunohistochemistry. IL1-beta gene injection increased proliferation of the lymphocytes by phytohemagglutinin (PHA). Macrophage functions, such as production of superoxide anion and phagocytosis, also were stimulated by IL-1beta gene injection. Moreover, an increase in resistance to Aeromonas hydrophila infection was recorded in IL-1beta-injected fish compared with control fish. Thus, the cloned homolog of IL-1beta from carp has all the functional similarities to the mammalian IL-1beta gene.

Cloning of a novel rainbow trout (Oncorhynchus mykiss) CC chemokine with a fractalkine-like stalk and a TNF decoy receptor using cDNA fragments containing AU-rich elements.

An activation-specific cDNA library was made from phytohaemagglutinin (PHA)-activated haematopoietic cells of the rainbow trout (Oncorhynchus mykiss) using the technique of suppression subtractive hybridization. Several immune system genes were identified, including an interleukin (IL)1 receptor related protein and two invariant chain-like proteins. Many clones showed no similarity by BLAST search, but had AU-rich elements. These fragments were labelled and used for hybridization with a PHA-activated head kidney cDNA library. Several immune system genes were isolated by this technique, including a tumour necrosis factor (TNF) decoy receptor and a novel chemokine, designated trout chemokine 2. The TNF receptor is 285 amino acids in length and is 32-36% identical to a brook trout and human homologue. The CC chemokine is 44% identical at the amino acid level to a carp CC chemokine and approximately 20% identical to several mammalian CC chemokines. However, it has a 91 amino acid stalk-like structure at its COOH end, which is similar to the glycosylated stalk of fractalkine, a mammalian CX(3)C chemokine. In summary, AU-rich fragments obtained from an activation-specific library proved useful as hybridization probes for isolating trout immune system genes.