The recombination activating gene 2 (RAG2) of the rainbow trout Oncorhynchus mykiss

Ontogeny and tissue specific expression profiles of recombination activating genes (RAGs) during development in Nile tilapia, Oreochromisniloticus

Recombination activating genes (RAGs) mediates the process of rearrangement and somatic recombination (V(D)J) to generate different antibody repertoire. Studies on the expression pattern of adaptive immune genes during ontogenic development are crucial for the formulation of fish immunization strategy. In the present study, Nile tilapia was taken to explore the relative expression profile of RAG genes during their developmental stages. The developmental stages of Nile tilapia, i.e., unfertilized egg, 0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28 and 30 days post-hatch (dph) and kidney, blood, gill, liver and spleen tissues from adult fish were collected and the cDNA synthesis was carried out. Gene specific primers for RAG-1 and RAG-2 of Nile tilapia were designed and their annealing temperature (Tm) was optimized by gradient PCR. Consequently, PCR was performed to confirm the specific amplification of RAG-1 and RAG-2 genes. Quantitative real-time PCR (qRT-PCR) gene expression of RAG-1 and RAG-2 were noticed in all the developmental stages; however, a significant increase was observed after 12 dph and peaked at 24 dph, followed by a gradual decrease until 30 dph. Tissue-specific gene expression profiling revealed that the highest expression of RAG-1 and RAG-2 was observed in the kidney, followed by spleen, gill, liver and blood. The findings of the study explored the suitable timing of lymphoid maturation that could be technically used for the adoption of strategies to improve disease resistance of fish larvae for mitigating larval mortality.

Rag1 and Rag2 Gene Expressions Identify Lymphopoietic Tissues in Larvae of Rice-Field Eel (Monopterus albus)

In immature lymphocytes, recombination activating genes 1 and 2 are necessary for antigen receptor V (D) J recombination, representing immature lymphocyte biomarkers. Herein, we cloned and sequenced rice-field eel rag1 and rag2 genes. Their expressions in the thymus, liver, and kidney were significant from 0 days post hatching (dph) to 45 dph, peaking at 45 dph in these three tissues. In situ hybridization detected high rag1 and rag2 expressions in the liver, kidney, and thymus of rice-field eel from 2 to 45 dph, suggesting that multiple tissues of rice-field eel contain lymphocyte lineage cells and undergo lymphopoiesis. Tissue morphology was used to observe lymphopoiesis development in these three tissues. The thymus primordium began to develop at 2 dph, while the kidney and liver have generated. Our findings verified that the thymus is the primary lymphopoietic tissue and suggested that, in rice-field eel, lymphocyte differentiation also occurs in the liver and kidney.

Effects of different pharmaceutical residues on embryos of fish species native to Central Europe

Environmental concentrations of pharmacologically active substances are increasing dramatically throughout the world, to the point where they are now considered a serious threat to the aquatic environment. This high occurrence of pharmaceutical residues in the aquatic environment is due to an increase in i) the prescription and consumption of drugs, and ii) their subsequent discharge into wastewater and its imperfect purification in wastewater treatment plants. Recent surveys have clearly shown that such substances can have serious negative effects on non-target organisms. In the present study, we tested the effects of several commonly used pharmaceuticals, such as antidepressants, analgesics and antibiotics, on the embryonic stages of different fishes. Specifically, we applied concentration ranges of tramadol, enrofloxacin and nortriptylined on a common toxicological model organism, the zebrafish (Danio rerio), and other species native to Central European freshwaters, i.e. common carp (Cyprinus carpio), catfish (Silurus glanis) and tench (Tinca tinca). Our results show that, though malformation and negative impacts on hatching and mortality were only observed at the highest test concentrations, gene expression indicated that even low environmentally relevant concentrations (0.1 μg/L) can cause significant changes in early development of embryo.

Immunoglobulins in teleosts

Immunoglobulins are glycoproteins which are produced as membrane-bound receptors on B-cells or in a secreted form, known as antibodies. In teleosts, three immunoglobulin isotypes, IgM, IgT, and IgD, are present, each comprising two identical heavy and two identical light polypeptide chains. The basic mechanisms for generation of immunoglobulin diversity are similar in teleosts and higher vertebrates. The B-cell pre-immune repertoire is diversified by VDJ recombination, junctional flexibility, addition of nucleotides, and combinatorial association of light and heavy chains, while the post-immune repertoire undergoes somatic hypermutation during clonal expansion. Typically, the teleost immunoglobulin heavy chain gene complex has a modified translocon arrangement where the Dτ-Jτ-Cτ cluster of IgT is generally located between the variable heavy chain (VH) region and the Dμ/δ-Jμ/δ-Cμ-Cδ gene segments, or within the set of VH gene segments. However, multiple genome duplication and deletion events and loss of some individual genes through evolution has complicated the IgH gene organization. The IgH gene arrangement allows the expression of either IgT or IgM/IgD. Alternative splicing is responsible for the regulation of IgM/IgD expression and the secreted versus transmembrane forms of IgT, IgD, and IgM. The overall structure of IgM and IgT is usually conserved across species, whereas IgD has a large variety of structures. IgM is the main effector molecule in both systemic and mucosal immunity and shows a broad range of concentrations in different teleost species. Although IgM is usually present in higher concentrations under normal conditions, IgT is considered the main mucosal Ig.

Revisiting the Teleost Thymus: Current Knowledge and Future Perspectives

Simple Summary

The thymus is the immune organ producing T lymphocytes that are essential to create immunity after encountering pathogens or vaccination. This review summarizes the thymus localization and histological studies, cell composition, and function in teleost fishes. We also describe how seasonal changes, photoperiod, water temperature fluctuations, and hormones can affect thymus development in fish species. Overall, the information helps identify future studies needed to understand thymus function in fish species and the immune system’s evolutionary origins. Since fish are exposed to pathogens, especially under aquaculture conditions, knowledge about the fish thymus and T lymphocyte can also help improve fish farming protocols, considering intrinsic and environmental conditions that can contribute to achieving the best vaccine responsiveness for disease resistance.

Abstract

The thymus in vertebrates plays a critical role in producing functionally competent T-lymphocytes. Phylogenetically, the thymus emerges early during evolution in jawed cartilaginous fish, and it is usually a bilateral organ placed subcutaneously at the dorsal commissure of the operculum. In this review, we summarize the current understanding of the thymus localization, histology studies, cell composition, and function in teleost fishes. Furthermore, we consider environmental factors that affect thymus development, such as seasonal changes, photoperiod, water temperature fluctuations and hormones. Further analysis of the thymus cell distribution and function will help us understand how key stages for developing functional T cells occur in fish, and how thymus dynamics can be modulated by external factors like photoperiod. Overall, the information presented here helps identify the knowledge gaps and future steps needed for a better understanding of the immunobiology of fish thymus.

Comparative study of cartilaginous fish divulges insights into the early evolution of primary, secondary and mucosal lymphoid tissue architecture

Cartilaginous fish are located at a pivotal point in phylogeny where the adaptive immune system begins to resemble that of other, more-derived jawed vertebrates, including mammals. For this reason, sharks and other cartilaginous fish are ideal models for studying the natural history of immunity. Insights from such studies may include distinguishing the (evolutionarily conserved) fundamental aspects of adaptive immunity from the (more recent) accessory. Some lymphoid tissues of sharks, including the thymus and spleen, resemble those of mammals in both appearance and function. The cartilaginous skeleton of sharks has no bone marrow, which is also absent in bony fish despite calcified bone, but cartilaginous fish have other Leydig's and epigonal organs that function to provide hematopoiesis analogous to mammalian bone marrow. Conserved across all vertebrate phylogeny in some form is gut-associated lymphoid tissues, or GALT, which is seen from agnathans to mammals. Though it takes many forms, from typhlosole in lamprey to Peyer's patches in mammals, the GALT serves as a site of antigen concentration and exposure to lymphocytes in the digestive tract. Though more complex lymphoid organs are not present in agnathans, they have several primitive tissues, such as the thymoid and supraneural body, that appear to serve their variable lymphocyte receptor-based adaptive immune system. There are several similarities between the adaptive immune structures in cartilaginous and bony fish, such as the thymus and spleen, but there are mechanisms employed in bony fish that in some instances bridge their adaptive immune systems to that of tetrapods. This review summarizes what we know of lymphoid tissues in cartilaginous fishes and uses these data to compare primary and secondary tissues in jawless, cartilaginous, and bony fishes to contextualize the early natural history of vertebrate mucosal immune tissues.

The Pronephros; a Fresh Perspective

Contemporary papers and book chapters on nephrology open with the assumption that human kidney development passes through three morphological stages: pronephros, mesonephros, and metanephros. Current knowledge of the human pronephros, however, appears to be based on only a hand full of human specimens. The ongoing use of variations in the definition of a pronephros hampers the interpretation of study results. Because of the increased interest in the anamniote pronephros as a genetic model for kidney organogenesis we aimed to provide an overview of the literature concerning kidney development and to clarify the existence of a pronephros in human embryos. We performed an extensive literature survey regarding vertebrate renal morphology and we investigated histological sections of human embryos between 2 and 8 weeks of development. To facilitate better understanding of the literature about kidney development, a referenced glossary with short definitions was composed. The most striking difference between pronephros versus meso- and metanephros is found in nephron architecture. The pronephros consists exclusively of non-integrated nephrons with external glomeruli, whereas meso- and metanephros are composed of integrated nephrons with internal glomeruli. Animals whose embryos have comparatively little yolk at their disposal and hence have a free-swimming larval stage do develop a pronephros that is dedicated to survival in aquatic environments. Species in which embryos do not have a free-swimming larval stage have embryos that are supplied with a large amount of yolk or that develop within the body of the parent. In those species the pronephros is usually absent, incompletely developed, and apparently functionless. Non-integrated nephrons were not identified in histological sections of human embryos. Therefore, we conclude that a true pronephros is not detectable in human embryos although the most cranial part of the amniote excretory organ is often confusingly referred to as pronephros. The term pronephros should be avoided in amniotes unless all elements for a functional pronephros are undeniably present.

The RAG2 gene of yellow catfish (Tachysurus fulvidraco) and its immune response against Edwardsiella ictaluri infection

Recombination-activating gene 2 (rag 2) allies with recombination-activating gene 1 (rag 1) and regulates the V(D)J recombination of immunoglobulin (Ig) and T-cell receptor (TCR) genes. Being a key player in the adaptive immune response of vertebrates, functional characterization of rag 2 from yellow catfish is beneficial for understanding the biological response towards the pathogens. In this report, we have cloned and characterized the rag 2 gene of yellow catfish, and a particular pattern of expression was analysed in the major tissues of yellow catfish. The results showed that the open reading frame (ORF) of yellow catfish rag 2 was 1596 bp in length, which encodes a peptide of 531 amino acids. The multiple sequence alignment and phylogenetic analysis of rag 2 of yellow catfish with other species showed the conserved regions and the classical taxonomic evolution among the different vertebrate species. The qRT-PCR and Western blot results revealed that rag 2 transcripts and proteins were present in various tissues of yellow catfish with relatively high expression in the tissues of the thymus, head-kidney, and spleen. The systematic distribution analysis of the rag 2 expression by immunohistochemistry (IHC) using the rabbit polyclonal antibody, exposed relatively high expression in head kidney, spleen and thymus tissues after infected with Edwardsiella ictaluri. Moreover, the temporal expression of rag 2 and pro-inflammatory cytokines (IL-1β and TNF-α) were significantly upregulated at different time points in the specific lymphoid tissues of yellow catfish following E. ictaluri infection. Our findings suggest that rag 2 potentially exhibited the immunological response in primary lymphoid tissues of yellow catfish against bacterial infection. This study will provide an essential source about rag 2 gene and its relationship with the inflammatory cytokines during infection.

Discovery of immunoglobulin T in Nile tilapia (Oreochromis niloticus): A potential molecular marker to understand mucosal immunity in this species

Immunoglobulin molecules play an important role in the immune defense system in all jawed vertebrates, by protecting the organism from a wide variety of pathogens. Nile tilapia (Oreochromis niloticus) is extensively cultivated worldwide, with a strong established market demand. It constitutes one of the model species for the study of fish immunology and its genome is currently fully sequenced. The presence of the immunoglobulin M gene in this species is well documented, as well as its major role in systemic immunity. To date, the IgT gene from O. niloticus has not been identified and, therefore, no information is available on the role of this immunoglobulin isotype in the immune response in tilapia. In the present work, novel secreted and membrane immunoglobulin T isotypes and a fragment of IgM were isolated from tilapia head kidney lymphocytes. Their transcriptional profiles were analyzed by quantitative PCR in larval development and in different tissues of healthy or lipopolysaccharide/Edwardsiella tarda-challenged tilapia adults. The presence of IgT and IgM were detected in early stages of larval development. Additionally, these genes exhibited differential expression profiles in basal conditions and after E. tarda infection in adult tilapia, in accord with the proposed effector functions of these immunoglobulins in the systemic and mucosal compartments. Our results suggest the potential involvement of this new Ig in mucosal immunity in tilapia.

Novel Insights on the Regulation of B Cell Functionality by Members of the Tumor Necrosis Factor Superfamily in Jawed Fish

Most ligands and receptors from the tumor necrosis factor (TNF) superfamily play very important roles in the immune system. In particular, many of these molecules are essential in the regulation of B cell biology and B cell-mediated immune responses. Hence, in mammals, it is known that many TNF family members play a key role on B cell development, maturation, homeostasis, activation, and differentiation, also influencing the ability of B cells to present antigens or act as regulators of immune responses. Evolutionarily, jawed fish (including cartilaginous and bony fish) constitute the first animal group in which an adaptive immune response based on B cells and immunoglobulins is present. However, until recently, not much was known about the expression of TNF ligands and receptors in these species. The sequences of many members of the TNF superfamily have been recently identified in different species of jawed fish, thus allowing posterior analysis on the role that these ligands and receptors have on B cell functionality. In this review, we summarize the current knowledge on the impact that the TNF family members have in different aspects of B cell functionality in fish, also providing an in depth comparison with functional aspects of TNF members in mammals, that will permit a further understanding of how B cell functionality is regulated in these distant animal groups.

Expression and purification of swine RAG2 in E. coli for production of porcine RAG2 polyclonal antibodies

Recombination activating gene 2 (RAG2) is necessary for immature B cell differentiation. Antibodies to human and rabbit RAG2 are currently commercially available, but antibodies to swine RAG remain unavailable to date. In this study, the swine RAG2 genes sequence was synthesized and then cloned into a pET-28a vector. The recombinant fusion protein was successfully expressed in E. coli, purified through nickel column chromatography, and further digested with Tobacco Etch Virus protease. The cleaved protein was purified by molecular-exclusion chromatography and named pRAG2. We used pRAG2 to immunize rabbits, collected the serum and purified rabbit anti-pRAG2 polyclonal antibodies. The rabbit anti-pRAG2 polyclonal antibodies were tested via immunofluorescence on eukaryotic cells overexpressing pRAG2 and also able to recognize pig natural RAG2 and human RAG2 protein in western blotting. These results indicated that the prepared rabbit anti-pRAG2 polyclonal antibodies may serve as a tool to detect immature B cell differentiation of swine.

Morphological and functional development of the interbranchial lymphoid tissue (ILT) in Atlantic salmon (Salmo salar L)

The interbranchial lymphoid tissue (ILT) of Atlantic salmon originates from an embryological location that in higher vertebrates gives rise to both primary and secondary lymphoid tissues. Still much is unknown about the morphological and functional development of the ILT. In the present work a standardized method of organ volume determination was established to study its development in relation to its containing gill and the thymus. Based on morphological findings and gene transcription data, the ILT shows no signs of primary lymphoid function. In contrast to the thymus, an ILT-complex first became discernible after the yolk-sac period. After its appearance, the ILT-complex constitutes 3-7% of the total volume of the gill (excluding the gill arch) with the newly described distal ILT constituting a major part, and in adult fish it is approximately 13 times larger than the thymus. Confined regions of T-cell proliferation are present within the ILT. Communication with systemic circulation through the distal ILT is also highly plausible thus offering both internal and external recruitment of immune cells in the growing ILT.

Recombination-activating gene 1 and 2 (RAG1 and RAG2) in flounder (Paralichthys olivaceus)

During the development of B and T lymphocytes, Ig and TCR variable region genes are assembled from germline V, D, and J gene segments by a site-specific recombination reaction known as V(D)J recombination. The process of somatic V(D)J recombination, mediated by the recombination-activating gene (RAG) products, is the most significant characteristic of adaptive immunity in jawed vertebrates. Flounder (Paralichthys olivaceus) RAG1 and RAG2 were isolated by Genome Walker and RT-PCR, and their expression patterns were analysed by RT-PCR and in situ hybridization on sections. RAG1 spans over 7.0 kb, containing 4 exons and 3 introns, and the full-length ORF is 3207 bp, encoding a peptide of 1068 amino acids. The first exon lies in the 5'-UTR, which is an alternative exon. RAG2 full-length ORF is 1062 bp, encodes a peptide of 533 amino acids, and lacks introns in the coding region. In 6-month old flounders, the expression of RAG1 and RAG2 was essentially restricted to the pronephros (head kidney) and mesonephros (truck kidney). Additionally, both of them were mainly expressed in the thymus. These results revealed that the thymus and kidney most likely serve as the primary lymphoid tissues in the flounder.

Geological events and Pliocene climate fluctuations explain the phylogeographical pattern of the cold water fish Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) in China

Background

Rhynchocypris oxycephalus is a cold water fish with a wide geographic distribution including the relatively warm temperate regions of southern China. It also occurs in second- and third-step geomorphic areas in China. Previous studies have postulated that high-altitude populations of R. oxycephalus in southern China are Quaternary glacial relics. In this study, we used the mitochondrial gene Cytb and the nuclear gene RAG2 to investigate the species phylogeographical patterns and to test two biogeographic hypotheses: (1) that divergence between lineages supports the three-step model and (2) climatic fluctuations during the Quaternary resulted in the present distribution in southern China.

Results

Phylogenetic analysis detected three major matrilines (A, B, and C); with matrilines B and C being further subdivided into two submatrilines. Based on genetic distances and morphological differences, matriline A potentially represents a cryptic subspecies. The geographic division between matrilines B and C coincided with the division of the second and third geomorphic steps in China, suggesting a historical vicariance event. Pliocene climatic fluctuations might have facilitated the southwards dispersal of R. oxycephalus in matriline C, with the subsequent warming resulting in its split into submatrilines C1 and C2, leaving submatriline C2 as a relic in southern China.

Conclusions

Our study demonstrates that geological events (three steps orogenesis) and climate fluctuations during the Pliocene were important factors in shaping phylogeographical patterns in R. oxycephalus. Notably, no genetic diversity was detected in several populations, all of which possessed unique genotypes. This indicates the uniqueness of local populations and calls for a special conservation plan for the whole species at the population level.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0225-9) contains supplementary material, which is available to authorized users.

Genome complexity in the coelacanth is reflected in its adaptive immune system

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

The teleost humoral immune response

Over the past 10 years our knowledge of cellular and molecular dynamics of teleost humoral immunity has increased enormously to now include: the existence of multiple isotypes, affinity-driven modulation of antibody structure and function, the unique trafficking patterns of each stage of B cell differentiation (including the plasma blast, short-lived and long-lived plasma cell, and the memory cell). Unfortunately the work which has generated the bulk of this information has generally employed defined antigens rather than vaccines. Thus, the focus of this review is to relate these aspects of immunity that are requisite for a mechanistic understanding of the generation of prophylactic immunity to the necessary analysis of responses to vaccines and vaccine candidates.

The astonishing diversity of Ig classes and B cell repertoires in teleost fish

With lymphoid tissue anatomy different than mammals, and diverse adaptations to all aquatic environments, fish constitute a fascinating group of vertebrate to study the biology of B cell repertoires in a comparative perspective. Fish B lymphocytes express immunoglobulin (Ig) on their surface and secrete antigen-specific antibodies in response to immune challenges. Three antibody classes have been identified in fish, namely IgM, IgD, and IgT, while IgG, IgA, and IgE are absent. IgM and IgD have been found in all fish species analyzed, and thus seem to be primordial antibody classes. IgM and IgD are normally co-expressed from the same mRNA through alternative splicing, as in mammals. Tetrameric IgM is the main antibody class found in serum. Some species of fish also have IgT, which seems to exist only in fish and is specialized in mucosal immunity. IgM/IgD and IgT are expressed by two different sub-populations of B cells. The tools available to investigate B cell responses at the cellular level in fish are limited, but the progress of fish genomics has started to unravel a rich diversity of IgH and immunoglobulin light chain locus organization, which might be related to the succession of genome remodelings that occurred during fish evolution. Moreover, the development of deep sequencing techniques has allowed the investigation of the global features of the expressed fish B cell repertoires in zebrafish and rainbow trout, in steady state or after infection. This review provides a description of the organization of fish Ig loci, with a particular emphasis on their heterogeneity between species, and presents recent data on the structure of the expressed Ig repertoire in healthy and infected fish.

Cloning and expression analysis of recombination activating genes (RAG1/2) in red snapper (Lutjanus sanguineus)

Recombination activating genes (RAG1 and RAG2), involved in the V(D)J recombination of immunoglobulin and T-cell receptor genes play a crucial role in the adaptive immune response in vertebrates. The expression of these genes was required for the proper development and maturity of lymphocytes so that they can be used as useful markers to evaluate the development of lymphoid organ. In this paper, the cDNA of RAG1 and RAG2 in red snapper, Lutjanus sanguineus were cloned by homological cloning and rapid amplification of cDNA ends (RACE) methods. Results showed the full length of RAG1 cDNA was 3944 bp, containing a 5' untranslated region (UTR) of 200 bp, a 3'-UTR of 561 bp and an open reading frame of 3183 bp encoding 1060 amino acids. Three important structural motifs, a RING/U-box domain, a RING/FYVE/PHD-type domain and a RAG Nonamer-binding domain were detected in the deduced amino acid sequence of RAG1 by InterProScan analysis. The full length of RAG2 cDNA was 2200 bp, consisting of a 141 bp 5'-UTR, a 457 bp 3'-UTR and an open reading frame of 1602 bp encoding 533 amino acids. Two important structural motifs, a Galactose oxidase/kelch, beta-propeller domain and a kelch-type beta-propeller domain were detected in the deduced amino acid sequence of RAG2 by InterProScan analysis. BLAST analysis revealed that the RAG1 and RAG2 in red snapper shared a high homology with other known RAG1 and RAG2 genes, while the greatest degree of identity was observed with Hippoglossus hippoglossus RAG1 at 82% and Takifugu rubripes RAG2 at 87%, respectively. The differential expressions of RAG1 and RAG2 in various tissues of red snapper were analyzed by fluorescent quantitative real-time PCR. The overall expression pattern of the two genes was quite similar. In healthy red snappers, the RAGs transcripts were mainly detected in thymus, following head kidney, spleen, intestine, liver and brain. After vaccinated with inactivated Vibrio alginolyticus 48 h later, the RAGs mRNA expression was significantly up-regulated in all studied tissues of red snapper. A clear time-dependent expression pattern of RAG1 and RAG2 after immunization and the expression reached the highest level at 48 h in thymus, 60 h in head kidney and spleen, respectively. These findings indicated that RAG1 and RAG2 could play an important role in the immune response to bacteria in red snapper.

Plasmablasts and plasma cells: reconsidering teleost immune system organization

Comparative immunologists have expended extensive efforts in the characterization of early fish B cell development; however, analysis of the post-antigen induction stages of antibody secreting cell (ASC) differentiation has been limited. In contrast, work with murine ASCs has resolved the physically and functionally distinct cells known as plasmablasts, the short-lived plasma cells and long-lived plasma cells. Teleost ASCs are now known to also possess comparable subpopulations, which can greatly differ in such basic functions as lifespan, antigen sensitivity, antibody secretion rate, differentiative potential, and distribution within the body. Understanding the mechanisms by which these subpopulations are produced and distributed is essential for both basic understanding in comparative immunology and practical vaccine engineering.

Expression of T-cell markers during Atlantic halibut (Hippoglossus hippoglossus L.) ontogenesis

The immune system of Atlantic halibut is relatively undeveloped at the time of hatching, and thus larvae are vulnerable to bacterial and viral diseases that can result in high mortalities. To enable establishment of effective prophylactic measures, it is important to know when the adaptive immune system is developed. This depends on both B- and T-cell functions. In the present study the expression of RAG1, TCRα, TCRβ, CD3γδ, CD3ɛ, CD3ζ, CD4, CD4-2, CD8α, CD8β, Lck, and ZAP-70 was analyzed in larval and juvenile stages during halibut development. Using real time RT-PCR, low basal mRNA levels of all 12 genes could be detected at early stages. An increase in mRNA transcripts for the genes was seen at different time points, from 38 days post hatching (dph) about the time when the first anlage of thymus is found, and onwards. The transcription patterns of the 12 mRNAs were found to be similar throughout the developmental stages tested. In situ hybridization on larval cross-sections showed that RAG1 and Lck could be detected in lymphocyte like cells within the thymus at 42 dph. CD4 expression could not be detected within the thymus before 66 dph, however, positive cells were restricted to the cortical region. At 87 dph, the zonation of the thymus in a cortical, cortico-medullary, and a medullary region seemed to be more evident with CD8α expressing cells found in all regions, indicating the presence of mature T-cells. This correlates with previous results describing thymus development and the appearance of IgM(+) cells during halibut ontogenesis.

Comparative analyses of B cell populations in trout kidney and mouse bone marrow: establishing "B cell signatures"

This study aimed to identify the frequency and distribution of developing B cell populations in the kidney of the rainbow trout, using four molecular B cell markers that are highly conserved between species, including two transcription factors, Pax5 and EBF1, recombination-activating gene RAG1, and the immunoglobulin heavy chain mu. Three distinct B cell stages were defined: early developing B cells (CLP, pro-B, and early pre-B cells), late developing B cell (late pre-B, immature B, and mature B cells), and IgM-secreting cells. Developmental stage-specific, combinatorial expression of Pax5, EBF1, RAG1 and immunoglobulin mu was determined in trout anterior kidney cells by flow cytometry. Trout staining patterns were compared to a well-defined primary immune tissue, mouse bone marrow, and using mouse surface markers B220 and CD43. A remarkable level of similarity was uncovered between the primary immune tissues of both species. Subsequent analysis of the entire trout kidney, divided into five contiguous segments K1-K5, revealed a complex pattern of early developing, late developing, and IgM-secreting B cells. Patterns in anterior kidney segment K1 were most similar to those of mouse bone marrow, while the most posterior part of the kidney, K5, had many IgM-secreting cells, but lacked early developing B cells. A potential second B lymphopoiesis site was uncovered in segment K4 of the kidney. The B cell patterns, or "B cell signatures" described here provide information on the relative abundance of distinct developing B cell populations in the trout kidney, and can be used in future studies on B cell development in other vertebrate species.

Lymphocyte differentiation in sea bass thymus: CD4 and CD8-alpha gene expression studies

Different developmental stages (from eggs to 1-year-old juveniles) of the teleost fish Dicentrarchus labrax (L.) were assayed for CD4 gene expression. RT-PCR revealed the appearance of CD4 transcripts in post-larvae from 51 days post-hatching (dph). This finding overlaps the first detection of CD8-alpha mRNA. Real-time PCR with specific primers quantified CD4, CD8-alpha and TCR-beta transcripts in larvae and post-larvae (25, 51, 75 and 92 dph) and 1-year-old thymus. At 92 dph, TcR-beta and CD8-alpha transcripts were significantly higher (P < 0.001) than in previous stages, as CD4 transcripts compared with 51 dph (P < 0.01). High levels of TCR-beta and CD8-alpha transcripts were found in the thymus, while CD4 transcripts were lower (P < 0.05 vs. TCR-beta). In situ hybridization identified CD4 mRNAs at 51 dph, localized in thymocytes of the outer and lateral zones of the thymic glands. From 75 dph on the signal was mainly detected in the outer region, drawing a cortex-medulla demarcation. Developmental expression of CD4 and CD8-alpha almost coincided. In each adult thymic lobe CD4(+) and CD8-alpha(+) thymocytes filled the cortex. The expression patterns of CD4 and CD8-alpha largely overlap, except in the medulla, where CD4(+) thymocytes were isolated, while CD8-alpha(+) ones mainly arranged in cords. These results provide new information about the thymic compartmentalization and lymphocyte differentiation pathways in a teleost, almost demonstrating that double negative thymocytes fill the cortex giving rise to further selection in the medulla.

Lymphoid tissue ontogeny in the mummichog, Fundulus heteroclitus

Most studies that examine the ontogeny of lymphoid organ development in teleostean fishes use species of interest to aquaculture or genetic research and, to date, have focused strictly on marine or freshwater species. The mummichog, Fundulus heteroclitus, also known as the estuarine killifish, is a unique model for studies on developmental immunobiology, because it is euryhaline, has a high degree of thermal tolerance, and has a unique reproductive strategy. Embryonic and larval mummichogs were examined for the ontogeny of lymphoid tissue development. The first lymphoid organ to appear was the head kidney at 1 dph, followed by the spleen at 1 wph, and then the thymus at 3 wph. Rag-1 was partially cloned and sequenced and shown to be highly conserved among other vertebrate Rag-1 genes. Using QT-PCR to monitor the temporal expression of Rag-1, it was shown to reach a maximum intensity at 3 and 4 wph and then to drop to pre-2-wph levels. Overall, this study suggests that juvenile mummichogs do not possess the ability to mount T- or B-cell responses until some time after 5 wph. Even though the estuarine killifish tolerates a wide range of salinities, the developmental patterns of lymphoid tissues are similar to what has been reported for strictly marine (stenohaline) teleosts. Thus, the mummichog should be a convenient model for understanding the developmental immunobiology of most marine teleosts.

Cell markers and determinants in fish immunology

Despite the impressive increase in the cloning and expression of genes encoding fish immunoregulatory molecules, the knowledge on "in vivo" and "in vitro" functional immunology of the corresponding peptide products is still at an initial stage. This is partly due to the lacking of specific markers for immunoregulatory peptides, that represent an indispensible tool to dissect immune reactions and to trace the fate of cellular events downstream of the activation. In this review we summarise the available information on functional immune activities of some teleost species and discuss the obtained data in an evolutionary and applied context.

Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes

Regulatory genes control the expression of other genes and are key components of developmental processes such as segmentation and embryonic construction of the skull in vertebrates. Here we examine the variability and evolution of three vertebrate regulatory genes, addressing issues of their utility for phylogenetics and comparing the rates of genetic change seen in regulatory loci to the rates seen in other genes in the parrotfishes. The parrotfishes are a diverse group of colorful fishes from coral reefs and seagrasses worldwide and have been placed phylogenetically within the family Labridae. We tested phylogenetic hypotheses among the parrotfishes, with a focus on the genera Chlorurus and Scarus, by analyzing eight gene fragments for 42 parrotfishes and eight outgroup species. We sequenced mitochondrial 12s rRNA (967 bp), 16s rRNA (577 bp), and cytochrome b (477 bp). From the nuclear genome, we sequenced part of the protein-coding genes rag2 (715 bp), tmo4c4 (485 bp), and the developmental regulatory genes otx1 (672 bp), bmp4 (488bp), and dlx2 (522 bp). Bayesian, likelihood, and parsimony analyses of the resulting 4903 bp of DNA sequence produced similar topologies that confirm the monophyly of the scarines and provide a phylogeny at the species level for portions of the genera Scarus and Chlorurus. Four major clades of Scarus were recovered, with three distributed in the Indo-Pacific and one containing Caribbean/Atlantic taxa. Molecular rates suggest a Miocene origin of the parrotfishes (22 mya) and a recent divergence of species within Scarus and Chlorurus, within the past 5 million years. Developmentally important genes made a significant contribution to phylogenetic structure, and rates of genetic evolution were high in bmp4, similar to other coding nuclear genes, but low in otx1 and the dlx2 exons. Synonymous and non-synonymous substitution patterns in developmental regulatory genes support the hypothesis of stabilizing selection during the history of these genes, with several phylogenetic regions of accelerated non-synonymous change detected in the phylogeny.

Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences

The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.

Cytotoxic activities of fish leucocytes

Like mammalian leucocytes, white blood cells of fish are able to kill altered (e.g. virus-infected) and foreign (allogeneic or xenogeneic) cells. The existence of natural killer (NK)-like and specific cytotoxic cells in fish was first shown using allogeneic and xenogeneic effector/target cell systems. In addition to in vivo and ex vivo studies, very important contributions were made by in vitro analysis using a number of different long-term cytotoxic cell lines established from channel catfish. In mammals, specific cell-mediated cytotoxicity (CMC) as part of the adaptive immune response requires a number of key molecules expressed on effector leucocytes and target cells. CD8+ T lymphocytes kill infected cells only, if their antigen receptor (TCR) matches the MHC class I with bound peptide of the target cell. Expression patterns of the fish gene homologues for TCR, CD8 and MHC class I, as well as related genes, are in agreement with similar function. Convenient systems for the analysis of specific CMC have only recently become available for fish with the combination of clonal fish with syngeneic or allogeneic but MHC class I matching cell lines. It was demonstrated that both, NK- and cytotoxic T (Tc) cells are involved in the killing of virus infected MHC class I matching and mismatching target cells. Analysis of these lymphocyte subsets is only starting for fish. There is also evidence that the different viral proteins trigger different subsets of killer cells. This review further discusses findings on fish CMC with regard to temperature/seasons and ontogeny.

Antibody repertoire development in teleosts--a review with emphasis on salmonids and Gadus morhua L

The group of teleosts is highly diverse, comprising more than 23000 extant species. Studies of the teleost antibody repertoire have been conducted in many different species within different orders, though some species and families have been better characterised than others. The Atlantic cod (Gadus morhua L.) and several species within the Salmoninae (e.g. Salmo salar and Oncorynchus mykiss) are among the best-studied teleosts in terms of the antibody repertoire. The estimated size of the repertoire, the organisation of immunoglobulin (IG) gene segments, the expressed IG repertoire, the IgM serum concentration, and the serum antibody responses reveal some fundamental differences between these species. The serum IgM concentration of G. morhua is some ten times higher than that of S. salar, though G. morhua is characterised as a 'low' (or 'non') responder in terms of specific antibody production. In contrast, an antibody response is readily induced in S. salar, although the response is strongly regulated by antigen induced suppression. The IGHD gene of G. morhua has a unique structure, while the IGHM and IGHD genes of S. salar have a characteristic genomic organisation in two parallel loci. In addition, salmonids, express a broad repertoire of IGH and IGI V-region gene segments, while a single V gene family dominates the expressed heavy and light chain repertoire of G. morhua. Little is known about the developing antibody repertoire during ontogeny, in different stages of B-cell maturation, or in separate B-cell subsets. Information on the establishment of the preimmune repertoire, and the possible role of environmental antigens is also sparse.

Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha: Teleostei)

Fishes of the Superorder Osteoglossomorpha (the "bonytongues") constitute a morphologically heterogeneous group of basal teleosts, including highly derived subgroups such as African electric fishes, the African butterfly fish, and Old World knifefishes. Lack of consensus among hypotheses of osteoglossomorph relationships advanced during the past 30 years may be due in part to the difficulty of identifying shared derived characters among the morphologically differentiated extant families of this group. In this study, we present a novel phylogenetic hypothesis for this group, based on the analysis of more than 4000 characters from five molecular markers (the mitochondrial cytochrome b, 12S and 16S rRNA genes, and the nuclear genes RAG2 and MLL). Our taxonomic sampling includes one representative of each extant non-mormyrid osteoglossomorph genus, one representative for the monophyletic family Mormyridae, and four outgroup taxa within the basal Teleostei. Maximum parsimony analysis of combined and equally weighted characters from the five molecular markers and Bayesian analysis provide a single, well-supported, hypothesis of osteoglossomorph interrelationships and show the group to be monophyletic. The tree topology is the following: (Hiodon alosoides, (Pantodon buchholzi, (((Osteoglossum bicirrhosum, Scleropages sp.), (Arapaima gigas, Heterotis niloticus)), ((Gymnarchus niloticus, Ivindomyrus opdenboschi), ((Notopterus notopterus, Chitala ornata), (Xenomystus nigri, Papyrocranus afer)))))). We compare our results with previously published phylogenetic hypotheses based on morpho-anatomical data. Additionally, we explore the consequences of the long terminal branch length for the taxon Pantodon buchholzi in our phylogenetic reconstruction and we use the obtained phylogenetic tree to reconstruct the evolutionary history of electroreception in the Notopteroidei.

Development and maturation of the immune system in zebrafish, Danio rerio: a gene expression profiling, in situ hybridization and immunological study

The development and maturation of the immune system in zebrafish was investigated using immune-related gene expression profiling by quantitative real-time polymerase chain reaction, in situ hybridization (ISH), immunoglobulin (Ig) detection by immuno-affinity purification and Western blotting as well as immersion immunization experiments. Ikaros expression was first detected at 1 day post-fertilization (dpf) and thereafter increased gradually to more than two-fold between 28 and 42dpf before decreasing to less than the initial 1dpf expression level in adult fish (aged 105dpf). Recombination activating gene-1 (Rag-1) expression levels increased rapidly (by 10-fold) between 3 and 17dpf, reaching a maximum between 21 and 28dpf before decreasing gradually. However, in adult fish aged 105dpf, the expression level of Rag-1 had dropped markedly, and was equivalent to the expression level at 3dpf. T-cell receptor alpha constant region and immunoglobulin light chain constant region (IgLC) isotype-1, 2 and 3 mRNAs were detected at low levels by 3dpf and their expression levels increased steadily to the adult range between 4 and 6 weeks post-fertilization (wpf). Using tissue-section ISH, Rag-1 expression was detected in head kidney by 2wpf while IgLC-1, 2 and 3 were detected in the head kidney and the thymus by 3wpf onwards. Secreted Ig was only detectable using immuno-affinity purification and Western blotting by 4wpf. Humoral response to T-independent antigen (formalin-killed Aeromonas hydrophila) and T-dependent antigen (human gamma globulin) was observed in zebrafish immunized at 4 and 6wpf, respectively, indicating that immunocompetence was achieved. The findings reveal that the zebrafish immune system is morphologically and functionally mature by 4-6wpf.

Characterization of the recombinase activating gene-1 and 2 locus in the Japanese pufferfish, Fugu rubripes

The recombinase activating genes (RAG1 and RAG2) encode nuclear proteins that directly mediate the mechanism V(D)J recombination process that occurs in T- and B-lymphocytes. The expression of RAG1 and RAG2 is required for the proper development of maturing lymphocytes. To identify evolutionary conserved regulatory regions adjacent to both genes we isolated and sequenced a cosmid clone containing 43kb of genomic DNA of the Japanese pufferfish, Fugu rubripes. Fugu has a haploid genome of 400Mb and contains the same number of genes as the genome of higher vertebrates. With low abundance of repetitive DNA, the genome of the pufferfish has shown to be ideal for comparative genomics. We found three complete genes, RAG1, RAG2 and ACS (a possible homologue of the plant 1-aminocyclopropane-carboxylate synthase gene). There is also the 5' exon of a prohormone convertase gene, possibly PACE4. The genetic structure of both RAG1 and RAG2 is identical to that found in other fish, but the size of the intergenic region is smaller in Fugu. Expression analysis by RT-PCR shows the presence of RAG transcripts in kidney of adult Fugu. The human ACS was identified in a cosmid assigned to chromosome 11p11, which is close to the location of the RAGs (11p12). This indicates conservation of linkage between human and pufferfish.

Molecular systematics of the african electric fishes (Mormyroidea: teleostei) and a model for the evolution of their electric organs

We present a new molecular phylogeny for 41 species of African mormyroid electric fishes derived from the 12S, 16S and cytochrome b genes and the nuclear RAG2 gene. From this, we reconstruct the evolution of the complex electric organs of these fishes. Phylogenetic results are generally concordant with earlier preliminary molecular studies of a smaller group of species and with the osteology-based classification of Taverne, which divides the group into the Gymnarchidae and the Mormyridae, with the latter including the subfamilies Petrocephalinae (Petrocephalus) and Mormyrinae (all remaining taxa). However, we find that several genera previously recognized by Taverne are non-monophyletic. Within the Mormyrinae, the genus Myomyrus is the sister group to all the remaining taxa. Other well-supported clades within this group are recovered. A reconstruction of electrocyte evolution on the basis of our best-supported topology suggests that electrocytes with penetrating stalks evolved once early in the history of the mormyrids followed by multiple paedomorphic reversals to electrocytes with non-penetrating stalks.

vig-1, a new fish gene induced by the rhabdovirus glycoprotein, has a virus-induced homologue in humans and shares conserved motifs with the MoaA family

We used mRNA differential display methodology to analyze the shift of transcription profile induced by the fish rhabdovirus, viral hemorrhagic septicemia virus (VHSV), in rainbow trout leukocytes. We identified and characterized a new gene which is directly induced by VHSV. This VHSV-induced gene (vig-1) encodes a 348-amino-acid protein. vig-1 is highly expressed during the experimental disease in lymphoid organs of the infected fish. Intramuscular injection of a plasmid vector expressing the viral glycoprotein results in vig-1 expression, showing that the external virus protein is sufficient for the induction. vig-1 expression is also obtained by a rainbow trout interferon-like factor, indicating that vig-1 can be induced through different pathways. Moreover, vig-1 is homologous to a recently described human cytomegalovirus-induced gene. Accordingly, vig-1 activation may represent a new virus-induced activation pathway highly conserved in vertebrates. The deduced amino acid sequence of vig-1 is significantly related to sequences required for the biosynthesis of metal cofactors. This suggests that the function of vig-1 may be involved in the nonspecific virus-induced synthesis of enzymatic cofactors of the nitric oxide pathway.

Ontogeny of lymphoid organs and immunoglobulin producing cells in Atlantic cod (Gadus morhua L.)

The ontogeny of lymphoid organs and the development of cells expressing immunoglobulin heavy chain (IgH) mRNA as well as cells containing immunoglobulin (IgM) were studied in Atlantic cod (Gadus morhua L.), a marine teleost. Head kidney and spleen appeared as the first lymphoid organs, present at the time of hatching, whereas thymus was observed in 9 mm larvae. Fully developed lymphoid organs were not achieved until after metamorphosis. Cells expressing IgH mRNA were detected in paraffin sections of larvae and juveniles by in situ hybridization. Positive cells were not detected in fish smaller than 33 mm (58 days after hatching). IgH mRNA expression coincided with the first appearance of immunoglobulin-positive cells as revealed by immunohistochemistry in the same animals.

Conservation of a master hematopoietic switch gene during vertebrate evolution: isolation and characterization of Ikaros from teleost and amphibian species

The generation of T, B and NK lymphocyte lineages from pluripotent hematopoietic stem cells is dependent upon the early expression of the Ikaros locus which by means of alternative splicing produces a variety of zinc finger DNA binding transcription factors. We assessed the general biological importance of Ikaros by studying its conservation and expression in teleost fish and amphibians. Portions of Ikaros cDNA from rainbow trout and Xenopus were amplified by reverse transcription-polymerase chain reaction (RT-PCR). They show roughly 75% conservation of the amino acid sequence with mammalian Ikaros. The trout fragment was then used to isolate full-length Ikaros clones from a trout thymocyte cDNA library. In mice and humans, Ikaros produces six alternatively spliced isoforms, but in trout two additional novel splice variants designated Ik-7 and Ik-8 were also found. Ik-7 is expressed in a similar fashion to Ik-1 and Ik-2, the predominant isoforms expressed in mammalian lymphocytes. In trout and zebrafish, as in mammals, Ikaros is a single-copy gene, but in Xenopus segregation analysis demonstrates that Ikaros has been duplicated, most likely a result of polyploidization. We then examined the expression of Ikaros in trout and Xenopus tumor T cell lines via Northern blot, RT-PCR, immunofluorescence and Western blot analysis. Overall, Ikaros is expressed in a lymphoid-specific fashion similar to that found in mice and humans. In addition Ikaros is expressed early in trout ontogeny, beginning roughly at days 3-4 in the yolk sac and at day 5-6 in the embryo proper. The conservation of Ikaros structure and expression confirms it as a master switch of hematopoiesis.

Model systems for the study of kidney development: use of the pronephros in the analysis of organ induction and patterning

Most vertebrate organs, once formed, continue to perform the function for which they were generated until the death of the organism. The kidney is a notable exception to this rule. Vertebrates, even those that do not undergo metamorphosis, utilize a progression of more complex kidneys as they grow and develop. This is presumably due to the changing conditions to which the organism must respond to retain what Homer Smith referred to as our physiological freedom. To quote, "Recognizing that we have the kind of blood we have because we have the kind of kidneys we have, we must acknowledge that our kidneys constitute the major foundation of our physiological freedom. Only because they work the way they do has it become possible for us to have bones, muscles, glands, and brains. Superficially, it might be said that the function of the kidneys is to make urine; but in a more considered view one can say that the kidneys make the stuff of philosophy itself" ("From Fish to Philosopher," Little, Brown and Co., Boston, 1953). Different kidneys are used to make the stuff of philosophy at different stages of development depending on the age and needs of the organism, rather than the usual approach of simply making embryonic organs larger as the animal grows. Although evolution has provided the higher vertebrates with complex adult kidneys, they continue to utilize simple kidneys in embryogenesis. In lower vertebrates with simple adult kidneys, even more simple versions are used during early developmental stages. In this review the anatomy, development, and gene expression patterns of the embryonic kidney, the pronephros, will be described and compared to the more complex kidney forms. Despite some differences in anatomy, similar developmental pathways seem to be responsible for the induction and the response to induction in both evanescent and permanent kidney forms. Gene expression patterns can, therefore, be added to the morphological and functional data indicating that all forms of the kidney are closely related structures. Given the similarities between the development of simple and complex kidneys, the embryonic kidneys may be an ideal model system in which to investigate the genesis of multicomponent organ systems.

Genomic organization of the TcR beta-chain diversity (Dbeta) and joining (Jbeta) segments in the rainbow trout: presence of many repeated sequences

This work describes a 5.5 kb genomic sequence of the rainbow trout T-cell receptor beta-chain locus. It includes, from 5' to 3', a Dbeta gene, 10 Jbeta genes and the 5'-end of the first Cbeta exon. The trout Dbeta-Jbeta-Cbeta locus is about the same size as the mouse, rat and human homologous loci, but it is less compact and contains 10 Jbeta segments instead of the 6-7 found in mammals. The trout Dbeta coding sequence is identical to those of the mouse, rat and human Dbeta, and the Dbeta recombination signal sequences (RSS) are also very well conserved. Each trout Jbeta segment is flanked in 5' by a 7-mer RSS, which matches with the canonical conserved 7-mer sequences of all RSS. However, 6 of the 10 Jbeta segments have no characteristic 9-mer RSS, although at least some of them are well expressed (Jbeta1 and Jbeta2). The Jbeta region of the trout TcRbeta locus contains numerous micro/minisatellite repeated DNA sequences; some of these repeats contain heptamer RSS-like sequences that could interfere with Jbeta expression. Knowledge of the germline boundaries of the trout Dbeta and Jbeta ends makes it possible to evaluate precisely the exonuclease activity and N-nucleotide addition at the Dbeta-Jbeta junctions of the rearranged TcRbeta chain genes. Many (40%) of the Dbeta-Jbeta junctions in the adult trout have no N-nucleotides, compared to 26.4% in adult mice, and 37% of the adult trout TcRbeta transcripts are out of frame. Thus, there may be major differences in the T-cell developmental kinetics and selection in fish and mammals.