Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: the class II cytokine receptors and their ligands in mammals and fish

Identification and expression analysis of interferon gamma genes in channel catfish

Multiple species of type I interferon (IFN) were recently identified in catfish (CF) (Ictalurus punctatus). Herein we extend these studies and report the existence of two distinct type II IFN genes in channel CF. As with zebrafish and the green spotted pufferfish, the two CF IFN-gamma genes are dissimilar in sequence but closely linked on the same chromosome. One of the genes (IFN-gamma2) encodes two distinct messages that likely arose via alternative splicing at two closely spaced splice donor sites within the first intron. Sequence analysis indicates that CF IFN-gamma genes contain the hallmarks of authentic IFN-gamma including: (1) a conserved nuclear localization site at the C terminus (CF IFN-gamma2 only), (2) an IFN-gamma signature sequence, (3) six putative helical regions within the mature protein, (4) one or more potential glycosylation sites, and (5) multiple mRNA instability motifs within the 3' untranslated region. Moreover, well-characterized CF T and NK cell clones were shown to synthesize IFN-gamma transcripts. This is the first unequivocal demonstration in any lower vertebrate species that NK and T cells synthesize IFN-gamma and is consistent with results in mammalian systems where T cells and NK cells are the major sources of type II IFN production. Collectively, these studies indicate that Siluriformes possess two evolutionarily conserved IFN-gamma genes and demonstrate that CF possess three key elements of the innate immune response: NK cells and types I and II IFN.

Identification and characterization of an interleukin-15 homologue from Tetraodon nigroviridis

Interleukin-15 (IL-15) plays an important role in adaptive immune systems in vertebrates with similar bioactivities to interleukin-2 (IL-2). Here we report molecular cloning, sequence analysis and distribution of an IL-15 homologue from a pufferfish (Tetraodon nigroviridis). It is located within a 3,088 bp genomic fragment, transcribed into a 1,056 bp mRNA including 158 bp 5'UTR (untranslated region), 519 bp ORF (open reading frame) and 379 bp 3'UTR. T. nigroviridis IL-15 is constitutively detectable in tissues and organs selected. Levels of transcripts were observed after various stimulations. Gene organization is similar to mammals and birds, and a high degree of conservation of chromosome synteny exists between them. Systematic genomics search against Takifugu rubripes genome supports our conclusions. The T. nigroviridis IL-15 precursor with 172aa (amino acids) contains a putative 53aa signal peptide, while the mature peptide has a calculated molecular mass of 13.36 kDa and a theoretical pI of 4.67. The protein sequence shares 13.3-62.1% identity with reported IL-15s. Phylogenetic analysis grouped Tetraodon with other fish on a separated branch, excluded from mammalian and avian IL-15s. In addition, our analysis on another annotated T. nigroviridis IL-15 demonstrated that it may be a paralogue of IL-15. To differentiate it from the known IL-15s, we described it as IL-15x.

The interferon system of teleost fish

Interferons (IFNs) are secreted proteins, which induce vertebrate cells into an antiviral state. In mammals, three families of IFNs (type I IFN, type II IFN and IFN-lambda) can be distinguished on the basis of gene structure, protein structure and functional properties. Type I IFNs, which include IFN-alpha and IFN-beta, are encoded by intron lacking genes and have a major role in the first line of defense against viruses. The human IFN-lambdas have similar biological properties as type I IFNs, but are encoded by intron containing genes. Type II IFN is identical to IFN-gamma, which is produced by T helper 1 cells in response to mitogens and antigens and has a key role in adaptive cell mediated immunity. IFNs, which show structural and functional properties similar to mammalian type I IFNs, have recently been cloned from Atlantic salmon, channel catfish, pufferfish, and zebrafish. Teleost fish appear to have at least two type I IFN genes. Phylogenetic sequence analysis shows that the fish type I IFNs form a group separated from the avian type I IFNs and the mammalian IFN-alpha, -beta and -lambda groups. Interestingly, the fish IFNs possess the same exon/intron structure as the IFN-lambdas, but show most sequence similarity to IFN-alpha. Recently, IFN-gamma genes have also been cloned from several fish species and shown to have the same exon/intron structure as mammalian IFN-gamma genes. The antiviral effect of mammalian type I IFN is exerted through binding to the IFN-alpha/beta-receptor, which triggers signal transduction through the JAK-STAT signal transduction pathway resulting in expression of Mx and other antiviral proteins. Putative IFN receptor genes have been identified in pufferfish. Several interferon regulatory factors and members of the JAK-STAT pathway have also been identified in various fish species. Moreover, Mx and several other interferon stimulated genes have been cloned and studied in fish. Furthermore, antiviral activity of Mx protein from Atlantic salmon and Japanese flounder has recently been demonstrated.

Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster

The IL-10 gene and homologs IL-19, IL-20, and IL-24 are expressed within a highly conserved 145-kb cytokine gene cluster. Like the Th2 IL-4 cytokine gene cluster, it is feasible that there is coordinate regulation of these cytokines by distal regulatory elements spanning the locus. We initiated a search to characterize regulatory elements within the IL-10 family locus and present data herein on a conserved 40-kb region between the IL-19 and IL-10 genes. We map the location of 17 DNase I-hypersensitive sites in different murine T cell populations and identify three enhancer elements, which function in T cells in vitro. Two of these enhancer elements, located 9 kb upstream and 6.45 kb downstream of IL-10, display cell-specific function in the Th1-Th2 cell clones AE7 and D10 and also exhibit basic promoter activity. The downstream element, IL-10CNS+6.45, binds AP-1 in the absence of NFAT and expresses intergenic RNA in a Th2-specific manner, further validating its role as a Th2-specific enhancer/promoter element. We show that the five most highly conserved noncoding sequences in the 40-kb region transcribe intergenic RNA; four of these regions possess promoter activity in vitro that could account for the expression of these transcripts. Hence, we speculate that these novel regulatory elements in the IL-10 family gene locus function via an intermediate regulatory RNA.

Performing quantitative reverse-transcribed polymerase chain reaction experiments

Quantitative polymerase chain reaction (PCR) is as old as PCR, but it has had to wait for the introduction of real-time PCR instruments to become widely used. These instruments allow monitoring of the PCR reaction on line; they involve the use of a fluorescent probe that allows quantification of the amplified DNA. Different fluorescent formats and different applications have been developed for quantitative PCR, but this chapter focuses on the use of the SYBR Green label for the quantification of specific cDNAs in reverse transcription mixes: RT-PCR. We propose optimal reaction conditions for the reactions to be performed on the different available instruments and discuss the important parameters for setting up experiments: specificity, efficiency, and reproducibility. We also introduce the reader to the problems of relative quantification.

Estimating the tempo and mode of gene family evolution from comparative genomic data

Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been attributed to the effects of natural selection, without a strong statistical basis for these conclusions. Here we use a model of stochastic birth and death for gene family evolution and show that it can be efficiently applied to multispecies genome comparisons. This model takes into account the lengths of branches on phylogenetic trees, as well as duplication and deletion rates, and hence provides expectations for divergence in gene family size among lineages. The model offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection in gene family expansion or contraction. We apply our method to data from the genomes of five yeast species to show its applicability.

Organization and promoter analysis of the zebrafish (Danio rerio) interferon gene

Interferon plays important roles in confronting viral infections as the first line of defense. For the purpose of understanding the molecular mechanism which controls transcription of the interferon gene, we cloned and sequenced the interferon promoter region of the zebrafish interferon gene and characterized its activity using firefly luciferase transient transfection expression assays. Different fragments of the zebrafish interferon 5'-flanking region were transfected into ZFL cells. In these cell lines, maximum promoter activity was located in 2.2 kb of the zebrafish interferon 5' flanking region of the ZFL cell line. In this study, we investigated whether the viral replicative intermediate double-stranded RNA (herein we used synthetic polyinosinic-polycytidylic acid [poly(I):poly(C)] modifies the effects of interferon on gene expression. For this purpose, all zebrafish interferon promoter fragments were treated with either 1, 10, or 100 microg/ml poly(I):poly(C). The results showed that after treatment with 10 microg/ml poly(I):poly(C), high promoter activity was observed in the -2.2-kb interferon promoter fragment. Several putative transcription factors were shown in the promoter region, including IRF-1, C/EBP, NFkappaB, and GATA-1. Further study of the in vivo expression of the interferon promoter during development was carried out in transgenic zebrafish expressing an interferon promoter-driven green fluorescent protein (GFP) encoding the GFP cDNA transgene. Morphological studies of transgenic zebrafish indicated that the interferon promoter-driven GFP transcripts appeared in the yolk, head, and lymphoid organs. These results indicate that the interferon promoter is active in a tissue-specific manner, and suggest that the interferon promoter plays an important role in virus resistance during teleost growth.

Experimental handling stress as infection-facilitating factor for the goldfish ulcerative disease

Experimental handling stress (EHS) was applied to clinically asymptomatic farmed goldfish (Carassius auratus L.). EHS affected the gills and skin integrity of the fish and was accompanied by increased levels of plasma glucose, cortisol and interleukin-10 (IL-10). EHS application was followed by highly significant enhancement of the rate of infection with a virulent Aeromonas salmonicida isolate. Cumulative ulceration at the initial phase of the ensuing goldfish ulcerative disease (GUD) evidenced a facilitating role of EHS in the onset of GUD. Host susceptibility to the pathogen increased from 40% in unstressed fish to 90% in the stressed fish. A. salmonicida could be reisolated from the early-stage skin lesions only, whereas opportunistic strains, other than A. salmonicida (A. sobria and A. hydrophila), were recovered from progressive-stage ulcers. The implication of these findings in fish aquaculture is discussed.

Molecular cloning and expression analysis of interferon regulatory factor-1 (IRF-1) of turbot and sea bream

The interferon regulatory factor (IRF) family comprises transcription factors that regulate the expression of interferon and interferon-related cytokines. Using the RACE technique, we have determined the complete cDNA sequence of turbot (Scophthalmus maximus) and sea bream (Sparus aurata) IRFs. These sequences shared characteristics with other IRFs of fish, mammals and birds, and showed high similarity with IRF-1. Indeed, they were included in the IRF-1 cluster of the phylogenetic tree constructed with IRF-1 and IRF-2 sequences of several organisms, and presented a low number of basic amino acid residues in the carboxy-terminal end of the proteins. All of these characteristics led to the identification of turbot and sea bream IRFs as IRF-1. Two IRF-1 sequences were obtained for both turbot and sea bream, and we named them turbot/sea bream IRF-1a and IRF-1b. Turbot IRF-1a differed from turbot IRF-1b in four nucleotides. The presence of both IRF types in cDNA from 45 turbot livers was determined by RFLP, suggesting the duplication of the gene. Sea bream IRF-1b presented a deletion of 121bp in its ORF compared to sea bream IRF-1a, and since both IRF types were present in all 25 cDNAs analyzed by PCR, we hypothesized that the truncated sea bream IRF-1b was probably an alternative splicing product. Turbot and sea bream IRF-1 expression was constitutive in every analyzed organ, as reported before for other fish species. Poly I:C significantly stimulated turbot IRF-1 expression in muscle, spleen and kidney 24 h post-treatment, while viral haemorrhagic septicemia virus (VHSV) induced a differential expression of this factor in kidney 8 h after infection. These results do not agree with those previously reported for flounder and trout IRF. Other expression experiments with turbot leukocytes stimulated in vitro with poly I:C and with brain and kidney of sea bream infected with nodavirus did not bring out differential IRF expression levels in stimulated samples with respect to controls.

Evolution of the Class 2 cytokines and receptors, and discovery of new friends and relatives

The sequencing of a wide variety of genomes and their transcripts has allowed researchers to determine how proteins or protein families evolved and how strongly during evolution a protein has been conserved. In this report, we analyze the evolution of the Class 2 ligands and their cognate receptors by analyzing Class 2 ligand and receptor chain gene sequences from a variety of DNA sequence databases. Both the Class 2 cytokines and receptor chains appear to have developed during the evolution of the chordate phyla: distant homologues of type I interferon (IFN) receptors are the only Class 2 cytokine receptors identified in the Ciona genomes, while a wide variety of Class 2 ligands and receptor chains are encoded in the currently available genomes of bony vertebrates (teleost fish, amphibians, reptiles, birds, mammals). Phylogenetic trees of ligands and ligand-binding receptor chains demonstrate that proteins involved in conferring antiviral activity diverged before those involved in adaptive immunity. Genes encoding IFNs and IFN receptors duplicated multiple times during chordate evolution, suggesting that duplication of genes encoding IFN activity conveyed an evolutionary advantage. Altogether, these data support a model whereby the original Class 2 cytokines and receptors evolved and duplicated during the evolution of the chordate innate immune response system; new receptor and ligand duplications evolved into signaling molecules to fulfill communication requirements of a highly specialized and differentiated vertebrate immune system. In addition, the genomic analysis led to the discovery of some new members of this family.

Interferons, interferon-like cytokines, and their receptors

Recombinant interferon-alpha (IFN-alpha) was approved by regulatory agencies in many countries in 1986. As the first biotherapeutic approved, IFN-alpha paved the way for the development of many other cytokines and growth factors. Nevertheless, understanding the functions of the multitude of human IFNs and IFN-like cytokines has just touched the surface. This review summarizes the history of the purification of human IFNs and the key aspects of our current state of knowledge of human IFN genes, proteins, and receptors. All the known IFNs and IFN-like cytokines are described [IFN-alpha, IFN-beta, IFN-epsilon, IFN-kappa, IFN-omega, IFN-delta, IFN-tau, IFN-gamma, limitin, interleukin-28A (IL-28A), IL-28B, and IL-29] as well as their receptors and signal transduction pathways. The biological activities and clinical applications of the proteins are discussed. An extensive section on the evolution of these molecules provides some new insights into the development of these proteins as major elements of innate immunity. The overall structure of the IFNs is put into perspective in relation to their receptors and functions.

A novel tumor necrosis factor (TNF) gene present in tandem with theTNF-? gene on the same chromosome in teleosts

Tumor necrosis factors (TNFs) are pleiotropic cytokines implicated in inflammation, apoptosis, cell proliferation, and a general stimulation of immune system. Although the TNF/lymphotoxin (LT) locus is present in the MHC region of the chromosome in mammals, no such locus has been described from teleosts. Furthermore, in teleosts only the TNF-alpha-like gene has been cloned and analyzed. In this study, for the first time in teleosts, a similar TNF locus has also been found in zebrafish and fugu. This locus harbors a new TNF ligand in tandem with TNF-alpha gene. The fugu and zebrafish TNF locus harbors TNF-alpha and TNF-N genes that are 7.5 kb and 19 kb apart from each other, respectively. Several genes associated with the TNF/LT locus in mammals are found conserved in fish as well. Fish TNF-alpha genes cloned possess a transmembrane domain, two conserved cysteines, and a conserved TNF family signature with a four-exon and three-intron genomic structure. The newly identified TNF-N genes from teleosts are present upstream of TNF-alpha genes in the same transcriptional orientation. However, the coding regions of these genes span into five and four exons in fugu and zebrafish, respectively. The transcription sites in the promoter regions of teleost TNF ligands are fairly conserved in comparison to mammals. Expression analysis indicates a constitutive expression of both the genes in fugu, while differential expression of TNF ligands is seen in zebrafish tissues.

IFN-inducible GTPases and immunity to intracellular pathogens

By eliciting host antimicrobial programs in nearly all nucleated cells interferons (IFNs) help orchestrate the innate immune response of mammals to a diverse array of microbial pathogens. Recent work has highlighted the complexity of this transcriptional repertoire and the emergence of several families of IFN-inducible guanosine 5' triphosphatases (GTPases)--p47, guanylate-binding protein (GBP), Mx and very large inducible GTPases (VLIG)--that subsume pathogen-specific roles. Such specificity arises from a combination of both the type and timing of inductive stimuli, target-cell population, subcellular binding partners and the infectious agent encountered. Evolution of different GTPase families to combat compartmentalized versus cytosolic pathogens reveals a hitherto unexpected level of intracellular discrimination during vertebrate host defense.

Interleukin-10 and related cytokines and receptors

The Class 2 alpha-helical cytokines consist of interleukin-10 (IL-10), IL-19, IL-20, IL-22, IL-24 (Mda-7), and IL-26, interferons (IFN-alpha, -beta, -epsilon, -kappa, -omega, -delta, -tau, and -gamma) and interferon-like molecules (limitin, IL-28A, IL-28B, and IL-29). The interaction of these cytokines with their specific receptor molecules initiates a broad and varied array of signals that induce cellular antiviral states, modulate inflammatory responses, inhibit or stimulate cell growth, produce or inhibit apoptosis, and affect many immune mechanisms. The information derived from crystal structures and molecular evolution has led to progress in the analysis of the molecular mechanisms initiating their biological activities. These cytokines have significant roles in a variety of pathophysiological processes as well as in regulation of the immune system. Further investigation of these critical intercellular signaling molecules will provide important information to enable these proteins to be used more extensively in therapy for a variety of diseases.

Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA

The combination of bioinformatic and biological approaches constitutes a powerful method for identifying gene regulatory elements. High-quality genome sequences are available in public databases for several vertebrate species. Comparative cross-species sequence analysis of these genomes shows considerable conservation of noncoding sequences in DNA. Biological analyses show that an unexpectedly high number of the conserved sequences correspond to functional cis-regulatory regions that influence gene transcription. Because research biologists are often unfamiliar with the bioinformatic resources at their disposal, this commentary discusses how to integrate biological and bioinformatic methods in the discovery of gene regulatory regions and includes a tutorial on widely available comparative genomics programs.

The use of zebrafish to understand immunity

For decades immunologists have relied heavily on the mouse model for their experimental designs. With the realization of the important role innate immunity plays in orchestrating immune responses, invertebrates such as worms and flies have been added to the repertoire. Here, we discuss the advent of the zebrafish as a powerful vertebrate model organism that promises to positively impact immunologic research.

The Class II cytokine receptor (CRF2) family: overview and patterns of receptor–ligand interactions

Expanded genomic information has driven the discovery of new members of the human Class II family of cytokine receptors (CRF2), which now includes 12 proteins. The corresponding cytokines have been identified, paired with their receptors and initially characterized for function. These cytokines include: a new human Type I IFN, IFN-kappa; molecules related to IL-10 (IL-19, IL-20, IL-22, IL-24, IL-26); and IFN-lambdas (IL-28/29), which have antiviral and cell stimulatory activities reminiscent of Type I IFNs, but act through a distinct receptor. In response to ligand binding, the CRF2 proteins form heterodimers, leading to cytokine-specific cellular responses; these diverse physiological functions are just beginning to be explored. Progress in structural and mutational analysis of ligand-receptor interactions now presents a more reliable framework for understanding receptor-ligand interactions, and for predicting key regions in less well studied members of the CRF2 family. The relationships between the CRF2 proteins will be summarized, as will the progress in identifying patterns of receptor interactions with ligands.

Tissue factor as an evolutionary conserved cytokine receptor: implications for inflammation and signal transduction

Tissue factor (TF) is a transmembrane protein that, in complex with factor VIIa (FVIIa), initiates coagulation. It also influences various other physiological and pathological events, such as inflammation, and negatively influences survival during sepsis. TF resembles a conserved class of pro-inflammatory cytokine receptors and activates a set of pro-inflammatory intracellular signal transduction routes. Interestingly, whereas the homology of TF to the class II cytokine receptors is reflected in a similar type of signal transduction, the mechanism by which the signal is transduced across the membrane differs greatly. This review discusses the role of TF and its ligand FVIIa in inflammation, sepsis, and signal transduction, and describes the way in which these processes interact.