Structural organization and sequence analysis of the globin locus in Atlantic salmon

Evolutionary pathway of pseudogenization of globin genes, α5 and β5, in genus Oryzias

Hemoglobin transports oxygen in many organisms and consists of α- and β-globin chains. Previously, using molecular phylogenetic analysis, we proposed that both α- and β-globins of teleost could be classified into four groups. We also showed that the Hd-rR strain of medaka (Oryzias latipes) inhabiting southern Japan had all four groups of globin genes but that the α- and β-globin genes of group III were pseudogenized (α5(ψα), β5(ψβ)). Based on the small degree of nucleotide variations, the pseudogenization of β5 was assumed to have occurred at a relatively late stage of evolution. Here, we compared the α5(ψα)-β5(ψβ) of two other strains of O. latipes and found that both α5(ψα) and β5(ψβ) of the northern Japanese and Korean strains were pseudogenized similar to those of Hd-rR. In a Philippine population (Oryzias luzonensis), α5(ψα) was also pseudogenized, but the structure was different from that of O. latipes, and β5(ψβ) was almost deleted. Interestingly, an Indonesian population (Oryzias celebensis) had α5 and β5 genes that were deduced to be functional. Indeed, they were expressed from the young to adult development stages, and this expression pattern was consistent with the expression of α2 and ad.α1 in Hd-rR. Because α2 and ad.α1 in Hd-rR were assigned to groups I and II, respectively, we speculate that their expression patterns might be altered by pseudogenization of group III genes. These results provide a basis for further investigations of recruiting and changing expression patterns of one globin gene after pseudogenization of other globin genes during evolution.

Interaction of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease, with host proteins in the kidney of Salmo trutta

Tetracapsuloides bryosalmonae (Myxozoa) is the causative agent of proliferative kidney disease in various species of salmonids which are found in Europe and North America. Less information about the interactions of T. bryosalmonae proteins with salmonid proteins during parasite development is known. In this study, anti-T. bryosalmonae monoclonal antibody-linked to N-hydroxysuccinimide-activated spin columns were used to purify parasite and host proteins from the kidneys of infected and non-infected brown trout (Salmo trutta) Linnaeus, 1758. The samples were next analyzed by electrospray ionization coupled to mass spectrometry to identify proteins that may be involved in the infection and proliferation of T. bryosalmonae within the brown trout host. A total of 6 parasite proteins and 40 different host proteins were identified in this analysis. The identified host proteins function in various processes, which include host defense, enzymatic, and structural components. In conjunction with modern molecular based tools, such siRNA, gene replacement, or gene disruption, this data can ultimately be used to develop novel control methods for T. bryosalmonae, based on the proteins or pathways identified in this study.

Differential modulation of host genes in the kidney of brown trout Salmo trutta during sporogenesis of Tetracapsuloides bryosalmonae (Myxozoa)

Tetracapsuloides bryosalmonae (Myxozoa) is the causative agent of proliferative kidney disease in various species of salmonids in Europe and North America. In Europe, spores of T. bryosalmonae develop in the kidney of infected brown trout Salmo trutta and are released via urine to infect the freshwater bryozoan Fredericella sultana. The transcriptomes of kidneys of infected and non-infected brown trout were compared by suppressive subtractive hybridization. Differential screening and a subsequent NCBI BLAST analysis of expressed sequence tags revealed 21 transcripts with functions that included cell stress and cell growth, ribonucleoprotein, signal transduction, ion transporter, immune response, hemoglobin and calcium metabolisms. Quantitative real time PCR was used to verify the presence of these selected transcripts in brown trout kidney at sporogonic stages of T. bryosalmonae development. Expression of cold-inducible RNA-binding protein, cyclin-dependent kinase inhibitor 2A, prothymosin alpha, transforming protein RhoA, immunoglobulin light chain and major histocompatibility complex class I were up-regulated significantly in infected brown trout. Expression of both the hemoglobin subunit beta and stanniocalcin precursor were down-regulated significantly in infected brown trout. This study suggests that cell stress and cell growth processes, signal transduction activities, erythropoiesis and calcium homeostasis of the host are modulated during sporogonic stages of parasite development, which may support the sporogenesis of T. bryosalmonae in the kidney of brown trout.

Phenotype-environment association of the oxygen transport system in trimorphic European whitefish (Coregonus lavaretus) populations

Replicated adaptive radiation events, typified by phenotypic divergence across resource axes, provide important insight into the eco-evolutionary dynamics that lead to the formation of new species. Here, we show that in trimorphic adaptive radiations of European whitefish (Coregonus lavaretus), divergence of the oxygen transport system has occurred across the pelagic/littoral (shallow)-profundal (deep) resource axis, and at multiple biological scales. Profundal whitefish exhibited significantly larger red blood cells (RBCs), a greater proportion of cathodic hemoglobin protein components, and higher hemoglobin transcript abundance in kidney compared to littoral and pelagic morphs. Hemoglobin transcript abundance in brain and gill, but not kidney, and anodic hemoglobin protein component diversity in blood were also linked to variation at an intronic single nucleotide polymorphism (SNP). As the whitefish morphs differ in population genetic structure at this SNP, hemoglobin transcript and protein divergence between profundal and pelagic/littoral morphs is likely being driven by genetic divergence. Our findings, along with our previous work on lake whitefish, highlight the importance of the oxygen transport system to the postglacial colonization of novel lacustrine environments by whitefish throughout the northern hemisphere.

Evolution and function of the globin intergenic regulatory regions of the antarctic dragonfishes (Notothenioidei: Bathydraconidae)

As the Southern Ocean cooled to -1.8 °C over the past 40 My, the teleostean clade Notothenioidei diversified and, under reduced selection pressure for an oxygen-transporting apparatus, became less reliant on hemoglobin and red blood cells. At the extreme of this trend, the crown group of Antarctic icefishes (Channichthyidae) lost both components of oxygen transport. Under the decreased selection scenario, we hypothesized that the Antarctic dragonfishes (Bathydraconidae, the red-blooded sister clade to the icefishes) evolved lower blood hemoglobin concentrations because their globin gene complexes (α- and β-globin gene pairs linked by a regulatory intergene) transcribe globin mRNAs less effectively than those of basal notothenioids (e.g., the Nototheniidae [notothens]). To test our hypothesis, we 1) sequenced the α/β-intergenes of the adult globin complexes of three notothen and eight dragonfish species and 2) measured globin transcript levels in representative species from each group. The typical nototheniid intergene was ∼3-4 kb in length. The bathydraconid intergenes resolved into three subclasses (long [3.8 kb], intermediate [3.0 kb], and short [1.5-2.3 kb]) that corresponded to the three subclades proposed for the taxon. Although they varied in length due to indels, the three notothen and eight dragonfish intergenes contained a conserved ∼90-nt element that we have previously shown to be required for globin gene transcription. Using the quantitative polymerase chain reaction, we found that globin mRNA levels in red cells from one notothen species and from one species of each dragonfish subclade were equivalent statistically. Thus, our results indicate that the bathydraconids have evolved adult globin loci whose regulatory intergenes tend to be shorter than those of the more basal nototheniids yet are equivalent in transcriptional efficacy. Their low blood hemoglobin concentrations are most likely due to reduction in hematocrit.

Genomic organization and gene expression of the multiple globins in Atlantic cod: conservation of globin-flanking genes in chordates infers the origin of the vertebrate globin clusters

Background

The vertebrate globin genes encoding the α- and β-subunits of the tetrameric hemoglobins are clustered at two unlinked loci. The highly conserved linear order of the genes flanking the hemoglobins provides a strong anchor for inferring common ancestry of the globin clusters. In fish, the number of α-β-linked globin genes varies considerably between different sublineages and seems to be related to prevailing physico-chemical conditions. Draft sequences of the Atlantic cod genome enabled us to determine the genomic organization of the globin repertoire in this marine species that copes with fluctuating environments of the temperate and Arctic regions.

Results

The Atlantic cod genome was shown to contain 14 globin genes, including nine hemoglobin genes organized in two unlinked clusters designated β5-α1-β1-α4 and β3-β4-α2-α3-β2. The diverged cod hemoglobin genes displayed different expression levels in adult fish, and tetrameric hemoglobins with or without a Root effect were predicted. The novel finding of maternally inherited hemoglobin mRNAs is consistent with a potential role played by fish hemoglobins in the non-specific immune response. In silico analysis of the six teleost genomes available showed that the two α-β globin clusters are flanked by paralogs of five duplicated genes, in agreement with the proposed teleost-specific duplication of the ancestral vertebrate globin cluster. Screening the genome of extant urochordate and cephalochordate species for conserved globin-flanking genes revealed linkage of RHBDF1, MPG and ARHGAP17 to globin genes in the tunicate Ciona intestinalis, while these genes together with LCMT are closely positioned in amphioxus (Branchiostoma floridae), but seem to be unlinked to the multiple globin genes identified in this species.

Conclusion

The plasticity of Atlantic cod to variable environmental conditions probably involves the expression of multiple globins with potentially different properties. The interspecific difference in number of fish hemoglobin genes contrasts with the highly conserved synteny of the flanking genes. The proximity of globin-flanking genes in the tunicate and amphioxus genomes resembles the RHBDF1-MPG-α-globin-ARHGAP17-LCMT linked genes in man and chicken. We hypothesize that the fusion of the three chordate linkage groups 3, 15 and 17 more than 800 MYA led to the ancestral vertebrate globin cluster during a geological period of increased atmospheric oxygen content.

Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

BACKGROUND

The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest.

RESULTS

We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced.

CONCLUSIONS

We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster after the whole genome duplication (WGD) at the base of the teleost radiation but prior to the salmonid-specific WGD, which then produced the duplicated copies seen today. We also propose that the relatively high number of hemoglobin genes as well as the presence of non-Bohr β hemoglobin genes may be due to the dynamic life history of salmon and the diverse environmental conditions that the species encounters.Data deposition: BACs S0155C07 and S0079J05 (fps135): GenBank GQ898924; BACs S0055H05 and S0014B03 (fps1046): GenBank GQ898925.

Organisation of the Hb 1 genes of the Antarctic skate Bathyraja eatonii: new insights into the evolution of globin genes

An extensive investigation of the organisation of globin genes has greatly contributed to the understanding of universal mechanisms of gene evolution and expression. Cartilaginous fish are the first organisms that have evolved the tetrameric form of hemoglobin (Hb). So far, there has been absolute lack of data about globin genes in chondrichthyans. Bathyraja is the dominant rajid south of 60 degrees S. In the framework of the investigations on globin genes of Antarctic red-blooded and Hb-less fish we obtained the cloning of the alpha- and beta-globin cDNAs of the main Hb (Hb 1) of the skate Bathyraja eatonii. Then, a genomic fragment of 6.2 kb was isolated where the Hb 1 alpha and beta genes are linked in a tail-to-head (3' to 5') orientation. The beta-globin gene promoter region and the chromosomal organisation of the Hb 1 genes of B. eatonii have been compared to their homologues in other vertebrates. The finding of a tail-to-head linkage of the Hb 1 alpha- and beta-globin genes in B. eatonii is the first characterisation of the organisation of globin genes in chondrichthyes; such finding offers a novel contribution to the understanding of the evolution of this class of genes. Moreover, the characterisation of chondrichthyan genes is very important for gaining insight into the ancestral state of vertebrate genomes.

Molecular cloning and sequencing of hemoglobin-beta gene of channel catfish, Ictalurus punctatus Rafinesque

The hemoglobin-beta gene of channel catfish, Ictalurus punctatus, was cloned and sequenced. Total RNA from head kidneys was isolated, reverse transcribed and amplified. The sequence of the channel catfish hemoglobin-beta gene consists of 600 nucleotides. Analysis of the nucleotide sequence reveals one open reading frame and 5'- as well as 3'-untranslated regions. The open reading frame of the sequence potentially encodes 148 amino acids with a calculated molecular mass of 16.3 kDa. The pI and charge at pH 7.0 of the deduced hemoglobin-beta protein were 7.28 and 0.47, respectively. Overall, 22 amino acid residues were conserved throughout the sequences, including His64 and His93, the sites for heme-binding. Unlike the counterpart of other common cultured fish such as Salmo salar, Oncorhynchus nerka, Oncorhynchus mykiss, Cyprinus carpio and Ctenopharyngodon idella, the hemoglobin-beta of channel catfish did not have cysteine. The amino acid sequence of channel catfish hemoglobin-beta shows 84% homology with that of Silurus asotus (both are in the order Siluriformes). However, comparison with those of other fish species shows homology ranging from 53 to 68%. Structural analysis by the 3D-PSSM program displays that channel catfish hemoglobin-beta has eight alpha-helices, A-H.

Evolution of globin genes of the medaka Oryzias latipes (Euteleostei; Beloniformes; Oryziinae)

Recently we cloned two globin gene clusters from the genome of medaka (Oryzias latipes): one designated the embryonic globin gene cluster (E1; (5')alpha0(3')-(3')beta1(5')-(5')alpha1(3')-(5')beta2(3')-(5')alpha2(3')-(3')alpha3(5')-(5')beta3(3')-(3')beta4(5')-(5')alpha4(3')-(3')psialpha(5')-(5')psibeta(3')) and the other the adult globin gene cluster (A1; (3')ad.alpha1(5')-(5')ad.beta1(3')-(3')ad.alpha2(5')). The E1 and A1 clusters map to linkage groups 8 and 19, respectively. The genes beta1/alpha1, alpha3/beta3, beta4/alpha4, psialpha/psibeta and ad.alpha1/ad.beta1 are organized in head-to-head orientation with respect to transcriptional polarity. The genes alpha0, alpha1 and alpha2 are arranged in tandem with the same orientation. The results suggest that a variety of events occurred in globin gene evolution such as chromosomal translocation, duplication of alpha/beta-paired genes, tandem duplication of single alpha genes and the transformation of one pair of alpha/beta-paired genes into pseudogenes (psialpha/psibeta). Amino acid sequences predicted from the genes were compared with those of 42 alpha and 55 beta teleostean globins using the neighbor-joining or maximum likelihood methods. The phylogenetic trees that were generated classified the teleostean globins into at least four groups, tentatively named 'Embryonic Hb Group (I)', 'Notothenioid Major Adult Hb Group (II)', 'Anodic Adult Hb Group (III)' and 'Cathodic Adult Hb Group (IV)'. The medaka genes alpha0, beta1, alpha1, alpha2, alpha3, beta3, beta4 and alpha4 belong to group I, and ad.alpha1 and ad.beta1 to group II. Further analysis suggests that psialpha/psibeta and beta2/ad.alpha2 belong to groups III and IV, respectively. Thus, globin genes in the medaka probably were diversified from four ancestral genes, one for each group. On the basis of the gene comparisons, we present a hypothetical pathway for globin gene evolution in the medaka.

Genomic organization and developmental expression of globin genes in the teleost Oryzias latipes

We isolated globin genes from a genomic DNA library of the drR strain of medaka Oryzias latipes, and walked on chromosome. The present study is the first demonstration of the full-length structure of globin gene locus in the teleosts. Two gene clusters were found. One cluster of 36 kbp consisted of nine globin genes and two pseudogenes. Based on structural and phylogenetic similarity of amino acid sequences, the cluster was named embryonic globin gene cluster (E1). The orientation of the genes was in (5')alpha0(3')-(3')beta1(5')-(5')alpha1(3')-(5')beta2(3')-(5')alpha2(3')-(3')alpha3(5')-(5')beta3(3')-(3')beta4(5')-(5')alpha4(3')-(3')psialpha(5')-(5')psibeta(3'). The other cluster of 20 kbp contained three globin genes ((3')ad.alpha1(5')-(5')ad.beta1(3')-(3')ad.alpha2(5')), and was named adult globin gene cluster (A1). Genetic linkage analysis clarified that E1 and A1 were mapped on linkage groups 8 and 19, respectively. The E1 cluster included other genes homologous to human EST clone KIAA0172, Sushi-1 retrotransposon, and protein 14 gene-like gene, while the A1 cluster linked to aquaporin-8 gene-like gene. The expression patterns of the genes were classified into four types: embryo-specific expression (alpha3, beta3, alpha4 and beta4), expression in embryo to young fish (alpha0, beta1, alpha1 and ad.alpha2), expression in young to adult fish (alpha2 and ad.alpha1) and successive expression in embryo to adult (ad.beta1).

Characterization of embryonic globin genes of the zebrafish

Hemoglobin switching is a complex process by which distinct globin chains are produced during stages of development. In an effort to characterize the process of hemoglobin switching in the zebrafish model system, we have isolated and characterized several embryonic globin genes. The embryonic and adult globin genes are found in clusters in a head-to-head configuration. One cluster of embryonic and adult genes is localized to linkage group 3, whereas another embryonic cluster is localized on linkage group 12. Several embryonic globin genes demonstrate an erythroid-specific pattern of expression early during embryogenesis and later are downregulated as definitive hematopoiesis occurs. We utilized electrospray mass spectroscopy to correlate globin genes and protein expression in developing embryonic red cells. The mutation, zinfandel, has a hypochromic microcytic anemia as an embryo, but later recovers in adulthood. The zinfandel gene maps to linkage group 3 near the major globin gene locus, strongly suggesting that zinfandel represents an embryonic globin defect. Our studies are the first to systematically evaluate the embryonic globins in the zebrafish and will ultimately be useful in evaluating zebrafish mutants with defects in hemoglobin production and switching.

EST-based identification of genes expressed in the liver of adult Atlantic salmon (Salmo salar)

A list of genes expressed in the liver of Atlantic salmon was compiled using the expressed sequence tag (EST) strategy. 733 ESTs, derived from 170 abundant and 563 rare mRNA encoding liver cDNA clones, were determined. Bioinformatic analysis revealed that 390 (53%) of the salmon liver ESTs could be ascribed to the transcriptional products of 93 identified genes including 7 previously described in the Atlantic salmon. The identified Atlantic salmon genes were classified with respect to cellular role which showed that 33 (36%) of the identified genes encoded proteins associated with primary liver functions such as transport, acute phase response, and blood clotting. Furthermore, comparative analysis revealed that 12 of the 16 salmon genes that were shown to encode abundant mRNA transcripts in liver had homologues that have also been shown to be highly expressed in mammalian liver systems. Finally, two cDNA variants corresponding to the two cDNA forms of the apolipoprotein A-I gene previously identified in rainbow trout were also found in Atlantic salmon.

The major adult alpha-globin gene of antarctic teleosts and its remnants in the hemoglobinless icefishes. Calibration of the mutational clock for nuclear genes

The icefishes of the Southern Ocean (family Channichthyidae, suborder Notothenioidei) are unique among vertebrates in their inability to synthesize hemoglobin. We have shown previously (Cocca, E., Ratnayake-Lecamwasam, M., Parker, S. K., Camardella, L., Ciaramella, M., di Prisco, G., and Detrich, H. W., III (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 1817-1821) that icefishes retain inactive genomic remnants of adult notothenioid alpha-globin genes but have lost the gene that encodes adult beta-globin. Here we demonstrate that loss of expression of the major adult alpha-globin, alpha1, in two species of icefish (Chaenocephalus aceratus and Chionodraco rastrospinosus) results from truncation of the 5' end of the notothenioid alpha1-globin gene. The wild-type, functional alpha1-globin gene of the Antarctic yellowbelly rockcod, Notothenia coriiceps, contains three exons and two A + T-rich introns, and its expression may be controlled by two or three distinct promoters. Retained in both icefish genomes are a portion of intron 2, exon 3, and the 3'-untranslated region of the notothenioid alpha1-globin gene. The residual, nonfunctional alpha-globin gene, no longer under positive selection pressure for expression, has apparently undergone random mutational drift at an estimated rate of 0.12-0.33%/million years. We propose that abrogation of hemoglobin synthesis in icefishes most likely resulted from a single mutational event in the ancestral channichthyid that deleted the entire beta-globin gene and the 5' end of the linked alpha1-globin gene.

Head-to-head linkage of carp alpha- and beta-globin genes

The alpha- and beta-globin gene variants are believed to have diverged from a single ancestral globin gene, and the divergence was primed by the duplication of the ancestral globin gene. To understand the process of gene duplication, we investigated the alpha- and beta-globin gene arrangement of a bony fish (carp). From a Southern analysis of seven previously prepared lambda phage clones (lambdaCG1-7) using radio-labelled alpha- or beta-globin gene probes, it was found that the clones included both the alpha- and beta-globin genes, and that they were located within a distance of 1 kb. Additionally, the linkage of two alpha-globin genes and two beta-globin genes in the clone lambdaCG1, 5 and 7 (e.g., alpha-beta-alpha-beta in lambdaCG5) revealed an arrangement that is different from the arrangement in higher vertebrates in which the alpha-globin and beta-globin genes generally occur at different loci. The distances between the detached alpha- to beta-globin genes were approximately 5 to 10 kb. DNA sequencing of the adjacently linked alpha- and beta-globin genes in lambdaCG3 showed that they were arranged in a head-to-head orientation. PCR amplification using primers for the internal region between the carp alpha- and beta-globin genes gave approximately 0.9-kb products from each of the clones lambdaCG1, 3, 4, 5, 6, and 7, and from the chromosomal DNA of German mirror carp, Saku carp, Suwa carp, and Yamato carp. This demonstrates the alternative arrangement of carp alpha- and beta-genes in the globin gene locus (i.e., 3'alpha5'-5'beta3'-3'alpha5'-5'beta3' in lambdaCG5), and the widespread distribution of head-to-head-linked alpha- and beta-globin genes in carp. Based on the above results, we hypothesize that the duplication of the ancestral globin gene (prior to the divergence of the a and beta forms) occurred in a head-to-head direction.