Developmental changes in the pattern of larval beta-globin gene expression in Xenopus laevis. Identification of two early larval beta-globin mRNA sequences

Molecular evolution of the hemoglobin gene family across vertebrates

Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α₂β₂) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean d_N/d_S (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.

Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis

RNA alternative polyadenylation contributes to the complexity of information transfer from genome to phenome, thus amplifying gene function. Here, we report the first X. tropicalis resource with 127,914 alternative polyadenylation (APA) sites derived from embryos and adults. Overall, APA networks play central roles in coordinating the maternal-zygotic transition (MZT) in embryos, sexual dimorphism in adults and longitudinal growth from embryos to adults. APA sites coordinate reprogramming in embryos before the MZT, but developmental events after the MZT due to zygotic genome activation. The APA transcriptomes of young adults are more variable than growing adults and male frog APA transcriptomes are more divergent than females. The APA profiles of young females were similar to embryos before the MZT. Enriched pathways in developing embryos were distinct across the MZT and noticeably segregated from adults. Briefly, our results suggest that the minimal functional units in genomes are alternative transcripts as opposed to genes.

Convergent evolution of hemoglobin switching in jawed and jawless vertebrates

Background

During development, humans and other jawed vertebrates (Gnathostomata) express distinct hemoglobin genes, resulting in different hemoglobin tetramers. Embryonic and fetal hemoglobin have higher oxygen affinities than the adult hemoglobin, sustaining the oxygen demand of the developing organism. Little is known about the expression of hemoglobins during development of jawless vertebrates (Agnatha).

Results

We identified three hemoglobin switches in the life cycle of the sea lamprey. Three hemoglobin genes are specifically expressed in the embryo, four genes in the filter feeding larva (ammocoete), and nine genes correspond to the adult hemoglobin chains. During the development from the parasitic to the reproductive adult, the composition of hemoglobin changes again, with a massive increase of chain aHb1. A single hemoglobin chain is expressed constitutively in all stages. We further showed the differential expression of other globin genes: Myoglobin 1 is most highly expressed in the reproductive adult, myoglobin 2 expression peaks in the larva. Globin X1 is restricted to the embryo; globin X2 was only found in the reproductive adult. Cytoglobin is expressed at low levels throughout the life cycle.

Conclusion

Because the hemoglobins of jawed and jawless vertebrates evolved independently from a common globin ancestor, hemoglobin switching must also have evolved convergently in these taxa. Notably, the ontogeny of sea lamprey hemoglobins essentially recapitulates their phylogeny, with the embryonic hemoglobins emerging first, followed by the evolution of larval and adult hemoglobins.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0597-0) contains supplementary material, which is available to authorized users.

Developmental regulation of hemoglobin synthesis in the green anole lizard Anolis carolinensis

Tetrapod vertebrates possess multiple α- and β-like globin genes that are ontogenetically regulated, such that functionally distinct hemoglobin (Hb) isoforms are synthesized during different stages of development. The α- and β-like globin genes of amphibians, birds and mammals are differentially expressed during embryonic development and postnatal life, but little is known about the developmental regulation of globin gene expression in non-avian reptiles. Here we report an investigation into the developmental regulation of Hb synthesis in the green anole lizard Anolis carolinensis. We tested two hypotheses derived from comparative genomic studies of the globin gene clusters in tetrapod vertebrates. First, we tested whether the product of the Anolis α(D)-globin gene is incorporated into embryonic Hb, thereby performing the role that would normally be performed by the embyronic α(E)-globin gene (which has been deleted from the green anole genome). Second, we tested whether two 'lizard-specific' β-globin paralogs have independently evolved a division of labor between an early-expressed embryonic gene and a later-expressed adult gene. Results of a proteomic analysis revealed that α- and β-like globin genes of the anole are differentially expressed during embryonic development. However, the same repertoire of α- and β-chain Hb isoforms was expressed during all stages of development and postnatal life, and the ontogenetic shifts in isoform composition were relatively subtle. In contrast to the pattern that has been documented in other tetrapod vertebrates, it appears that the developmental regulation of Hb synthesis in the green anole lizard does not involve discrete, stage-specific switches in gene activation and gene silencing.

Lineage-specific patterns of functional diversification in the alpha- and beta-globin gene families of tetrapod vertebrates

The alpha- and beta-globin gene families of jawed vertebrates have diversified with respect to both gene function and the developmental timing of gene expression. Phylogenetic reconstructions of globin gene family evolution have provided suggestive evidence that the developmental regulation of hemoglobin synthesis has evolved independently in multiple vertebrate lineages. For example, the embryonic beta-like globin genes of birds and placental mammals are not 1:1 orthologs. Despite the similarity in developmental expression profiles, the genes are independently derived from lineage-specific duplications of a beta-globin pro-ortholog. This suggests the possibility that other vertebrate taxa may also possess distinct repertoires of globin genes that were produced by repeated rounds of lineage-specific gene duplication and divergence. Until recently, investigations into this possibility have been hindered by the dearth of genomic sequence data from nonmammalian vertebrates. Here, we report new insights into globin gene family evolution that were provided by a phylogenetic analysis of vertebrate globins combined with a comparative genomic analysis of three key sauropsid taxa: a squamate reptile (anole lizard, Anolis carolinensis), a passeriform bird (zebra finch, Taeniopygia guttata), and a galliform bird (chicken, Gallus gallus). The main objectives of this study were 1) to characterize evolutionary changes in the size and membership composition of the alpha- and beta-globin gene families of tetrapod vertebrates and 2) to test whether functional diversification of the globin gene clusters occurred independently in different tetrapod lineages. Results of our comparative genomic analysis revealed several intriguing patterns of gene turnover in the globin gene clusters of different taxa. Lineage-specific differences in gene content were especially pronounced in the beta-globin gene family, as phylogenetic reconstructions revealed that amphibians, lepidosaurs (as represented by anole lizard), archosaurs (as represented by zebra finch and chicken), and mammals each possess a distinct independently derived repertoire of beta-like globin genes. In contrast to the ancient functional diversification of the alpha-globin gene cluster in the stem lineage of tetrapods, the physiological division of labor between early- and late-expressed genes in the beta-globin gene cluster appears to have evolved independently in several tetrapod lineages.

The amphibian globin gene repertoire as revealed by the Xenopus genome

The draft genome sequence of the Western clawed frog Xenopus (Silurana) tropicalis facilitates the identification, expression analysis and phylogenetic classification of the amphibian globin gene repertoire. Frog and mammalian neuroglobin display about 67% protein sequence identity, with the expected predominant expression in frog brain and eye. Frog and mammalian cytoglobins share about 69% of their amino acids, but the frog protein lacks the mammalian-type extension at the C-terminus. Like in mammals, X. tropicalis cytoglobin is expressed in many organs including neural tissue. Neuroglobin and cytoglobin genomic regions are syntenically conserved in all vertebrate classes. Frog and fish globin X show only 57% amino acid identity, but gene synteny analysis confirms orthology. The expression pattern of X. laevis globin X differs from that in fish, with a prominent expression in the eye and weak expression in most other examined tissues. Globin X is possibly present as two paralogous copies in X. tropicalis, with one copy showing transition stages of non-functionalization. The amphibian genome contains a previously unknown globin type (tentatively named 'globin Y') which is expressed in a broad range of tissues and is distantly related to the cytoglobin lineage. The globin Y gene is linked to a cluster of larval and adult hemoglobin alpha and beta genes which contains substantially more paralogous hemoglobin gene copies than previously published. Database and gene synteny analyses confirm the absence of a myoglobin gene in X. tropicalis.

Distinctive gene profiles occur at key points during natural metamorphosis in the Xenopus laevis tadpole tail

Thyroid hormones (THs) are essential for tadpole metamorphosis into a juvenile frog; however, a complex interplay between additional hormones and signaling events also contributes to this dramatic developmental phase. A major mechanism of TH action is the nuclear receptor-mediated regulation of gene transcription of responsive genes. By using the precocious metamorphic model, several genes have been identified as TH responsive in the regressing tail. Many of these genes also exhibit altered expression during natural metamorphosis. Although identification of these genes provides insight into the mechanism whereby TH acts, complex interplay between TH and other hormones and the developmental stage-dependency of tissue responses contribute to the timing and coordination of metamorphic events. We investigated the temporal gene expression profile in Xenopus laevis tadpole tails from premetamorphosis through metamorphic climax by using a combination of a novel frog cDNA array containing 420 genes and quantitative real-time PCR. Seventy-nine genes were identified whose steady-state mRNA expression levels were altered in the tadpole tail during natural metamorphosis, of which 34 have previously been identified to be TH responsive in frogs or mammals. Of these genes, 75 clustered into 13 groups that displayed distinct developmental expression profiles. The levels of 28 transcripts were altered during premetamorphosis, 31 during prometamorphosis, and 43 with the onset of tail regression. This work establishes an important baseline for determining the mechanisms whereby tissues undergo differing metamorphic fates.

Humoral regulation of hemoglobin transition from larval to adult types in a salamander, Hynobius retardatus

In amphibians hemoglobin (Hb) transition from larval to adult types occurs during metamorphosis. Hemoglobin transition in the salamander Hynobius retardatus also occurs during metamorphosis, but depends on activity of the pituitary gland, rather than that of the thyroid gland. These findings were supported by the fact that the transplanted pituitary gland to hypophysectomized (Hx) larvae exerted accelerating effects on Hb transition. Contrary to this, a homogenate of the pituitary gland from Xenopus laevis had no accelerating effect on Hb transition when injected into Hx larvae of H. retardatus. Whereas exogeneously applied triiodothyronine (T3) or a combination of T3 and hydrocortisone had an accelerating effect on Hb transition in the Hx larvae, a single treatment with hydrocortisone in the Hx larvae had no effect. When an inhibitor of synthesis of adrenocortico-steroid hormones, metyrapone, was applied in combination with goitrogens to intact larvae, Hb transition from larval to adult types was suppressed compared with normal controls, suggesting that the thyroid-corticoid system is involved in Hb transition. These results suggest that Hb transition in H. retardatus is controlled by two independent accelerating factors, from both the pituitary gland and the thyroid-corticoid system. These control mechanisms are different from the general regulation of metamorphosis that occurs in many amphibians. A tentative model of hormonal controls in Hb transition from larval to adult types during the metamorphosis in H. retardatus is presented.

Over-expression of GATA-6 in Xenopus embryos blocks differentiation of heart precursors

Xenopus GATA-6 transcripts are first detected at the beginning of gastrulation in the mesoderm, and subsequent domains of expression include the field of cells shown to have heart-forming potential. In this region, GATA-6 expression continues only in those cells that go on to form the heart; however, a decrease occurs prior to terminal differentiation. Artificial elevation of GATA-6, but not GATA-1, prevents expression of both cardiac actin and heart-specific myosin light chain. This effect is heart-specific because cardiac actin expression is unaffected in somites. Expression of the earlier marker XNkx-2.5 was unaffected and morphological development of the heart was initiated independently of the establishment of the contractile machinery. We conclude that a reduction in the level of GATA-6 is important for the progression of the cardiomyogenic differentiation programme and that GATA-6 may act to maintain heart cells in the precursor state. At later stages, when the elevated GATA-6 levels had decayed, differentiation ensued but the number of cells contributing to the myocardium had increased, suggesting either that the blocked cells had proliferated or that additional cells had been recruited.

Heterochrony and neotenic salamanders: possible clues for understanding the animal development and evolution

A synthesis of developmental genetics with evolutionary genetics is now making possible to understand significant evolutionary changes in multicellular organisms. The key concept for unifying the two must be heterochrony. Heterochrony causes evolutionary modifications due to changes in timing and/or rate of development. The heterochrony is conventionally categorized into three patterns as neoteny (retardation in somatic development), progenesis (acceleration in gonadal development), and direct development (acceleration in somatic development, resulting in lack of larval or tadpole stages). A lot of species showing neoteny are known in urodeles, but not in anurans. Neotenic urodeles are also divided into three categories; permanent or obligate, "inducible" obligate and facultative neotenies. Hynobius retardatus, a specific population of which had been reported to show neoteny but is believed to be extinct at present, has become to be used for experimental analysis of heterochronic expression of several adult characters during its ontogeny. Gonadal maturation and a transition of globin subunits from larval to adult types have been shown to occur independently on the morphological metamorphosis in H. retardatus. Mechanisms underlying the heterochrony, including morphogenetic clock, heterochronic genes in Drosophila and C. elegans, temporal colinearity in Hox gene complex in mice, and atavistic transformation induced by altered expression of Hox genes are discussed in terms of current molecular biology.

Expression of GATA-binding proteins during embryonic development in Xenopus laevis

Proteins that recognize the core sequence GATA are important regulators of hematopoietic-specific gene transcription. We have characterized cDNAs encoding the Xenopus laevis homologues of three related transcription factors, designated GATA-1, -2, and -3. Comparative sequence analysis reveals strong conservation of the zinc-finger DNA-binding domain among all vertebrate GATA-binding proteins. GATA-2 and GATA-3 polypeptides are homologous throughout their entire sequences, whereas GATA-1 sequence is conserved only in the region responsible for DNA binding. In Xenopus, RNAs encoding GATA-binding proteins are expressed in both larval and adult erythroid cells. GATA-1, -2, and -3 RNAs are first detectable in early gastrula (Nieuwkoop developmental stage 11). This is earlier than the appearance of the early larval alpha T1 globin RNA (stage 15), beta T1 globin RNA (stage 26), or blood island formation (stage 30). The expression of GATA-1, -2, and -3 in early development may signal an early commitment of mesoderm to form hematopoietic tissue.

Expression of adult and tadpole specific globin genes from Xenopus laevis in transgenic mice

Transgenic mice were generated which carried the adult alpha and beta-globin genes and the major tadpole specific beta-globin gene of Xenopus laevis. The adult specific alpha and beta genes were found to express in erythroid tissues in adult mice, while the major tadpole specific beta gene (beta T1) was expressed in blood from 12.5 day embryos. The pattern of expression of the beta T1 gene during mouse development was consistent with its being regulated as an embryonic globin gene in the mouse. This observation suggests that some of the factors mediating globin switching have been conserved during the evolution of modern amphibia and mammals and raises interesting questions concerning the evolution of vertebrate globin gene switching.

Sequence analysis of the upstream regions of Xenopus laevis beta-globin genes and arrangement of repetitive elements within the globin gene clusters

The globin gene clusters of Xenopus laevis are interspersed by various different repetitive DNA elements. A specific repeat, the JH12 element, has been mapped by Southern analysis and some of its locations have been subsequently confirmed by nucleotide sequencing. JH12 family members seem to represent mobile genetic elements and display a high degree of divergence. The nucleotide sequences upstream to the adult beta I-globin gene and to the two coordinately expressed larval beta I- and beta II-globin genes have been determined and compared to those of the adult alpha-genes. Besides some repetitive DNA elements and a short sequence of rather weak homology we have found no characteristic sequence motifs to be common to the adult alpha- and beta-genes. The two larval beta-genes share one short sequence element being absent from the adult genes. This might reflect completely different sequence requirements for protein interactions and for the regulation of adult and larval globin gene expression.

Transient activation of oocyte 5S RNA genes in Xenopus embryos by raising the level of the trans-acting factor TFIIIA

The concentration of the trans-acting factor, TFIIIA, required for the activation of 5S RNA genes in Xenopus can be elevated in developing embryos by injecting a synthetic full-length mRNA into fertilized eggs. 5S RNA genes are activated by the increased factor concentration at the mid-blastula transition through mid-gastrulation. The activated oocyte 5S RNA genes are then inactivated, leaving the TFIIIA-enhanced embryos with the same profile of differential 5S RNA gene activity as control embryos, i.e., synthesizing mainly somatic 5S RNA. Inactivation of the oocyte 5S RNA genes is complete by neurulation and can occur in the absence of DNA replication. We propose that this loss of gene activity is due at least in part to destabilization of transcription complexes that are associated with oocyte 5S RNA genes.

Sequence analysis of the larval beta II-globin gene of Xenopus laevis

The 1822 bp sequence of the larval Xenopus laevis beta II-globin gene is reported together with 240 bp upstream of the gene and 190 bp beyond the site of polyadenylation. The mRNA start point was determined by primer extension as well as nuclease S1 mapping and the polyadenylation site by comparison of the gene sequence to the mRNA sequence derived from a corresponding cDNA clone. Like other vertebrate globin genes, this gene comprises three exons interrupted by two intervening sequences (IVS). IVS I spans over 582 nucleotides and interrupts the exon sequences within codon 30. IVS II is located between the codons 104/105 and spans over 617 nucleotides. The 5' region of the gene contains the canonical TATAA homology at position -31. Comparison of the upstream sequence to that of Xenopus laevis larval beta I-globin gene revealed a conserved sequence, located between nucleotide positions -60 and -87, which might function as regulatory element of transcription. Whereas the upstream region of the larval beta II-globin gene does not contain a CAAT box, we notice a reiterated AAATGA motif and discuss its possible significance.