DNA content in the genus Xenopus

The power of amphibians to elucidate mechanisms of size control and scaling

Size is a fundamental feature of biology that affects physiology at all levels, from the organism to organs and tissues to cells and subcellular structures. How size is determined at these different levels, and how biological structures scale to fit together and function properly are important open questions. Historically, amphibian systems have been extremely valuable to describe scaling phenomena, as they occupy some of the extremes in biological size and are amenable to manipulations that alter genome and cell size. More recently, the application of biochemical, biophysical, and embryological techniques to amphibians has provided insight into the molecular mechanisms underlying scaling of subcellular structures to cell size, as well as how perturbation of normal size scaling impacts other aspects of cell and organism physiology.

Similar Ratios of Introns to Intergenic Sequence across Animal Genomes

One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.

Heart regeneration in adult Xenopus tropicalis after apical resection

Background

Myocardium regeneration in adult mammals is very limited, but has enormous therapeutic potentials. However, we are far from complete understanding the cellular and molecular mechanisms by which heart tissue can regenerate. The full functional ability of amphibians to regenerate makes them powerful animal models for elucidating how damaged mature organs are naturally reconstituted in an adult organism. Like other amphibians, such as newts and axolotls, adult Xenopus displays high regenerative capacity such as retina. So far, whether the adult frog heart processes regenerative capacity after injury has not been well delineated.

Results

We examined the regeneration of adult cardiac tissues of Xenopus tropicalis after resection of heart apex. We showed, for the first time, that the adult X. tropicalis heart can regenerate perfectly in a nearly scar-free manner approximately 30 days after injury via apical resection. We observed that the injured heart was sealed through coagulation immediately after resection, which was followed by transient fibrous tissue production. Finally, the amputated area was regenerated by cardiomyocytes. During the regeneration process, the cardiomyocytes in the border area of the myocardium adjacent to the wound exhibited high proliferation after injury, thus contribute the newly formed heart tissue.

Conclusions

Establishing a cardiac regeneration model in adult X. tropicalis provides a powerful tool for recapitulating a perfect regeneration phenomenon and elucidating the underlying molecular mechanisms of cardiac regeneration in an adult heart, and findings from this model may be applicable in mammals.

Electronic supplementary material

The online version of this article (10.1186/s13578-017-0199-6) contains supplementary material, which is available to authorized users.

Basal bodies in Xenopus

Xenopus has been one of the earliest and most important vertebrate model organisms for investigating the role and structure of basal bodies. Early transmission electron microscopy studies in Xenopus revealed the fine structures of Xenopus basal bodies and their accessory structures. Subsequent investigations using multiciliated cells in the Xenopus epidermis have further revealed many important features regarding the transcriptional regulation of basal body amplification as well as the regulation of basal body/cilia polarity. Future basal body research using Xenopus is expected to focus on the application of modern genome editing techniques (CRISPR/TALEN) to characterize the components of basal body proteins and their molecular functions.

Identification and characterization of cryptochrome4 in the ovary of western clawed frog Xenopus tropicalis

CRY proteins can be classified into several groups based on their phylogenetic relationships, and they function as a photoreceptor, a photolyase, and/or a transcriptional repressor of the circadian clock. In order to elucidate the expression profile and functional diversity of CRYs in vertebrates, we focused on XtCRY4, a member of the uncharacterized cryptochrome family CRY4 in Xenopus tropicalis. XtCRY4 cDNA was isolated by RT-PCR, and a phylogenetic analysis of deduced sequence of XtCRY4 suggested that the vertebrate Cry4 genes evolved at much higher evolutionary rates than mammalian-type Cry genes, such as the CRY1 and CRY2 circadian clock molecules. A transcriptional assay was performed to examine the transcriptional regulatory function as circadian repressor, and XtCRY4 had marginal effects on the transactivation of XtCLOCK/XtBMAL1 via E-box element. In situ hybridization and quantitative RT-PCR was performed to detect mRNA expression in native tissues. Quantitative RT-PCR revealed that XtCry4 mRNA was highly transcribed in the ovary. In situ hybridization showed the presence of XtCry4 transcripts in the oocytes, testis, renal tubules, the visual photoreceptors, and the retinal ganglion cells. A specific antiserum to XtCRY4 was developed to detect endogeneous expression of XtCRY4 protein in the ovary. The expression level was estimated by immunoblot analysis, and this is the first detection and estimation of endogenous expression of CRY protein in the ovary. These results suggest that X. tropicalis ovary may respond to blue-light by using XtCRY4.

Spindle assembly on immobilized chromatin micropatterns

We describe a method to assemble meiotic spindles on immobilized micropatterns of chromatin built on a first layer of biotinylated BSA deposited by microcontact printing. Such chromatin patterns routinely produce bipolar spindles with a yield of 60%, and offer the possibility to follow spindle assembly dynamics, from the onset of nucleation to the establishment of a quasi steady state. Hundreds of spindles can be recorded in parallel for different experimental conditions. We also describe the semi-automated image analysis pipeline, which is used to analyze the assembly kinetics of spindle arrays, or the final morphological diversity of the spindles.

Xenopus tropicalis: an ideal experimental animal in amphibia

Studies using amphibians have contributed to the progress of life science including developmental biology and cell biology for more than one hundred years. Since the 1950s Xenopus laevis in particular has been used by scientists in many fields for experiments, resulting in the development of various techniques such as microsurgery on early embryos, biosynthesis of gene-encoded protein in oocytes by mRNA injection, misexpression experiments by mRNA injection into embryos, gene knockdown studies by injection of morpholino anti-sense oligonucleotide into fertilized eggs, transgenesis by the I-SceI meganuclease method, and so on. In this paper we will introduce Xenopus tropicalis as an alternative experimental animal. It has a shorter generation time and smaller diploid genome, together with whole-genome sequence data. The procedures available for Xenopus laevis can work well with Xenopus tropicalis, and embryos of both species develop at similar rates according to the developmental staging system of Nieuwkoop and Faber. Experimental systems of Xenopus tropicalis will pave the way for a new era of vertebrate genomics and genetics.

Control of DNA replication by anomalous reaction-diffusion kinetics

We propose a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions. Analyzing recent data from Xenopus frog embryos, we find that the initiation rate is reaction limited until nearly the end of replication, when it becomes diffusion limited. Initiation of origins is suppressed when the diffusion-limited search time dominates. To fit the experimental data, we find that the interaction between DNA and the rate-limiting protein must be subdiffusive.

How Xenopus laevis embryos replicate reliably: investigating the random-completion problem

DNA synthesis in Xenopus frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the time to complete and may lead to cell death if replication takes longer than the cell cycle time ( approximately 25 min) . Surprisingly, although the typical replication time is about 20 min , in vivo experiments show that replication fails to complete only about 1 in 300 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two solutions to this "random-completion problem." The first solution uses randomly located origins but increases their rate of initiation as S phase proceeds, while the second uses regularly spaced origins. In this paper, we investigate the random-completion problem using a type of model first developed to describe the kinetics of first-order phase transitions. Using methods from the field of extreme-value statistics, we derive the distribution of replication-completion times for a finite genome. We then argue that the biologists' first solution to the problem is not only consistent with experiment but also nearly optimizes the use of replicative proteins. We also show that spatial regularity in origin placement does not alter significantly the distribution of replication times and, thus, is not needed for the control of replication timing.

Development of metamorphosis assay using Silurana tropicalis for the detection of thyroid system-disrupting chemicals

The West African clawed frog (Silurana tropicalis), which resembles the South African clawed frog (Xenopus laevis), but is somewhat smaller, has a diploid genome and a shorter generation time. Therefore, S. tropicalis has the potential for use as a new model in ecotoxicology. We demonstrated a S. tropicalis metamorphosis assay based on Xenopus Metamorphosis Assay (XEMA) using 1 microg/L thyroxine (T4) and 75 mg/L propylthiouracil (PTU). Tadpoles at developmental stages 48-50 were exposed to chemicals for 28 days and total body length, developmental stage, and hind limb length were recorded every 7 days. Significant differences in developmental stage and total body length were found for both T4 and PTU after 7-day exposure, which were similar to the results of the XEMA ring-test using the same chemicals. Moreover, in the present study, we measured hind limb length as a new endpoint of thyroid axis. Significant differences in the hind limb length were encountered in both T4 and PTU treatments after 7 days of exposure. These results suggest that S. tropicalis can be used in a XEMA-like protocol to detect agonist and antagonist effects of chemicals on the thyroid system. Hind limb length is also a suitable endpoint in such protocols. A new test protocol detecting both thyroid disruption and reproductive effects of chemicals using S. tropicalis should be established in the near future.

A selective block of nuclear actin export stabilizes the giant nuclei of Xenopus oocytes

Actin is a major cytoskeletal element and is normally kept cytoplasmic by exportin 6 (Exp6)-driven nuclear export. Here, we show that Exp6 recognizes actin features that are conserved from yeast to human. Surprisingly however, microinjected actin was not exported from Xenopus laevis oocyte nuclei, unless Exp6 was co-injected, indicating that the pathway is inactive in this cell type. Indeed, Exp6 is undetectable in oocytes, but is synthesized from meiotic maturation onwards, which explains how actin export resumes later in embryogenesis. Exp6 thus represents the first example of a strictly developmentally regulated nuclear transport pathway. We asked why Xenopus oocytes lack Exp6 and observed that ectopic application of Exp6 renders the giant oocyte nuclei extremely fragile. This effect correlates with the selective disappearance of a sponge-like intranuclear scaffold of F-actin. These nuclei have a normal G2-phase DNA content in a volume 100,000 times larger than nuclei of somatic cells. Apparently, their mechanical integrity cannot be maintained by chromatin and the associated nuclear matrix, but instead requires an intranuclear actin-scaffold.

A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution

The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent rainforest refugia probably acted as "lifeboats" that preserved existing species, rather than "species pumps" where many new successful lineages originated. We estimate that polyploidization occurred at least six times in clawed frogs.

Xenopus, the next generation: X. tropicalis genetics and genomics

A small, fast-breeding, diploid relative of the frog Xenopus laevis, Xenopus tropicalis, has recently been adopted for research in developmental genetics and functional genomics. X. tropicalis shares advantages of X. laevis as a classic embryologic system, but its simpler genome and shorter generation time make it more convenient for multigenerational genetic, genomic, and transgenic approaches. Its embryos closely resemble those of X. laevis, except for their smaller size, and assays and molecular probes developed in X. laevis can be readily adapted for use in X. tropicalis. Genomic manipulation techniques such as gynogenesis facilitate genetic screens, because they permit the identification of recessive phenotypes after only one generation. Stable transgenic lines can be used both as in vivo reporters to streamline a variety of embryologic and molecular assays, or to experimentally manipulate gene expression through the use of binary constructs such as the GAL4/UAS system. Several mutations have been identified in wild-caught animals and during the course of generating inbred lines. A variety of strategies are discussed for conducting and managing genetic screens, obtaining mutations in specific sequences, achieving homologous recombination, and in developing and taking advantage of the genomic resources for Xenopus tropicalis.

Analyzing gene regulation in ascidian embryos: new tools for new perspectives

Ascidians are marine protochordates at the evolutionary boundary between invertebrates and vertebrates. Ascidian larvae provide a simple system for unraveling gene regulation networks underlying the formation of the basic chordate body plan. After being used for over a century as a model for embryological studies, ascidians have become, in the past decade, an increasingly popular organism for studying gene regulation. Part of the renewed appeal of this system is the use of electroporation to introduce transgenic DNAs into developing embryos. This method is considerably more efficient than conventional microinjection assays and permits the simultaneous transformation of hundreds of embryos. Electroporation has allowed the identification and characterization of cis-regulatory DNAs that mediate gene expression in a variety of tissues, including the notochord, tail muscles, CNS, and endoderm. Electroporation has also provided a simple method for misexpressing patterning genes and producing dominant mutant phenotypes. Recent studies have used electroporation to create "knock-out" phenotypes by overexpressing dominant negative forms of particular proteins. Here we review the past and present uses of electroporation in ascidian development, and speculate on potential future uses.

The NIEHS Xenopus maternal EST project: interim analysis of the first 13,879 ESTs from unfertilized eggs

The sequencing of expressed sequence tags (ESTs) from Xenopus laevis has lagged behind efforts on many other common experimental organisms and man, partly because of the pseudotetraploid nature of the Xenopus genome. Nonetheless, large collections of Xenopus ESTs would be useful in gene discovery, oligonucleotide-based knockout studies, gene chip analyses of normal and perturbed development, mapping studies in the related diploid frog X. tropicalis, and for other reasons. We have created a normalized library of cDNAs from unfertilized Xenopus eggs. These cells contain all of the information necessary for the first several cell divisions in the early embryo, as well as much of the information needed for embryonic pattern formation and cell fate determination. To date, we have successfully sequenced 13,879 ESTs out of 16,607 attempts (83.6% success rate), with an average sequence read length of 508 bp. Using a fragment assembly program, these ESTs were assembled into 8,985 'contigs' comprised of up to 11 ESTs each. When these contigs were used to search publicly available databases, 46.2% bore no relationship to protein or DNA sequences in the database at the significance level of 1e-6. Examination of a sample of 100 of the assembled contigs revealed that most ( approximately 87%) were comprised of two apparent allelic variants. Expression profiles of 16 of the most prominent contigs showed that 12 exhibited some degree of zygotic expression. These findings have implications for sequence-specific applications for Xenopus ESTs, particularly the use of allele-specific oligonucleotides for knockout studies, differential hybridization techniques such as gene chip analysis, and the establishment of accurate nomenclature and databases for this species.

Evolution of structure, ontogeny of gene expression, and function of Xenopus laevis transthyretin

Xenopus laevis transthyretin (xTTR) cDNA was cloned and sequenced. The derived amino acid sequence was very similar to those of other vertebrate transthyretins (TTR). TTR gene expression was observed during metamorphosis in X. laevis tadpole liver but not in tadpole brain nor adult liver. Recombinant xTTR was synthesized in Pichia pastoris and identified by amino acid sequence, subunit molecular mass, tetramer formation, and binding to retinol-binding protein. Contrary to mammalian xTTRs, the affinity of xTTR was higher for L-triiodothyronine than for L-thyroxine. The regions of the TTR genes coding for the NH(2)-terminal sections of the polypeptide chains of TTR seem to have evolved by stepwise shifts of mRNA splicing sites between exons 1 and 2, resulting in shorter and more hydrophilic NH(2) termini. This may be one molecular mechanism of positive Darwinian evolution. Open reading frames with xTTR-like sequences in the genomes of C. elegans and several microorganisms suggested evolution of the TTR gene from ancestor TTR gene-like "DNA modules." Increasing preference for binding of L-thyroxine over L-triiodothyronine may be associated with evolving tissue-specific regulation of thyroid hormone action by deiodination.

Isolation of Xenopus frizzled-10A and frizzled-10B genomic clones and their expression in adult tissues and embryos

Frizzled genes, encoding WNT receptors, play key roles in cell fate determination. Here, we isolated two Xenopus frizzled genes (Xfz10A and Xfz10B), probably reflecting pseudotetraploidy in Xenopus. Xfz10A (586 amino acids) and Xfz10B (580 amino acids) both encoded by a single exon, consisted of the N-terminal cysteine-rich domain, seven transmembrane domains, and the C-terminal Ser/Thr-X-Val motif. Xfz10A and Xfz10B were 97.0% identical at the amino acid level, and Xfz10B was 100% identical to previously reported Xfz9, yet Xfz10A was 85.3% and 62.4% identical to FZD10 and FZD9, respectively. Xfz10 mRNA appeared as 3.4 kb in adult tissues and embryos. RT-PCR analyses revealed the expression of more Xfz10A mRNA in stomach, kidney, eye, skeletal muscle, and skin, and more Xfz10B mRNA in heart and ovary, but in embryos, two mRNAs were equally expressed from the blastula stage with their peak expression at the late gastrula stage. The main site of Xfz10 mRNA expression was neural fold at the neurula stage and the dorsal region of midbrain, hindbrain, and spinal cord at the tadpole stage. These results suggest that Xfz10 has important roles in neural tissue formation.

Cloning and characterization of mRNA capping enzyme and mRNA (Guanine-7-)-methyltransferase cDNAs from Xenopus laevis

The mRNA cap structure, which is synthesized by a series of reactions catalyzed by capping enzyme, mRNA (guanine-7-)-methyltransferase, and mRNA (ribose-2'-O-)-methyltransferase, has crucial roles for RNA processing and translation. Methylation of the cap structure is also implicated in polyadenylation-mediated translational activation during Xenopus oocyte maturation. Here we isolated two Xenopus laevis cDNAs, xCAP1a and xCAP1b, for mRNA capping enzyme and one cDNA for mRNA (guanine-7-)-methyltransferase, xCMT1, which encode 598, 511, and 402 amino acids, respectively. The deduced amino acid sequence of xCAP1a was highly homologous to that of human capping enzyme hCAP1a, having all the characteristic regions including N-terminal RNA 5'-triphosphatase as well as C-terminal mRNA guanylyltransferase domains which are conserved among animal mRNA guanylyltransferases, whereas in xCAP1b the most C-terminal motif was missing. The amino acid sequence of xCMT1 was also similar to human (guanine-7-)-methyltransferase, hCMT1a, with all the conserved motifs among cellular (guanine-7-)-methyltransferases, except for its N-terminal portion. The recombinant xCAP1a and xCMT1 exhibited cap formation and mRNA (guanine-7-)-methyltransferase activities, respectively. RT-PCR analysis showed that mRNA for xCAP1a and xCMT1 exist abundantly in fertilized eggs as maternal mRNAs, but xCMT1 mRNA gradually decreased in its amount in later stages of early development.

Structure of the Xenopus laevis TFF-gene xP4.1, differentially expressed to its duplicated homolog xP4.2

TFF-peptides (formerly P-domain peptides, trefoil factors) represent major secretory products of mucous epithelia in mammals and amphibia. The nucleotide sequence of a large portion of a gene encoding the TFF-peptide xP4.1 from Xenopus laevis and its genomic organization were determined in the present study. The peptide xP4.1 containing four TFF-domains is thought to represent the functional frog homolog of human TFF2 (formerly hSP). The xP4.1 gene analyzed spans a region of about 7 kb and consists of six exons. Each TFF-domain is encoded by a single exon flanked by type 1 introns typical of shuffled modules. The 5'-upstream region contains a TATA-box, and potential binding sites for hepatocyte nuclear factor 3 and AP-1. Furthermore, the cDNA sequence of a transcript named xP4.2 with 91% similarity to xP4.1 is presented. RT-PCR analysis revealed that xP4.1 and xP4.2 genes are differentially expressed. xP4.1 transcripts are detectable only in the stomach, but not in the esophagus, whereas xP4.2 transcripts are found both in the esophagus and in the stomach with a descending gradient from fundus to antrum.

Background adaptation by Xenopus laevis: a model for studying neuronal information processing in the pituitary pars intermedia

This review is concerned with recent literature on the neural control of the pituitary pars intermedia of the amphibian Xenopus laevis. This aquatic toad adapts skin colour to the light intensity of its environment, by releasing the proopiomelanocortin (POMC)-derived peptide alpha-MSH (alpha-melanophore-stimulating hormone) from melanotrope cells. The activity of these cells is controlled by brain centers of which the hypothalamic suprachiasmatic and magnocellular nuclei, respectively, inhibit and stimulate both biosynthesis and release of alpha-MSH. The suprachiasmatic nucleus secretes dopamine, GABA, and NPY from synaptic terminals on the melanotropes. The structure of the synapses depends on the adaptation state of the animal. The inhibitory transmitters act via cAMP. Under inhibition conditions, melanotropes actively export cAMP, which might have a first messenger action. The magnocellular nucleus produces CRH and TRH. CRH, acting via cAMP, and TRH stimulate POMC-biosynthesis and POMC-peptide release. ACh is produced by the melanotrope cell and acts in an autoexcitatory feedback on melanotrope M1 muscarinic receptors to activate secretory activity. POMC-peptide secretion is driven by oscillations of the [Ca2+]i, which are initiated by receptor-mediated stimulation of Ca2+ influx via N-type calcium channels. The hypothalamic neurotransmitters and ACh control Ca2+ oscillatory activity. The structural and functional aspects of the various neural and endocrine steps in the regulation of skin colour adaptation by Xenopus reveal a high degree of plasticity, enabling the animal to respond optimally to the external demands for physiological adaptation.

Intronic U14 snoRNAs of Xenopus laevis are located in two different parent genes and can be processed from their introns during early oogenesis

U14 is a member of the rapidly growing family of intronic small nucleolar RNAs (snoRNAs) that are involved in pre-rRNA processing and ribosome biogenesis. These snoRNA species are encoded within introns of eukaryotic protein coding genes and are synthesized via an intron processing pathway. Characterization of Xenopus laevis U14 snoRNA genes has revealed that in addition to the anticipated location of U14 within introns of the amphibian hsc70 gene (introns 4, 5 and 7), additional intronic U14 snoRNAs are also found in the ribosomal protein S13 gene (introns 3 and 4). U14 is thus far a unique intronic snoRNA in that it is encoded within two different parent genes of a single organism. Northern blot analysis revealed that U14 snoRNAs accumulate during early oocyte development and are rapidly expressed after the mid-blastula transition of developing embryos. Microinjection of hsc70 pre-mRNAs into developing oocytes demonstrated that oocytes as early as stages II and III are capable of processing U14 snoRNA from the pre-mRNA precursor. The ability of immature oocytes to process intronic snoRNAs is consistent with the observed accumulation of U14 during oocyte maturation and the developmentally regulated synthesis of rRNA during oogenesis.

Translocon-associated protein TRAP delta and a novel TRAP-like protein are coordinately expressed with pro-opiomelanocortin in Xenopus intermediate pituitary

In the intermediate pituitary gland of Xenopus laevis, the expression levels of the prohormone pro-opiomelanocortin (POMC) can be readily manipulated. When the animal is placed on a black background, the gene for POMC is actively transcribed, whereas on a white background the gene is virtually inactive. In this study, we characterized two genes whose transcript levels in the intermediate pituitary are regulated in coordination with that for POMC. One of these codes for a protein homologous to translocon-associated protein TRAP delta, a subunit of a transmembrane protein complex located at the site where nascent secretory proteins enter the endoplasmic reticulum (ER). Both Xenopus and mice were found to express an alternatively spliced transcript that gives rise to a previously unknown version of the TRAP delta protein. The product of the second gene is a novel and highly conserved protein with structural similarity to glycoprotein gp25L, a constituent of another translocon-associated protein complex. A database search revealed the existence of a novel family of gp25L-related proteins whose members occur throughout the animal kingdom. Together, our data imply that (i) the group of ER proteins surrounding translocating polypeptide chains may be far more complex than previously expected, and (ii) a number of the accessory components of the translocon participate in early steps of prohormone biosynthesis.

Exon-intron organization of Xenopus MHC class II beta chain genes

The amphibian Xenopus laevis is the most primitive vertebrate in which the major histocompatibility complex (MHC) has been defined at the biochemical, functional, and molecular genetic levels. We previously described the isolation and characterization of cDNA clones encoding X. laevis MHC class II beta chains. In the present study, genomic clones encoding class II beta chains were isolated from X. laevis homozygous for the MHC f haplotype. Three class II beta chain genes, designated Xela-DAB, Xela-DBB, and Xela-DCB, were identified. Sequence analysis of these genes showed that Xela-DBB and Xela-DCB correspond to the previously characterized cDNA clones F3 and F8, respectively, whereas Xela-DAB encodes a third, hitherto unidentified class II beta chain of the MHC f haplotype. As a representative of X. laevis class II beta chain genes, the Xela-DAB gene underwent detailed structural analysis. In addition, the nucleotide sequence of Xela-DABf cDNA clones was determined. The Xela-DAB gene is made up of at least six exons, with an exon-intron organization similar to that of a typical mammalian class II beta chain gene. The 5'-flanking region of the Xela-DAB gene contains transcriptional control elements known as X1, X2, and Y, but lacks typical TATA or CCAAT boxes. A notable feature of the X. laevis class II beta chain genes is that the sizes of the introns are larger than those of their mammalian counterparts. As assessed by northern blot analysis, the three class II beta chain genes had similar expression patterns, with the highest level of transcription detected in the intestine. Identification of the Xela-DAB, -DBB, and -DCB genes is consistent with our previous observations, which suggested that the MHC of the tetraploid frog X. laevis is diploidized at the genomic level and contains three class II beta chain genes per haplotype that cross-hybridize to one another under reduced stringency conditions.

Differential display analysis of gene expression in developing embryos of Xenopus laevis

Differential display (DD), an arbitrarily primed RT-PCR fingerprinting technique, is a novel approach for the search of differentially expressed transcripts. Using our improved DD protocol, reproducible cDNA fingerprints were successfully obtained from RNAs of Xenopus laevis embryos at six representative stages. Parallel comparison among the fingerprints revealed a number of bands with differential expression patterns. Analysis with clones of three randomly chosen bands confirmed that their expression patterns were faithfully reflected on fingerprints, thereby proving the reliability and validity of the approach. Nucleotide sequencing of these clones revealed that one is identical with a known transcript (cardiac actin), the second is a novel developmentally regulated gene showing no significant homology with those reported previously, and the last is a close but unique relative of XK endo B gene showing somewhat different spatial expression pattern. These results indicated that the DD analysis provides a rapid and reliable way for the identification of novel differentially expressed genes as well as a unique 'scope' for the survey of the changes in overall gene expression profiles occurring in the early embryonic development of Xenopus as well as of other organisms.

Role of TFIIIA zinc fingers in vivo: analysis of single-finger function in developing Xenopus embryos

The Xenopus 5S RNA gene-specific transcription factor IIIA (TFIIIA) has nine consecutive Cys2His2 zinc finger motifs. Studies were conducted in vivo to determine the contribution of each of the nine zinc fingers to the activity of TFIIIA in living cells. Nine separate TFIIIA mutants were expressed in Xenopus embryos following microinjection of their respective in vitro-derived mRNAs. Each mutant contained a single histidine-to-asparagine substitution in the third zinc ligand position of an individual zinc finger. These mutations result in structural disruption of the mutated finger with little or no effect on the other fingers. The activity of mutant proteins in vivo was assessed by measuring transcriptional activation of the endogenous 5S RNA genes. Mutants containing a substitution in zinc finger 1, 2, or 3 activate 5S RNA genes at a level which is reduced relative to that in embryos injected with the message for wild-type TFIIIA. Proteins with a histidine-to-asparagine substitution in zinc finger 5 or 7 activate 5S RNA genes at a level that is roughly equivalent to that of the wild-type protein. Zinc fingers 8 and 9 appear to be critical for the normal function of TFIIIA, since mutations in these fingers result in little or no activation of the endogenous 5S RNA genes. Surprisingly, proteins with a mutation in zinc finger 4 or 6 stimulate 5S RNA transcription at a level that is significantly higher than that mediated by similar concentrations of wild-type TFIIIA. Differences in the amount of newly synthesized 5S RNA in embryos containing the various mutant forms of TFIIIA result from differences in the relative number and/or activity of transcription complexes assembled on the endogenous 5S RNA genes and, in the case of the finger 4 and finger 6 mutants, result from increased transcriptional activation of the normally inactive oocyte-type 5S RNA genes. The remarkably high activity of the finger 6 mutant can be reproduced in vitro when transcription is carried out in the presence of 5S RNA. Disruption of zinc finger 6 results in a form of TFIIIA that exhibits reduced susceptibility to feedback inhibition by 5S RNA and therefore increases the availability of the transcription factor for transcription complex formation.

Role of TFIIIA zinc fingers in vivo: analysis of single-finger function in developing Xenopus embryos

The Xenopus 5S RNA gene-specific transcription factor IIIA (TFIIIA) has nine consecutive Cys2His2 zinc finger motifs. Studies were conducted in vivo to determine the contribution of each of the nine zinc fingers to the activity of TFIIIA in living cells. Nine separate TFIIIA mutants were expressed in Xenopus embryos following microinjection of their respective in vitro-derived mRNAs. Each mutant contained a single histidine-to-asparagine substitution in the third zinc ligand position of an individual zinc finger. These mutations result in structural disruption of the mutated finger with little or no effect on the other fingers. The activity of mutant proteins in vivo was assessed by measuring transcriptional activation of the endogenous 5S RNA genes. Mutants containing a substitution in zinc finger 1, 2, or 3 activate 5S RNA genes at a level which is reduced relative to that in embryos injected with the message for wild-type TFIIIA. Proteins with a histidine-to-asparagine substitution in zinc finger 5 or 7 activate 5S RNA genes at a level that is roughly equivalent to that of the wild-type protein. Zinc fingers 8 and 9 appear to be critical for the normal function of TFIIIA, since mutations in these fingers result in little or no activation of the endogenous 5S RNA genes. Surprisingly, proteins with a mutation in zinc finger 4 or 6 stimulate 5S RNA transcription at a level that is significantly higher than that mediated by similar concentrations of wild-type TFIIIA. Differences in the amount of newly synthesized 5S RNA in embryos containing the various mutant forms of TFIIIA result from differences in the relative number and/or activity of transcription complexes assembled on the endogenous 5S RNA genes and, in the case of the finger 4 and finger 6 mutants, result from increased transcriptional activation of the normally inactive oocyte-type 5S RNA genes. The remarkably high activity of the finger 6 mutant can be reproduced in vitro when transcription is carried out in the presence of 5S RNA. Disruption of zinc finger 6 results in a form of TFIIIA that exhibits reduced susceptibility to feedback inhibition by 5S RNA and therefore increases the availability of the transcription factor for transcription complex formation.

Molecular cloning and expression of a metallothionein mRNA in Xenopus laevis

Metallothioneins (MT) are expressed during early development in species of several groups. To understand MT function in developmental processes, we studied the MT system of Xenopus laevis, a model vertebrate species in experimental embryology. We first purified and sequenced the liver MT from copper-treated animals. This 62-amino-acid protein shares the main structural properties of known vertebrate MT, and is more closely related to avian than to fish or mammalian MT. Using this sequence, we designed oligonucleotide primers to amplify and isolate a MT clone from a XL2 cell line cDNA library. This 752-bp cDNA encodes a putative 62-amino-acid-long protein that is 100% identical with the sequenced MT. Zinc, cadmium, and copper ions are very efficient inducers of MT mRNA accumulation in Xenopus liver and cell lines.

Proopiomelanocortin gene expression as a neural marker during the embryonic development of Xenopus laevis

Proopomelanocortin (POMC) is the precursor protein for a number of peptide hormones and neuropeptides, and the POMC gene is transcriptionally very active in the pars intermedia of the pituitary of the amphibian Xenopus laevis (Xenopus). We analysed the expression of this gene during Xenopus embryogenesis, in order to examine whether it can function as a (novel) neural marker. We investigated the spatio-temporal distribution of POMC mRNA, using a single-stranded probe that corresponds to the 3' untranslated region of Xenopus POMC gene B mRNA. Gene transcripts were first detected at stage 25 of development via RNase protection assays. In situ hybridization analysis performed at stage 46 showed clearly that these transcripts are localised in a region representing the future pars intermedia of the pituitary. Experiments using Xenopus explants indicate that the POMC gene can be used successfully as an indirect marker in studies on neural induction: in the absence of interactions with mesoderm, ectoderm fails to express the POMC gene, whereas POMC transcripts are readily detectable in conjugates of ectoderm and mesoderm. Artificial application of two different signals, which are likely to be relevant for neural differentiation (namely retinoic acid and the activation of protein kinase C via phorbol ester), was not effective in evoking POMC gene expression in cultured ectoderm explants. However, retinoic acid treatment of conjugates of Xenopus ectoderm and mesoderm successfully prevented POMC expression. We conclude that POMC gene expression can be used as an indirect marker for anterior neural differentiation in Xenopus.

DNA content in Eurasian sturgeon species determined by flow cytometry

The nuclear DNA content in 10 species of chondrostean fishes was measured by flow cytometry. The sterlet Acipenser ruthenus blood cells were used as an internal standard. The sterlet DNA content was calculated on the basis of comparison with the Xenopus laevis blood cells, 2C = 6.30 pg. In the tetraploid A. ruthenus and A. stellatus the DNA content comprises 3.74 pg/nucleus and is practically invariant; in Huso dauricus it is almost the same, 3.74-3.81 pg; and in A. nudiventris it is a little higher, 3.88-4.04 pg. In the oldest chondrostean, Pseudoscaphirhynchus kaufmanni, the nuclear DNA content is slightly lower, 2C = 3.46-3.48 pg, and in the American paddlefish Polyodon spathula it is lower still, 3.17 pg. In two octoploid sturgeons, A. baeri and A. gueldenstaedti, the DNA content is twice as high as that of the sterlet, 8.29-8.31 and 7.86-7.88 pg, respectively; a very similar amount, 8.24-8.42 pg, was determined in the hybrid Huso huso x A. ruthenus. In the Sakhalin sturgeon, A. medirostris (= A. mikadoi), the DNA content is two times higher than in the octoploids, 13.93-14.73 pg; therefore its ploidy may be 16n and the number of chromosomes could be 500.

The LIM domain-containing homeo box gene Xlim-1 is expressed specifically in the organizer region of Xenopus gastrula embryos

A novel cysteine-rich motif, named LIM, has been identified in the homeo box genes lin-11, Isl-1, and mec-3; the mec-3 and lin-11 genes determine cell lineages in Caenorhabditis elegans. We isolated LIM class homeo box genes from Xenopus laevis that are closely related to lin-11 and mec-3 in the LIM and homeo domains. This paper deals with one of these genes, Xlim-1. Xlim-1 mRNA is found at low abundance in the unfertilized egg, has a major expression phase at the gastrula stage, decreases, and rises again during the tadpole stage. In adult tissues the brain shows the highest abundance, by far, of Xlim-1 mRNA. The maternal and late expression phases of the Xlim-1 gene suggest that it has multiple functions at different stages of the Xenopus life cycle. In the gastrula embryo, Xlim-1 mRNA is localized in the dorsal lip and the dorsal mesoderm, that is, in the region of Spemann's organizer. Explant experiments showed that Xlim-1 mRNA is induced by the mesoderm-inducer activin A and by retinoic acid, which is not a mesoderm inducer but affects patterning during Xenopus embryogenesis; application of activin A and retinoic acid together results in synergistic induction. The structure, inducibility, and localized expression in the organizer of the Xlim-1 gene suggest that it has a role in establishing body pattern during gastrulation.

Presence of Vi-transposon-like elements in the proopiomelanocortin gene A of Xenopus laevis does not affect gene activity

Restriction mapping of the two proopiomelanocortin (POMC) genes of the South African clawed toad Xenopus laevis revealed that POMC gene A is much larger than POMC gene B. Here we report that this size difference is mainly due to the presence of four vitellogenin (Vi)-transposon-like elements in POMC gene A, while Vi elements are absent from POMC gene B. Alignment of these elements with other Vi elements revealed a consensus sequence of 463 bp, which is bounded by a 16 bp inverted repeat and flanked by a 3 bp direct repeat. Since the amounts of mRNA produced by both POMC genes in the pars intermedia of the Xenopus pituitary are similar, the presence of the Vi-transposon-like elements in POMC gene A apparently has no effect on POMC gene expression at transcriptional or post-transcriptional levels.

Chromosome banding in Amphibia. XVI. High-resolution replication banding patterns in Xenopus laevis

High-resolution replication banding patterns were induced in prometaphase and prophase chromosomes of Xenopus laevis by treating kidney cell lines with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT) in succession. Up to 650 early and late replicating bands per haploid karyotype were demonstrated in the very long prophase chromosomes. This permits an exact identification of all chromosome pairs of X. laevis. Late replicating heterochromatin was located by analysing the time sequence of replication throughout the second half of S-phase. Neither heteromorphic sex chromosomes nor sex chromosome-specific replication bands were demonstrated in the heterogametic ZW females of X. laevis. A detailed examination of the BrdU/dT-labelled prometaphases and prophases revealed that the X. laevis chromosomes can be arranged in groups of four (quartets), most of which show conspicuous similarities in length, centromere position, and replication pattern. This is interpreted as further evidence for an ancient allotetraploid origin of X. laevis.

Involvement of proliferating cell nuclear antigen (cyclin) in DNA replication in living cells

Proliferating cell nuclear antigen (PCNA) (also called cyclin) is known to stimulate the activity of DNA polymerase delta but not the other DNA polymerases in vitro. We injected a human autoimmune antibody against PCNA into unfertilized eggs of Xenopus laevis and examined the effects of this antibody on the replication of injected plasmid DNA as well as egg chromosomes. The anti-PCNA antibody inhibited plasmid replication by up to 67%, demonstrating that PCNA is involved in plasmid replication in living cells. This result further implies that DNA polymerase delta is necessary for plasmid replication in vivo. Anti-PCNA antibody alone did not block plasmid replication completely, but the residual replication was abolished by coinjection of a monoclonal antibody against DNA polymerase alpha. Anti-DNA polymerase alpha alone inhibited plasmid replication by 63%. Thus, DNA polymerase alpha is also required for plasmid replication in this system. In similar studies on the replication of egg chromosomes, the inhibition by anti-PCNA antibody was only 30%, while anti-DNA polymerase alpha antibody blocked 73% of replication. We concluded that the replication machineries of chromosomes and plasmid differ in their relative content of DNA polymerase delta. In addition, we obtained evidence through the use of phenylbutyl deoxyguanosine, an inhibitor of DNA polymerase alpha, that the structure of DNA polymerase alpha holoenzyme for chromosome replication is significantly different from that for plasmid replication.

Involvement of proliferating cell nuclear antigen (cyclin) in DNA replication in living cells

Proliferating cell nuclear antigen (PCNA) (also called cyclin) is known to stimulate the activity of DNA polymerase delta but not the other DNA polymerases in vitro. We injected a human autoimmune antibody against PCNA into unfertilized eggs of Xenopus laevis and examined the effects of this antibody on the replication of injected plasmid DNA as well as egg chromosomes. The anti-PCNA antibody inhibited plasmid replication by up to 67%, demonstrating that PCNA is involved in plasmid replication in living cells. This result further implies that DNA polymerase delta is necessary for plasmid replication in vivo. Anti-PCNA antibody alone did not block plasmid replication completely, but the residual replication was abolished by coinjection of a monoclonal antibody against DNA polymerase alpha. Anti-DNA polymerase alpha alone inhibited plasmid replication by 63%. Thus, DNA polymerase alpha is also required for plasmid replication in this system. In similar studies on the replication of egg chromosomes, the inhibition by anti-PCNA antibody was only 30%, while anti-DNA polymerase alpha antibody blocked 73% of replication. We concluded that the replication machineries of chromosomes and plasmid differ in their relative content of DNA polymerase delta. In addition, we obtained evidence through the use of phenylbutyl deoxyguanosine, an inhibitor of DNA polymerase alpha, that the structure of DNA polymerase alpha holoenzyme for chromosome replication is significantly different from that for plasmid replication.

Primary structure and evolutionary relationship between the adult alpha-globin genes and their 5'-flanking regions of Xenopus laevis and Xenopus tropicalis

To investigate the evolution of globin genes in the genus Xenopus, we have determined the primary structure of the related adult alpha I- and alpha II-globin genes of X. laevis and of the adult alpha-globin gene of X. tropicalis, including their 5'-flanking regions. All three genes are comprised of three exons and two introns at homologous positions. The exons are highly conserved and code for 141 amino acids. By contrast, the corresponding introns vary in length and show considerable divergence. Comparison of 900 bp of the 5'-flanking region revealed that the X. tropicalis gene contains a conserved proximal 310-bp promoter sequence, comprised of the canonical TATA and CCAAT motifs at homologous positions, and five conserved elements in the same order and at similar positions as previously shown for the corresponding genes of X. laevis. We therefore conclude that these conserved upstream elements may represent regulatory sequences for cell-specific regulation of the adult Xenopus globin genes.

Kinetics of histone gene expression during early development of Xenopus laevis

Using literature data for transcriptional and translational rate constants, gene copy numbers, DNA concentrations, and stability constants, we have calculated the expected concentrations of histones and histone mRNA during embryogenesis of Xenopus laevis. The results led us to conclude that: (i) for X. laevis the gene copy number of the histone genes is too low to ensure the synthesis of sufficient histones during very early development, inheritance from the oocyte of either histone protein or histone mRNA (but not necessarily both) is necessary; (ii) from the known storage of histones in the oocyte and the rates of histone synthesis determined by Adamson & Woodland (1977), there would be sufficient histones to structure the newly synthesized DNA up to gastrulation but not thereafter (these empirical rates of histone synthesis may be underestimates); (iii) on the other hand, the amount of H3 mRNA recently observed during early embryogenesis (Koster, 1987, Koster et al., 1988) could direct a higher and sufficient synthesis of H3 protein, also after gastrulation. We present a quantitative model that accounts both for the observed H3 mRNA concentration as a function of time during embryogenesis and for the synthesis of sufficient histones to structure the DNA throughout early embryogenesis. The model suggests that X. laevis exhibits a major (i.e. some 14-fold) reduction in transcription of histone genes approximately 11 hours after fertilization. This reduction could be due to a decrease in the number of transcribed histone genes, a decreased rate constant of transcription with continued transcription of all the histone genes, and/or a reduction in the time during the cell cycle in which histone mRNA synthesis takes place. Alternatively, the histone mRNA stability might decrease approximately 16-fold 11 hours after fertilization.

Expression of a histone H1-like protein is restricted to early Xenopus development

Genes whose expression is restricted to oogenesis and early development may have important functions in these processes. Northern analysis showed that Xenopus B4 mRNA is expressed in oogenesis and embryogenesis through to the neurula stage. Immunocytochemistry with anti-B4 antibodies showed that B4 protein is only detectable in preneurula stages; it is localized to nuclei and is associated with metaphase chromosomes. Immunoblotting revealed approximately constant levels of B4 protein per embryo for the first 2 days of development. Thus, as the number of nuclei increases during early development, the amount of B4 protein per nucleus is diluted out. Sequencing of two B4 cDNA clones revealed that the predicted B4 translation product is a 29-kD protein with 29% identity with histone H1, distributed over the entire length of its sequence. The B4 protein also has certain other H1 protein characteristics--a tripartite structure consisting of a mainly hydrophobic central domain flanked by an amino-terminal segment and a long hydrophilic carboxyterminal tail containing a tandemly repeated amino acid motif. However, in contrast to histone H1 mRNA, B4 mRNA has a classic polyadenylation signal, is polyadenylated, and lacks the histone H1 3' noncoding consensus sequence involved in RNA processing.

Oocyte and somatic 5S ribosomal RNA and 5S RNA encoding genes in Xenopus tropicalis

We have investigated the structure of oocyte and somatic 5S ribosomal RNA and of 5S RNA encoding genes in Xenopus tropicalis. The sequences of the two 5S RNA families differ in four positions, but only one of these substitutions, a C to U transition in position 79 within the internal control region of the corresponding 5S RNA encoding genes, is a distinguishing characteristic of all Xenopus somatic and oocyte 5S RNAs characterized to date, including those from Xenopus laevis and Xenopus borealis. 5S RNA genes in Xenopus tropicalis are organized in clusters of multiple repeats of a 264 base pair unit; the structural and functional organization of the Xenopus tropicalis oocyte 5S gene is similar to the somatic but distinct from the oocyte 5S DNA in Xenopus laevis and Xenopus borealis. A comparative sequence analysis reveals the presence of a strictly conserved pentamer motif AAAGT in the 5'-flanking region of Xenopus 5S genes which we demonstrate in a separate communication to serve as a binding signal for an upstream stimulatory factor.

Amino acid sequence microheterogeneities of a type I cytokeratin of Mr 51,000 from Xenopus laevis epidermis

The complete cDNA-derived sequence of a type I cytokeratin (designated no. 3) from Xenopus laevis skin is described. The deduced protein has an Mr of 51,888 and consists of a glycine-rich head domain, a well-conserved alpha-helical region and a tail rich in hydroxyamino acid residues. Various cDNA clones encoding two different mRNAs were isolated that differed by short deletions/insertions and point mutations. These microheterogeneities are mainly located in a 'hypervariable region' at the C-terminal non-alpha-helical region.

Enolase isoenzymes in adult and developing Xenopus laevis and characterization of a cloned enolase sequence

As part of a study of glycolysis during early development we have examined the pattern of expression of enolase isoenzymes in Xenopus laevis. In addition, the nucleotide sequence of a cDNA clone coding for the complete amino acid sequence of one enolase gene (ENO1) in X. laevis was determined. X. laevis ENO1 shows highest homology to mammalian non-neuronal enolase. Analysis of enolase isoenzymes in X. laevis by non-denaturing electrophoresis on cellulose acetate strips revealed five isoenzymes. One form was present in all tissues tested, two additional forms were expressed in oocytes, embryos, adult liver and adult brain, and two further forms were restricted to larval and adult muscle. Since enolase is a dimer, three different monomers (gene products) could account for the observed number of isoenzymes. This pattern of enolase isoenzyme expression in X. laevis differs from that of birds and mammals. In birds and mammals the most acidic form is neuron-specific and there is only one major isoenzyme expressed in the liver. RNAase protection experiments showed the presence of ENO1 mRNA in oocytes, liver and muscle, suggesting that it codes for a non-tissue-restricted isoenzyme. ENO1 mRNA concentrations are high in early oocytes, decrease during oogenesis and decrease further after fertilization. Enolase protein, however, is maintained at high concentrations throughout this period.