Early Stage Of Vertebrate Evolution Research Articles

Foxn1 is not essential for T-cell development in teleosts.

In mammals, T-cell development depends on the activity of the Foxn1 transcription factor in the thymic epithelium; mutations in the vertebrate-specific Foxn1 gene are associated with profound T-cell lymphopenia and fatal immunodeficiency. Here, we examined the extent of T-cell development in teleosts lacking a functional foxn1 gene. In zebrafish carrying a deleterious internal deletion of foxn1, reduced but robust lymphopoietic activity is maintained in the mutant thymus. Moreover, pseudogenization or loss of foxn1 in the genomes of deep-sea anglerfishes is independent of the presence or absence of the canonical signatures of the T-cell lineage. Thus, in contrast to the situation in mammals, the teleost thymus can support foxn1-independent lymphopoiesis, most likely through the activity of the Foxn4, an ancient metazoan paralog of Foxn1. Our results imply that during the early stages of vertebrate evolution, genetic control of thymopoiesis was functionally redundant and thus robust; in mammals, the genetic network was reorganized to become uniquely dependent on the FOXN1 transcription factor.

Heterochrony of the Expression of Lanf and Foxg1 in the Lamprey Confirms the Appearance of the Telencephalon as an Evolutionarily Young Superstructure in the Central Nervous System of Vertebrates

One of the most important evolutionary innovations of vertebrates is a complexly structured telencephalon, which provides higher forms of nervous activity in animals and humans. This work is devoted to the study of the appearance of the telencephalon in the early stages of vertebrate evolution. At the same time, there is reason to believe that lampreys, due to their evolutionary antiquity, could retain some ancient expression patterns of genes that regulate the development of the brain in the very first vertebrates. The study of the features of spatio-temporal expression patterns of key genes that regulate the development of the forebrain in lampreys compared with other vertebrates can help to understand the molecular mechanisms underlying the appearance and evolutionary development of this unique structure of vertebrates. This paper presents the results from analyzing the gene-expression dynamics of Lanf, FoxG1, Otx2, Goosecoid, and HoxB9 in the early stages of development of the European river lamprey Lampetra fluviatilis. It was shown that lamprey genes involved in telencephalon differentiation (Lanf and FoxG1) exhibit heterochrony of expression compared with more evolutionarily advanced representatives of vertebrates. This fact confirms the idea that the telencephalon, being evolutionarily the youngest part of the brain, could appear in vertebrate ancestors as a superstructure in the late stages of their embryonic development.

Double maternal-effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, with essential but distinct functions are shared by fish and tetrapods

BackgroundNucleoplasmin 2 (npm2) is an essential maternal-effect gene that mediates early embryonic events through its function as a histone chaperone that remodels chromatin. Recently, two npm2 (npm2a and npm2b) genes have been annotated in zebrafish. Thus, we examined the evolution of npm2a and npm2b in a variety of vertebrates, their potential phylogenetic relationships, and their biological functions using knockout models via the CRISPR/cas9 system.ResultsWe demonstrated that the two npm2 duplicates exist in a wide range of vertebrates, including sharks, ray-finned fish, amphibians, and sauropsids, while npm2a was lost in coelacanth and mammals, as well as some specific teleost lineages. Using phylogeny and synteny analyses, we traced their origins to the early stages of vertebrate evolution. Our findings suggested that npm2a and npm2b resulted from an ancient local gene duplication, and their functions diverged although key protein domains were conserved. We then investigated their functions by examining their tissue distribution in a wide variety of species and found that they shared ovarian-specific expression, a key feature of maternal-effect genes. We also demonstrated that both npm2a and npm2b are maternally-inherited transcripts in vertebrates, and that they play essential, but distinct, roles in early embryogenesis using zebrafish knockout models. Both npm2a and npm2b function early during oogenesis and may play a role in cortical granule function that impact egg activation and fertilization, while npm2b is also involved in early embryogenesis.ConclusionThese novel findings will broaden our knowledge on the evolutionary history of maternal-effect genes and underlying mechanisms that contribute to vertebrate reproductive success. In addition, our results demonstrate the existence of a newly described maternal-effect gene, npm2a, that contributes to egg competence, an area that still requires further comprehension.

Editorial: A Comparative Survey of the RF-Amide Peptide Superfamily.

The first member of the RF-amide peptide superfamily to be characterized, in 1977, was the cardioexcitatory peptide, FMRFamide, isolated from the ganglia of the clam Macrocallista nimbosa (1). Since then, a large number of such peptides, designated after their C-terminal arginine (R) and amidated phenylalanine (F) residues, have been identified in representative species of all major phyla. The discovery, 12 years ago, that the RF-amide peptide kisspeptin, acting via GPR54, was essential for the onset of puberty and reproduction, has been a major breakthrough in reproductive physiology (2–4). It has also put in front of the spotlights RF-amide peptides and has invigorated research on this superfamily of regulatory neuropeptides. The present Research Topic aims at illustrating major advances achieved, through comparative studies in (mammalian and non-mammalian) vertebrates and invertebrates, in the knowledge of RF-amide peptides in terms of evolutionary history and physiological significance.

Functional roles of evolutionary conserved motifs and residues in vertebrate chemokine receptors.

Chemokine receptors regulate cell migration and homing. They belong to the rhodopsin-like family of GPCRs. Their ancestor genes emerged in the early stages of vertebrate evolution. Since then, the family has been greatly expanded through whole and segmental genome duplication events. During evolution, many amino acid changes have been introduced in individual chemokine receptors, but certain motifs and residues are highly conserved. Previously, we proposed a nomenclature system of the vertebrate chemokine receptors based on their evolutionary history and phylogenetic analyses. With the use of this classification system, we are now able to confidently assign the species orthologs of vertebrate chemokine receptors. Here, we systematically analyze conserved motifs and residues of each group of orthologous chemokine receptors that may play important roles in their signaling and biologic functions. Our present analysis may provide useful information on how individual chemokine receptors are activated upon ligand binding.

Unexpected multiplicity of QRFP receptors in early vertebrate evolution.

The neuropeptide QRFP, also called 26RFa, and its G protein-coupled receptor GPR103 have been identified in all vertebrates investigated. In mammals, this peptide-receptor pair has been found to have several effects including stimulation of appetite. Recently, we reported that a QRFP peptide is present in amphioxus, Branchiostoma floridae, and we also identified a QRFP receptor (QRFPR) that mediates a functional response to sub-nanomolar concentrations of the amphioxus peptide as well as short and long human QRFP (Xu et al., submitted). Because the ancestral vertebrate underwent two tetraploidizations, it might be expected that duplicates of the QRFP gene and its receptor gene may exist. Indeed, we report here the identification of multiple vertebrate QRFPR genes. Three QRFPR genes are present in the coelacanth Latimeria chalumnae, representing an early diverging sarcopterygian lineage. Three QRFPR genes are present in the basal actinopterygian fish, the spotted gar. Phylogenetic and chromosomal analyses show that only two of these receptor genes are orthologous between the two species, thus demonstrating a total of four distinct vertebrate genes. Three of the QRFPR genes resulted from the early vertebrate tetraploidizations and were copied along with syntenic neuropeptide Y receptor genes. The fourth QRFPR gene may be an even older and distinct lineage. Because mammals and birds have only a single QRFPR gene, this means that three genes have been lost in these lineages, and at least one of these was lost independently in mammals and birds because it is still present in a turtle. In conclusion, these results show that the QRFP system gained considerable complexity in the early stages of vertebrate evolution and still maintains much of this in some lineages, and that it has been secondarily reduced in mammals.

Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations

The age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint differences, genes in different functional categories might show dissimilar retention patterns after duplication. It is known that genes in some functional categories are highly duplicated in the early stage of vertebrate evolution. However, the correlations of the age distribution pattern of gene duplication between the different functional categories are still unknown. To investigate this issue, we developed a robust pipeline to date the gene duplication events in the human genome. We successfully estimated about three-quarters of the duplication events within the human genome, along with the age distribution pattern in each Gene Ontology (GO) slim category. We found that some GO slim categories show different distribution patterns when compared to the whole genome. Further hierarchical clustering of the GO slim functional categories enabled grouping into two main clusters. We found that human genes located in the duplicated copy number variant regions, whose duplicate genes have not been fixed in the human population, were mainly enriched in the groups with a high proportion of recently duplicated genes. Moreover, we used a phylogenetic tree-based method to date the age of duplications in three signaling-related gene superfamilies: transcription factors, protein kinases and G-protein coupled receptors. These superfamilies were expressed in different subcellular localizations. They showed a similar age distribution as the signaling-related GO slim categories. We also compared the differences between the age distributions of gene duplications in multiple subcellular localizations. We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome.

Extensive genome duplications in sturgeons: new evidence from microsatellite data

Summary Genome duplications and polyploidization events are thought to have played relevant roles in the early stages of vertebrate evolution, in particular near the time of divergence of the lamprey lineage. Additional genome duplications, specifically in ray-finned fish, may have occurred before the divergence of the teleosts. The role of polyploidization in vertebrate genome evolution is a thriving area of research. Sturgeons (order Acipenseriformes) provide a unique model for the investigation of genome duplication, with existing species possessing 120, 250 or 360 chromosomes. In the present study, data from 240 sturgeon specimens representing 11 species were used for analysis of ploidy levels. Allele numbers were assessed at eleven microsatellite loci. The results provide further evidence for functional diploidy, tetraploidy and hexaploidy in species possessing 120, 250 and 360 chromosomes, respectively. The analysis also uncovered novel evidence for functional hexaploidy in the shortnose sturgeon (Acipenser brevirostrum). In conclusion, the process of functional genome reduction is demonstrated to be an on-going process in this fish lineage.

Trunk exoskeleton in teleosts is mesodermal in origin

The vertebrate mineralized skeleton is known to have first emerged as an exoskeleton that extensively covered the fossil jawless fish. The evolutionary origin of this exoskeleton has long been attributed to the emergence of the neural crest, but experimental evaluation for this is still poor. Here we determine the embryonic origin of scales and fin rays of medaka (teleost trunk exoskeletons) by applying long-term cell labelling methods, and demonstrate that both tissues are mesodermal in origin. Neural crest cells, however, fail to contribute to these tissues. This result suggests that the trunk neural crest has no skeletogenic capability in fish, instead highlighting the dominant role of the mesoderm in the evolution of the trunk skeleton. This further implies that the role of the neural crest in skeletogenesis has been predominant in the cephalic region from the early stage of vertebrate evolution.

Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution

BackgroundDNA methylation by the Dnmt family occurs in vertebrates and invertebrates, including ascidians, and is thought to play important roles in gene regulation and genome stability, especially in vertebrates. However, the global methylation patterns of vertebrates and invertebrates are distinctive. Whereas almost all CpG sites are methylated in vertebrates, with the exception of those in CpG islands, the ascidian genome contains approximately equal amounts of methylated and unmethylated regions. Curiously, methylation status can be reliably estimated from the local frequency of CpG dinucleotides in the ascidian genome. Methylated and unmethylated regions tend to have few and many CpG sites, respectively, consistent with our knowledge of the methylation status of CpG islands and other regions in mammals. However, DNA methylation patterns and levels in vertebrates and invertebrates have not been analyzed in the same way.ResultsUsing a new computational methodology based on the decomposition of the bimodal distributions of methylated and unmethylated regions, we estimated the extent of the global methylation patterns in a wide range of animals. We then examined the epigenetic changes in silico along the phylogenetic tree. We observed a gradual transition from fractional to global patterns of methylation in deuterostomes, rather than a clear demarcation between vertebrates and invertebrates. When we applied this methodology to six piscine genomes, some of which showed features similar to those of invertebrates.ConclusionsThe mammalian global DNA methylation pattern was probably not acquired at an early stage of vertebrate evolution, but gradually expanded from that of a more ancient organism.

The evolution of somatostatin in vertebrates

Somatostatins (SS) play important roles in the regulation of growth in vertebrates. In the present study, we identified six SS genes in zebrafish and named them SS1, SS2, SS3, SS4, SS5 and SS6. We subsequently found that five SS genes ( SS1, SS2, SS3, SS4 and SS5) also existed in stickleback, medaka, Takifugu and Tetraodon. Phylogenetic analysis showed that vertebrate SS genes were grouped into five clades. Using a comparative genomic approach, we further investigated the evolutionary origin of these SS genes in vertebrates, and the results revealed that: (1) SS1, SS2 and SS5 were generated by two rounds of genome duplications (2R) that happened during the early stages of vertebrate evolution; (2) SS4 is an SS1 paralog generated by a third genome duplication (3R) that occurred to most teleost fish; and (3) SS3 and SS6 were produced by tandem duplication of SS1 and SS2 in teleost fish. RT-PCR analysis revealed that all six SS genes were functionally expressed in different zebrafish tissues. These data indicate that both genome-wide duplication and local duplication contribute to the expansion of SS genes in vertebrates.

Comparison of two kinds of functional asymmetry in the roach Rutilus rutilus (Teleostei: Cyprinidae)

In the higher vertebrates, asymmetries of different functions of individual are poorly connected with each other. At present it is unknown whether this poor link is a secondary phenomenon or it is characteristic of different kinds of functional asymmetry already at early stages of vertebrate evolution. In connection with this problem, in the roach Rutilus rutilus we studied asymmetry of two behavioral reactions--movements in an annular corridor and of the C-shaped body bending at a sudden action of electrical stimulus. Different individuals prefer a certain direction of movement in the corridor (to the right or to the left). Comparison of these two kinds of asymmetry in the same individuals has shown the absence of significant association between asymmetries of different reactions. The obtained data indicate that already in the lower vertebrates, different kinds of functional asymmetry are controlled by different mechanisms and are poorly associated with each other.

Phylogenesis of brain-derived neurotrophic factor ( BDNF)‏ in vertebrates

Brain-derived neurotrophic factor (BDNF) belongs to neurotrophin family, a class of molecules playing key roles in neuronal development, survival and regeneration, neurite growth and plasticity: memory processes are mainly affected, and mutations of the human BDNF gene are associated to cognitive and behavioural disturbances. All neurotrophins contain a highly conserved C-terminal domain and bind to the same receptor family. Both correct folding and post-translational processing of the entire preproprotein are pivotal for sorting to the extracellular space, dimerization and receptor binding. Evolutionary studies conducted so far demonstrate that a single ancestor gene underwent two independent duplication events at an early stage of vertebrate evolution, leading to the formation of the current neurotrophins. However, works focusing on BDNF evolution are scarce and fragmentary, mainly in lower vertebrates . In this work, we report cloning of eight DNA sequences from amphibians and teleosts, and analysis of the entire coding regions (cDNA sequences) of BDNF from 35 organisms, from teleosts to mammals. A phylogenetic tree was constructed and the analysis of non-synonymous–synonymous substitution rates performed for the different branches. Our results suggest that natural selection is acting on mammals, separating them from other classes. Since preproprotein cleavage and 3D structure of mature protein are important for functional activity of BDNF, we also propose a de novo prediction of the 3D structure of translates in at least one species for each class, in order to get hints about the functional constraints of the protein.

Gene Structure and Functional Characterization of Growth Hormone in Dogfish, Squalus acanthias

Dogfish (Squalus acanthias) growth hormone (GH) was identified by cDNA cloning and protein purification from the pituitary gland. Dogfish GH cDNA encoded a prehormone of 210 amino acids (aa). Sequence analysis of purified GH revealed that the prehormone is composed of a signal peptide of 27 aa and a mature protein of 183 aa. Dogfish GH showed 94% sequence identity with blue shark GH, and also showed 37-66%, 26%, and 48-67% sequence identity with GH from osteichtyes, an agnathan, and tetrapods. The site of production was identified through immunocytochemistry to be cells of the proximal pars distalis of the pituitary gland. Dogfish GH stimulates both insulin-like growth factor-I and II mRNA levels in dogfish liver in vitro. The dogfish GH gene consisted of five exons and four introns, the same as in lamprey, teleosts such as cypriniforms and siluriforms, and tetrapods. The 5'-flanking region within 1082 bp of the transcription start site contained consensus sequences for the TATA box, Pit-1/GHF-1, CRE, TRE, and ERE. These results show that the endocrine mechanism for growth stimulation by the GH-IGF axis was established at an early stage of vertebrate evolution, and that the 5-exon-type gene organization might reflect the structure of the ancestral gene for the GH gene family.

Opioid-induced depression in the lamprey respiratory network

The role of opioid receptors in modulating respiratory activity was investigated in in vitro brainstem preparations of adult lampreys by bath application of agonists and antagonists. The vagal motor output was used to monitor respiratory activity. Neuronal recordings were also performed to characterize the rostrolateral trigeminal region that has been suggested to be critical for respiratory rhythmogenesis. Microinjections of the μ-opioid receptor agonist [ d-Ala 2, N-Me-Phe 4, Gly 5-ol]-enkephalin (DAMGO) were also made into this region and at different locations within the brainstem. Bath application of DAMGO (0.5–2 μM) caused marked decreases in respiratory frequency up to complete apnea. Bath application of the δ-opioid receptor agonist [ d-Pen 2,5]-enkephalin (DPDPE) at 10–40 μM induced less pronounced depressant respiratory effects, while no changes in respiratory activity were induced by the κ-opioid receptor agonist trans-(1S,2S)-3,4-dichloro-N-methyl-N-[2-(1-pyrrolidinyl)cyclohexyl] benzeneacetamide (U50488) at 10–40 μM. Bath application of the opioid receptor antagonists naloxone and naltrindole did not affect baseline respiratory activity, but prevented agonist-induced effects. DAMGO microinjections (1 mM; 0.5–1 nl) at sites rostrolateral to the trigeminal motor nucleus, where respiration-related neuronal activity was recorded, abolished the respiratory rhythm. The results show that opioids may have an important role in the lamprey respiratory network and that μ-opioid receptor activation is the most effective in causing respiratory depression. They also indicate that endogenous opioids are not required for the generation of baseline respiratory activity. Apneic responses induced by DAMGO microinjections support the hypothesis that a specific opioid-sensitive region rostrolateral to the trigeminal motor nucleus, that we have termed the paratrigeminal respiratory group (pTRG), likely has a pivotal role in respiratory rhythmogenesis. Since the lamprey diverged from the main vertebrate line around 450 million years ago, our results also imply that the inhibitory role of opioids on respiration is present at an early stage of vertebrate evolution.

Agouti‐Related Proteins (AGRPs) and Agouti‐Signaling Peptide (ASIP) in Fish and Chicken

We performed an intensive search on sequence databases to identify orthologues of ASIP and AGRP peptides in a number of different species, revealing a number of genomic fragments coding for the C-terminal part of agouti-related motifs, different from annotated peptide sequences, including one fragment from chicken, two from zebrafish, two from Fugu (Takifugu rubripes), and three from Tetraodon (Tetraodon nigroviridis). We have thus shown for the first time that both AGRP and ASIP genes exist in many species in "lower vertebrates" and were most probably present in early stages of vertebrate evolution.

New insights into the genomic organization and origin of the major histocompatibility complex: role of chromosomal (genome) duplication in the emergence of the adaptive immune system.

Recently, it became clear that the human and mouse genomes contain at least three regions paralogous to the major histocompatibility complex (MHC) region. This observation led us to the proposal that the MHC region emerged as a result of chromosomal duplication that took place at an early stage of vertebrate evolution. Here I briefly review this proposal. Accumulating evidence indicates that (a) genome-wide duplication(s) took place close to the origins of vertebrates. Taking this and others into account, I suggest that the duplication(s) involving the MHC region probably took place as a part of the genome-wide duplication(s). The human T cell receptor (TCR) and immunoglobulin (Ig) genes also appear to be located on paralogous chromosomal segments. These findings raise the possibility that the genome-wide duplication provided a major impetus not only to the emergence of the full-fledged MHC system, but also to the appearance of other key molecules of the adaptive immune system such as TCR and Ig.

Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci.

Genome duplications may have played a role in the early stages of vertebrate evolution, near the time of divergence of the lamprey lineage. Additional genome duplication, specifically in ray-finned fish, may have occurred before the divergence of the teleosts. The common carp (Cyprinus carpio) has been considered tetraploid because of its chromosome number (2n = 100) and its high DNA content. We studied variation using 59 microsatellite primer pairs to better understand the ploidy level of the common carp. Based on the number of PCR amplicons per individual, about 60% of these primer pairs are estimated to amplify duplicates. Segregation patterns in families suggested a partially duplicated genome structure and disomic inheritance. This could suggest that the common carp is tetraploid and that polyploidy occurred by hybridization (allotetraploidy). From sequences of microsatellite flanking regions, we estimated the difference per base between pairs of alleles and between pairs of paralogs. The distribution of differences between paralogs had two distinct modes suggesting one whole-genome duplication and a more recent wave of segmental duplications. The genome duplication was estimated to have occurred about 12 MYA, with the segmental duplications occurring between 2.3 and 6.8 MYA. At 12 MYA, this would be one of the most recent genome duplications among vertebrates. Phylogenetic analysis of several cyprinid species suggests an evolutionary model for this tetraploidization, with a role for polyploidization in speciation and diversification.

Identification of growth hormone in the sea lamprey, an extant representative of a group of the most ancient vertebrates.

GH was identified in the sea lamprey, an extant representative of a group of the most ancient vertebrates, the Agnatha. A putative GH-cDNA was cloned from the pituitary by RT-PCR. The entire coding region comprised an open-reading frame of 203 amino acids (aa). The mature protein was also isolated from pituitaries, and fractionated by gel filtration and reverse-phase HPLC. A putative GH was monitored by Western blotting with a rabbit antiserum against a synthetic peptide corresponding to pre-GH sequence (aa 29-45). Sequence analysis of the purified protein demonstrated that the prehormone consists of a signal peptide of 22 aa and the mature protein of 181 aa, which shows 25% sequence identity with sturgeon GH. The site of production was identified through immunohistochemistry to be cells of the dorsal half of the proximal pars distalis of the pituitary. Following cDNA cloning of lamprey IGF cDNA, it was shown using RT-PCR that lamprey GH stimulates IGF expression in lamprey liver. This is the first study in which a member of the GH/prolactin/somatolactin family has been identified in an agnathan. In addition, GH appears to be the only member of this hormone family in the sea lamprey. Evidence suggests that GH is the ancestral hormone in the molecular evolution of the GH family and that the endocrine mechanism for growth stimulation was established at an early stage of vertebrate evolution.

Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution

The classical (two-round) hypothesis of vertebrate genome duplication proposes two successive whole-genome duplication(s) (polyploidizations) predating the origin of fishes, a view now being seriously challenged. As the debate largely concerns the relative merits of the 'big-bang mode' theory (large-scale duplication) and the 'continuous mode' theory (constant creation by small-scale duplications), we tested whether a significant proportion of paralogous genes in the contemporary human genome was indeed generated in the early stage of vertebrate evolution. After an extensive search of major databases, we dated 1,739 gene duplication events from the phylogenetic analysis of 749 vertebrate gene families. We found a pattern characterized by two waves (I, II) and an ancient component. Wave I represents a recent gene family expansion by tandem or segmental duplications, whereas wave II, a rapid paralogous gene increase in the early stage of vertebrate evolution, supports the idea of genome duplication(s) (the big-bang mode). Further analysis indicated that large- and small-scale gene duplications both make a significant contribution during the early stage of vertebrate evolution to build the current hierarchy of the human proteome.