Molecular evolution and characterization of hepcidin gene products in vertebrates

Antimicrobial peptides (AMPs) include a diverse group of gene-encoded molecules that play a role in innate defense in many organisms. Evolutionary analyses of the AMP genes can be challenging because of gene duplication and diversification. Recently discovered, hepcidins are small, cysteine-rich antimicrobial peptides that also function as hormonal regulators of iron homeostasis. In this paper we investigated the organization, expression and molecular evolution of hepcidin. From searches of the literature and public genomic databases we collected 68 different hepcidin gene products from 51 different species, all among the vertebrates. Although some species have multiple hepcidin homologues, we suggest that each contains only one copy that functions as an iron regulator. Despite the recent report of hepcidin sequences in the pigeon (Fu, Y.M., Li, S.P., Wu, Y.F., Chang, Y.Z., 2007. Identification and expression analysis of hepcidin-like cDNAs from pigeon (Columba livia). Mol. Cell. Biochem. 305, 191-197.), searches of the chicken genomic, EST, and HTGS databases did not reveal any evidence of the presence of this gene in birds. This, along with the absence of reported avian transferrin receptor 2 and hemojuvelin sequences, suggests that iron homeostasis in birds may be regulated by an alternative mechanism.     

Sex chromosome evolution in non-mammalian vertebrates

Birds, reptiles, amphibia and fish have an enormous variety of chromosomal sex determination mechanisms that apparently do not follow any phylogenetic or taxonomic scheme. A similar picture is now emerging at the molecular level. Most genes that function downstream of the mammalian master sex-determining gene, Sry, have been found in non-mammalian vertebrates. Although the components of the machinery that determines sex seem to be conserved, their interaction and most importantly the initial trigger is not the same in all vertebrates. This variety is the consequence of the extremely dynamic process of the evolution of sex determination mechanisms and sex chromosomes, which is prone to create differences rather than uniformity.     

Ancient evolution of stress-regulating peptides in vertebrates

Recent studies on genomic sequences have led to the discovery of novel corticotropin-releasing factor (CRF) type 2 receptor-selective agonists, stresscopin (SCP)/urocortin III (UcnIII), and stresscopin-related peptide (SRP)/urocortin II (UcnII). In addition, analyses of vertebrate genomes showed that the CRF peptide family includes four distinct genes, CRF, urocortin/urotensin I, SCP/UcnIII, and SRP/UcnII. Each of these four genes is highly conserved during evolution and the identity between mammalian and teleost orthologs ranges from >96% for CRF to >55% for SCP. Phylogenetic studies showed that the origin of each of these peptides predates the evolution of tetrapods and teleosts, and that this family of peptide hormones evolved from an ancestor gene that developed the CRF/urocortin and SCP/SRP branches through an early gene duplication event. These two ancestral branches then gave rise to additional paralogs through a second round of gene duplication. Consequently, each of these peptides participates in the regulation of stress responses over the 550 million years of vertebrate evolution. The study also suggested that the fight-or-flight and stress-coping responses mediated mainly by CRF types 1 and 2 receptors evolved early in chordate evolution. In addition, we hypothesize that the CRF/CRF receptor signaling evolved from the same ancestors that also gave rise to the diuretic hormone/diuretic hormone receptors in insects. Thus, a complete inventory of CRF family ligands and their receptors in the genomes of different organisms provides an opportunity to reveal an integrated view of the physiology and pathophysiology of the CRF/SCP family peptides, and offers new insights into the evolution of stress regulation in vertebrates.     

LINEs.

LINEs are ubiquitous transposable elements of eukaryotes. Significant information has accumulated in the past year concerning the mechanism of transposition and the intermediates involved. In addition, progress has been made in the understanding of LINE structure and evolution, and several laboratories have exploited the interspersed, repetitive nature of LINEs for use in genome mapping.     

Molecular evolution and functional characterization of the orexigenic peptide 26RFa and its receptor in vertebrates

Several neuropeptides possessing the RFamide motif at their C-termini (designated RFamide peptides) have been characterized in the hypothalamus of a variety of vertebrates. To date, five groups of the RFamide peptide family have been shown to exert several important neuroendocrine, behavioral, sensory, and autonomic functions. Since the discovery of the 26-amino acid RFamide peptide (termed 26RFa) from the frog brain, 26RFa has been shown to exert orexigenic activity in mammals and to be a ligand of the previously identified orphan G-protein-coupled receptor GPR103. Recently, 26RFa and its cognate receptor GPR103 have been identified in the brain of birds. This mini-review summarizes the advances in the identification, localization, and functions of 26RFa and its cognate receptor GPR103 in vertebrates and highlights recent progress made in birds.     

Molecular mechanisms of early neurogenesis in vertebrates

Recent studies revealed a great variety of genes which control the early development of the central nervous system in vertebrates, including neural induction and differentiation of primary neurons. Most of these genes were first identified inDrosophila melanogaster, then their structural and functional homologs were found in vertebrates. Modern data on the molecular-genetic mechanisms of vertebrate neurogenesis are reviewed. The neurogenetic mechanisms are compared for vertebrates and invertebrates. Widely discussed hypotheses are considered along with the commonly accepted mechanisms.     

Brain insulin receptors in the evolution of vertebrates

Studies have been made on 125I-insulin binding for brain membranes from cyclostomes (the lamprey Lampetra fluviatilis), fish (pink salmon Oncorhynchus gorbuscha) and mammals (rats). The species studied differed by the level of binding (the highest in the rat and the lowest in the lamprey), which was due mainly to differences in the number of binding sites per membrane protein. Qualitative properties of the receptors in the species studied were found to be very similar. All three types of the receptors were capable of differentiating between the insulins from pig, pink salmon and lamprey, all of them binding porcine insulin more readily than the salmon one and the latter better than the insulin from the lamprey. It means that these insulins reacted not to the species specific properties of the hormone, but to biological activity of the insulin. The data obtained indicate that functionally mature insulin receptor may be found already in the brain of cyclostomes and that in the course of animal evolution from cyclostomes to mammals functional properties of this receptor did not undergo any significant changes.     

The evolution of feeding motor patterns in vertebrates

Despite considerable skepticism, researchers have found that the patterns of muscle activation that control feeding behaviors of lower vertebrates have been surprisingly conserved during evolution. This tendency for conservation among taxa appears in the face of marked flexibility of motor patterns within individuals. One interpretation of these apparently conflicting trends is that the most effective motor pattern for any given feeding situation is the same across substantial phylogenetic distances and morphological differences. The novel evolutionary insight provided by this research is that historical changes to motor patterns are a relatively infrequent source of trophic innovation. The spectacular diversity of feeding abilities and feeding ecology in lower vertebrates is based mostly on axes of variation, and on the innovations in the organization of muscles and the skeletal linkage systems that they drive.     

Molecular evolution of Cide family proteins: Novel domain formation in early vertebrates and the subsequent divergence

Background  

Cide family proteins including Cidea, Cideb and Cidec/Fsp27, contain an N-terminal CIDE-N domain that shares sequence similarity to the N-terminal CAD domain (NCD) of DNA fragmentation factors Dffa/Dff45/ICAD and Dffb/Dff40/CAD, and a unique C-terminal CIDE-C domain. We have previously shown that Cide proteins are newly emerged regulators closely associated with the development of metabolic diseases such as obesity, diabetes and liver steatosis. They modulate many metabolic processes such as lipolysis, thermogenesis and TAG storage in brown adipose tissue (BAT) and white adipose tissue (WAT), as well as fatty acid oxidation and lipogenesis in the liver.     

Molecular evolution of ankyrin: gain of function in vertebrates by acquisition of an obscurin/titin-binding-related domain

Ankyrins form a family of modular adaptor proteins that link between integral membrane proteins and the cytoskeleton. They evolved within the Metazoa as an adaptation for organizing membrane microstructure and directing membrane traffic. Molecular cloning has identified one Caenorhabditis elegans (unc-44), two Drosophila (Dank1, Dank2), and three mammalian (Ank1, Ank2, Ank3) genes. We have previously identified a 76-amino acid (aa) alternatively spliced sequence that is present in muscle polypeptides encoded by the rat Ank3 gene. A closely related sequence in a muscle Ank1 product binds the cytoskeletal muscle proteins obscurin and titin. This obscurin/titin-binding-related domain (OTBD) contains repeated modules of 18 aa: three are encoded by Ank1 and Ank2, two by Ank3; this pattern is conserved throughout vertebrate ankyrin genes. The C. elegans ankyrin, UNC-44, contains one 18-aa module as does the ankyrin gene in the urochordate Ciona intestinalis, but the insect ankyrins contain none. Our data indicate that an ancestral ankyrin acquired an 18-aa module which was preserved in the Ecdysozoa/deuterostome divide, but it was subsequently lost from arthropods. Successive duplications of the module led to a gain of function in vertebrates as it acquired obscurin/titin-binding activity. We suggest that the OTBD represents an adaptation of the cytoskeleton that confers muscle cells with resilience to the forces associated with vertebrate life.     

Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

Summary By using complete sequence data of mitochondrial DNAs, three Markov models (Day-hoff, Proportional, and Poisson models) for amino acid substitutions during evolution were applied in maximum likelihood analyses of mitochondrially encoded proteins to estimate a phylogenetic tree depicting human, cow, whale, and murids (mouse and rat), with chicken, frog, and carp as outgroups. A cow/whale clade was confirmed with a more than 99.8% confidence level by any of the three models, but the branching order among human, murids, and the cow/whale clade remained uncertain. It turned out that the Dayhoff model is by far the most appropriate model among the alternatives in approximating the amino acid substitutions of mitochondrially encoded proteins, which is consistent with a previous analysis of a more limited data set. It was shown that the substitution rate of mitochondrially encoded proteins has increased in the order of fishes, amphibians, birds, and mammals and that the rate in mammals is at least six times, probably an order of magnitude, higher than that in fishes. The higher evolutionary rate in birds and mammals than in amphibians and fishes was attributed to relaxation of selective constraints operating on proteins in warm-blooded vertebrates and to high mutation rate of bird and mammalian mitochondrial DNAs.Offprint requests to: M. Hasegawa     

Dynamic evolution of bitter taste receptor genes in vertebrates

Background  

Sensing bitter tastes is crucial for many animals because it can prevent them from ingesting harmful foods. This process is mainly mediated by the bitter taste receptors (T2R), which are largely expressed in the taste buds. Previous studies have identified some T2R gene repertoires, and marked variation in repertoire size has been noted among species. However, the mechanisms underlying the evolution of vertebrate T2R genes remain poorly understood.     

Structure and evolution of the horizontal septum in vertebrates

Although the horizontal septum (HS) has been identified as playing a role in fish biomechanics and in path finding of cells during zebrafish development, its morphology is poorly known. However, it is generally regarded as an evolutionarily conserved structure. To test this idea, we applied a novel combination of techniques to analyse the HS of 35 species from all major gnathostome clades in which is visualized its collagen fibre architecture. Results show that the HS is a conserved trait only with respect to the presence of caudolateral [= epicentral] and craniolateral [= posterior oblique] collagen fibre tracts, but differs remarkably with respect to the specifications of these tracts. Our data revealed several evolutionary changes within vertebrates. In the gnathostome ancestor, the two tracts are represented by evenly distributed epicentral fibres (ECFs) and posterior oblique fibres (POFs). ECFs are condensed to distinct epicentral tendons (ECTs) in the actinopteran ancestor. POFs independently evolved to distinct posterior oblique tendons (POTs) at least two times within teleosts. Within basal teleostomes, POFs as well as ECFs or ECTs were lost two times independently. POTs were lost at least three times independently within teleosts. This view of a homoplastic HS remains stable regardless of the competing phylogenies used for analysis. Our data make problematic any generalization of biomechanical models on fish swimming that include the HS. They indicate that the pathfinding role of the HS in zebrafish may be extended to gnathostome fishes, but not to agnathans, sarcopterygian fishes and tetrapods.