Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions

One important mechanism for functional innovation during evolution is the duplication of genes and entire genomes. Evidence is accumulating that during the evolution of vertebrates from early deuterostome ancestors entire genomes were duplicated through two rounds of duplications (the 'one-to-two-to-four' rule). The first genome duplication in chordate evolution might predate the Cambrian explosion. The second genome duplication possibly dates back to the early Devonian. Recent data suggest that later in the Devonian, the fish genome was duplicated for a third time to produce up to eight copies of the original deuterostome genome. This last duplication took place after the two major radiations of jawed vertebrate life, the ray-finned fish (Actinopterygia) and the sarcopterygian lineage, diverged. Therefore the sarcopterygian fish, which includes the coelacanth, lungfish and all land vertebrates such as amphibians, reptiles, birds and mammals, tend to have only half the number of genes compared with actinopterygian fish. Although many duplicated genes turned into pseudogenes, or even 'junk' DNA, many others evolved new functions particularly during development. The increased genetic complexity of fish might reflect their evolutionary success and diversity.     

The structure and evolution of the melanocortin and MCH receptors in fish and mammals

Zebrafish are an excellent genetic model system for studying developmental and physiological processes. Pigment patterns in zebrafish are affected by mutations in three types of chromatophores. The behavior of these cells is influenced by alpha-melanocyte-stimulating hormone (alphaMSH) and melanin-concentrating hormone (MCH). Mammals have five alphaMSH receptors (melanocortin receptors) and one or two MCH receptors. We have identified the full complement of melanocortin and MCH receptors in both zebrafish and the pufferfish, Fugu. Zebrafish have six melanocortin receptors, including two MC5R orthologues, while Fugu, lacking MC3R, has only four. We also demonstrate that Fugu and zebrafish have two and three MCHR genes, respectively. MC2R and MC5R are physically linked in all species examined. Unlike other species, we find the Fugu genes contain introns, one of which is in a conserved location and is probably ancestral. We also detail the differential expression of the zebrafish genes throughout development.     

Role of iron in the pathogenicity of Vibrio damsela for fish and mammals

Abstract The ability to obtain iron of 14 isolates of Vibrio damsela with different degrees of virulence for mice and turbot ( Scophthalmus maximus ) has been evaluated in artificial and natural iron-restricted environments. All strains were capable of utilizing haemoglobin (Hb) and ferric ammonium citrate (FAC) as the sole iron sources in vitro. However, only virulent V. damsela strains were able to resist the bacterioslatic and bactericidal effects of human and turbot sera, their growth being enhanced by the addition of Hb and FAC. The inhibitory effect of these sera on the growth of the non-pathogenic strain (ATCC 35083), however, was reversed by heat treatment (56°C for 60 min). The role of iron-availability on the virulence was investigated in iron-overloaded animals. The iron-treatment before the infection resulted in a significant reduction in the LD₅₀ of virulent strains. This fact demonstrates a positive correlation between iron availability in host fluids and degree of virulence in the species Vibrio damsela .     

Process of exotrophy in fish. Effects of the heavy metals Zn and Cu

The review summarizes for the first time the information on effects of Zn and Cu on various links of the fish exotrophy process. It has been shown that essential metals, like the nonessential ones, can produce negative effects on various aspects of the feeding behavior, on sensor systems providing feeding behavior, and on the digestive enzymes realizing digestion in fish of different ecological groups. A particular attention is paid to their different effects on proteinases functioning in stomach and intestine of various fish species as well as on hydrolase activities in their potential food objects (fish and invertebrate animals). Several mechanisms are considered which allow decreasing the negative action of Zn and Cu on the process of fish exotrophy.     

Molecular evolution and functional divergence of the cytochrome P450 3 (CYP3) Family in Actinopterygii (ray-finned fish)

Background

The cytochrome P450 (CYP) superfamily is a multifunctional hemethiolate enzyme that is widely distributed from Bacteria to Eukarya. The CYP3 family contains mainly the four subfamilies CYP3A, CYP3B, CYP3C and CYP3D in vertebrates; however, only the Actinopterygii (ray-finned fish) have all four subfamilies and detailed understanding of the evolutionary relationship of Actinopterygii CYP3 family members would be valuable.

Methods and Findings

Phylogenetic relationships were constructed to trace the evolutionary history of the Actinopterygii CYP3 family genes. Selection analysis, relative rate tests and functional divergence analysis were combined to interpret the relationship of the site-specific evolution and functional divergence in the Actinopterygii CYP3 family. The results showed that the four CYP3 subfamilies in Actinopterygii might be formed by gene duplication. The first gene duplication event was responsible for divergence of the CYP3B/C clusters from ancient CYP3 before the origin of the Actinopterygii, which corresponded to the fish-specific whole genome duplication (WGD). Tandem repeat duplication in each of the homologue clusters produced stable CYP3B, CYP3C, CYP3A and CYP3D subfamilies. Acceleration of asymmetric evolutionary rates and purifying selection together were the main force for the production of new subfamilies and functional divergence in the new subset after gene duplication, whereas positive selection was detected only in the retained CYP3A subfamily. Furthermore, nearly half of the functional divergence sites appear to be related to substrate recognition, which suggests that site-specific evolution is closely related with functional divergence in the Actinopterygii CYP3 family.

Conclusions

The split of fish-specific CYP3 subfamilies was related to the fish-specific WGD, and site-specific acceleration of asymmetric evolutionary rates and purifying selection was the main force for the origin of the new subfamilies and functional divergence in the new subset after gene duplication. Site-specific evolution in substrate recognition was related to functional divergence in the Actinopterygii CYP3 family.     

The role of fish parasites in fresh-water ecosystems exemplified by a parasite of the smelt (Osmerus eperlanus)

The European smelt Osmerus eperlanus had been accidentally introduced into the ecosystem of the Syamozero Lake (Karelia). The population of this species has achieved a high density and caused serious changes in the structure and trophic relationships of fish community of the Syamozero ecosystem. The microsporidia Glugea hertwigi Weisenberg, 1921 has become a new and super-dominant parasite of the european smelt in this ecosystem. The invasion of microsporidia has caused a mass death of fishes, that has led to changes in population structure of the smelt and lowered a fish catch. The present study suggests to show a role of parasites in the ichthyocenosis structure regulation in freshwater ecosystem.     

Inner retinal photoreceptors (IRPs) in mammals and teleost fish.

Research over the past decade has provided overwhelming evidence that photoreception in the vertebrate eye is not confined to the rods and cones. The discovery of non-rod, non-cone ocular photoreceptors in mammals and fish arose from quite different lines of investigation. In transgenic mice entirely lacking functional rod and cone photoreceptors a range of responses to light, including the regulation of the circadian system and a pupillary light reflex, are preserved. Electrophysiological and imaging approaches were then able to characterise a coupled plexus of directly light sensitive ganglion cells. Most recently action spectroscopy has shown that a novel 'blue-light' sensitive photopigment based upon opsin/vitamin A (OP480) mediates these responses to light. Several candidate genes have emerged for OP480, with melanopsin being by far the strongest. A definitive link, however, between this gene and OP480 has still to be established. In contrast to the mammals, the discovery of inner retinal photoreceptors (IRPs) in fish started with the discovery of a new gene family (VA opsin). The teleost VA opsins form functional photopigments and are expressed in several different types of inner retinal neuron, including retinal horizontal cells. Recent studies have investigated the electrical properties of these photosensitive neurones, but their light-sensing role remains a matter of speculation. Thus the study of IRP is developing along quite separate lines. In the mammals the research is directed towards a molecular identification of the photopigment (OP480) and its cascade, whilst in fish the major effort is directed towards identifying a role for these novel photoreceptors using physiological approaches. The discovery of IRPs in the vertebrates tells us that despite 150 years of research, we still have much to learn about how the eye processes light.     

Role of a single amino acid in the evolution of glycans of invertebrates and vertebrates

Structures of glycoconjugate N-glycans and glycolipids of invertebrates show significant differences from those of vertebrates. These differences are due largely to the vertebrate beta1,4-galactosyltransferase-1 (beta4Gal-T1), which is found as a beta1,4-N-acetylgalactosaminyltransferase (beta4GalNAc-T1) in invertebrates. Mutation of Tyr285 to Ile or Leu in human beta4Gal-T1 converts the enzyme into an equally efficient beta4GalNAc-T1. A comparison of all the human beta4Gal-T1 ortholog enzymes shows that this Tyr285 residue in human beta4Gal-T1 is conserved either as Tyr or Phe in all vertebrate enzymes, while in all invertebrate enzymes it is conserved as an Ile or Leu. We find that mutation of the corresponding Ile residue to Tyr in Drosophila beta4GalNAc-T1 converts the enzyme to a beta4Gal-T1 by reducing its N-acetylgalactosaminyltransferase activity by nearly 1000-fold, while enhancing its galactosyltransferase activity by 80-fold. Furthermore, we find that, similar to the vertebrate/mammalian beta4Gal-T1 enzymes, the wild-type Drosophila beta4GalNAc-T1 enzyme binds to a mammary gland-specific protein, alpha-lactalbumin (alpha-LA). Thus, it would seem that, during the evolution of vertebrates from invertebrates over 500 million years ago, beta4Gal-T1 appeared as a result of the single amino acid substitution of Tyr or Phe for Leu or Ile in the invertebrate beta4GalNAc-T1. Subsequently, the pre-existing alpha-LA-binding site was utilized during mammalian evolution to synthesize lactose in the mammary gland during lactation.     

The angiosomes of the mammals and other vertebrates.

This is a comparative study of the vasculature of the integument and underlying deep tissues of a range of mammals and other vertebrates. The investigation was conducted in the pig, monkey, dog, cat, possum, guinea pig, rat, rabbit, duck, and toad. The results from each are compared not only to each other, but also to previously performed human studies. The arterial network of the fresh animal cadaver was injected with a mixture of lead oxide and gelatin. The vascular anatomy of the skin, deep tissues, and individual muscles was defined by dissection, cutaneous perforator counts, photography, and radiography. A similar pilot study of the venous framework was performed in the pig, dog, and rabbit that included maps of the sites and orientations of the valves. The vasculature of the integument and deep tissues was correlated, and we found that we were able to define angiosomes (composite blocks of tissue supplied by the same source vessel) in each animal. Results revealed a marked dissimilarity of the overlying cutaneous vessels in many cases, yet a striking resemblance of the vascular architecture of the deep tissues. The size and density of the cutaneous perforators bore a close relation to the degree of the skin mobility, being large and sparse where the skin was mobile and smaller and more densely grouped where the integument was tethered or fixed. The cutaneous vasculature of the human resembled that of the monkey closely, was similar to that of the dog, cat, and possum, and was dissimilar to that of the pig, rat, guinea pig, and rabbit. Studies of the amphibian and bird bore many resemblances to those of the mammals. They provided basic concepts regarding modification of the animals' vascular anatomy in response to the functional demands of the species. In each animal, the arteries formed an unbroken network throughout the body. This consisted of anatomic territories linked by anastomotic vessels that were usually of reduced caliber. The pattern of the venous system was almost identical. Valved venous territories were linked by avalvular (oscillating) veins. The common denominator in the vascular system is the capillary bed. Conceptually, the anatomic arrangement of the arteries and veins, reproduced in each species, appears to be a sophisticated mechanism to allow equilibration of flow and pressure arriving at and departing from the capillary bed. The angiosome concept is reinforced by the animal studies. Although this investigation is essentially a detailed pilot study, it embraces many animals commonly used for experimentation and provides a reference atlas of their vasculature.(ABSTRACT TRUNCATED AT 400 WORDS)     

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.     

The ecology of communities of related animal species (research approaches and methods exemplified by terrestrial vertebrates)]

The review is dedicated to some old and modern problems in studying of the assemblages of phylogenetically related species among terrestrial vertebrates. The classical approach by Robert Mac-Arthur, discussed elsewhere summarized briefly. Although an explanative potential of competition theory seems exhausted there is no new paradigm that can simply explain species diversity in natural communities. From the beginning of 90's community ecology became very complex and controversial discipline. At the same time it is still a pioneering science. We have not enough comparative data on geo2 graphically distinct communities studied under the unified methods of data collection and analysis. Some recent results of intercontinental comparisons signify to the high degree of individualism in structure of geographically isolated communities. This makes doubtful any extrapolation from one region to another. Examination and explanation of processes is still the most contradictory field in community ecology. Confusion of causes and effects is continuing to be serious methodological problem. Much of attention was paid recently to the macroecological approach. A desire for reconsideration of some "old rules" of biodiversity is explained by advances in paleozoology, biogeography and systematic, as well as by some unsatisfactory explanations within the framework of competition theory.     

AZFY-like sequence in fish,with comments on the evolution of theZFY family of genes in vertebrates

ZFY-like genes have been observed in a variety of vertebrate species. Although originally implicated as the primary testis-determining gene in humans and other placental mammals, more recent evidence indicates a role(s) outside that of testis determination. In this study, DNA from five species of fish,Carasius auratus, Rivulus marmoratus, Xiphophorus maculatus, X. milleri, andX. nigrensis was subjected to Southern blot analysis using a PCR-amplified fragment of mouseZFY-like sequence as a probe. Restriction fragment patterns were not polymorphic between sexes in any one species but showed a different pattern for each species. With one exception,Rivulus, a 3.1-kb band from theEcoRI digestion was common to all. Sequence and open reading frame analysis of this fragment showed a strong homology to other known vertebrateZFY-like genes. Of particular interest in this gene is a novel third finger domain similar to one human and one alligatorZFY-like gene. Our studies and others provide evidence for a family of vertebrateZFY genes, with those having this novel third finger being representative of the ancestral condition.     

A new locality of Late Cretaceous snakes, mammals and other vertebrates in Africa (western Libya)

s sp. nov. (Reptilia sp. nov. (Reptilia, Serpentes, Simoliopheidae) is described from the Upper Cretaceous ‘unnamed’ beds of the Mizdah Formation (Santonian-Campanian) at Draa Ubari in western Libya. The accompanying fauna consists of an undetermined mammal represented by a caudal vertebra, of hybodontoid, ganopristid and lamnoid sharks, as well as dipnoans, lepisosteids, pycnodonts, enchodontids, turtles, crocodiles and ?dinosaurs.

Résumé

Une nouvelle localité de serpents, mammifères et autres vertébrés du Crétacé supérieur en Afrique (Libye occidentale). s sp. nov. (Reptilia sp. nov. (Reptilia, Serpentes, Simoliopheidae) est décrit dans des grès de la formation Mizdah (Santonien-Campanien), à Draa Ubari en Libye occidentale. Les mêmes couches ont livré une vertèbre caudale de mammifère indéterminé, ainsi que des restes de requins hybodontoïdes, ganopristidés et lamnoïdes, de dipneustes, lépisostéïdes, pycnodontes, enchodontidés, tortues, crocodiles et? dinosaures.     

The evolution of pepsinogen C genes in vertebrates: duplication, loss and functional diversification

Background

Aspartic proteases comprise a large group of enzymes involved in peptide proteolysis. This collection includes prominent enzymes globally categorized as pepsins, which are derived from pepsinogen precursors. Pepsins are involved in gastric digestion, a hallmark of vertebrate physiology. An important member among the pepsinogens is pepsinogen C (Pgc). A particular aspect of Pgc is its apparent single copy status, which contrasts with the numerous gene copies found for example in pepsinogen A (Pga). Although gene sequences with similarity to Pgc have been described in some vertebrate groups, no exhaustive evolutionary framework has been considered so far.

Methodology/Principal Findings

By combining phylogenetics and genomic analysis, we find an unexpected Pgc diversity in the vertebrate sub-phylum. We were able to reconstruct gene duplication timings relative to the divergence of major vertebrate clades. Before tetrapod divergence, a single Pgc gene tandemly expanded to produce two gene lineages (Pgbc and Pgc2). These have been differentially retained in various classes. Accordingly, we find Pgc2 in sauropsids, amphibians and marsupials, but not in eutherian mammals. Pgbc was retained in amphibians, but duplicated in the ancestor of amniotes giving rise to Pgb and Pgc1. The latter was retained in mammals and probably in reptiles and marsupials but not in birds. Pgb was kept in all of the amniote clade with independent episodes of loss in some mammalian species. Lineage specific expansions of Pgc2 and Pgbc have also occurred in marsupials and amphibians respectively. We find that teleost and tetrapod Pgc genes reside in distinct genomic regions hinting at a possible translocation.

Conclusions

We conclude that the repertoire of Pgc genes is larger than previously reported, and that tandem duplications have modelled the history of Pgc genes. We hypothesize that gene expansion lead to functional divergence in tetrapods, coincident with the invasion of terrestrial habitats.