One melanocortin 4 and two melanocortin 5 receptors from zebrafish show remarkable conservation in structure and pharmacology

We report the cloning, genome mapping, functional expression, pharmacology and anatomical distribution of three melanocortin (MC) receptors from zebrafish (z). Phylogenetic analysis showed with high bootstrap support that these genes represent one MC4 receptor and two MC5 receptors. Chromosomal mapping showed conserved synteny between regions containing zMC4 and human (h) MC4 receptors, whereas the two zMC5 receptor genes map on chromosome segments in which the zebrafish has several genes with two orthologues of a single mammalian gene. It is likely that the two copies of zMC5 receptors arose through a separate duplication in the teleost lineage. The zMC4, zMC5a, and zMC5b receptors share 70-71% overall amino acid identity with the respective human orthologues and over 90% in three TM regions believed to be most important for ligand binding. All three zebrafish receptors also show pharmacological properties remarkably similar to their human orthologues, with similar affinities and the same potency order, when expressed and characterized in radioligand binding assay for the natural MSH) peptides alpha-, beta-, and gamma-MSH. Stimulation of transfected mammalian cells with alpha-MSH caused a dose-dependent increase in intracellular cAMP levels for all three zebrafish receptors. All three genes were expressed in the brain, eye, ovaries and gastrointestinal tract, whereas the zMC5b receptor was also found in the heart, as determined by RT-PCR. Our studies, which represent the first characterization of MC receptors in a nonamniote species, indicate that the MC receptor subtypes arose very early in vertebrate evolution. Important pharmacological and functional properties, as well as gene structure and syntenic relationships have been highly conserved over a period of more than 400 million years implying that these receptors participate in vital physiological functions.     

Cytogenetics, conserved synteny and evolution of chicken fucosyltransferase genes compared to human

Fucosyltransferases appeared early in evolution, since they are present from bacteria to primates and the genes are well conserved. The aim of this work was to study these genes in the bird group, which is particularly attractive for the comprehension of the evolution of the vertebrate genome. Twelve fucosyltransferase genes have been identified in man. The orthologues of theses genes were looked for in the chicken genome and cytogenetically localized by FISH. Three families of fucosyltransferases: alpha6-fucosyltransferases, alpha3/4-fucosyltransferases, and protein-O-fucosyltransferases, were identified in the chicken with their associated genes. The alpha2-fucosyltransferase family, although present in some invertebrates and amphibians was not found in birds. This absence, also observed in Drosophila, may correspond to a loss of these genes by negative selection. Of the eight chicken genes assigned, six fell on chromosome segments where conservation of synteny between human and chicken was already described. For the two remaining loci, FUT9 and FUT3/5/6, the location may correspond to a new small syntenic area or to an insertion. FUT4 and FUT3/5/6 were found on the same chicken chromosome. These results suggest a duplication of an ancestral gene, initially present on the same chromosome before separation during evolution. By extension, the results are in favour of a common ancestor for the alpha3-fucosyltransferase and the alpha4-fucosyltransferase activities. These observations suggest a general mechanism for the evolution of fucosyltransferase genes in vertebrates by duplication followed by divergent evolution.     

Comparative study on synteny between yeasts and vertebrates

We studied synteny conservation between 18 yeast species and 13 vertebrate species in order to provide a comparative analysis of the chromosomal plasticity in these 2 phyla. By computing the regions of conserved synteny between all pairwise combinations of species within each group, we show that in vertebrates, the number of conserved synteny blocks exponentially increases along with the divergence between orthologous protein and that concomitantly; the number of genes per block exponentially decreases. The same trends are found in yeasts but only when the mean protein divergence between orthologs remains below 36%. When the average protein divergence exceeds this threshold, the total number of recognizable synteny blocks gradually decreases due to the repeated accumulation of rearrangements. We also show that rearrangement rates are on average 3-fold higher in vertebrates than in yeasts, and are estimated to be of 2 rearrangements/Myr. However, the genome sizes being on average 200 times larger in vertebrates than in yeasts, the normalized rates of chromosome rearrangements (per Mb) are about 50-fold higher in yeast than in vertebrate genomes.     

Neuropeptide Y-family receptors Y6 and Y7 in chicken. Cloning, pharmacological characterization, tissue distribution and conserved synteny with human chromosome region

The peptides of the neuropeptide Y (NPY) family exert their functions, including regulation of appetite and circadian rhythm, by binding to G-protein coupled receptors. Mammals have five subtypes, named Y1, Y2, Y4, Y5 and Y6, and recently Y7 has been discovered in fish and amphibians. In chicken we have previously characterized the first four subtypes and here we describe Y6 and Y7. The genes for Y6 and Y7 are located 1 megabase apart on chromosome 13, which displays conserved synteny with human chromosome 5 that harbours the Y6 gene. The porcine PYY radioligand bound the chicken Y6 receptor with a K(d) of 0.80 +/- 0.36 nm. No functional coupling was demonstrated. The Y6 mRNA is expressed in hypothalamus, gastrointestinal tract and adipose tissue. Porcine PYY bound chicken Y7 with a K(d) of 0.14 +/- 0.01 nm (mean +/- SEM), whereas chicken PYY surprisingly had a much lower affinity, with a Ki of 41 nm, perhaps as a result of its additional amino acid at the N terminus. Truncated peptide fragments had greatly reduced affinity for Y7, in agreement with its closest relative, Y2, in chicken and fish, but in contrast to Y2 in mammals. This suggests that in mammals Y2 has only recently acquired the ability to bind truncated PYY. Chicken Y7 has a much more restricted tissue distribution than other subtypes and was only detected in adrenal gland. Y7 seems to have been lost in mammals. The physiological roles of Y6 and Y7 remain to be identified, but our phylogenetic and chromosomal analyses support the ancient origin of these Y receptor genes by chromosome duplications in an early (pregnathostome) vertebrate ancestor.     

Analysis of the conservation of synteny between Fugu and human chromosome 12

Background

The pufferfish Fugu rubripes (Fugu) with its compact genome is increasingly recognized as an important vertebrate model for comparative genomic studies. In particular, large regions of conserved synteny between human and Fugu genomes indicate its utility to identify disease-causing genes. The human chromosome 12p12 is frequently deleted in various hematological malignancies and solid tumors, but the actual tumor suppressor gene remains unidentified.

Results

We investigated approximately 200 kb of the genomic region surrounding the ETV6 locus in Fugu (fETV6) in order to find conserved functional features, such as genes or regulatory regions, that could give insight into the nature of the genes targeted by deletions in human cancer cells. Seven genes were identified near the fETV6 locus. We found that the synteny with human chromosome 12 was conserved, but extensive genomic rearrangements occurred between the Fugu and human ETV6 loci.

Conclusion

This comparative analysis led to the identification of previously uncharacterized genes in the human genome and some potentially important regulatory sequences as well. This is a good indication that the analysis of the compact Fugu genome will be valuable to identify functional features that have been conserved throughout the evolution of vertebrates.

     

Association of feather colour with constitutively active melanocortin 1 receptors in chicken.

Seven alleles of the chicken melanocortin (MC) 1 receptor were cloned into expression vectors, expressed in mammalian cells and pharmacologically characterized. Four of the clones e(+R), e(+B&D), e(wh)/e(y), E(Rfayoumi) gave receptors to which melanocortin stimulating hormone (alpha-MSH) and NDP-MSH bound with similar IC50 values and responded to alpha-MSH by increasing intracellular cAMP levels in a dose-dependent manner. Three of the cMC1 receptors; e(b), E and E(R), did not show any specific binding to the radioligand, but were found to be constitutively active in the cAMP assay. The E and E(R) alleles are associated with black feather colour in chicken while the eb allele gives rise to brownish pigmentation. The three constitutively active receptors share a mutation of Glu to Lys in position 92. This mutation was previously found in darkly pigmented sombre mice, but constitutively active MC receptors have not previously been shown in any nonmammalian species. We also inserted the Glu to Lys mutation in the human MC1 and MC4 receptors. In contrast with the chicken clones, the hMC1-E94K receptor bound to the ligand, but was still constitutively active independently of ligand concentration. The hMC4-E100K receptor did not bind to the MSH ligand and was not constitutively active. The results indicate that the structural requirements that allow the receptor to adapt an active conformation without binding to a ligand, as a consequence of this E/K mutation, are not conserved within the MC receptors. The results are discussed in relationship to feather colour in chicken, molecular receptor structures and evolution. We suggest that properties for the 'E92K switch' mechanism may have evolved in an ancestor common to chicken and mammals and were maintained over long time periods through evolutionary pressure, probably on closely linked structural features.     

Conserved synteny of mammalian imprinted genes in chicken, frog, and fish genomes

Conservation of synteny of mammalian imprinted genes between chicken and human suggested that highly conserved gene clusters were selected long before these genes were recruited for genomic imprinting in mammals. Here we have applied in silico mapping of orthologous genes in pipid frog, zebrafish, spotted green and Japanese pufferfish to show considerable conservation of synteny in lower vertebrates. More than 400 million years ago in a common ancestor of teleost fish and tetrapods, 'preimprinted' chromosome regions homologous to human 6q25, 7q21, 7q32, 11p15, and 15q11-->q12 already contained most present-day mammalian imprinted genes. Interestingly, some imprinted gene orthologues which are isolated from imprinted clusters in mouse and human could be linked to preimprinted regions in lower vertebrates, indicating that separation occurred during mammalian evolution. On the contrary, newly arisen genes by segmental duplication in the mammalian lineage, i.e. SNRPN and FRAT3, were transposed or translocated to imprinted clusters and recruited for parent-specific activity. By analysis of currently available sequences of non-mammalian vertebrates, the imprinted gene clusters homologous to human chromosomes 14q32 and 19q12 are only poorly conserved in chicken, frog, and fish and, therefore, may not have evolved from ancestral preimprinted gene arrays. Evidently, evolution of imprinted gene clusters is an ongoing and dynamic process in mammals. In general, imprinted gene orthologues do not show a higher degree of synteny conservation in vertebrates than non-imprinted genes interspersed with or adjacent to an imprinted cluster.     

Deletions of the N-terminal regions of the human melanocortin receptors

The non-homologous N-terminal regions of four human melanocortin (MC) receptors were truncated in order to investigate their putative participation in ligand binding. Eleven constructs were made, where different numbers of residues from the N terminus were deleted. These constructs were used for transient expression experiments in COS cells and analysed by ligand binding. The results show that 27, 25, 28, and 20 amino acids could be deleted from the N terminus of the human MC1, MC3, MC4 and MC5 receptors, respectively, including all potential N-terminal glycosylation sites in the MC1 and the MC4 receptors, without affecting ligand binding or expression levels. The results indicate that the N-terminal regions of the human MC1, MC3, MC4 and MC5 receptors, do not play an important role for the ligand binding properties of these receptors.     

Pharmacological comparison of rat and human melanocortin 3 and 4 receptors in vitro

The melanocortin 3 and 4 receptors are G-protein-coupled receptors found in the hypothalamus with important role in regulation of the energy balance. In this study, we performed pharmacological comparison of the rat and human melancortin (MC) 3 and MC4 receptors. We transiently expressed the genes for these receptors individually in a mammalian cell line and determined the binding affinities to several MSH peptides. The results showed no major difference between the rat and human MC3 receptors while the rat MC4 receptor had higher affinity to several peptides compared with the human MC4 receptor. NDP-, alpha-, beta-, gamma-MSH, ACTH(1-24), HS014 and MTII had from 5- to 34-fold higher affinity for the rat MC4 receptor, while SHU9119, HS024 and HS028 had similar affinity for both the MC4 receptors. Pharmacological species difference have earlier been reported for the MC1 and MC5 receptors but this is the first report showing important differences between the rat and human MC4 receptors.     

Measures of synteny conservation between species pairs

Measures of conserved synteny are important for estimating the relative rates of chromosomal evolution in various lineages. We present a natural way to view the synteny conservation between two species from an Oxford grid--an r x c table summarizing the number of orthologous genes on each of the chromosomes 1 through r of the first species that are on each of the chromosomes 1 through c of the second species. This viewpoint suggests a natural statistic, which we denote by rho and call syntenic correlation, designed to measure the amount of synteny conservation between two species. This measure allows syntenic conservation to be compared across many pairs of species. We improve the previous methods for estimating the true number of conserved syntenies given the observed number of conserved syntenies by taking into account the dependency of the numbers of orthologues observed in the chromosome pairings between the two species and by determining both point and interval estimators. We also discuss the application of our methods to genomes that contain chromosomes of highly variable lengths and to estimators of the true number of conserved segments between species pairs.     

Functional characterization of the modified melanocortin peptides responsible for ligand selectivity at the human melanocortin receptors

The melanocortin system plays an important role in energy homeostasis as well as skin pigmentation, steroidogenesis and exocrine gland function. In this study, we examined eight Ac-His-Phe-Arg-Trp-NH(2) tetrapeptides that were modified at the Phe position and pharmacologically characterized their activities at the human MCR wild-types and their mutants. Our results indicate that at the hMC1R, all D stereochemical modified residues at the Phe position of peptides increase cAMP production in a dose-dependent manner. At the hMC3R, the DPhe peptide dose dependently increases cAMP production but all other three tetrapeptides were not. At the hMC4R, both the DPhe and DNal(1') peptides induce cAMP production. However, both DTyr and DNal(2') were not able to induce cAMP production. Further studies indicated that at the hMC1R M128L mutant receptor, the all D-configured tetrapeptides reduce their potencies as compared to that of hMC1R wild-type. However, at the hMC3R and hMC4R L165M and L133M mutant receptors, the DNal(2') and DTyr tetrapeptides possess agonist activity. These findings indicate that DPhe in tetrapeptide plays an important role in ligand selectivity and specific residue TM3 of the melanocortin receptors is crucial for ligand selectivity.     

Expression of endothelin receptors in frog, chicken, mouse and human pigment cells

Several reports have shown the participation of vasoactive endothelins (ETs) in the regulation of vertebrate pigment cells. In the present study, we identified ET receptors in pigment cells of vertebrate species by RT-PCR assays, and compared the differential expression of the various subtypes in each species by quantitative PCR. RT-PCR was performed with specific primers for ETC, ETA(X) or ETA in Xenopus laevis melanophores, ETA or ETB(2) in chicken melanocytes, ETA or ETB in murine (B-16, S-91 or Melan-A) or human (SK-Mel 23 or SK-Mel 28) melanoma cells, and the products obtained were confirmed by cloning and sequencing. The results showed the presence of ETA(X), but not ETA mRNA, and confirmed the expression of ETC in X. laevis melanophores. ETA and ETB(2) mRNAs were also demonstrated in chicken melanocytes. ETA and ETB receptor were identified in S-91, B16 and Melan-A murine cells. In human melanoma cells, SK-Mel 23 and SK-Mel 28, we confirmed the presence of ETB mRNA, and also found ETA mRNA. The comparison between the two subtypes present in the pigment cell of each species and among species demonstrated that the expression of ETAs in chicken, mouse, and human melanocytes is negligible, as is the expression of ETA(X) in Xenopus melanophores. The relative expression, as determined by quantitative PCR, was as follows: chicken ETB>SK-Mel 23 ETB>S91 ETB>Xenopus ETC, suggesting that the endothelin system plays a major role in avian and mammalian pigment cell regulation, as compared to lower vertebrates. The phylogenetic analysis revealed that subtype A receptors were probably the most primitive ET receptors, directly deriving from the ancestral type; all the other receptors, B subtypes and C, originated from diverse derivative molecules.     

Evolutionary conservation of KLF transcription factors and functional conservation of human gamma-globin gene regulation in chicken

The Krüppel-like factors (KLFs) are a family of Cys2His2 zinc-finger DNA binding proteins with homology to Drosophila Krüppel. KLFs can bind to CACCC elements, which are important in controlling developmental programs. The CACCC promoter element is critical for the developmental regulation of the human gamma-globin gene. In the present study, chicken homologues of the human KLF2, 3, 4, 5, 9, 11, 12, 13, and 15 genes were identified. Phylogenetic analysis confirms that these genes are more closely related to their human homologues than they are to other chicken KLFs. This work also represents the first systematic study of the expression patterns of KLFs during erythroid development. In addition, transient transfections of human globin constructs into 5-day (primitive) chicken red blood cells show that human gamma-globin expression is regulated via its CACCC promoter element. This indicates that a CACCC-binding factor(s) important for gamma-globin expression functions in 5-day chicken red cells.     

Semi-rigid tripeptide agonists of melanocortin receptors

A series of 30 RCO–HfR–NH₂ derivatives show preference for the mouse MC1R vs MC3-5Rs. trans-4-HOC₆H₄CHCHCO–HfR–NH₂ (13) [EC₅₀ (nM): MC1R 83, MC3R 20500, MC4R 18130 and MC5R 935; ratio 1:246:217:11] is 11 times more potent than the lead compound LK-394 Ph(CH₂)₃CO–HfR–NH₂ (2) and only 11 times less potent than the native tridecapeptide α-MSH at mMC1R. Differences in conformations of 2 and 13 are discussed.     

Functional conservation of hematopoietic factors in Drosophila and vertebrates

The GATA, Friend of GATA, and Runt homology domain protein families function during hematopoiesis to promote progenitor cell development and regulate lineage commitment and differentiation. The hematopoietic functions of these factors have been remarkably conserved across taxonomic groups, ranging from flies to humans. Furthermore, aspects of hematopoiesis and hemocyte function appear to be conserved. Thus, comparative studies using Drosophila and vertebrate models should enhance our understanding of blood cell development.