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Abstract: Gene duplication is thought to facilitate increasing complexity in the evolution of life. The fate of most duplicated genes is nonfunctionalization: functional decay resulting from the accumulation of mutations. [...]

The fatty acid-binding protein (fabp) genes belong to the multigene family of intracellular lipid-binding proteins. To date, 12 different FABPs have been identified in vertebrate genomes. Owing to the teleost-specific genome duplication event, many fishes have duplicated copies of the fabp genes. Here, we identified and characterized the fabp genes of spotted green pufferfish (Tetraodon nigroviridis). Seven fabp genes were identified, out of which, two were retained in the pufferfish genome as duplicated copies. Each putative pufferfish Fabp protein shares greatest sequence identity and similarity with their teleost and tetrapod orthologs, and clustered together as a distinct clade in phylogenetic analysis. Conserved gene synteny was evident between the pufferfish fabp genes and the orthologs of human, zebrafish, three-spined stickleback, and medaka FABP/fabp genes, providing evidence that the duplicated copies of pufferfish fabp genes most likely arose as a result of the teleost- specific genome duplication event. The differential tissue-specific distribution of pufferfish fabp transcripts suggests divergent spatial regulation of duplicated pairs of fabp genes. Key words: spotted green pufferfish, fatty acid-binding protein, teleost-specific genome duplication. Les genes codant pour des proteines de liaison aux acides gras (fabp) appartiennent a une famille multigenique de proteines intracellulaires de liaison des lipides. A ce jour, 12 FABP differents ont ete identifies au sein des genomes de vertebres. En raison de l'evenement de duplication genomique specifique des teleosteens, plusieurs poissons ont des copies dupliquees des genes fabp. Dans ce travail, les auteurs identifient et caracterisent les genes fabp chez le tetraodon vert (Tetraodon nigroviridis). Sept genes fapb ont ete identifies, dont deux representent des copies dupliquees qui ont ete conservees au sein du genome du tetraodon. Chaque proteine Fabp putative chez le tetraodon presente une identite et une similarite maximale avec son orthologue chez les teleosteens et les tetrapodes, de maniere a former un clade distinct en analyse phylogenetique. Une syntenie genique etait evidente entre les genes fabp du tetraodon et leurs orthologues chez l'humain, le poisson zebre, l'epinoche a trois epines et le medaka, ce qui suggere que les copies dupliquees des genes FABP/fabp chez le tetraodon sont vraisemblablement le resultat de l'evenement de duplication genomique specifique des teleosteens. La distribution tissus-specifique differentielle des transcrits fabp suggere une regulation spatiale divergente des paires de genes fabp dupliques. [Traduit par la Redaction] Mots-cles: tetraodon vert, proteine de liaison des acides gras, duplication genomique specifique des teleosteens., Introduction The members of the family of intracellular lipid-binding proteins (iLBP) are known to play vital roles in the transport of hydrophobic ligands such as long-chain fatty acids and retinoid [...]

A whole-genome duplication (WGD) early in the teleost fish lineage makes fish ideal organisms to study the fate of duplicated genes and underlying evolutionary trajectories that have led to the retention of ohnologous gene duplicates in fish genomes. Here, we compare the genomic organization and tissue-specific transcription of the ohnologous fabp7 and fabp10 genes in medaka, three-spined stickleback, and spotted green pufferish to the well-studied duplicated fabp7 and Fabp10 genes of zebrafish. Teleost fabp7 and fabp10 genes contain four exons interrupted by three introns. Polypeptide sequences of Fabp7 and Fabp10 show the highest sequence identity and similarity with their orthologs from vertebrates. Orthology was evident as the ohnologous Fabp7 and Fabp10 polypeptides of teleost fishes each formed distinct clades and clustered together with their orthologs from other vertebrates in a phylogenetic tree. Furthermore, ohnologous teleost fabp7 and fabp10 genes exhibit conserved gene synteny with human FABP7 and chicken FABP10, respectively, which provides compelling evidence that the duplicated fabp7 and fabp10 genes of teleost fishes most likely arose from the well-documented WGD. The tissue-specific distribution of fabp7a, fabp7b, fabp10a, and fabp10b transcripts provides evidence of diverged spatial transcriptional regulation between ohnologous gene duplicates of fabp7 and fabp10 in teleost fishes. Keywords: ohnologs, fabp7, fabp10, teleost, whole-genome duplication. Une duplication du genome entier qui s'est produite tot dans l'evolution des poissons teleosteens fait des poissons des organismes ideaux pour etudier le sort des genes dupliques et les trajectoires evolutives qui ont mene a la retention de ces genes dupliques, les ohnologues, au sein des genomes des poissons. Dans ce travail, les auteurs ont compare l'organisation genomique et le profil de transcription tissulaire des genes ohnologues fabp7 etfabp10 chez le medaka, l'epinoche a trois epines et le Tetraodon simulans a ceux rapportes pour leurs homologues largement etudies chez le poisson zebre, fabp7 etfabp10. Les genes fabp7 etfabp10 chez les teleosteens comptent quatre exons interrompus par trois introns. Les sequences proteiques de Fabp7 et de Fabp10 presentent les plus fortes identite et similarite de sequence avec leurs orthologues chez les vertebres. L'orthologie etait evidente chez les proteines ohnologues Fabp7 et Fabp10 des teleosteens, lesquelles formaient des clades distincts et etaient groupees avec leurs orthologues des autres vertebres au sein d'un arbre phylogenetique. De plus, les ohnologues fabp7 et fabp10 teleosteens presentaient respectivement une syntenie genique conservee avec les genes FABP7 humain et FABP10 du poulet, ce qui represente une preuve convaincante que les genes dupliques fabp7 et fabp10 des teleosteens seraient le fruit de la duplication genomique bien documentee. La repartition des transcrits fabp7a, fabp7b, fabp10a et fabp10b au sein des tissus fournit des evidences d'une regulation transcriptionnelle divergente entre ces genes dupliques ohnologues chez les teleosteens. [Traduit par la Redaction] Mots-cles: ohnologues, fabp7, fabp10, teleosteen, duplication du genome entier., Introduction Fatty acid binding proteins (FABPs) are abundant small intracellular proteins found in many tissues of vertebrates (Ockner et al. 1972; Veerkamp and Maatman 1995; Bernlohr et al. 1997). FABPs [...]

Here we describe the evolutionary relationship of the duplicated intestinal fatty acid binding protein genes fabp2a and fabp2b from medaka and three-spined stickleback by comparing them to the well-studied fabp2 gene from zebrafish. The duplicated fabp2 genes from medaka and three-spined stickleback consist of four exons separated by three introns, which code for a polypeptide of 132 amino acids. Fabp2a and Fabp2b of medaka and three-spined stickleback share highest sequence identity with zebrafish Fabp2. All Fabp2/FABP2 sequences from vertebrates form a distinct clade in a neighbor-joining phylogenetic tree with a robust 100% bootstrap value, which indicates that the medaka and three-spined stickleback fabp2a and fabp2b are orthologs of zebrafish fabp2. The syntenic genes of fabp2a and fabp2b from medaka and three-spined stickleback were shown to be conserved with the syntenic genes of fabp2/FABP2 from zebrafish and human, evidence that the duplicated fabp2 genes from medaka and three-spined stickleback most likely arose from the teleost-specific whole-genome duplication. The tissue- specific distribution of medaka and three-spined stickleback fabp2a and fabp2b transcripts, and zebrafish fabp2 transcripts, assayed by RT-qPCR suggests the acquisition of new function(s) by the medaka fabp2a, and the distinct evolution of fabp2b compared with fabp2a in the medaka and three-spined stickleback genomes. Key words: fabp2, medaka, three-spined stickleback, teleost, whole-genome duplication. Dans ce travail, les auteurs decrivent les relations evolutives de genes dupliques codant pour des proteines intestinales de liaison aux acides gras fabp2a etfabp2b chez le medaka et l'epinoche en les comparant au gene fabp2 bien etudie chez le poisson zebre. Les genes fabp2 dupliques chez le medaka et l'epinoche comptent quatre exons separes par trois introns et ils codent pour un polypeptide de 132 acides amines. Fabp2a et Fabp2b du medaka et de l'epinoche presentent la plus grande similarite de sequence avec Fabp2 du poisson zebre. Toutes les sequences Fabp2/FABP2 chez d'autres vertebres forment un clade distinct au sein des arbres phylogenetiques obtenus lors d'une analyse neighbor-joining avec une valeur de re-echantillonnage de 100%, ce qui indique que les genes fabp2a et fabp2b du medaka et de l'epinoche sont les orthologues de fabp2 du poisson zebre. Les genes synteniques avec fabp2a et fabp2b chez le medaka et l'epinoche sont conserves avec les genes synteniques avec fabp2/FABP2 chez le poisson zebre et l'humain, ce qui suggere que les genes fabp2 dupliques chez le medaka et l'epinoche seraient vraisemblablement le produit d'une duplication genomique specifique des teleosteens. L'analyse de l'expression tissulaire des genes fabp2a et fabp2b du medaka et de l'epinoche ainsi que fabp2 du poisson zebre, tel que mesuree par RT-qPCR, suggere l'acquisition de nouvelle(s) fonction(s) pour le gene fabp2a du medaka et une evolution distincte du gene fabp2b par rapport a fabp2a au sein des genomes du medaka et de l'epinoche. [Traduit par la Redaction] Mots-cles: fabp2, medaka, epinoche, teleosteen, duplication genomique., Introduction Fatty acids are an important source of energy in almost all vertebrates (EFSA Panel on Dietetic Products, Nutrition, and Allergies 2010). Owing to the hydrophobicity of fatty acids, they [...]

We describe a fatty acid-binding protein 1 (fabp1b.2) gene and its tissue-specific expression in zebrafish embryos and adults. The 3.5 kb zebrafish fabp1b.2 gene is the paralog of the previously described zebrafish fabp1a and fabp1b genes. Using the LN54 radiation hybrid mapping panel, we assigned the zebrafish fabp1b.2 gene to linkage group 8, the same linkage group to which fabp1b.1 was mapped. fabp1b.1 and fabp1b.2 appear to have arisen by a tandem duplication event. Whole-mount in situ hybridization of a riboprobe to embryos and larvae detected fabp1b.2 transcripts in the diencephalon and as spots in the periphery of the yolk sac. In adult zebrafish, in situ hybridization revealed fabp1b.2 transcripts in the anterior intestine and skin, and reverse transcription PCR (RT-PCR) detected fabp1b.2 transcripts in the intestine, brain, heart, ovary, skin, and eye. By contrast, fabp1b.1 transcripts were detected by RT-PCR in the liver, intestine, heart, testis, ovary, and gills. The tissue-specific distribution of transcripts for the tandemly duplicated fabp1b.1 and fabp1b.2 genes in adult tissues and during development suggests that the duplicated fabp1b genes of zebrafish have acquired additional functions compared with the ancestral fabp1 gene, i.e., by neofunctionalization. Furthermore, these functions were subsequently divided between fabp1b.1 and fabp1b.2 owing to subfunctionalization. Key words: whole genome duplication, Fabp1, L-Fabp, duplicated genes, tandem duplication, diencephalon, zebrafish. Les auteurs decrivent une proteine se liant aux acides gras (fabp1b.2) et son expression tissulaire chez les embryons et adultes du poison zebre. Le gene fabp1b.2 du poison zebre mesure 3,5 kb et il est le paralogue des genes fabp1a et fabp1b deja decrits. Au moyen du panel d'hybrides d'uradiation LN54, les auteurs ont assigne le gene fabp1b.2 au groupe de liaison 8, le meme groupe portant egalement fabp1b.1. fabp1b.1 et fabp1b.2 semblent provenir dune duplication en tandem. Des hybridations in situ au moyen dune sonde d'ARN marque sur des embryons et des larvas a detecte des transcrits de fabp1b.2 dans le diencephale et des signaux ponctuels dans la peripherie du sac vitellin. Chez les adultes, fhybridation in situ revele la presence de transcrits fabp1b.2 dans fintestin anterieur et la peau, et la RT-PCR detecte des transcrits fabp1b.2 dans fintestin, le cerveau, le coeur, l'ovaire, la peau et les yeux. Par ailleurs, des transcrits de fabp1b.1 ont ete detectes en RT-PCR dans le foie, fintestin, le coeur, les testicules, l'ovaire et les branchies. L'expression tissulaire specifique des genes dupliques en tandem fabp1b.1 et fabp1b.2 au sein des tissus adultes et au tours du developpement suggere que ces genes dupliques auraient acquis des fonctions additionnelles par rapport au gene ancestral fabp1, c'est-adire par neo-fonctionnalisation. De plus, ces fonctions auraient ensuite ete partagees entre fabp1b.1 et fabp1b.2 par voie de sub-fonctionnalisation. Mots-cles : duplication genomique, Fabp1, L-Fabp, genes dupliques, duplication en tandem, diencephale, poison zebre. [Traduit par la Redaction], Introduction Fatty acid-binding proteins (FABPs), members of the multigene family of intracellular lipid-binding proteins (iLBPs), are involved in the intracellular trafficking and se questering of fatty acids (Bernlohr et al. [...]

Abstract Background Force, Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions (subfunctionalization) and acquisition of novel functions (neofunctionalization) were the two primary mechanisms for the retention of duplicated genes. The DDC model was tested by analyzing the transcriptional induction of the duplicated fatty acid-binding protein (fabp) genes by clofibrate in zebrafish. Clofibrate is a specific ligand of the peroxisome proliferator-activated receptor (PPAR); it activates PPAR which then binds to a peroxisome proliferator response element (PPRE) to induce the transcriptional initiation of genes primarily involved in lipid homeostasis. Zebrafish was chosen as our model organism as it has many duplicated genes owing to a whole genome duplication (WGD) event that occurred ~230-400 million years ago in the teleost fish lineage. We assayed the steady-state levels of fabp mRNA and heterogeneous nuclear RNA (hnRNA) transcripts in liver, intestine, muscle, brain and heart for four sets of duplicated fabp genes, fabp1a/fabp1b.1/fabp1b.2, fabp7a/fabp7b, fabp10a/fabp10b and fabp11a/fabp11b in zebrafish fed different concentrations of clofibrate. Result Electron microscopy showed an increase in the number of peroxisomes and mitochondria in liver and heart, respectively, in zebrafish fed clofibrate. Clofibrate also increased the steady-state level of acox1 mRNA and hnRNA transcripts in different tissues, a gene with a functional PPRE. These results demonstrate that zebrafish is responsive to clofibrate, unlike some other fishes. The levels of fabp mRNA and hnRNA transcripts for the four sets of duplicated fabp genes was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). The level of hnRNA coded by a gene is an indirect estimate of the rate of transcriptional initiation of that gene. Clofibrate increased the steady-state level of fabp mRNAs and hnRNAs for both the duplicated copies of fabp1a/fabp1b.1, and fabp7a/fabp7b, but in different tissues. Clofibrate also increased the steady-state level of fabp10a and fabp11a mRNAs and hnRNAs in liver, but not for fabp10b and fabp11b. Conclusion Some duplicated fabp genes have, most likely, retained PPREs, but induction by clofibrate is over-ridden by an, as yet, unknown tissue-specific mechanism(s). Regardless of the tissue-specific mechanism(s), transcriptional control of duplicated zebrafish fabp genes by clofibrate has markedly diverged since the WGD event.

Abstract Background In the Duplication-Degeneration-Complementation (DDC) model, subfunctionalization and neofunctionalization have been proposed as important processes driving the retention of duplicated genes in the genome. These processes are thought to occur by gain or loss of regulatory elements in the promoters of duplicated genes. We tested the DDC model by determining the transcriptional induction of fatty acid-binding proteins (Fabps) genes by dietary fatty acids (FAs) in zebrafish. We chose zebrafish for this study for two reasons: extensive bioinformatics resources are available for zebrafish at zfin.org and zebrafish contains many duplicated genes owing to a whole genome duplication event that occurred early in the ray-finned fish lineage approximately 230-400 million years ago. Adult zebrafish were fed diets containing either fish oil (12% lipid, rich in highly unsaturated fatty acid), sunflower oil (12% lipid, rich in linoleic acid), linseed oil (12% lipid, rich in linolenic acid), or low fat (4% lipid, low fat diet) for 10 weeks. FA profiles and the steady-state levels of fabp mRNA and heterogeneous nuclear RNA in intestine, liver, muscle and brain of zebrafish were determined. Result FA profiles assayed by gas chromatography differed in the intestine, brain, muscle and liver depending on diet. The steady-state level of mRNA for three sets of duplicated genes, fabp1a/fabp1b.1/fabp1b.2, fabp7a/fabp7b, and fabp11a/fabp11b, was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). In brain, the steady-state level of fabp7b mRNAs was induced in fish fed the linoleic acid-rich diet; in intestine, the transcript level of fabp1b.1 and fabp7b were elevated in fish fed the linolenic acid-rich diet; in liver, the level of fabp7a mRNAs was elevated in fish fed the low fat diet; and in muscle, the level of fabp7a and fabp11a mRNAs were elevated in fish fed the linolenic acid-rich or the low fat diets. In all cases, induction of the steady-state level of fabp mRNAs by dietary FAs correlated with induced levels of hnRNA for a given fabp gene. As such, up-regulation of the steady-state level of fabp mRNAs by FAs occurred at the level of initiation of transcription. None of the sister duplicates of these fabp genes exhibited an increase in their steady-state transcript levels in a specific tissue following feeding zebrafish any of the four experimental diets. Conclusion Differential induction of only one of the sister pair of duplicated fabp genes by FAs provides evidence to support the DDC model for retention of duplicated genes in the zebrafish genome by either subfunctionalization or neofunctionalization.