Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates

Piscine aquaporins: an overview of recent advances

Aquaporins are a superfamily of integral membrane proteins that facilitate the rapid and yet highly selective flux of water and other small solutes across biological membranes. Since their discovery, they have been documented throughout the living biota, with the majority of research focusing on mammals and plants. Here, we review available data for piscine aquaporins, including Agnatha (jawless fish), Chondrichthyes (chimaeras, sharks, and rays), Dipnoi (lungfishes), and Teleostei (ray-finned bony fishes). Recent evidence suggests that the aquaporin superfamily has specifically expanded in the chordate lineage consequent to serial rounds of whole genome duplication, with teleost genomes harboring the largest number of paralogs. The selective retention and dichotomous clustering of most duplicated paralogs in Teleostei, with differential tissue expression profiles, implies that novel or specialized physiological functions may have evolved in this clade. The recently proposed new nomenclature of the piscine aquaporin superfamily is discussed in relation to the phylogenetic signal and genomic synteny, with the teleost aquaporin-8 paralogs used as a case study to illustrate disparities between the underlying codons, molecular phylogeny, and physical locus. Structural data indicate that piscine aquaporins display similar channel restriction residues found in the tetrapod counterparts, and hence their functional properties seem to be conserved. However, emerging evidence suggests that regulation of aquaporin function in teleosts may have diverged in some cases. Cell localization and experimental studies imply that the physiological roles of piscine aquaporins extend at least to osmoregulation, reproduction, and early development, although in most cases their specific functions remain to be elucidated.

Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes

Background

The central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by multiple isozymes encoded by a multigene family. Several isozymes in this pathway are expressed only during spermatogenesis, and gene targeting studies indicate that they are essential for sperm function and male fertility in mouse. At least three of the novel glycolytic isozymes are encoded by retrogenes (Pgk2, Aldoart1, and Aldoart2). Their restricted expression profile suggests that retrotransposition may play a significant role in the evolution of sperm glycolytic enzymes.

Results

We conducted a comprehensive genomic analysis of glycolytic enzymes in the human and mouse genomes and identified several intronless copies for all enzymes in the pathway, except Pfk. Within each gene family, a single orthologous gene was typically retrotransposed frequently and independently in both species. Several retroposed sequences maintained open reading frames (ORFs) and/or provided evidence of alternatively spliced exons. We analyzed expression of sequences with ORFs and <99% sequence identity in the coding region and obtained evidence for the expression of an alternative Gpi1 transcript in mouse spermatogenic cells.

Conclusions

Our analysis detected frequent, recent, and lineage-specific retrotransposition of orthologous glycolytic enzymes in the human and mouse genomes. Retrotransposition events are associated with LINE/LTR and genomic integration is random. We found evidence for the alternative splicing of parent genes. Many retroposed sequences have maintained ORFs, suggesting a functional role for these genes.

Aromatase in the brain of teleost fish: expression, regulation and putative functions

Unlike that of mammals, the brain of teleost fish exhibits an intense aromatase activity due to the strong expression of one of two aromatase genes (aromatase A or cyp19a1a and aromatase B or cyp19a1b) that arose from a gene duplication event. In situ hybridization, immunohistochemistry and expression of GFP (green fluorescent protein) in transgenic tg(cyp19a1b-GFP) fish demonstrate that aromatase B is only expressed in radial glial cells (RGC) of adult fish. These cells persist throughout life and act as progenitors in the brain of both developing and adult fish. Although aromatase B-positive radial glial cells are most abundant in the preoptic area and the hypothalamus, they are observed throughout the entire central nervous system and spinal cord. In agreement with the fact that brain aromatase activity is correlated to sex steroid levels, the high expression of cyp19a1b is due to an auto-regulatory loop through which estrogens and aromatizable androgens up-regulate aromatase expression. This mechanism involves estrogen receptor binding on an estrogen response element located on the cyp19a1b promoter. Cell specificity is achieved by a mandatory cooperation between estrogen receptors and unidentified glial factors. Given the emerging roles of estrogens in neurogenesis, the unique feature of the adult fish brain suggests that, in addition to classical functions on brain sexual differentiation and sexual behaviour, aromatase expression in radial glial cells could be part of the mechanisms authorizing the maintenance of a high proliferative activity in the brain of fish.

Evolution of the nuclear-encoded cytochrome oxidase subunits in vertebrates

Vertebrate mitochondrial cytochrome c oxidase (COX) possesses 10 nuclear-encoded subunits. Six subunits have paralogs in mammals, but the origins and distribution of isoforms among vertebrates have not been analyzed. We used Bayesian phylogenetic analysis to interpret the origins of each subunit, inferring the roles of gene and genome duplications. The paralogous ancestries of five genes were identical throughout the major vertebrate taxa: no paralogs of COX6c and COX7c, two paralogs of COX4 and COX6a, and three paralogs of COX7a. Two genes had an extra copy in teleosts (COX5a, COX5b), and three genes had additional copies in mammals (COX6b, COX7b, COX8). Focusing on early vertebrates, we examined structural divergence and explored transcriptional profiles across zebrafish tissues. Quantitative transcript profiles revealed dramatic differences in transcript abundance for different subunits. COX7b and COX4 transcripts were typically present at very low levels, whereas COX5a and COX8 were in vast excess in all tissues. For genes with paralogs, two general patterns emerged. For COX5a and COX8, there was ubiquitous expression of one paralog, with the other paralog in lower abundance in all tissues. COX4 and COX6a shared a distinct expression pattern, with one paralog dominant in brain and gills and the other in muscles. The isoform profiles in combination with phylogenetic analyses show that vertebrate COX isoform patterns are consistent with the hypothesis that early whole genome duplications in basal vertebrates governed the isoform repertoire in modern fish and tetrapods, though more recent lineage-specific gene/genome duplications also play a role in select subunits.

Perspectives on fish gonadotropins and their receptors

Teleosts lack a hypophyseal portal system and hence neurohormones are carried by nerve fibers from the preoptic region to the pituitary. The various cell types in the teleost pituitary are organized in discrete domains. Fish possess two gonadotropins (GtH) similar to FSH and LH in other vertebrates; they are heterodimeric hormones that consist of a common alpha subunit non-covalently associated with a hormone-specific beta subunit. In recent years the availability of molecular cloning techniques allowed the isolation of the genes coding for the GtH subunits in 56 fish species representing at least 14 teleost orders. Advanced molecular engineering provides the technology to produce recombinant GtHs from isolated cDNAs. Various expression systems have been used for the production of recombinant proteins. Recombinant fish GtHs were produced for carp, seabream, channel and African catfish, goldfish, eel, tilapia, zebrafish, Manchurian trout and Orange-spotted grouper. The hypothalamus in fishes exerts its regulation on the release of the GtHs via several neurohormones such as GnRH, dopamine, GABA, PACAP, IGF-I, norepinephrine, NPY, kisspeptin, leptin and ghrelin. In addition, gonadal steroids and peptides exert their effects on the gonadotropins either directly or via the hypothalamus. All these are discussed in detail in this review. In mammals, the biological activities of FSH and LH are directed to different gonadal target cells through the cell-specific expression of the FSH receptor (FSHR) and LH receptor (LHR), respectively, and the interaction between each gonadotropin-receptor couple is highly selective. In contrast, the bioactivity of fish gonadotropins seems to be less specific as a result of promiscuous hormone-receptor interactions, while FSHR expression in Leydig cells explains the strong steroidogenic activity of FSH in certain fish species.

An exon-based comparative variant analysis pipeline to study the scale and role of frameshift and nonsense mutation in the human-chimpanzee divergence

Chimpanzees and humans are closely related but differ in many deadly human diseases and other characteristics in physiology, anatomy, and pathology. In spite of decades of extensive research, crucial questions about the molecular mechanisms behind the differences are yet to be understood. Here I report ExonVar, a novel computational pipeline for Exon-based human-chimpanzee comparative Variant analysis. The objective is to comparatively analyze mutations specifically those that caused the frameshift and nonsense mutations and to assess their scale and potential impacts on human-chimpanzee divergence. Genomewide analysis of human and chimpanzee exons with ExonVar identified a number of species-specific, exon-disrupting mutations in chimpanzees but much fewer in humans. Many were found on genes involved in important biological processes such as T cell lineage development, the pathogenesis of inflammatory diseases, and antigen induced cell death. A “less-is-more” model was previously established to illustrate the role of the gene inactivation and disruptions during human evolution. Here this analysis suggested a different model where the chimpanzee-specific exon-disrupting mutations may act as additional evolutionary force that drove the human-chimpanzee divergence. Finally, the analysis revealed a number of sequencing errors in the chimpanzee and human genome sequences and further illustrated that they could be corrected without resequencing.

Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields

The electrostatic potential of an enzyme is a key determinant of its substrate interactions and catalytic turnover. Here we invoke comparative analysis of protein electrostatic potentials, along with sequence and structural analysis, to classify and characterize all the enzymes in an entire pathway across a set of different organisms. The electrostatic potentials of the enzymes from the glycolytic pathway of 11 eukaryotes were analyzed by qPIPSA (quantitative protein interaction property similarity analysis). The comparison allows the functional assignment of neuron-specific isoforms of triosephosphate isomerase from zebrafish, the identification of unusual protein surface interaction properties of the mosquito glucose-6-phosphate isomerase and the functional annotation of ATP-dependent phosphofructokinases and cofactor-dependent phosphoglycerate mutases from plants. We here show that plants possess two parallel pathways to convert glucose. One is similar to glycolysis in humans, the other is specialized to let plants adapt to their environmental conditions. We use differences in electrostatic potentials to estimate kinetic parameters for the triosephosphate isomerases from nine species for which published parameters are not available. Along the core glycolytic pathway, phosphoglycerate mutase displays the most conserved electrostatic potential. The largest cross-species variations are found for glucose-6-phosphate isomerase, enolase and fructose-1,6-bisphosphate aldolase. The extent of conservation of electrostatic potentials along the pathway is consistent with the absence of a single rate-limiting step in glycolysis.

Zebrafish RNase T2 genes and the evolution of secretory ribonucleases in animals

Background

Members of the Ribonuclease (RNase) T2 family are common models for enzymological studies, and their evolution has been well characterized in plants. This family of acidic RNases is widespread, with members in almost all organisms including plants, animals, fungi, bacteria and even some viruses. While several biological functions have been proposed for these enzymes in plants, their role in animals is unknown. Interestingly, in vertebrates most of the biological roles of plant RNase T2 proteins are carried out by members of a different family, RNase A. Still, RNase T2 proteins are conserved in these animals

Results

As a first step to shed light on the role of animal RNase T2 enzymes, and to understand the evolution of these proteins while co-existing with the RNase A family, we characterized RNase Dre1 and RNase Dre2, the two RNase T2 genes present in the zebrafish (Danio rerio) genome. These genes are expressed in most tissues examined, including high expression in all stages of embryonic development, and their expression corresponds well with the presence of acidic RNase activities in every tissue analyzed. Embryo expression seems to be a conserved characteristic of members of this family, as other plant and animal RNase T2 genes show similar high expression during embryo development. While plant RNase T2 proteins and the vertebrate RNase A family show evidences of radiation and gene sorting, vertebrate RNase T2 proteins form a monophyletic group, but there is also another monophyletic group defining a fish-specific RNase T2 clade.

Conclusion

Based on gene expression and phylogenetic analyses we propose that RNase T2 enzymes carry out a housekeeping function. This conserved biological role probably kept RNase T2 enzymes in animal genomes in spite of the presence of RNases A. A hypothetical role during embryo development is also discussed.

Cyclostome and chondrichthyan adrenomedullins reveal ancestral features of the adrenomedullin family

The adrenomedullin (AM) family is a newly identified group of regulatory peptides involved in various aspects of homeostasis. Different forms of AMs are the result of genome duplication during vertebrate evolution, but nothing is known about the AM genes before divergence of bony fish. In the present study, we identified novel AM genes in cyclostomes (a hagfish and two lamprey species) and chondrichthyes (a holocephalan and two elasmobranch species). The AM of cyclostomes possessed features of both AM1 and AM2, with gene structure and overall precursor sequence more similar to AM1 of teleosts and tetrapods but mature sequence more similar to AM2. A sequence reminiscent of proAM N-terminal 20 peptide (PAMP), another bioactive peptide present in the prosegment of AM1 precursors, exists in the lamprey AM precursor. An AM gene with both AM1 and AM2 characteristics was also found in chondrichthyes, and an additional AM5-like gene was detected in Squalus acanthias. The hybrid-type AM gene from cyclostomes and chondrichthyes was expressed ubiquitously in all tissues examined including the skeletal muscle, while the Squalus AM5-like gene transcripts were detected more specifically in the liver. Taken together, the ancestral gene of the AM family appears to possess both AM1 and AM2 characteristics as observed in the lamprey AM gene, and the general structure including PAMP was retained by the extant AM1 genes, but the mature sequence was retained by the extant AM2 genes.

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses

BACKGROUND

Sorghum is the first C4 plant and the second grass with a full genome sequence available. This makes it possible to perform a whole-genome-level exploration of C4 pathway evolution by comparing key photosynthetic enzyme genes in sorghum, maize (C4) and rice (C3), and to investigate a long-standing hypothesis that a reservoir of duplicated genes is a prerequisite for the evolution of C4 photosynthesis from a C3 progenitor.

RESULTS

We show that both whole-genome and individual gene duplication have contributed to the evolution of C4 photosynthesis. The C4 gene isoforms show differential duplicability, with some C4 genes being recruited from whole genome duplication duplicates by multiple modes of functional innovation. The sorghum and maize carbonic anhydrase genes display a novel mode of new gene formation, with recursive tandem duplication and gene fusion accompanied by adaptive evolution to produce C4 genes with one to three functional units. Other C4 enzymes in sorghum and maize also show evidence of adaptive evolution, though differing in level and mode. Intriguingly, a phosphoenolpyruvate carboxylase gene in the C3 plant rice has also been evolving rapidly and shows evidence of adaptive evolution, although lacking key mutations that are characteristic of C4 metabolism. We also found evidence that both gene redundancy and alternative splicing may have sheltered the evolution of new function.

CONCLUSIONS

Gene duplication followed by functional innovation is common to evolution of most but not all C4 genes. The apparently long time-lag between the availability of duplicates for recruitment into C4 and the appearance of C4 grasses, together with the heterogeneity of origins of C4 genes, suggests that there may have been a long transition process before the establishment of C4 photosynthesis.

Evolution of the Ikaros gene family: implications for the origins of adaptive immunity

Members of the Ikaros family of transcription factors are important for immune system development. Analysis of Ikaros-related genes from a range of species suggests the Ikaros family derived from a primordial gene, possibly related to the present-day protostome Hunchback genes. This duplicated before the divergence of urochordates to produce two distinct lineages: one that generated the Ikaros factor-like (IFL) 2 genes of urochordates/lower vertebrates and the Pegasus genes of higher vertebrates, and one that generated the IFL1 genes of urochordates/lower vertebrates, the IKFL1 and IKFL2 genes of agnathans and the remaining four Ikaros members of higher vertebrates. Expansion of the IFL1 lineage most likely occurred via the two intervening rounds of whole genome duplication. A proposed third whole genome duplication in teleost fish produced a further increase in complexity of the gene family with additional Pegasus and Eos members. These findings question the use of IFL sequences as evidence for the existence of adaptive immunity in early chordates and vertebrates. Instead, this study is consistent with a later emergence of adaptive immunity coincident with the appearance of the definitive lymphoid markers Ikaros, Aiolos, and Helios.

Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia

The compact genome of the unicellular eukaryote Paramecium tetraurelia contains noncoding DNA (ncDNA) distributed into >39,000 intergenic sequences and >90,000 introns of 390 base pairs (bp) and 25 bp on average, respectively. Here we analyzed the molecular features of the ncRNA genes, introns, and intergenic sequences of this genome. We mainly used computational programs and comparative genomics possible because the P. tetraurelia genome had formed throughout whole-genome duplications (WGDs). We characterized 417 5S rRNA, snRNA, snoRNA, SRP RNA, and tRNA putative genes, 415 of which map within intergenic sequences, and two, within introns. The evolution of these ncRNA genes appears to have mainly involved purifying selection and gene deletion. We then compared the introns that interrupt the protein-coding gene duplicates arisen from the recent WGD and identified a population of a few thousands of introns having evolved under most stringent constraints (>95% of identity). We also showed that low nucleotide substitution levels characterize the 50 and 80-115 base pairs flanking, respectively, the stop and start codons of the protein-coding genes. Lower substitution levels mark the base pairs flanking the highly transcribed genes, or the start codons of the genes of the sets with a high number of WGD-related sequences. Finally, adjacent to protein-coding genes, we characterized 32 DNA motifs able to encode stable and evolutionary conserved RNA secondary structures and defining putative expression controlling elements. Fourteen DNA motifs with similar properties map distant from protein-coding genes and may encode regulatory ncRNAs.

Characterization of a cis-acting element involved in cell-specific expression of the zebrafish brain aromatase gene

The cytochrome P450 Aromatase is the key enzyme catalyzing the conversion of androgens into estrogens. In zebrafish, the brain aromatase is encoded by cyp19b. Expression of cyp19b is restricted to radial glial cells bordering forebrain ventricles and is strongly stimulated by estrogens during development. At the promoter level, we have previously shown that an estrogen responsive element (ERE) is required for induction by estrogens. Here, we investigated the role of ERE flanking regions in the control of cell-specific expression. First, we show that a 20 bp length motif, named G x RE (glial x responsive element), acts in synergy with the ERE to mediate the estrogenic induction specifically in glial cells. Second, we demonstrate that, in vitro, this sequence binds factors exclusively present in glial or neuro-glial cells and is able to confer a glial specificity to an artificial estrogen-dependent gene. Taken together, these results contribute to the understanding of the molecular mechanisms allowing cyp19b regulation by estrogens and allowed to identify a promoter sequence involved in the strong estrogen inducibility of cyp19b which is specific for glial cells. The exceptional aromatase activity measured in the brain of teleost fish could rely on such mechanisms.

Evolutionary history of the UCP gene family: gene duplication and selection

Background

The uncoupling protein (UCP) genes belong to the superfamily of electron transport carriers of the mitochondrial inner membrane. Members of the uncoupling protein family are involved in thermogenesis and determining the functional evolution of UCP genes is important to understand the evolution of thermo-regulation in vertebrates.

Results

Sequence similarity searches of genome and scaffold data identified homologues of UCP in eutherians, teleosts and the first squamates uncoupling proteins. Phylogenetic analysis was used to characterize the family evolutionary history by identifying two duplications early in vertebrate evolution and two losses in the avian lineage (excluding duplications within a species, excluding the losses due to incompletely sequenced taxa and excluding the losses and duplications inferred through mismatch of species and gene trees). Estimates of synonymous and nonsynonymous substitution rates (dN/dS) and more complex branch and site models suggest that the duplication events were not associated with positive Darwinian selection and that the UCP is constrained by strong purifying selection except for a single site which has undergone positive Darwinian selection, demonstrating that the UCP gene family must be highly conserved.

Conclusion

We present a phylogeny describing the evolutionary history of the UCP gene family and show that the genes have evolved through duplications followed by purifying selection except for a single site in the mitochondrial matrix between the 5^th and 6^th α-helices which has undergone positive selection.

Translational machinery of senegalese sole (Solea senegalensis Kaup) and Atlantic halibut (Hippoglossus hippoglossus L.): comparative sequence analysis of the complete set of 60s ribosomal proteins and their expression

Ribosomal proteins (RPs) comprise a large set of highly evolutionarily conserved proteins that are often over-represented in complementary DNA libraries. They have become very useful markers in comparative genomics, genome evolution, and phylogenetic studies across taxa. In this study, we report the sequences of the complete set of 60S RPs in Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus), two commercially important flatfish species. Amino-acid sequence comparisons of the encoded proteins showed a high similarity both between these two flatfish species and with respect to other fish and human counterparts. Expressed sequence tag analysis revealed the existence of paralogous genes for RPL3, RPL7, RPL41, and RPLP2 in Atlantic halibut and RPL13a in Senegalese sole as well as RPL19 and RPL22 in both species. Phylogenetic analysis of paralogs revealed distinct evolutionary histories for each RP in agreement with three rounds of genome duplications and lineage-specific duplications during flatfish evolution. Steady-state transcript levels for RPL19 and RPL22 RPs were quantitated during larval development and in different tissues of sole and halibut using a real-time polymerase chain reaction approach. All paralogs were expressed ubiquitously although at different levels in different tissues. Most RP transcripts increased coordinately after larval first-feeding in both species but decreased progressively during the metamorphic process. In all cases, expression profiles and transcript levels of orthologous genes in Senegalese sole and Atlantic halibut were highly congruent. The genomic resources and knowledge developed in this survey will be useful for the study of Pleuronectiformes evolution.

Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after?

Two rounds of whole-genome duplications are thought to have played an important role in the establishment of gene repertoires in vertebrates. These events occurred during chordate evolution after the split of the urochordate and cephalochordate lineages but before the radiation of extant gnathostomes (jawed vertebrates). During this interval, diverse agnathans (jawless fishes), including cyclostomes (hagfishes and lampreys), diverged. However, there is no solid evidence for the timing of these genome duplications in relation to the divergence of cyclostomes from the gnathostome lineage. We conducted cDNA sequencing in diverse early vertebrates for members of homeobox-containing (Dlx and ParaHox) and other gene families that would serve as landmarks for genome duplications. Including these new sequences, we performed a molecular phylogenetic census using the maximum likelihood method for 55 gene families. In most of these gene families, we detected many more gene duplications before the cyclostome-gnathostome split, than after. Many of these gene families (e.g., visual opsins, RAR, Notch) have multiple paralogs in conserved, syntenic genomic regions that must have been generated by large-scale duplication events. Taken together, this indicates that the genome duplications occurred before the cyclostome-gnathostome split. We propose that the redundancy in gene repertoires possessed by all vertebrates, including hagfishes and lampreys, was introduced primarily by genome duplications. Apart from subsequent lineage-specific modifications, these ancient genome duplication events might serve generally to distinguish vertebrates from invertebrates at the genomic level.

Electric charge divergence in proteins: insights into the evolution of their three-dimensional properties

Previous studies of protein evolution have identified important mutations in various proteins that affect a small number of residues, but dramatically alter protein function. However, the evolutionary process underlying the three-dimensional protein properties, which are determined by a much larger number of residues, remains unclear. Based on a comparative evolutionary analysis of teleost phosphoglucose isomerases (PGIs; EC 5.3.1.9), we previously demonstrated that the relatively weak selection on many amino acid sites has played an important role in the evolution of protein electric charge as a model of three-dimensional protein properties. To ascertain the generality of this finding, we sought further evidence of this type of protein evolution. For this purpose, we analyzed the vertebrate isoforms of fructose-1,6-bisphosphate aldolase (ALD; EC 4.1.2.13), for which electric charges are known to have diverged after gene duplication. The results showed that the divergence in electric charge between the ALD isoforms was also driven by weak selection on many amino acid sites, as in PGI, confirming the generality of earlier findings. To obtain further insights, ALD and PGI were compared to the proteins pancreatic ribonuclease (EC 3.1.27.5) and triose-phosphate isomerase (EC 5.3.1.1), for which electric charges likely evolved through a well-defined mode of molecular evolution; namely, strong selection on specific amino acid sites. Comparison of the number and composition of amino acids on the protein surface suggested that the absolute number of evolutionarily changeable amino acids in a protein affects the strength of selection pressure acting on individual amino acid sites.

Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196(T)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.

Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR

Background

Flatfish metamorphosis involves major physiological and morphological changes. Due to its importance in aquaculture and as a model for developmental studies, some gene expression studies have focused on the understanding of this process using quantitative real-time PCR (qRT-PCR) technique. Therefore, adequate reference genes for accurate normalization are required.

Results

The stability of 12 potential reference genes was examined during larval development in Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus) to determine the most suitable genes for qRT-PCR analysis. Transcription levels of genes encoding β-Actin (ACTB), glyceraldehyde-3P-dehydrogenase (GAPDH), annexin A2 (ANXA2), glutathione S-transferase (GST), ornithine decarboxylase (ODC), hypoxanthine phosphoribosyltransferase (HPRT1), ubiquitin (UBQ), elongation factor 1 alpha (eEF1A1), 18S ribosomal RNA, and the ribosomal proteins S4 (RPS4) and L13a (RPL13a) were quantitated. Two paralogous genes for ACTB were analyzed in each of both flatfish species. In addition, two paralogous genes for GAPDH were studied in Senegalese sole. RPL13a represented non-orthologous genes between both flatfish species. GeNorm and NormFinder analyses for expression stability revealed RPS4, UBQ and eEF1A1 as the most stable genes in Senegalese sole, Atlantic halibut and in a combined analysis. In all cases, paralogous genes exhibited differences in expression stability.

Conclusion

This work suggests RPS4, UBQ, and eEF1A1 genes as useful reference genes for accurate normalization in qRT-PCR studies in Senegalese sole and Atlantic halibut larvae. The congruent results between both species in spite of the drastic differences in larval development suggest that selected housekeeping genes (HKGs) could be useful in other flatfish species. However, the finding of paralogous gene copies differentially expressed during development in some HKGs underscores the necessity to identify orthologous genes.

Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Solea senegalensis Kaup): differential gene expression and thyroid hormones dependence during metamorphosis

BACKGROUND

Eukaryotic elongation factor 1 alpha (eEF1A) is one of the four subunits composing eukaryotic translation elongation factor 1. It catalyzes the binding of aminoacyl-tRNA to the A-site of the ribosome in a GTP-dependent manner during protein synthesis, although it also seems to play a role in other non-translational processes. Currently, little information is still available about its expression profile and regulation during flatfish metamorphosis. With regard to this, Senegalese sole (Solea senegalensis) is a commercially important flatfish in which eEF1A gene remains to be characterized.

RESULTS

The development of large-scale genomics of Senegalese sole has facilitated the identification of five different eEF1A genes, referred to as SseEF1A1, SseEF1A2, SseEF1A3, SseEF1A4, and Sse42Sp50. Main characteristics and sequence identities with other fish and mammalian eEF1As are described. Phylogenetic and tissue expression analyses allowed for the identification of SseEF1A1 and SseEF1A2 as the Senegalese sole counterparts of mammalian eEF1A1 and eEF1A2, respectively, and of Sse42Sp50 as the ortholog of Xenopus laevis and teleost 42Sp50 gene. The other two elongation factors, SseEF1A3 and SseEF1A4, represent novel genes that are mainly expressed in gills and skin. The expression profile of the five genes was also studied during larval development, revealing different behaviours. To study the possible regulation of SseEF1A gene expressions by thyroid hormones (THs), larvae were exposed to the goitrogen thiourea (TU). TU-treated larvae exhibited lower SseEF1A4 mRNA levels than untreated controls at both 11 and 15 days after treatment, whereas transcripts of the other four genes remained relatively unchanged. Moreover, addition of exogenous T4 hormone to TU-treated larvae increased significantly the steady-state levels of SseEF1A4 with respect to untreated controls, demonstrating that its expression is up-regulated by THs.

CONCLUSION

We have identified five different eEF1A genes in the Senegalese sole, referred to as SseEF1A1, SseEF1A2, SseEF1A3, SseEF1A4, and Sse42Sp50. The five genes exhibit different expression patterns in tissues and during larval development. TU and T4 treatments demonstrate that SseEF1A4 is up-regulated by THs, suggesting a role in the translational regulation of the factors involved in the dramatic changes that occurs during Senegalese sole metamorphosis.

Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites

Background

The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization). Nonetheless, how a subfunctionalized protein can evolve into a more adaptive protein is poorly understood, mainly due to the limitations of current analytical methods, which can detect only strong selection for amino acid substitutions involved in adaptive molecular evolution. In this study, we employed a comparative evolutionary approach to this question, focusing on differences in the structural properties of a protein, specifically the electric charge, encoded by fish-specific duplicated phosphoglucose isomerase (Pgi) genes.

Results

Full-length cDNA cloning, RT-PCR based gene expression analyses, and comparative sequence analyses showed that after subfunctionalization with respect to the expression organ of duplicate Pgi genes, the net electric charge of the PGI-1 protein expressed mainly in internal tissues became more negative, and that of PGI-2 expressed mainly in muscular tissues became more positive. The difference in net protein charge was attributable not to specific amino acid sites but to the sum of various amino acid sites located on the surface of the PGI molecule.

Conclusion

This finding suggests that the surface charge evolution of PGI proteins was not driven by strong selection on individual amino acid sites leading to permanent fixation of a particular residue, but rather was driven by weak selection on a large number of amino acid sites and consequently by steady directional and/or purifying selection on the overall structural properties of the protein, which is derived from many modifiable sites. The mode of molecular evolution presented here may be relevant to various cases of adaptive modification in proteins, such as hydrophobic properties, molecular size, and electric charge.

The warm temperature acclimation protein Wap65 as an immune response gene: its duplicates are differentially regulated by temperature and bacterial infections

The warm temperature acclimation related 65kDa protein (Wap65) in teleost fish shares high structural similarities with mammalian hemopexins. Recent studies using microarray analysis indicated that this temperature acclimation protein may also be involved in immune responses. To provide evidence of its potential involvement in immune responses after bacterial infections, we have identified and characterized two types of Wap65 genes in channel catfish, referred to as Wap65-1 and Wap65-2, respectively. While Wap65-1 and Wap65-2 are both structurally similar to the mammalian hemopexins, they exhibit highly differential patterns of spatial expression. Wap65-1 was expressed in a wide range of tissues, whereas Wap65-2 was only expressed in the liver. Their regulation with warm temperature and bacterial infections was also highly different: Wap65-1 was constitutively expressed, whereas Wap65-2 was highly regulated by both warm temperature and bacterial infections, and warm temperature and bacterial infections appeared to synergistically induce the expression of Wap65-2. The great contrast of expression patterns and regulation of the two catfish Wap65 genes suggested both neofunctionalization and partitioning of their functions. Phylogenetic analysis indicated that the duplicated catfish Wap65 genes were evolved not only from whole genome duplication, but also from tandem, intrachromosomal gene duplications. Taken together, the results of this study suggest that Wap65 genes are not only important for its classical role as a warm temperature acclimation protein, but more importantly, may also function as an immune response protein.

Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (sseKer1 and sseKer2) in the flatfish Senegalese sole (Solea senegalensis Kaup)

BACKGROUND

Keratins make up the largest subgroup of intermediate filaments, and, in chordates, represent the most abundant proteins in epithelial cells. They have been associated with a wide range of functions in the cell, but little information is still available about their expression profile and regulation during flatfish metamorphosis. Senegalese sole (Solea senegalensis) is a commercially important flatfish in which no keratin gene has been described yet.

RESULTS

The development of large-scale genomics of Senegalese sole has facilitated the identification of two different type I keratin genes referred to as sseKer1 and sseKer2. Main characteristics and sequence identities with other fish and mammal keratins are described. Phylogenetic analyses grouped sseKer1 and sseKer2 in a significant clade with other teleost epidermal type I keratins, and have allowed for the identification of sseKer2 as a novel keratin. The expression profile of both genes was studied during larval development and in tissues using a real-time approach. sseKer1 and sseKer2 mRNA levels were significantly higher in skin than in other tissues examined. During metamorphosis, sseKer1 transcripts increased significantly at first stages, and reduced thereafter. In contrast, sseKer2 mRNA levels did not change during early metamorphosis although a significant drop at metamorphosis climax and late metamorphosis was also detected. To study the possible regulation of sseKer gene expressions by thyroid hormones (THs), larvae were exposed to the goitrogen thiourea (TU). TU-treated larvae exhibited higher sseKer1 and sseKer2 mRNA levels than untreated control at both 11 and 15 days after treatment. Moreover, addition of exogenous T4 hormone to TU-treated larvae restored or even reduced the steady-state levels with respect to the untreated control, demonstrating that expression of both genes is negatively regulated by THs.

CONCLUSION

We have identified two keratin genes, referred to as sseKer1 and sseKer2, in Senegalese sole. Phylogenetic analyses revealed sseKer2 as a novel keratin. Although they exhibit different expression patterns during larval development, both of them are negatively regulated by THs. The co-regulation by THs could explain the reduction of both keratin transcripts after the metamorphosis climax, suggesting their role in the tissue remodelling processes that occur during metamorphosis.

Differential gene expression and dependence on thyroid hormones of two glyceraldehyde-3-phosphate dehydrogenases in the flatfish Senegalese sole (Solea senegalensis Kaup)

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential enzyme of the glycolytic pathway. The application of large-scale genomics to Senegalese sole (Solea senegalensis) has facilitated the identification of two different genes referred to as GAPDH-1 and GAPDH-2. Main characteristics and sequence similarities with other fish and mammals are described. Phylogenetic analyses grouped both genes into two separate clusters with their mammalian counterparts as a sister clade. The expression profiles of both genes were studied during larval development and in juvenile tissues using a real-time PCR approach. In juvenile fish, GAPDH-1 was expressed mainly in muscle and GAPDH-2 in brain. During metamorphosis, GAPDH-2 mRNA levels did not change. In contrast, GAPDH-1 transcripts increased significantly between S1 and S2 metamorphic stages and reduced their levels thereafter. A treatment with the goitrogen thiourea indicated that GAPDH-1 expression was negatively regulated by thyroid hormones. The possible role of GAPDHs in metamorphosis is discussed.

Three male germline-specific aldolase A isozymes are generated by alternative splicing and retrotransposition

Enzymes in the glycolytic pathway of mammalian sperm are modified extensively and are localized in the flagellum, where several are tightly bound to the fibrous sheath. This study provides the first evidence for three novel aldolase isozymes in mouse sperm, two encoded by Aldoart1 and Aldoart2 retrogenes on different chromosomes and another by Aldoa_v2, a splice variant of Aldoa. Phylogenetic analyses and comparative genomics indicate that the retrogenes and splice variant have remained functional and have been under positive selection for millions of years. Their expression is restricted to the male germline and is tightly regulated at both transcriptional and translational levels. All three isozymes are present only in spermatids and sperm and have distinctive features that may be important for localization in the flagellum and/or altered metabolic regulation. Both ALDOART1 and ALDOA_V2 have unusual N-terminal extensions not found in other aldolases. The N-terminal extension of ALDOA_V2 is highly conserved in mammals, suggesting a conserved function in sperm. We hypothesize that the N-terminal extensions are responsible for localizing components of the glycolytic pathway to the fibrous sheath and that this localization is required to provide sufficient ATP along the length of the flagellum to support sperm motility.

GnRH and GnRH receptors in metazoa: a historical, comparative, and evolutive perspective

About 50years after Harris's first demonstration of its existence, GnRH has strongly stimulated the interest and imagination of scientists, resulting in a high number of studies in an increasing number of species. For the endocrinologist, GnRH, via its actions on the synthesis and release of pituitary gonadotrophins, is first an essential hormone for the initiation and maintenance of the reproductive axis, but recent data suggest that GnRH emerged in animals lacking a pituitary. In this context, this review intends to explore the current status of knowledge on GnRH and GnRH receptors in metazoa in order to see if it is possible to draw an evolutive scenario according to which GnRH actions progressively evolved from the control of simple basic functions in early metazoa to an indirect mean of controlling gonadal activity in vertebrates through a sophisticated network of finely tuned neurons developing in a rather fascinating way. This review also intends to provide an evolutive scenario based on the recent advances of whole genome sequencing possibly explaining the number of GnRH and GnRH receptor variants according to the 2R and 3R theories accompanied by gene losses.

Increased glycolytic flux as an outcome of whole-genome duplication in yeast

After whole-genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy number of some glycolytic genes could have conferred an almost immediate selective advantage to an ancestor of Saccharomyces cerevisiae, providing a rationale for the success of the WGD. We propose that the loss of other redundant genes throughout the genome resulted in incremental dosage increases for the surviving duplicated glycolytic genes. This increase gave post-WGD yeasts a growth advantage through rapid glucose fermentation; one of this lineage's many adaptations to glucose-rich environments. Our hypothesis is supported by data from enzyme kinetics and comparative genomics. Because changes in gene dosage follow directly from post-WGD deletions, dosage selection can confer an almost instantaneous benefit after WGD, unlike neofunctionalization or subfunctionalization, which require specific mutations. We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD.

Comparative sequence analysis of the complete set of 40S ribosomal proteins in the Senegalese sole (Solea senegalensis Kaup) and Atlantic halibut (Hippoglossus hippoglossus L.) (Teleostei: Pleuronectiformes): phylogeny and tissue- and development-specific expression

Background

Ribosomal proteins (RPs) are key components of ribosomes, the cellular organelle responsible for protein biosynthesis in cells. Their levels can vary as a function of organism growth and development; however, some RPs have been associated with other cellular processes or extraribosomal functions. Their high representation in cDNA libraries has resulted in the increase of RP sequences available from different organisms and their proposal as appropriate molecular markers for phylogenetic analysis.

Results

The development of large-scale genomics of Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus), two commercially important flatfish species, has made possible the identification and systematic analysis of the complete set of RP sequences for the small (40S) ribosome subunit. Amino acid sequence comparisons showed a high similarity both between these two flatfish species and with respect to other fish and human. EST analysis revealed the existence of two and four RPS27 genes in Senegalese sole and Atlantic halibut, respectively. Phylogenetic analysis clustered RPS27 in two separate clades with their fish and mammalian counterparts. Steady-state transcript levels for eight RPs (RPS2, RPS3a, RPS15, RPS27-1, RPS27-2, RPS27a, RPS28, and RPS29) in sole were quantitated during larval development and in tissues, using a real-time PCR approach. All eight RPs exhibited different expression patterns in tissues with the lowest levels in brain. On the contrary, RP transcripts increased co-ordinately after first larval feeding reducing progressively during the metamorphic process.

Conclusion

The genomic resources and knowledge developed in this survey will provide new insights into the evolution of Pleuronectiformes. Expression data will contribute to a better understanding of RP functions in fish, especially the mechanisms that govern growth and development in larvae, with implications in aquaculture.

Evolution of pigment synthesis pathways by gene and genome duplication in fish

BACKGROUND

Coloration and color patterning belong to the most diverse phenotypic traits in animals. Particularly, teleost fishes possess more pigment cell types than any other group of vertebrates. As the result of an ancient fish-specific genome duplication (FSGD), teleost genomes might contain more copies of genes involved in pigment cell development than tetrapods. No systematic genomic inventory allowing to test this hypothesis has been drawn up so far for pigmentation genes in fish, and almost nothing is known about the evolution of these genes in different fish lineages.

RESULTS

Using a comparative genomic approach including phylogenetic reconstructions and synteny analyses, we have studied two major pigment synthesis pathways in teleost fish, the melanin and the pteridine pathways, with respect to different types of gene duplication. Genes encoding three of the four enzymes involved in the synthesis of melanin from tyrosine have been retained as duplicates after the FSGD. In the pteridine pathway, two cases of duplicated genes originating from the FSGD as well as several lineage-specific gene duplications were observed. In both pathways, genes encoding the rate-limiting enzymes, tyrosinase and GTP-cyclohydrolase I (GchI), have additional paralogs in teleosts compared to tetrapods, which have been generated by different modes of duplication. We have also observed a previously unrecognized diversity of gchI genes in vertebrates. In addition, we have found evidence for divergent resolution of duplicated pigmentation genes, i.e., differential gene loss in divergent teleost lineages, particularly in the tyrosinase gene family.

CONCLUSION

Mainly due to the FSGD, teleost fishes apparently have a greater repertoire of pigment synthesis genes than any other vertebrate group. Our results support an important role of the FSGD and other types of duplication in the evolution of pigmentation in fish.

Evolution of pigment synthesis pathways by gene and genome duplication in fish

BACKGROUND

Coloration and color patterning belong to the most diverse phenotypic traits in animals. Particularly, teleost fishes possess more pigment cell types than any other group of vertebrates. As the result of an ancient fish-specific genome duplication (FSGD), teleost genomes might contain more copies of genes involved in pigment cell development than tetrapods. No systematic genomic inventory allowing to test this hypothesis has been drawn up so far for pigmentation genes in fish, and almost nothing is known about the evolution of these genes in different fish lineages.

RESULTS

Using a comparative genomic approach including phylogenetic reconstructions and synteny analyses, we have studied two major pigment synthesis pathways in teleost fish, the melanin and the pteridine pathways, with respect to different types of gene duplication. Genes encoding three of the four enzymes involved in the synthesis of melanin from tyrosine have been retained as duplicates after the FSGD. In the pteridine pathway, two cases of duplicated genes originating from the FSGD as well as several lineage-specific gene duplications were observed. In both pathways, genes encoding the rate-limiting enzymes, tyrosinase and GTP-cyclohydrolase I (GchI), have additional paralogs in teleosts compared to tetrapods, which have been generated by different modes of duplication. We have also observed a previously unrecognized diversity of gchI genes in vertebrates. In addition, we have found evidence for divergent resolution of duplicated pigmentation genes, i.e., differential gene loss in divergent teleost lineages, particularly in the tyrosinase gene family.

CONCLUSION

Mainly due to the FSGD, teleost fishes apparently have a greater repertoire of pigment synthesis genes than any other vertebrate group. Our results support an important role of the FSGD and other types of duplication in the evolution of pigmentation in fish.

Novelties in hybrid zones: crossroads between population genomic and ecological approaches

BACKGROUND

Interspecific hybridization is widespread, occurring in a taxonomically diverse array of species. The Cyprinidae family, which displays more than 30% hybridization, is a good candidate for studies of processes underlying isolation and speciation, such as genetic exchange between previously isolated lineages. This is particularly relevant in the case of recent hybridization between an invasive species, Chondrostoma nasus nasus (from Eastern Europe), and C. toxostoma toxostoma (a threatened species endemic to southern France), in which bidirectional introgressive hybridization has been demonstrated.

METHODOLOGY/PRINCIPAL FINDINGS

We studied 128 specimens from reference populations and 1495 hybrid zone specimens (two years of sampling and four stations), using five molecular markers (one mitochondrial gene, four nuclear introns), morphology (meristic and plastic characters) and life history traits (weight, size, coefficient of condition, sex, age, shoaling). We identified 65 hybrid combinations and visualized spatial and temporal changes in composition. The direction of mitochondrial introgression was density-dependent in favor of the rarer species and we demonstrate that the sexual selection hypothesis is a preponderant explanation in the asymmetry of introgression. Despite genomic evolution in the hybrid zone, convergence was observed for body shape and coefficient of condition, indicating changes in foraging behavior with respect to reference populations, reflecting strong environmental pressure.

CONCLUSIONS/SIGNIFICANCE

The complex rules of hybrid zone dynamics are established very early in the contact zone. We propose "inheritance from the rare species" as a new evolutionary hypothesis for animal models. The endemic species was not assimilated by the invasive species. Survival rates for this species were highest in the middle of the river (the warmest part) due to a trade-off between food availability and fecundity. The environment-independent hybrid combination may result from nuclear-mitochondrial interactions involving the Tpi1b gene or a gene linked to this gene (Chromosome 16). This genomic region is also responsible for shoaling behavior in Danio rerio and is a promising zone for studies of changes in population dynamics and advances in integrated studies of hybrid zones.

Vertebrate vitellogenin gene duplication in relation to the "3R hypothesis": correlation to the pelagic egg and the oceanic radiation of teleosts

The spiny ray-finned teleost fishes (Acanthomorpha) are the most successful group of vertebrates in terms of species diversity. Their meteoric radiation and speciation in the oceans during the late Cretaceous and Eocene epoch is unprecedented in vertebrate history, occurring in one third of the time for similar diversity to appear in the birds and mammals. The success of marine teleosts is even more remarkable considering their long freshwater ancestry, since it implies solving major physiological challenges when freely broadcasting their eggs in the hyper-osmotic conditions of seawater. Most extant marine teleosts spawn highly hydrated pelagic eggs, due to differential proteolysis of vitellogenin (Vtg)-derived yolk proteins. The maturational degradation of Vtg involves depolymerization of mainly the lipovitellin heavy chain (LvH) of one form of Vtg to generate a large pool of free amino acids (FAA 150-200 mM). This organic osmolyte pool drives hydration of the ooctye while still protected within the maternal ovary. In the present contribution, we have used Bayesian analysis to examine the evolution of vertebrate Vtg genes in relation to the "3R hypothesis" of whole genome duplication (WGD) and the functional end points of LvH degradation during oocyte maturation. We find that teleost Vtgs have experienced a post-R3 lineage-specific gene duplication to form paralogous clusters that correlate to the pelagic and benthic character of the eggs. Neo-functionalization allowed one paralogue to be proteolyzed to FAA driving hydration of the maturing oocytes, which pre-adapts them to the marine environment and causes them to float. The timing of these events matches the appearance of the Acanthomorpha in the fossil record. We discuss the significance of these adaptations in relation to ancestral physiological features, and propose that the neo-functionalization of duplicated Vtg genes was a key event in the evolution and success of the teleosts in the oceanic environment.