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Cloning and Comparative Analyses of the Zebrafish Ugt Repertoire Reveal Its Evolutionary Diversity

  • Haiyan Huang,

    Affiliations Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China

  • Qiang Wu

    qwu123@gmail.com

    Affiliations Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai, China

Cloning and Comparative Analyses of the Zebrafish Ugt Repertoire Reveal Its Evolutionary Diversity

  • Haiyan Huang, 
  • Qiang Wu
PLOS
x

Abstract

UDP-glucuronosyltransferases (Ugts) are a supergene family of phase II drug-metabolizing enzymes that catalyze the conjugation of numerous hydrophobic small molecules with the UDP-glucuronic acid, converting them into hydrophilic molecules. Here, we report the identification and cloning of the complete zebrafish Ugt gene repertoire. We found that the zebrafish genome contains 45 Ugt genes that can be divided into three families: Ugt1, Ugt2, and Ugt5. Both Ugt1 and Ugt2 have two unlinked clusters: a and b. The Ugt1a, Ugt1b, Ugt2a, and Ugt2b clusters each contain variable and constant regions, similar to that of the protocadherin (Pcdh), immunoglobulin (Ig), and T-cell receptor (Tcr) clusters. Cloning the full-length coding sequences confirmed that each of the variable exons is separately spliced to the set of constant exons within each zebrafish Ugt cluster. Comparative analyses showed that both a and b clusters of the zebrafish Ugt1 and Ugt2 genes have orthologs in other teleosts, suggesting that they may be resulted from the “fish-specific” whole-genome duplication event. The Ugt5 genes are a novel family of Ugt genes that exist in teleosts and amphibians. Their entire open reading frames are encoded by single large exons. The zebrafish Ugt1, Ugt2, and Ugt5 genes can generate additional transcript diversity through alternative splicing. Based on phylogenetic analyses, we propose that the ancestral tetrapod and teleost Ugt1 clusters contained multiple Ugt1 paralogs. After speciation, these ancestral Ugt1 clusters underwent lineage-specific gene loss and duplication. The ancestral vertebrate Ugt2 cluster also underwent lineage-specific duplication. The intronless Ugt5 open reading frames may be derived from retrotransposition followed by gene duplication. They have been expanded dramatically in teleosts and have become the most abundant Ugt family in these lineages. These findings have interesting implications regarding the molecular evolution of genes with diversified variable exons in vertebrates.

Introduction

Natural selection plays an essential role in the evolution of vertebrate genomes. At the molecular level, DNA duplication provides important genetic materials upon which Darwinian positive selection can act. Vertebrate genomes contain a unique set of gene clusters that are organized into variable and constant regions. These gene clusters include the immunoglobulin (Ig), T-cell receptor (Tcr), Protocadherin (Pcdh), and UDP-glucuronosyltransferase (Ugt) genes [1]. Their variable region contains a tandem array of highly similar exons which are of about the same length. Each of the variable exons is combined with a single set of downstream constant exons to generate enormous molecular diversity required for the survival of the organisms. In the acquired immune system, DNA rearrangement, somatic mutation, and positive selection of the Ig and Tcr clusters provide unlimited diversity for defense against foreign antigens and for protection of our body from viral infections [2], [3]. Similarly, alternative splicing, gene conversion, and adaptive selection of the Pcdh clusters generate enormous diversity for the construction of trillions of specific neuronal connectivity in the central nervous system [4][7].

The human Pcdh α and γ clusters each contain more than a dozen variable exons and a common set of three constant exons [4]. Each “variable” exon is separately spliced to the set of downstream “constant” exons within each cluster to generate diverse functional mRNAs [4]. Each variable exon is preceded by a distinct promoter and promoter choice determines which variable exon is included in a Pcdh mRNA [5]. This unusual genomic organization of Pcdh clusters may provide a molecular foundation for generating enormous cellular diversity and complex neural connectivity in the brain.

The Ugt cluster encodes a diverse set of enzymes required for drug clearance, detoxification of xenobiotics, and metabolism of endobiotics, including phenolic compounds, environmental toxins, bilirubin, steroids, and bile acids [8]. Ugt1 and Ugt2 are the two Ugt families identified in mammals [9][11]. The mammalian Ugt1 clusters are organized into variable and constant regions, similar to the organization of the Pcdh clusters [1], [12], [13]. Each variable exon is preceded by its own promoter and is separately spliced to a common set of four downstream constant exons. Each variable exon encodes a signal peptide and the amino-terminal aglycone-recognition domain. The constant exons encode a highly conserved donor-binding domain, which binds the UDP-glucuronic acid (UDPGA), and the carboxyl-terminal endoplasmic-reticulum(ER)-anchoring transmembrane segment. Therefore, the encoded family of diverse Ugt1 enzymes can catalyze the conjugation of a vast number of lipophilic xenobiotics and endobiotics with the UDP-glucuronic acid. This glucuronidation reaction converts hydrophobic aglycones to water-soluble glucuronides and enhances their excretion from the body [8], [11].

Mammalian and avian genomes contain a single Ugt1 cluster divided into two major groups: constant-proximal bilirubin group and constant-distal phenol group [13], [14]. Members within the bilirubin or phenol group are highly similar and appear to be duplicated recently. Consistent with the whole genome duplication (WGD) in the teleost fishes [15][17] and similar to the duplication of the teleost Pcdh clusters [6], [7], [18], [19], the zebrafish Ugt1 cluster has been duplicated into Ugt1a and Ugt1b clusters, each organized into variable and constant regions [14], [20]. Both clusters span a region of about 35 kb genomic sequences, much smaller than mammals and avians. Members of the zebrafish Ugt1 clusters do not display orthologous relationships to those of the mammalian and avian clusters [14], [20].

Members of the Ugt2 family are clustered in one locus in human, mouse and rat, and are probably evolved by duplication of the entire gene [14]. The human UGT2 cluster includes three UGT2A genes and twelve UGT2B genes, five of which are pseudogenes [10], [11], [14], [21]. In contrast to the Ugt1 family, each Ugt2b gene consists of six exons. The exons 1 and 2 of the Ugt2b genes correspond to one variable exon of the Ugt1 cluster. Similar to the Ugt1 cluster, Ugt2a1 and Ugt2a2 genes are organized into variable and constant regions, which contain two variable exons and five constant exons, respectively [9], [14].

The human UGT genes play important roles in drug metabolism. For example, the UGT1A1 gene is essential in metabolizing the colorectal cancer drug irinotecan. Thus, the UGT1A1 genotyping has been used to determine the personalized irinotecan dosage for the treatment of colorectal cancer patients [22]. As in humans, each nonhuman vertebrate species lives in different ecological niches and has distinctive dietary. For example, many fish populations thrive at unique aquatic environments. Thus, each organism interacts with unique sets of environmental “drugs” or toxins. Therefore, each species might evolve a unique set of Ugt genes to detoxify them. Recently, zebrafish emerged as an important model organism in the toxicological research [23]. They are small, fecund, and morphologically and physiologically similar to mammals. In addition, they have transparent, externally developing embryos that facilitate their usages in developmental toxicology [23].

In this report, we cloned the complete zebrafish Ugt gene repertoire, which encodes at least 40 distinct yet highly similar enzymes. In addition, sequencing their full-length coding regions revealed many novel splice variants. To gain insight into the Ugt evolution, we performed comprehensive comparative analyses of the Ugt repertoire in teleosts and lower tetrapods. We found that the vertebrate Ugt1 clusters have undergone lineage-specific gene loss and duplication, while vertebrate Ugt2 clusters have undergone only lineage-specific gene duplication. Finally, we discovered a novel class of genes, designated Ugt5, whose entire protein sequences are encoded by single large exons. Interestingly, the vertebrate Ugt5 genes are only found in teleosts and amphibians, and have been extensively expanded in teleosts.

Results and Discussion

Identification and Cloning of the Complete Zebrafish Ugt Gene Repertoire

We identified 45 zebrafish Ugt genes through a combination of iterative BLAST searches of genomic sequences with comprehensive cloning of Ugt cDNA sequences (Tables S1 and S2). These genes constitute the complete repertoire of zebrafish Ugt genes (Fig. 1). They include two duplicated Ugt2 clusters (Fig. 1A), 17 single-exon Ugt5 genes (Fig. 1B), and two duplicated Ugt1 clusters (Fig. 1C). They are located in at least ten different chromosomes. Five of them are pseudogenes (Fig. 1 and data not shown). The other 40 genes are all transcribed in the adult zebrafish as we have successfully cloned all of their full-length coding sequences. All of the encoded Ugt proteins have the typical two-Rossmann-fold-domain structures that bind donor and acceptor molecules.

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Figure 1. The repertoire of the zebrafish Ugt genes.

Shown are the genomic organizations of the zebrafish Ugt 2a and 2b clusters (A), the Ugt5 genes (B), and the Ugt 1a and 1b clusters (C). Orange boxes represent variable exons or Ugt5 exons, and blue boxes represent constant exons. Gray boxes represent pseudogenes (p) or relics (r). The approximate length for each cluster is also shown. Transcription directions are indicated by an arrow above each gene. Chromosomal or scaffold locations are shown on the right by the letter “C” representing chromosome or “S” representing scaffold. Var, variable; Con, constant; Kb, kilobase pairs. The phylogenetic trees are based on the polypeptide sequences encoded by the zebrafish (z) and human (h) variable regions (D) or constant regions (E). The trees are unrooted. The tree branches are labeled with the percentage support on the basis of 1,000 bootstrap replicates. Only bootstrap values (>50%) of the major nodes are shown. The scale bar equals a distance of 0.1.

https://doi.org/10.1371/journal.pone.0009144.g001

We previously predicted four zebrafish Ugt2a (2a1 to 2a4) genes that are organized in a cluster containing variable and constant regions [14]. The variable region contains four highly similar exons that are organized in a tandem array. The constant region contains a set of five small exons located downstream of the variable region. We cloned the full-length coding sequences for all of the four zebrafish Ugt2a genes and confirmed that each of the four Ugt2a variable exons is separately spliced to the same set of downstream constant exons (Fig. 1A). In addition, we identified two additional Ugt2a (2a5 and 2a6) genes that are located downstream of the tandem-arrayed Ugt2a genes. Cloning of their full-length coding region and comparing them with the zebrafish genomic sequences revealed that both the Ugt2a5 and Ugt2a6 genes are organized into six exons and that they do not share any constant exon. Their first exons are highly similar to the variable exons of the tandem-arrayed Ugt2a genes. The next five exons are each similar to the five respective constant exons of the tandem-arrayed Ugt2a genes. However, the transcriptional directions are opposite to that of the tandem-arrayed Ugt2a genes (Fig. 1A).

We identified a novel cluster of zebrafish Ugt2 genes. This Ugt2b cluster contains a variable region of four variable first exons, 2b1 to 2b4, and a constant region with a set of five downstream constant exons (Fig. 1A). Cloning and sequencing of the full-length coding sequences revealed that, similar to the Ugt2a (2a1 to 2a4) cluster, each of the Ugt2b variable exons is separately spliced to the common set of downstream constant exons. However, the Ugt2b2 and Ugt2b4 genes appear to be pseudogenes because their variable exons are frame-shifted due to insertions. This cluster of Ugt2b genes is followed by two single Ugt genes: Ugt2b5 and Ugt2b6 (Fig. 1A). The Ugt 2b5 and 2b6 genes contain six exons, each of which is similar to the corresponding exons in the tandem-arrayed Ugt2b genes. Contrary to the Ugt2a cluster, the transcriptional directions of the Ugt5b and Ugt6b genes are the same as the tandem-arrayed Ugt2b genes. Finally, we identified a pseudogene, Ugt2b7p, which is located in the same scaffold as that of the Ugt2b cluster (data not shown).

We identified 18 unusual Ugt-like genes, designated Ugt5, located in six different chromosomes. The encoded protein sequences show high similarity to that of the Ugt1 and Ugt2 enzymes. Each predicted Ugt5 protein contains an acceptor-binding domain preceded by an N-terminal signal peptide, and a donor-binding domain followed by an ER-anchoring transmembrane segment. Each Ugt5 protein also contains the essential catalytic histidine and aspartic acid residues [14] in its acceptor-binding domain. However, we cannot rule out the possibility that these proteins might use donor sugars other than that of the Ugt1 and Ugt2 enzymes.

In contrast to multiple coding exons of the Ugt1 and Ugt2 genes, the open reading frame of each of the Ugt5 genes (except Ugt5g2) is encoded by a single large exon (Fig. 1B). Five of them, Ugt 5a1 to 5a5, are clustered on the chromosome 25. Similarly, the five Ugt5b (5b1 to 5b5) genes are clustered on the chromosome 1; however, the Ugt5b5 gene has four nonsense mutations and two frameshift mutations and appears to be a pseudogene. Nevertheless, it is transcribed because we have cloned its cDNA. Three of the Ugt5c genes, 5c1 to 5c3, are clustered on the chromosome 18. The other four Ugt5 genes, 5d1, 5e1, 5f1, and 5g1, are nonclustered single genes. Finally, we found that the Ugt5g2 gene contains two coding exons (Fig. 1B).

We previously identified two duplicated zebrafish Ugt1 clusters, 1a and 1b. Each of these clusters contains a variable region and a constant region [14]. We predicted that each of the Ugt1 variable exons is alternatively spliced to a single set of constant exons. We have cloned the full-length coding sequences of all of the members of the Ugt 1a and 1b clusters and confirmed that each member of the zebrafish Ugt 1a and 1b clusters is separately spliced to the respective set of constant exons (Fig. 1C).

To examine the evolutionary relationship of the zebrafish and human Ugt genes, we reconstructed their phylogenetic trees based on amino acid sequences corresponding to those encoded by the Ugt2 variable exons (Fig. 1D) or the Ugt1 constant exons (Fig. 1E). In both trees, the zebrafish Ugt superfamily is divided into three separate clades: Ugt1, Ugt2, and Ugt5. The zebrafish Ugt1 and Ugt2 genes are closely related to the human UGT1 and UGT2 genes, respectively. The zebrafish Ugt5 genes form a separate branch in both trees, suggesting that the Ugt5 genes are a novel Ugt subfamily that does not exist in humans (Fig. 1D and 1E).

Additional Ugt Diversity Generated by Alternative Splicing

In addition to the cDNAs containing both variable and constant regions, we also cloned a set of unusual short-form cDNAs from the adult zebrafish for each member of the clustered Ugt1 and Ugt2 genes. These short-form cDNAs correspond to the variable exons and their immediate downstream intronic sequences (Fig. 2A). Such short-form cDNAs have also been found for members of the Pcdh α and γ clusters, corresponding to the Pcdh variable exons and their immediate downstream intronic sequences [4], [24]. However, the physiological function for the encoded short-form Pcdh proteins remains to be established.

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Figure 2. Alternative splicing of the zebrafish Ugt genes.

(A) Each Ugt1 or Ugt2 member has a short-form transcript which corresponds to the variable exon (orange box) and its immediate downstream intronic sequences (purple box). Red triangles indicate the potential translational stop codons. Gray box indicates pseudogene. Transcription directions are marked by an arrow above each gene. (B) Detection of the short-form cDNA by RT-PCR and agarose electrophoresis. “+” and “−” indicate with and without reverse transcriptase, respectively. Amplification bands are detected only in “+” lanes. M: 1 kb marker. (C) Alternatively spliced variants for the Ugt2a1, and Ugt 2b1 and 2b5 genes. The exon length is shown in each box. (D) Alternative splicing of the zebrafish Ugt5 genes. Green boxes represent 5′ noncoding exons or short noncoding exonic sequences immediate upstream of the ATG codon.

https://doi.org/10.1371/journal.pone.0009144.g002

All of the Ugt1 and Ugt2 cDNAs have these short variants (Fig. 2B). However, we do not know whether the RNA molecules corresponding to these cDNAs are polyadenylated. In addition, we found that few EST sequences match these short-form variants of the Ugt cDNAs. Nevertheless, they may encode short-form polypeptides containing only the N-terminal signal peptide and the aglycone-recognition domain, but lacking the donor-binding domain and the ER-anchoring transmembrane segment. Therefore, they do not have intrinsic UDP-glucuronosyltransferase activities. However, they may form hetero- or homo-oligomers with full-length Ugt proteins. It has long been suggested that Ugts functions in ER membranes as dimers in monoglucuronide formation, and may form tetramers in diglucuronide formation [25], [26]. The amino terminal domain has been suggested to be involved in human UGT2B1 dimerization [27]. Alternatively, the short Ugt RNA variants may play some roles in the regulation of the Ugt gene expression and never encode any polypeptide. For example, they may be processed to small regulatory RNA molecules such as miRNAs. However, we could not find any miRNA sequence in the public miRNA databases matching these short Ugt RNA variants. Further experiments need to be performed to elucidate their physiological functions.

Each of the full-length Ugt2 mRNAs is generated by splicing of one variable exon to the set of five constant exons (Figs. 1A and 2C). Interestingly, cloning the full-length coding sequences revealed at least four additional transcripts (v2 to v5) (Fig. 2C). Ugt2a1_v2 is an intron-retention transcript that retained the entire 64-nucleotide intronic sequences between the constant exons 2 and 3. Ugt2a1_v3 contains an additional 215-nucleotide alternative exon within the intronic sequences between the constant exons 1 and 2. Cloning of the Ugt2b1_v4 transcript revealed an alternative 5′ splice site within the variable exon that splices directly to the first constant exon to generate an 81-nucleotide shorter mRNA molecule. Finally, we cloned a cDNA molecule (Ugt2b1_v5) that retained the entire 188-nucleotide intronic sequences between the constant exons 3 and 4. All of these four types of alternatively spliced transcripts may encode short-form Ugt proteins (Fig. 2C). Interestingly, the Guillemette's group has recently identified a novel alternative exon at the 3′ end of the mammalian Ugt1 cluster which generates a new set of Ugt1a isoforms [28], [29]. These isoforms can decrease the enzymatic activity of the normal Ugt1 proteins [28], [29].

The transcription start site of each member of the Ugt1 and Ugt2 clusters has been mapped to the immediate upstream of the corresponding variable exon. Each variable exon of these two Ugt gene clusters is associated with its own promoter. Therefore, these Ugt1 and Ugt2 genes belong to a large class of genes whose expression patterns are determined by their respective promoters of multiple variable first exons [1]. By contrast, sequencing of the cloned Ugt 5a1 to 5a4 cDNAs and comparing them with the genomic DNA sequences revealed that a common 5′ noncoding exon is spliced to each of the four mutually exclusive coding exons (Fig. 2D). Therefore, the Ugt 5a1 to 5a4 share a common upstream noncoding exon and are actually transcribed from a single promoter (Fig. 2D). Each of these four transcripts appears to be separately polyadenylated. For example, two clones (BC109447 and BC124407) that correspond to two of these four transcripts contain poly(A) tails. Therefore, this cluster of Ugt5 genes belongs to a class of genes that are alternatively polyadenylated [30]. Interestingly, their downstream paralogous Ugt5a5 gene has two different 5′ noncoding exons (Fig. 2D).

The genomic organization of the Ugt 5b1 to 5b4 is the most complex. In addition to the first 5′ noncoding exon u1, we also found an alternative 5′ noncoding exon u2 (Fig. 2D) that can be included into each of the Ugt5b1 to 5b4 mRNAs. This second 5′ noncoding exon is 364 bp in length and is located at about 3.4 kb downstream of the first 5′ noncoding exon u1 and about 1.7 kb upstream of the Ugt5b1 coding region. The u2 exon can also be skipped in a second set of Ugt5b transcripts. Thus, the exclusion or inclusion of the exon u2 generates two sets of mRNA variants for each member of the Ugt 5b1 to 5b4 cluster. In addition, we discovered two additional constitutively included 5′ noncoding exons (Fig. 2D, u4 and u5) located between the protein-coding region of the Ugt 5b2 and 5b3. The noncoding exon u1 is spliced to the noncoding exon u4, followed by the noncoding exon u5 and the protein-coding exon to generate a set of the Ugt 5b3 and 5b4 mRNAs. Alternatively, inclusion of the noncoding exon u2 generates a second set of the Ugt 5b3 and 5b4 mRNAs that are 364-bp longer. Finally, we identified a novel 5′ noncoding exon (Fig. 2D, u3) that is located at the immediate upstream of the noncoding exon u4, potentially generating the third set of the Ugt 5b3 and 5b4 mRNAs. Indeed, cloning and sequencing the Ugt 5b3 and 5b4 cDNAs (Table S2, Ugt5b3_v3 and Ugt5b4_v3) confirmed that u3 is spliced to u4, followed by u5 and the protein-coding exon. In total, three sets of different mRNAs could be generated by alternative splicing for these Ugt5 genes. The downstream paralogous Ugt5b5p pseudogene does not share any 5′-UTR exon with Ugt 5b1 to 5b4, but has its own 5′ noncoding exon u6 (Fig. 2D).

The Ugt 5b1 to 5b4 are likely derived from one common ancestral Ugt5 gene that has 5′ noncoding exons. This ancestral gene may have experienced multiple rounds of coding-exon duplications, generating three more duplicated Ugt exons (Fig. 1D and 2D). The 5′ splice sites of the upstream 5′ noncoding exons are then spliced to the 3′ splice sites of these mutually exclusive exons, thus generating molecular diversity in the 5′-UTRs of Ugt 5b1 to 5b4. These dynamic 5′-UTR structure might play an important role in regulating mRNA stability or their translation efficiency, thus may determine the spatial or temporal expression patterns of the Ugt5b genes. The Ugt 5a1 to 5a4 cluster may evolve similarly.

The clustered Ugt5c genes each have its own 5′ noncoding exons. Despite of high similarity among their coding regions, their 5′ noncoding exons do not show any sequence similarity. Their introns differ sharply from each other either in length or sequences. Similar to members of the Ugt5c family, Ugt 5d1, 5e1, and 5f1 each have its own 5′ nonconding exon. Finally, the Ugt5g1 gene contains three distinct 5′ noncoding exons. The second and third of these noncoding exons are only 58 bp and 71 bp, respectively. The splicing of each of these 5′ noncoding exons has been confirmed by cloning and sequencing (Table S2). Similar genomic organizations have been found for other family genes. For example, the entire coding sequences of hundreds of vertebrate olfactory receptor genes are also encoded by single exons. Moreover, the olfactory receptor genes appear to have 5′ noncoding exons [31].

Lineage-Specific Birth and Death Evolution of the Vertebrate Ugt1 Genes

Members of the zebrafish Ugt1 do not display orthologous relationships to those of the mammalian and avian Ugt1 clusters [14]. To determine their evolutionary history, we annotated the complete Ugt1 gene repertoire in other teleosts such as fugu, tetraodon, medaka, and stickleback, as well as in a wide variety of lower tetrapods. Each teleost has two Ugt1 loci, designated 1a and 1b (Fig. 3). To our surprise, the Ugt1 genes in none of these four teleosts are organized into variable and constant regions. Instead, they are single genes each organized into multiple exons (Fig. 3A). As in zebrafish, the Ugt1a genes in euteleosts each contain five exons. All of the corresponding exons are highly similar among members of the teleost Ugt1a genes.

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Figure 3. The evolution of the vertebrate Ugt1 genes.

(A) Comparison of the vertebrate Ugt1 clusters with species names indicated on the left. The exons are indicated by boxes with different colors. Pseudogene (p) and relic (r) are indicated by gray boxes. The directions of transcription are indicated by arrows. Chromosomal or scaffold locations are shown on the right. Small gaps are represented by light blue lines and possible exons in the gaps by dotted boxes. The hypothetical ancestral teleost and tetrapod Ugt1 clusters are shown with orthologous variable exons shaded in the same background color. (B) Phylogenetic tree of the zebrafish (z), fugu (f), tetraodon (t), medaka (m), stickleback (s), xenopus (x), lizard (l), zebra finch (zf), and human (h) Ugt1 genes. The tree branches are labeled with the percentage support on the basis of 1,000 bootstrap replicates. Only bootstrap values (>50%) of the major nodes are shown. The trees are unrooted. The scale bar equals a distance of 0.1. The seven Ugt1 groups (1aI to 1aVII) are indicated with the same color as shaded in the panel A.

https://doi.org/10.1371/journal.pone.0009144.g003

The coding regions of the euteleosts Ugt1a first exons are 861 bp in length; however, the corresponding sequences in their Ugt1b genes are organized into five small exons (Fig. 3A). Although these Ugt1b genes display close relationships with the zebrafish Ugt1b genes in the phylogenetic tree (Fig. 3B), we cannot rule out that they may not be the zebrafish Ugt1b orthologs. The first exon of these euteleost Ugt1b genes appears to be a little longer than the corresponding Ugt1a region (Fig. S1). Thus, the mature proteins of the fugu 1b1 and 1b2, tetraodon 1b1, medaka 1b1 and 1b2, and stickleback 1b1 could contain 34, 34, 29, 29, 27, and 42 more amino acid residues than that of the Ugt1a proteins, respectively.

Xenopus contains at least six Ugt1 genes (Fig. 3A). The Ugt 1a1 to 1a4 genes are organized into variable and constant regions and the Ugt1a5 and Ugt1a6 genes are single genes organized into five exons. The Ugt 1a1 to 1a4 genes appear to be generated by tandem duplication of variable exons while the Ugt1a5 and Ugt1a6 genes seem to arise from the duplication of the entire five ancestral Ugt1a exons (Fig. 3A). Similar to humans, the green lizards and the zebra finches each contain a single Ugt1 cluster, organized into variable and constant regions. Lizards contain seven Ugt1 variable exons, much less than those in zebra finches and humans (Fig. 3A).

To determine the evolutionary history of the vertebrate Ugt1 genes, we performed phylogenetic analyses using polypeptides (Fig. S1) encoded by the variable regions of the Ugt1 clusters and the corresponding first exons of other Ugt1 genes (Fig. 3B). The tree demonstrates that the vertebrate Ugt1 variable exons can be grouped into seven clades, Ugt 1aI to 1aVII (Fig. 3B), each may be derived from an ancestral variable exon. Teleosts have the clades 1aVI and 1aVII; while tetrapods have the clades 1aI to 1aV (Fig. 3A). In addition, the teleost and tetrapod Ugt1 genes do not have any overlapping clade. Therefore, we propose that the ancestral teleost Ugt1 cluster contained two variable exons (1aVI and 1aVII) and that the ancestral tetrapod Ugt1 cluster contained five variable exons (1aI to 1aV) (Fig. 3A). Both zebrafish Ugt 1a and 1b clusters maintained 1aVI and 1aVII after the fish-specific WGD. By contrast, the euteleosts lost 1aVII in the Ugt1a cluster and lost 1aVI in the Ugt1b cluster. Finally, members of the zebrafish Ugt1 clusters expanded greatly through tandem duplication of the 1aVI and 1aVII variable exons (Fig. 3A).

The ancestral xenopus Ugt1 cluster contains the Ugt 1aI and 1aII variable exons. The Ugt1aI has been greatly expanded into five variable exons (1a1, and 1a3 to la6) (Fig. 3A). Lizards have the 1aII, 1aIII, 1aIV, and 1aV groups but have lost the other three ancestral variable exons. Zebra finches also have the ancestral 1aII variable exon. In addition, this exon might have been duplicated before the divergence of zebra finches and lizards. Moreover, the Ugt 1aIV and 1aV have also been duplicated in zebra finches and lizards. The Ugt1aIII was unique in lizards and might have been lost in other species. The humans have tandem duplications of Ugt 1aIV and 1aV but have lost all of the other three Ugt1 ancestral genes (Fig. 3A).

The mammalian Ugt1 genes can be divided into constant-proximal bilirubin group and constant-distal phenol group [13], [14]. For example, human UGT 1A1 to 1A5 genes belong to the bilirubin group and 1A6 to 1A10 belong to the phenol group. Thus, 1aIV and 1aV might correspond to the ancestors of the bilirubin and phenol groups, respectively (Fig. 3A). These evolutionary dynamics of the Ugt1 clusters in different lineages of vertebrates might have contributed to their adaptation to specific habitats.

Lineage-Specific Duplication of the Vertebrate Ugt2 Genes

We have analyzed the evolution of the vertebrate Ugt2 clusters. Zebrafish, fugu, and medaka have two unlinked Ugt2 clusters, 2a and 2b (Fig. 4A). We only found one Ugt2 cluster in the draft genomic sequences of stickleback. There may be a second stickleback Ugt2 cluster that have not been sequenced yet. In the phylogenetic tree based on polypeptides (Fig. S2) encoded by the Ugt2 variable exons, almost all of the vertebrate Ugt2 display paralogous relationships (Fig. 4B). This suggests that members of the Ugt2 clusters have undergone lineage-specific gene duplication.

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Figure 4. The evolution of the vertebrate Ugt2 genes.

(A) Comparison of the vertebrate Ugt2 clusters with species indicated on the left. The exons are indicated by boxes with different colors. Pseudogenes (p) are indicated by gray boxes. The directions of transcription are indicated by arrows. Chromosomal or scaffold locations are shown on the right. (B) Phylogenetic tree of the zebrafish (z), fugu (f), medaka (m), stickleback (s), xenopus (x), lizard (l), zebra finch (zf), and human (h) Ugt2 genes. The trees are unrooted. Bootstrap values (>50%) of only the major nodes are shown. The scale bar equals a distance of 0.1.

https://doi.org/10.1371/journal.pone.0009144.g004

Like the teleost Ugt1 clusters, only zebrafish Ugt 2a and 2b clusters contain variable and constant regions (Fig. 4A). In the zebrafish Ugt2a cluster, the variable exons are resulted from tandem duplication of an ancient variable exon. The variable exons 2a3 and 2a4 seem to be duplicated most recently. Similarly, the six-exon Ugt 2a5 and 2a6 genes appear to be duplicated recently (Fig. 4B). In the zebrafish Ugt2b cluster, the six-exon Ugt 2b5 and 2b6 genes are likely duplicated early. The variable exons 2b1 to 2b4 may be resulted from tandem duplication of an ancient variable exon (Fig. 4A).

The euteleost Ugt2b genes are single genes that are each organized into six exons. However, the euteleost Ugt2a genes are each organized into seven exons (Fig. 4A). The sizes of the first two Ugt2a exons are 231 and 490 bp in fugu, and 246 and 490 bp in medaka, respectively, corresponding to the 712∼733 bp in length of the zebrafish Ugt2a variable exons. The encoded amino acid sequences are highly similar to those encoded by the other teleost Ugt 2a and 2b genes (Fig. S2). Compared to the variable and constant genomic organization of the zebrafish Ugt2a cluster, the fugu and medaka Ugt2a each contain only one single gene. A distinct feature of the euteleost Ugt2 genes is that none of them share common constant exons or contain multiple variable exons (Fig. 4A).

Mammals have three Ugt2a and multiple Ugt2b genes [10], [11], [14]. The human UGT2A genes have orthologs in mice and rats, while the human UGT2B genes display paralogous relationship to those of mouse and rat [14]. Chicken and zebra finch have three Ugt2a variable exons (Fig. 4A). Each of these three variable exons displays strict orthologous relationships in the phylogenetic tree, indicating that their expansion occurred before the divergence of chicken and zebra finch. Lizard and Xenopus have two functional Ugt2a variable exons and these exons display paralogous relationships (Fig. 4B). Zebrafish has four Ugt2a variable exons and they display paralogous relationships (Fig. 4B). Because the variable exons encode the aglycone-recognition domains, these dynamic evolution of variable exons may be an adaptation of each organisms to its specific environmental niches.

The Ugt5 Genes Are Only Found in Lower Vertebrates

The teleost Ugt5 family can be divided into eight groups, Ugt 5a to 5h, based on their sequence divergence (Fig. 5A). Members of the zebrafish Ugt 5a, 5b, or 5c groups are clustered (Fig. 5A). All of the other members of the zebrafish Ugt5 family are not clustered. Ugt 5d to 5f are single genes. The Ugt5g group contains two members: 5g1 and 5g2.

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Figure 5. The Ugt5 genes are expanded in teleosts.

(A) Vertebrate Ugt5 genes in teleosts and xenopus. Members of each Ugt5 subfamily (5a to 5h) are indicated by colored boxes. Pseudogene (p) and relic (r) are indicated by gray boxes. Transcription directions are indicated by arrows. Chromosomal or scaffold locations are shown on the right. Small gaps are represented by light blue lines and possible exons in the gaps by dotted boxes. (B) Phylogenetic tree of the zebrafish (z), fugu (f), tetraodon (t), medaka (m), stickleback (s), and xenopus (x) Ugt5 genes. Genes labeled with same colors belong to the same subfamily. The trees are unrooted. Only bootstrap values (>50%) of the major nodes are shown. The scale bar equals a distance of 0.1.

https://doi.org/10.1371/journal.pone.0009144.g005

One striking feature of members of the Ugt5 family is that their entire open reading frames are encoded by single large exons. The only exception is the Ugt5g2 gene which contains two exons that are 123 and 1482 bp in length (Fig. 5A). The zebrafish Ugt5 family has eighteen members, representing about 40% of the total number of the zebrafish Ugt genes. To determine the evolutionary history of the Ugt5 family, we searched a wide variety of vertebrate genomes. We identified Ugt5 genes in amphibians and teleosts but could not find any Ugt5-like gene in reptiles, birds, and mammals (Fig. 5A).

Each teleost species has more than ten Ugt5 genes (Fig. 5A). However, xenopus has only two Ugt5 genes (Fig. 5A). It appears that the Ugt5 genes decreased from teleosts to amphibians. Thus, a large number of Ugt5 genes were lost during the transition from teleosts to amphibians. By contrast, the Ugt1 and Ugt2 families were expanded to generate diversity during the transition from amphibians to sauropsids and mammals.

We reconstructed a phylogenetic tree based on the full-length sequences of the encoded Ugt5 proteins (Fig. 5B; Fig. S3). The tree shows that the teleost Ugt5 genes form eight clades. In each clade, zebrafish Ugt5 genes occupy a basal phylogenetic position among the teleost species. This is consistent with that zebrafish belongs to Otocephala while fugu, tetraodon, medaka, and stickleback belong to Euteleostei. All subfamilies of the zebrafish Ugt5 genes have orthologs in other fishes. The Ugt5a orthologs in Euteleostei are grouped into two subclades. One subclade contains fugu 5a1 to 5a4, tetraodon 5a1 and 5a2, medaka 5a1, and stickleback 5a1. The other contains fugu 5a5 and stickleback 5a2 (Fig. 5B). The fugu 5a1 to 5a4 and tetraodon 5a1 to 5a3 genes are clustered, suggesting that they are resulted from tandem duplication of an ancient Ugt5 gene. The Ugt5b orthologs are found in pufferfish species but not in Smegmamorpha (medaka and stickleback). Fugu Ugt5b genes have at least two members: 5b1 and 5b2. The 5b1 gene appears to be a pseudogene because of a nonsense mutation. Tetraodon contains five tandem-arrayed Ugt5b genes two of which have frame-shift mutations and appear to be pseudogenes.

The Ugt5c and Ugt5f genes are present in the genomes of zebrafish, fugu, medaka, and stickleback, but are absent in the tetraodon genome. Like Ugt5a, the Ugt5c genes in euteleosts can be grouped into two subclades in the phylogenetic tree (Fig. 5B). One subclade contains the fugu 5c1, medaka 5c1 to 5c4, and stickleback 5c1. The other contains the fugu 5c2, medaka 5c5 to 5c7, and stickleback 5c2. Interestingly, we found that, in the medaka and stickleback genomes, the Ugt5c genes in the second subclade are always located directly upstream of the Ugt5f genes (data not shown).

The Ugt5d genes seem to be lost in pufferfishes (fugu and tetraodon) and duplicated in tandem in medaka. Surprisingly, the medaka and stickleback Ugt5d genes have three exons which are 288, 714, and 585 bp in length. The stickleback Ugt5d gene appears to be a pseudogene because it lacks the coding sequences for the N-terminal signal peptide. Ugt5e and Ugt5g exist in all of the five teleosts. The tetraodon and medaka Ugt5e and stickleback Ugt5g genes have been duplicated recently. Other fishes only contain one copy of the Ugt5e and Ugt5g gene. Finally, Ugt5h is absent in zebrafish and medaka but present as single copies in the fugu, tetraodon, and stickleback genomes.

A Possible Mechanism for the Expansion of Ugt5 Genes in Teleosts

How did so many Ugt5 genes occur in the teleost genomes? We posit that retrotransposon might play a role in their expansion. If a retrotransposon inserts into a site near an ancient multi-exon Ugt gene, such as the ancestral Ugt1 or Ugt2 gene, the encoded retrotransposon proteins could reverse-transcribe the spliced mRNA sequences containing the full-length ORF from this Ugt gene. The reverse transcribed cDNA sequences are subsequently integrated into a new site downstream from a promoter [32]. Because the length of the 5′ noncoding sequences depends on the distance between the upstream promoter and the integration site, the initial 5′ noncoding region in the primary transcript could be very large in size [33]. Subsequently, 5′ and 3′ splice sites could be generated by mutations or the insertions of a retronuon (a nuon is any definable nucleic acid sequence) carrying such potential splice sites such as Alu sequences [33]. Splicing between these 5′ and 3′ splice sites could reduce the size of 5′-UTR in the mature mRNA. Recombination or additional rounds of retrotansposition might generate multiple teleost Ugt5 genes. Similar mechanisms have been proposed to be involved in the expansion of G-protein coupled receptor superfamily with intronless protein coding regions [32], [33], such as the olfactory receptor genes [31], in the vertebrate genomes.

This mechanism is consistent with three observations of the zebrafish Ugt5 genes. First, we found a polyprotein-like coding sequence located at the immediate upstream of the zebrafish Ugt5c cluster (data not shown). The encoded polyprotein contains the domains of protease, reverse transcriptase, and retroviral integrase, which could have retrotransposase activities. Second, the Ugt5 genes were scattered at many loci in the zebrafish genome. Third, each of the zebrafish Ugt5 genes contain at least one 5′ noncoding exon (Fig. 2D). Thus, the Ugt5 loci appear to be hotspots for retrotransposition.

Conclusions

We have identified and cloned the complete zebrafish Ugt repertoire. Zebrafish contains 45 Ugt genes that can be divided into three families: Ugt1, Ugt2, and Ugt5. Both Ugt1 and Ugt2 are organized into two unlinked clusters: a and b. Phylogenetic analyses show that both a and b clusters have orthologs in other teleost species, indicating that they may be resulted from the “fish-specific” WGD event that occurred in the ray-finned fish (Actinopterygii) lineage about 350 million years ago [17], [34]. We also cloned five distinct isoforms for members of the zebrafish Ugt1 and Ugt2 clusters. The coding region of the zebrafish Ugt5 genes is encoded by a single large exon. These coding exons are each preceded by small 5′ noncoding exons. Finally, several of the 5′ noncoding exons can be alternatively spliced to generate additional diversity for the Ugt5b mRNAs. The diverse 5′-UTR sequences may play an important role in the regulation of the Ugt5 mRNA stability or their translation efficiency.

Based on the inferred phylogenetic relationships of the vertebrate Ugt1 genes, we propose that the Ugt1 clusters in the teleost and tetrapod ancestors contained multiple Ugt1 paralogous genes. In addition, these ancestral Ugt1 loci have experienced differential gene loss and duplication in different vertebrate lineages. Moreover, the ancestral vertebrate Ugt2 gene has undergone lineage-specific duplications. Finally, the Ugt5 genes appear to be present only in lower vertebrates and have been expanded dramatically in teleosts. The dynamic evolution of the Ugt genes in different vertebrate lineages may contribute to the development of chemical defense system for their adaptation to ecological habitats.

Materials and Methods

Sequence Annotation

The zebrafish Ugt genomic sequences were identified by iterative BLAST search of the zebrafish genome assembly (Danio rerio Zv8) using the published vertebrate UGT protein sequences as queries and annotated as previously described [1], [14]. The Ugt genomic sequences of fugu, tetraodon, medaka, stickleback, xenopus, lizard, zebra finch, and chicken were identified and annotated similarly (Takifugu rubripes v4.0, Tetraodon nigroviridis v7, Oryzias latipes v1.0, Gasterosteus aculeatus v1.0, Xenopus tropicalis v4.1, Anolis carolinensis v1.0, Taeniopygia guttata v3.2.4, and Gallus gallus v2.1).

Cloning and Sequencing of the Zebrafish Ugt Genes

Total RNA was prepared from the whole adult zebrafish with the Trizol reagent (Invitrogen, USA), treated with DNase I (Takara, Japan), and reverse-transcribed by using the Superscript III reverse transcriptase (Invitrogen, USA) with Ugt-specific primers. The full-length coding sequences were amplified by PCR with Taq DNA polymerase (Takara, Japan), cloned into the pGEM-T vector (Promega, USA), and sequenced in both directions. The primers used for reverse transcription and PCR reactions are listed in Tables S1 and S2. Sequences of the zebrafish Ugt cDNAs have been submitted to the GenBank. All of the zebrafish cDNAs and their accession numbers are listed in Table S2.

Phylogenetic Analyses

The cloned or predicted Ugt coding sequences were translated, and the resulting amino acid sequences were aligned by using the ClustalX software (Version 2.0.11) [35]. Phylogenetic trees were reconstructed by using the Neighbor-joining method based on sequence distance matrix, and the trees were displayed using the NJplot program (http://pbil.univ-lyon1.fr/software/njplot.html). The robustness of the tree partitions was evaluated by using the bootstrap analysis with a neighbor-joining search.

Supporting Information

Table S1.

Sequences of primers used. All of the primers used to clone the zebrafish Ugt repertoire are listed. Their sequences are also shown.

https://doi.org/10.1371/journal.pone.0009144.s001

(0.04 MB DOC)

Table S2.

The GenBank accession numbers for all of the zebrafish Ugt clones. The zebrafish Ugt cDNA clones and their GenBank accession numbers are shown. The primers used in the RT-PCR reactions for each clone are also listed.

https://doi.org/10.1371/journal.pone.0009144.s002

(0.04 MB DOC)

Figure S1.

An alignment of the vertebrate Ugt1 protein sequences. The zebrafish (z), fugu (f), tetraodon (t), medaka (m), stickleback (s), xenopus (x), lizard (l), zebra finch (zf), and human (h) Ugt1 polypeptides were aligned by using the ClustalX software. The Ugt1 sequence names are indicated on the left and are presented according to the seven groups shown on the Figure 3. The amino acid residues are represented by capitalized single-letters with the degree of conservation indicated above the alignment.

https://doi.org/10.1371/journal.pone.0009144.s003

(7.28 MB PDF)

Figure S2.

An alignment of the vertebrate Ugt2 protein sequences. The zebrafish (z), fugu (f), medaka (m), stickleback (s), xenopus (x), lizard (l), zebra finch (zf), and human (h) Ugt2 polypeptides were aligned by using the ClustalX. The amino acid residues are represented by capitalized single-letters with the degree of conservation highlighted by different colors. The Ugt2 sequence names are indicated on the left.

https://doi.org/10.1371/journal.pone.0009144.s004

(0.21 MB PDF)

Figure S3.

An alignment of the vertebrate Ugt5 protein sequences. The zebrafish (z), fugu (f), tetraodon (t), medaka (m), stickleback (s), and xenopus (x) Ugt2 polypeptides were aligned by using the ClustalX. The amino acid residues are represented by capitalized single-letters with the degree of conservation highlighted by differential coloring. The names of the Ugt5 proteins are indicated on the left and presented according to the order of the eight Ugt5 groups (Ugt5a to Ugt5h) shown on the Figure 5.

https://doi.org/10.1371/journal.pone.0009144.s005

(0.28 MB PDF)

Acknowledgments

We thank Renjie Jiao for providing zebrafish and Hualin Fu for critical reading of the manuscript. We also thank Yuanming Wang for excellent assistance.

Author Contributions

Conceived and designed the experiments: HH QW. Performed the experiments: HH. Analyzed the data: HH QW. Wrote the paper: HH QW.

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