Expression of phosphatase of regenerating liver family genes during embryogenesis: an evolutionary developmental analysis among Drosophila, amphioxus, and zebrafish
© Lin et al.; licensee BioMed Central Ltd. 2013
Received: 25 January 2013
Accepted: 29 April 2013
Published: 4 May 2013
Phosphatase of regenerating liver (PRL) family is classified as class IVa of protein tyrosine phosphatase (PTP4A) that removes phosphate groups from phosphorylated tyrosine residues on proteins. PRL phosphatases have been implicated in a number of tumorigenesis and metastasis processes and are highly conserved. However, the understanding of PRL expression profiles during embryonic development is very limited.
In this study, we demonstrated and characterized the comprehensive expression pattern of Drosophila PRL, amphioxus PRL, and zebrafish PRLs during embryonic development by either whole mount immunostaining or in situ hybridization. Our results indicate that Drosophila PRL is mainly enriched in developing mid-guts and central nervous system (CNS) in embryogenesis. In amphioxus, initially PRL gene is expressed ubiquitously during early embryogenesis, but its expression become restricted to the anterior neural tube in the cerebral vesicle. In zebrafish, PRL-1 and PRL-2 share similar expression patterns, most of which are neuronal lineages. In contrast, the expression of zebrafish PRL-3 is more specific and preferential in muscle.
This study, for the first time, elucidated the embryonic expression pattern of Drosophila, amphioxus, and zebrafish PRL genes. The shared PRL expression pattern in the developing CNS among diverse animals suggests that PRL may play conserved roles in these animals for CNS development.
KeywordsPhosphatase of regenerating liver PTP4A Embryogenesis Drosophila Zebrafish Amphioxus
Phosphatase of regenerating liver (PRL) family is classified as class IVa of protein tyrosine phosphatase (PTP4A) that removes phosphate groups from phosphorylated tyrosine residues on proteins. Mammalian PRL family consists of three PRL members. PRL-1 (PTP4A1) was originally identified as an immediate-early growth response gene in the nucleus of regenerating rat liver and mitogen-treated 3T3 mouse fibroblasts [1, 2]. PRL-2 (PTP4A2) and PRL-3 (PTP4A3) were subsequently discovered through database searches for sequences homologous to PRL-1 .
Overexpression of PRL family members has been implicated in cancer progression. For example, PRL-3 up-regulation clearly correlates with colon carcinoma metastases, gastric carcinoma with nodal metastasis, ovarian carcinoma, breast carcinoma, and liver carcinoma cells (reviewed in ). Notably, PRL-3 expression level in primary colorectal cancers has prognostic significance in predicting the development of liver and lung metastases . PRL-1 has been found to elevate in renal carcinoma, melanoma, pancreatic cancer cells, and ovarian lymphoma cells [6–8]. In addition to PRL-1 and PRL-3, PRL-2 overexpression is associated with prostate malignancies  and breast cancer [10, 11]. These observations indicate that PRL family proteins play important roles in metastasis and a variety of cancers [4, 12].
Although the PRL family members are known to be involved in cancer progression and metastasis, the understanding of normal PRL expression patterns during embryonic development is limited. Most of previous studies were focused on examining PRL expression in adult tissues. For example, rat Prl-1 is mainly expressed in brain, skeletal muscle [1, 13], and a number of digestive epithelial tissues [14, 15]. Rat Prl-2 mRNA is widely expressed in adult tissues including the anterior pituitary, brain cortex, adrenal gland, kidney, testis, and heart . Rat PRL-3 protein has not yet been examined in adult normal tissues but is found to be expressed in fetal heart . In mouse, Prl-1 mRNA is expressed at all stages examined from E10.5 through E18.5 in a variety of tissues except heart and skeletal muscle . In contrast, mouse Prl-2 mRNA is preferentially expressed in skeletal muscle and Prl-3 mRNA is mainly expressed both in the skeletal muscle and heart . In addition, mouse PRL-3 is also expressed in villus epithelial cells of the small intestine . Similar to mouse Prl-1, human PRL-1 and PRL-2 are almost ubiquitously expressed in adult human tissues, except that PRL-1 is absent in the brain cortex . In contrast to the ubiquitous expression pattern, human PRL-3 mRNA is most enriched in the heart and skeletal muscle and moderately expressed in the pancreas . These observations indicate that the expressions of PRL members can be varied in a tissue specific manner in mammals.
To our knowledge, no study has yet described and compared the expression patterns of PRLs in Drosophila and zebrafish model animals during embryonic development. Here, we demonstrated and characterized, for the first time, the comprehensive expression pattern of both Drosophila PRL and zebrafish PRLs during embryonic development by either whole mount immunostaining or in situ hybridization. To further understand the evolution of PRL gene in the chordate lineage, we also identify the single PRL orthologue in the basal chordate amphioxus and study its embryonic expression. Our study reveals evolutionary conserved as well as lineage specific PRL expression patterns during embryonic development among Drosophila, amphioxus, and lower vertebrate zebrafish.
Drosophila, amphioxus, and zebrafish PRL phosphatases are highly conserved
Summary of PRL/PTP4A family proteins from selected species
Gene names (species)
Coding region (aa)
GenBank accession number
Previous studies indicate that PRL phosphatases contain conserved WPD loop and C(X)5R catalytic motif required for its phosphatase enzymatic activity [24, 25]. In addition, the C-terminal region consists of a polybasic region together with a C-terminal prenylation motif which are required for its association with plasma membrane and early endosome [19, 26, 27]. The multiple sequence alignment reveals that Drosophila, amphioxus and zebrafish PRLs also contain these highly conserved signatures (Figure 1B).
DrosophilaPRL is expressed in developing mid-gut and CNS in embryogenesis and localized on the plasma membrane
To analyze the expression pattern and subcelluar localization of Drosophila PRL protein, we generated an anti-dmPRL antibody. The full length dmPRL CDS with 176 codons was subcloned into pET-32a vector for producing recombinant dmPRL proteins which were used to generate dmPRL antiserum from rabbits. The dmPRL antiserum preferentially recognized a protein band that represents dmPRL in embryo lysates around 22 kDa on Western blots (Additional file 2: Figure S2, arrowhead). The antibody specificity of dmPRL antiserum was further proved by its recognition of GFP-PRL fusion proteins in ovary lysate (Additional file 2: Figure S2, arrow). To explore the embryonic expression of dmPRL protein, we preformed whole mount immunostaining. At embryonic stage 5, dmPRL is mainly localized in the apical membrane of blastoderm embryos (Figure 2E). In stage 9 embryos, dmPRL is ubiquitously expressed in the germ band and evenly distributed in the plasma membrane of the cells (Figure 2F). At stage 13, the dmPRL expression is enriched in VNC (Figure 2G). In addition, dmPRL expression can be detected in the developing anterior and posterior mid-guts (Figure 2G, arrows). In stage 15 embryos, dmPRL expression persisted in the VNC (Figure 2H, arrow) but the mid-gut expression of dmPRL had vanished (Figure 2H). To confirm the expression of dmPRL in VNC, we dissected VNC of stage 15 embryos and performed double immunostaining with anti-dmPRL and anti-BP102, an axonal marker, antibodies. The dmPRL signal colocalized with BP102 staining perfectly (Figures 2I-K), indicating dmPRL expression is indeed in VNC. In summary, our data suggest that dmPRL begins to enrich in the axon of VNC by embryonic stage 13.
Zebrafish PRL-1 and PRL-2are mainly expressed in neuronal cell lineages
Zebrafish PRL-3transcripts are expressed in brain, somites, blood island, and head muscles in developing embryos
Amphioxus PRLis initially expressed throughout the embryo but later concentrated to the anterior neural tube in the larva
PRL is an evolutionary conserved protein family that is widely distributed in many species among the protostomes and deuterostomes. Through database search, it is evident that all of the examined vertebrate genomes possess three PRL genes, whereas invertebrate animals including C. elegans, Drosophila, Sea urchin, and the basal chordate amphioxus Branchiostoma floridae have only one PRL gene. Our molecular phylogenetic analysis suggests that the three vertebrate PRL genes may be the product of gene duplication events that happened at the base of the vertebrate lineage. By comparing whole-genome synteny patterns, it has been shown that the vertebrate genome had undergone two rounds of whole-genome duplication during early vertebrate evolution . We analyzed the synteny patterns between amphioxus and human genomic regions around PRL genes and found that the single amphioxus PRL gene is located on the Branchiostoma floridae genomic scaffold 233 (Additional file 3: Figure S3A), while the three human PRL paralogues are located on three different chromosomes. We identified some conserved synteny patterns among amphioxus PRL and human PRL-1 and PRL-2 (Additional file 3: Figure S3B); however, no synteny conservation could be identified around the genomic region harboring PRL-3 on human chromosome 8, which may be due to genomic rearrangement after duplication. In fact, we also detected extensive genomic rearrangements that may have caused translocation (such as MDGA1 on human chromosome 6) and tandem duplication of genes (such as AGO1, AGO3 on AGO4 on human chromosome 1) around the vertebrate PRL-1 and PRL-2 genomic regions (Additional file 3: Figure S3B), suggesting that after two rounds of whole-genome duplication, vertebrate genomes have experienced extensive rearrangements during evolution.
Expression profiles of PRL family genes in embryos, larvae, and adult normal tissues
Embryonic and/or larval expression domains
Expression in adult tissue
Ubiquitous expression 
Fetal heart 
Most tissues except heart and skeletal muscle 
Preferential in skeletal muscle 
Ubiquitous expression except brain cortex 
Ubiquitous expression 
Mainly in neuronal cell lineage
Mainly in neuronal cell lineage
Mainly in skeletal muscle
Ubiquitous in embryos; Central nervous system in larvae
Developing mid-gut and central nervous system in embryos; Imaginal discs in larvae
In contrast to general neuronal expression of PRL-1, PRL-2, the expression of mammalian and zebrafish PRL-3 phosphatases are preferential in mesodermal cell lineage, such as heart, skeletal muscle, and pre-erythrocytes (Table 2 and Figure 6). Thus, we propose that the ancestral PRL is predominantly expressed in neuronal cell lineage, especially in the central nervous system. In the vertebrate lineage, two of the duplicated PRL paralogues, PRL-1 and PRL-2, retained this neuronal expression, while the third paralogue, PRL-3, may have evolved new function and obtained more specific expression in the mesodermal cell lineage.
In summary, our study characterizes the distinct expression patterns of three structurally related zebrafish PRL genes and those of Drosophila and amphioxus PRL homologues. Our comparisons provide interesting insight into the evolution of PRL genes and their embryonic expression patterns, and highlight the possible consequence of gene duplication events on the neofunctionalization of duplicated genes during vertebrate evolution.
To generate a rabbit anti-PRL antibody, we subcloned the full length dmPRL CDS from cDNA clone RE40268 into pET-32a vector for producing recombinant His-tagged dmPRL proteins in E.coli. The dmPRL recombinant protein purification together with the generation of the anti-dmPRL polyclonal rabbit antiserum were performed by GeneTex International Corp. approved by the Industrial Development & Investment Promotion Committee of Hsin-Chu City, Taiwan.
Drosophilawhole mount immunostaining
For embryo immunostaining, collected embryos were washed with 0.4% NaCl, 0.1% Triton X-100, dechorionated with 100% bleach for 2 min, and washed with deionized water. Embryos were fixed for 20 min in 4% formaldehyde with heptane. After removal of the fixative, embryos were washed with methanol several times and rehydrated into phosphate buffered Tris. Embryos were blocked with 2% bovine serum albumin in PBT (PBS containing 0.2% Tween-20) for 1 hour, and incubated overnight at 4°C in primary antibody diluted in PBS. The embryos were then washed 3 times for 20 min each in PBT, and then incubated for 2 h at room temperature in secondary antibody in PBT. Following three 30 min washes in PBT, the embryos were mounted in anti-fade mounting solution (PBS containing 50% glycerol and 2% DABCO). For eye disc immunostaining, hand dissected eye discs were fixed for 20 min in 4% formaldehyde. After removal of the fixative, embryos were washed several times in PBST (PBS containing 0.3% Triton X-100). Eye discs were blocked with 2% bovine serum albumin in PBST for 1 hour, and incubated overnight at 4°C in primary antibody diluted in PBS. The eye discs were then washed 3 times for 20 min each in PBST, and then incubated for 2 h at room temperature in secondary antibody in PBST. Following three 30 min washes in PBT, the discs were mounted in anti-fade mounting solution. The following primary antibodies were used: rabbit anti-PRL, rat anti-ELAV (Developmental Studies Hybridoma Bank), mouse anti-HRP (Jackson Labs). Fluorescent-labeled secondary antibodies used goat-anti-rabbit Alexa Fluor 488 (Invitrogen), goat anti-rat Alexa Fluor 633 (Invitrogen), and goat anti-mouse Alexa Fluor 633 (Invitrogen). F-actin was labeled by Alexa Flour 633 conjugated phalloidin (Invitrogen).
Drosophila whole mount in situhybridization
The full length CDS of dmPRL cDNA were cloned into pGEM-3Z vector and used to synthesize digoxigenin (DIG) labeled RNA probes for in situ hybridization. Template preparation, probe synthesis, and procedure for whole mount in situ hybridization were performed as previously described . All embryos were observed under a Nikon Eclipse E800 microscope equipped with Nomarski differential interference contrast optics and a CCD camera.
Zebrafish strain and embryo staging
Mature zebrafish (AB strain) were raised at the zebrafish facility of the Life Sciences Development Center, Tamkang University. All animal experiments in this study were approved by Tamkang University and performed in accordance with the “Animal Research: Reporting in vivo Experiments” guideline issued by regional animal ethic committee. The fish were maintained at 28°C with a photoperiod of 14 h light and 10 h dark, in an aquarium supplied with freshwater and aeration . Embryos were produced using standard procedures and were staged according to standard criteria .
Zebrafish whole mount in situhybridization, cryosection and imaging
The procedures for whole mount in situ hybridization, and cryosection have been described previously , except that the full length of individual zebrafish PRL-1, PRL-2, and PRL-3 coding sequences were used to produce digoxigenin-labeled probes. All embryos were observed under a Leica DM 2500 microscope equipped with Nomarski differential interference contrast optics (Kramer Scientific) and a digital camera (Cannon, Japan).
Identification of amphioxus PRL homologue and whole mount in situhybridization
Amphioxus homologue of PRL gene was identified from Branchiostoma floridae draft genome  by BLAST search using Drosophila PRL protein as queries. Identified Gene models were subsequently used to search the amphioxus EST database and cDNA collection (B. floridae Gene Collection Release 1 ) to isolate the corresponding cDNA clones. The identified cDNA clones were sequenced from both ends by M13 forward and reverse primers as well as internal primers to obtain the complete nucleotide sequence of the inserts. At the end, we identified three different cDNA isoforms (amphioxus cDNA ID: bfad016c08, bfad039b03, and bfad043g05) representing one single PRL gene in amphioxus (see Results).
Gravid animals of the amphioxus (B. floridae) were collected in Tampa Bay, Florida USA, during the summer breeding season. Gametes were obtained by electric stimulation. Fertilization and subsequent culturing of the embryos were carried out as previously described . Amphioxus PRL cDNA clones isolated from the aforementioned cDNA collection were used to synthesize digoxigenin (DIG) labeled anti-sense and sense RNA probes for in situ hybridization. Template preparation, probe synthesis, and procedure for single-color in situ hybridization were performed as previously described . Whole-mount in situ hybridization on amphioxus embryos was performed as previously described . Images of embryos were taken using a Zeiss Axio Imager A1 microscope with a Zeiss AxioCam MRc CCD camera. Probes generated from the three amphioxus PRL cDNA isoforms gave us identical pattern, thus we only present results from one cDNA clone, bfad016c08, which gave us the strongest signals.
Central nervous system
Hours post fertilization
Phosphatase of regenerating liver
Ventral nerve cord.
We are grateful to the Fly Core in Taiwan for fly stocks and reagents. We thank the technical supports provided by sequencing core facility of the National Yang-Ming University Genome Research Center (YMGC). The Sequencing Core Facility is supported by National Research Program for Genomic Medicine (NRPGM), National Science Council. The confocal microscopy was provided by the office of research and development at Tzu-Chi University. This work is supported by the National Sciences Council (NSC) of Taiwan (NSC101-2311-B-320-001-MY3) and Tzu Chi Foundation (610300239) to Ming-Der Lin. NSC99-2627-B-001-003, NSC101-2923-B-001-004-MY2, and the Career Development Award (AS-98-CDA-L06) from Academia Sinica, Taiwan, to Jr-Kai Yu. NSC101-2313-B-032-001-MY3 to Yau-Hung Chen.
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