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MOLECULAR, CELLULAR, AND DEVELOPMENTAL BIOLOGY |
Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100094
2 Corresponding author: nyang{at}cau.edu.cn
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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and THRSPß. In the current study, cDNA sequences of the duplicated duck THRSP genes were cloned by real-time PCR and rapid amplification of cDNA ends. Duck THRSP and THRSPß were predicted to encode peptides with 133 amino acids, which had 74 and 68% sequence identity at cDNA level, 78 and 74% identity at amino acid level to the chicken counterparts, respectively. A high percentage (73.1%) of G and C nucleotides were found in the 3' untranslated region of duck THRSPß cDNA. Although a low similarity of peptide composition was shared between ducks and mammals, and a moderate similarity was shared between ducks and chickens, many predicted properties of THRSP, including the pI, subcellular localization and functional domains seemed to be highly conserved. The present study demonstrated that the duck THRSP gene duplicates into the 2 paralogs as in chickens. Phylogenetic analysis indicated that the duplication for THRSP paralogs appeared to have taken place preceding the chicken–duck split, and the diverging rate between THRSP paralogs seemed faster in the chicken genome than that in the duck genome. Expression analysis by real-time quantitative PCR showed that THRSP paralogs in ducks were more actively transcribed in fat tissues (i.e., s.c. fat and abdominal fat) than in liver, and the mRNA concentrations of THRSPß were higher than that of THRSP in liver and s.c. fat.
Key Words: thyroid hormone responsive Spot 14 • paralog • complementary deoxyribonucleic acid • expression • duck
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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The chicken THRSP gene was found by microarray analysis as a differentially regulated EST in livers of chickens divergently selected for fast or slow growth rates (Cogburn et al., 2000), and its expression was regulated by thyroid hormone status (Wang et al., 2002). The gene was mapped to a chromosomal region (1q41–44; Carre et al., 2001) harboring QTL for s.c. fatness (Ikeobi et al., 2002) and abdominal fatness (Lagarrigue et al., 2003). Recently, the chicken THRSP gene was cloned by in silico EST assembling and was identified to duplicate into 2 paralogs, THRSP and THRSPß (Wang et al., 2004). Furthermore, Cogburn et al. (2003) and Wang et al. (2004) observed that the polymorphisms in the coding regions of the paralogous genes were associated with the abdominal fatness of chicken. Sequence analysis of mammal and chicken THRSP genes demonstrated that both of them shared a similar gene organization, with 2 exons and an intron, but the deduced chicken THRSP peptide had a low similarity (less than 30% of identities and 50% of positives) to the THRSP amino acid sequences of mammals and fishes (Grillasca et al., 1997; Wang et al., 2004). In addition, the ortholog of chicken THRSPß hasn’t been identified in other vertebrates.
Ducks and chickens belong to sister avian orders, and both of them share de novo fatty acid biosynthesis, mainly in the liver. Although comparative fluorescence in situ hybridization mapping suggests poor conservation between the chicken and duck genes (Yuan et al., 2005), it is of interest to explore if the gene organization and duplication episode of the chicken THRSP are shared in the duck genome. In addition, THRSP may play an important role in avian adipogenesis, and it is necessary to get cDNA sequence and expression profiles of duck THRSP for future functional genomic investigations. To this end, we carried out the present study to identify and characterize the duplicated THRSP genes in the duck genome.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Primer Design
As low sequence similarities in both nucleotides and amino acids are shared by chickens and mammals, primers were designed only based on the available sequences of chicken THRSP and THRSPß cDNA, with GenBank Accession no. AY568628
[GenBank]
for THRSP and AY568630
[GenBank]
for THRSPß (Wang et al., 2004). The gene-specific primers to clone the 3' ends of THRSP and THRSPß cDNA using the rapid amplification of cDNA ends (RACE) procedure were first designed from the nucleotides encoding the conservative domains of the chicken THRSP peptides. The primers for 5'-RACE of THRSP or amplifying open reading frame (ORF) of THRSPß were designed from the nucleotides sequenced from the 3'-RACE products and those encoding conservative N-terminus of THRSPß in chickens. The primers amplifying the full-length cDNA of THRSP paralogs and intron sequence of THRSP were designed according to the assembled sequences of RACE products. Primers for real-time PCR were designed using Primer Express 2.0 software (Applied Biosystems, Foster City, CA). All primers were synthesized with ABI 3900 DNA/RNA Synthesizer (Applied Biosystems), and they are listed in Table 1
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3 and ß 3) and abridge universal amplification primer. A touchdown PCR was used with a PTC-200 thermocycler (MJ Research, Watertown, MA), and temperature profile was set as follows: 1 cycle of 95°C for 5 min; 5 cycles of 95°C for 45 s, 70°C for 45 s (–2°C per cycle), and 72°C for 1 min; 20 cycles of 95°C for 45 s, 60°C for 45 s, and 72°C for 1 min; 1 cycle of 72°C for 10 min. Due to the high GC content in the 3' untranslated region (UTR) of chicken THRSPß, Takara LA Taq with GC buffer (Takara, Tokyo, Japan) was used in performing the hot start condition, with 98°C at the first denaturation step to clone the duck THRSPß 3'-UTR.
For 5'-RACE of THRSP, 2 µg of liver RNA were primed by using the obtained cDNA sequence (primer 5–1) and reverse transcribed as described above. After the cDNA synthesis, RNase H was used to degrade the remainder of the RNA template. The first-strand cDNA was purified by spin cartridge column. A homopolymeric C tail was then added to the 3' end of the cDNA, using deoxycytidine triphosphate (dCTP) and terminal deoxynucleotide transferase. The first-round PCR amplification was performed with 5' abridged anchor primer and the nested primer 5–2. The obtained primary PCR product was diluted and reamplified using abridge universal amplification primer and the nested primer 5–3. The thermal profile for the first-round PCR process consisted of an initial 94°C denaturation step for 2 min followed by 35 cycles of denaturation (94°C for 30 s), annealing (55°C for 50 s), and extension (72°C for 1 min). Finally, a 7-min 72°C step was used before holding at 4°C. The nested PCR amplification for the final 5'-RACE result was conducted as the touchdown protocol outlined above. A degenerated sense primer ß ICF For was designed to amplify the ORF and partial 3'-UTR of THRSPß with antisense primer ß ICF Rev together, and the initial annealing temperature was set at 59°C in touchdown PCR. The PCR products were separated by electrophoresis in 1.5% agarose, stained with ethidium bromide and visualized with a UV transilluminator gel documentation system (BioRad, Richmond, CA). The separated PCR products were purified with the QIAquick DNA purification kit (Qiagene, Hilden, Germany) and directly sequenced or ligated into the pMD18-T Vector (Takara). Multiple clones for each fragment were bidirectionally sequenced using Big Dye Terminator v 3.1 reagents on an Applied Biosystems 3730 DNA analyzer (Applied Biosystems) by the dideoxy-mediated chain-termination method (Sanger et al., 1977).
After the overlapping cDNA fragments were assembled according to the sequencing results, the full-length or complete cDNA sequences of THRSP and THRSPß were con-firmed by amplifying the cDNA templates with the primer sets PS For and PS Rev and PS ß For and PS ß Rev, respectively. The primers of I For and I Rev were used to amplify the intron sequence of THRSP in genomic level. Simultaneously, the duck THRSP gene containing 2 exons and 1 intron was amplified using genomic DNA templates and the primers of PS For and PS Rev. A 50-µL volume of Takara LA Taq with GC buffer (Takara) was chosen to perform the similar touchdown PCR protocol depicted above with the different initial annealing temperatures displayed in Table 1
. Following the consecutive steps of purification and clone sequencing for the PCR products, the integrity of cDNA of THRSP paralogs was confirmed by the alignment of the full-length nucleotides sequenced with the assembling nucleotides and exhibiting the gel picture of the PCR products.
Sequence and Phylogenetic Analysis
Nucleotide sequences of 3'- and 5'-RACE clones were assembled and identified by the NCBI BLAST search program, and the overall cDNA sequences were aligned using the DNAMAN software package (Lynnon Biosoft, Quebec, Canada). The amino acid similarity, including identities and positives, was analyzed using the BLASTp program with BLOSUM62 scoring matrix. The alignment of multiple peptides was created with the ClustalW multiple sequences alignment program and displayed using the BOX-SHADE 3.21 program (http://www.ch.embnet.org). After the ClustalW alignment using amino acid sequences of THRSP, the phylogenetic tree was constructed by MEGA software version 3.0,using maximum parsimony methods (Kumar et al., 2004). The p-distances (proportion of differences) with a high resolution of branching pattern were calculated (Nei and Kumar, 2000). The reliability of the constructed tree was tested by bootstrap analysis implemented in MEGA.
Expression Profiling by Real-Time PCR
The mRNA levels of THRSP paralogs were measured using the QuantiTect SYBR Green PCR Kit (Qiagen, Tokyo, Japan) and the ABI PRISM 7900 Sequence Detection System (Applied Biosystems). The quantities of THRSP and THRSPß messages from different tissues were normalized with the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA to compensate for variations in input RNA amounts. Eight serial dilutions (from 1 x 102 to 1 x 109 copies per µl) of a plasmid from the GAPDH clone were selected as the templates to generate a standard curve. All reactions were carried out in a 15-µL volume containing 7.5 µL of SYBR Green Master Mix (Qiagen), 5.5 µL of water, 5 pmol of each primer, 1 µL of serial diluted GAPDH plasmids, or 1 µL of cDNA derived from reverse transcription of each tissue RNA using Moloney murine leukemia virus reverse transcriptase (Promega Corp., Madison, WI). Real-time PCR was performed to amplify each cDNA sample in duplicate, the negative control, and 8 diluted GAPDH plasmids within the same 96-well microplates. The amplification program recommended by the manufacturer was used. Specificity of the real-time PCR was evaluated by both high-resolution gel electrophoresis and melting-curve analysis. Normalization was conducted by dividing the average copies of each isoform of THRSP paralogs by the average copies of GAPDH in each tissue. The relative mRNA concentrations of THRSP paralogs were determined by transformation of common logarithm for the 1,000-fold normalized values and represented in arbitrary units.
Statistical Analysis
Relative mRNA levels of THRSP genes in the duck adipogenic tissues were subject to ANOVA. The expression of THRSP paralogs in same tissue was analyzed by Student’s t-test. Analysis of variance and Student’s t-test were performed using SAS 8.2 package (SAS Institute Inc., Cary, NC). The data were presented as means ± SEM.
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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and 402 bp for THRSPß were generated by 3'-RACE, and 5'-RACE for THRSP yielded a 282-bp fragment. The full-length THRSP cDNA, with 817 nucleotides, was obtained by assembling the overlapping 3'-RACE and 5'-RACE sequences. The ORF for THRSP cDNA comprises 402 nucleotides deducing a peptide with 133 amino acids (Figure 1, panel A).The THRSP peptide was predicted to have a molecular weight of 14.7 kDa and an isoelectric point of 4.44 by using Compute pI/Mw tool (http://ca.expasy.org/tools/pi_tool.html). The ORF is flanked by a 5'-UTR, which is 21 nucleotides long, and a 3'-UTR, which is 394 nucleotides long. The integrity of the full-length THRSP cDNA was confirmed by real-time PCR using the primers of PS For and PS Rev (Figure 2, lane 2) and sequencing. A pair of primers of I For and I Rev allowed amplification of a 1,008-bp fragment containing the intron sequence of duck THRSP based on the overall organization of the chicken THRSP gene (Figure 2, lane 4). As a result, a 739 bp of intron of duck THRSP gene was obtained, corresponding to a homolog of 637 bp found in chicken genome by searching in Genome Browser Gateway (http://genome.ucsc.edu/cgi-bin/hgGateway?org=chicken). The boundaries between the exon and intron conform to the GT-AG rule (data not shown). A 1,556-bp fragment (Figure 2, lane 5), which was amplified using the primers of PS For and PS Rev in genomic DNA level, was found to be composed of a 817-bp transcript and a 739-bp intron of the duck THRSP by sequencing and alignment.
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, panel B). The attempt to amplify the 5'-UTR of duck THRSPß cDNA by 5'-RACE assay failed to yield the predicted products due to high GC content and high similarity in ORF (91% identity) between THRSP paralogs. However, the 711-bp fragment of THRSPß cDNA, which was amplified using the primers of PS ß For and PS ß Rev (Figure 2, lane 3) and sequenced, demonstrated that the complete cDNA sequence of the duck THRSPß was as desired. Similar to the duck THRSP isoform, the predicted THRSPß protein is acidic (pI of 4.53), with a molecular weight of 14.8 kDa. Without exception, the conserved AATAAA hexanucleotide polyadenylation signal (Proudfoot and Brownlee, 1976) was detected 18 nucleotides away from the poly(dA) tracts of both THRSP and THRSPß cDNA.
The duck THRSP and THRSPß were found to have 74 and 68% nucleotide sequence identities at the cDNA level as compared with the chicken orthologs, respectively. Higher similarities of nucleotide sequence (91%) and amino acid sequence (85% identities; 90% positives) in the putative coding region were detected between the duck THRSP paralogs (Figure 1, panel C) corresponding to those of nucleotide (80%) and amino acid (70% identities; 79% positives) between the chicken THRSP paralogs (Wang et al., 2004). Analysis with BLASTp revealed that the duck THRSP peptide shared a moderate similarity (78% identities; 83% positives) to the chicken THRSP protein and low similarity to that of humans (33% identities; 50% positives; Grillasca et al., 1997) and zebrafish (30% identities; 45% positives; zTC192887 found in TIGR: http://www.tigr.org/tdb/tgi/zgi). The duck THRSPß peptide is similar to the homologous amino acid sequences of the chicken (74% identities; 80% positives), the human (34% identities; 46% positives), and the zebrafish (33% identities; 45% positives). Both THRSP and THRSPß peptides in ducks were predicted to localize in the nucleus and have a Leu zipper motif in the C-terminus by the PSORT II program (http://psort.ims.u-tokyo.ac.jp/), which is similar to the THRSP proteins of the chicken and other vertebrates.
The alignment of multiple amino acid sequences exhibited structural similarity of THRSP orthologs among the zebrafish, duck, chicken, bovine, human, mouse, and rat (Figure 3). The THRSP amino acid sequence is weakly conserved in vertebrates, as described above, but both isoforms of duck THRSP also share 3 conserved domains with the orthologs of the chicken and other vertebrates, which include a highly hydrophobic domain 1 near N-terminus, a second hydrophobic domain 2 in the middle, and a Leu zipper domain 3 in the carboxyl terminus. No difference of amino acids was found in the 2 hydrophobic regions of either THRSP isoform between duck and chicken. Leucine zipper motif, which confers DNA-binding ability of THRSP and conducts homodimerization of THRSP with the first hydrophobic domain (Cunningham et al., 1997), is more classical in ducks and chickens than in mammals and fish in terms of the number of Leu. As suggested by Compe et al. (2001), homodimers of THRSP interact with chicken ovalbumin upstream promoter-transcription factor 1 and upregulate the expression of L-type pyruvate kinase gene through a specificity protein 1 binding site localized in the proximal promoter.
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). The duck THRSP paralogs were clustered into the same orthologous group with the chicken THRSP and THRSPß. The duplication episode of THRSP occurred only in the genomes of both duck and chicken among different vertebrate species. Duplicated THRSP paralogs were not found in the mammalian genome when performing homologous searching by using the BLAST program in GenBank. No counterpart of THRSPß isoform was found in other vertebrate genomes by searching for the homologs in the protein database. Comparison of human genome sequence to that of chicken showed a similar number of older duplications in both species genomes, but there were significantly fewer paralogs specific to the chicken lineage than those specific to the human lineage (International Chicken Genome Sequencing Consortium, 2004). The overall stability of avian genomes is indicated by a low rate of gene duplication (Ellegren, 2005). Although many extant orders of birds date the divergence between chicken and duck back to 89.8 ± 6.97 million years (Tuinen and Hedges, 2001), Lynch and Conery (2000) estimated that gene duplication occurred and was fixed in populations at an average rate of about 1 per gene per 100 million years in eukaryotes. Thus, the genetic event generating the THRSP paralogs appeared to have taken place in the last common progenitor of both the duck and the chicken.
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and THRSPß evolve independently in chickens and ducks. A larger genetic distance between duplicated THRSP paralogs in chickens (0.185) than that in ducks (0.111) was observed, implying a faster divergence for duplicated THRSP genes in the chicken genome than in the duck genome. Different functional constraints might have contributed to the phenomenon that 1 copy evolves faster than the other at the amino acid level after the gene duplication (Zhang et al., 2003). Gene duplication is an important mechanism that enables the morphological and functional innovation in evolution, and it may lead to distinct function for each copy by accumulating mutations that arose widely in the genome evolution (Tatusov et al., 1997).
Expression Analysis of THRSP Paralogs in Ducks
The expression profiles of the duck THRSP genes were examined by real-time PCR using the specific For/ Rev primer set for THRSP, and ß For/ß Rev for THRSPß (Figure 5). Gel electrophoresis revealed single bands of expected sizes for THRSP (72 bp), THRSPß (137 bp), and GAPDH (108 bp) products amplified from adipogenic tissues or liver (Figure 5, panel D). The expression data of THRSP and THRSPß subjected to the normalization and logarithm transformation showed the positive values only in adipogenic tissues including abdominal fat, s.c. fat, and the liver. The remaining tissues expressed THRSP genes at extremely low rates and showed negative values of relative expression (data not shown). The highest expression levels of both THRSP and THRSPß mRNA were found identically in the fat tissues (i.e., abdominal fat or s.c. fat) of 6-wk-old Pekin ducks. The mRNA concentrations of the duck THRSP and THRSPß were 1.5 to 2 times greater in fat tissues than that in liver (P < 0.01, Figure 5, panels A and B), but there was no difference between s.c. and abdominal fat tissues for THRSP paralog mRNA (P > 0.05). Expression concentrations of THRSP and THRSPß in the duck abdominal fat were almost equal.
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were 2 to 3 times greater than that of THRSPß in liver and abdominal fat, respectively (Wang et al., 2004). In the current study, intensive expression of THRSP mRNA was observed in adipogenic tissues of 6-wk-old ducks, as reported for the 5-wk-old chickens. However, the THRSP paralogs in 6-wk-old ducks were more actively transcribed in adipose tissues than in liver. In contrast to the expression patterns of THRSP orthologs in 5-wk-old chickens, the relative mRNA levels of THRSPß in liver and s.c. fat of 6-wk-old ducks were significantly higher than those of THRSP (P < 0.01, Figure 5, panel C). In mammals, the presence of lineage-specific gene duplications could increase the human–mouse divergence of the expression patterns in the corresponding tissues of both species (Huminiecki and Wolfe, 2004). The present study on THRSP paralogs exhibited the similar picture of expression differences of duplicate genes in avian species. There is a distinct character on fat deposition and distribution in ducks when compared with the chickens, although both of them belong to the avian class. A large mass of s.c. fat can be deposited in ducks, corresponding to the excessive abdominal fat in chickens. The changes in gene expression were proposed to play a key role in the evolution course of vertebrate species (Schulte, 2004). Gu et al. (2004) pointed out that the expression patterns of duplicate genes were, in general, expected to diverge faster between species than those of single-copy gene, because changes in gene expression may lead to important phenotypic evolution. To date, the exact mechanism of THRSP involved in mammalian and avian lipid metabolism has not been well characterized. Therefore, the expression difference of THRSP mRNA in adipogenic tissues of avian species and their relationship with gene duplication awaits further investigation. In conclusion, the current study demonstrated that the duplication of the THRSP gene is not a unique case in chickens, but it also exists in ducks and is possible in other avian species. Comparison of nucleotide and amino acid sequences in the putative coding region between the 2 paralogs showed that less difference was present in the duck THRSP compared with that of the chicken. Furthermore, expression differences of duplicated THRSP genes were presented in adipogenic tissues of the duck and the chicken. It is, therefore, the objective for further functional genomics studies to determine the physiological roles of the 2 THRSP paralogs.
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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reported in this paper have been submitted to Gen-Bank nucleotide sequence database and assigned Accession no. DQ227766
[GenBank]
for THRSP, DQ227767
[GenBank]
for THRSPß, and DQ334339
[GenBank]
for the intron of THRSP. 
Received for publication January 9, 2006. Accepted for publication June 1, 2006.
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