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SAGE-Hindawi Access to Research Genetics Research International Volume 2011, Article ID 436138, 7 pages doi:10.4061/2011/436138 Research Article Characterization and In Silico Analysis of Pregnancy-Associated Glycoprotein-1 Gene of Buffalo (Bubalus bubalis) Jerome A., 1 S. K. Singh, 1 S. K. Agarwal, 1 Mohini Saini, 2 and Ashwin Raut 3 1 Division of Animal Reproduction, Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India 2 Centre for Wildlife, Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India 3 Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India Correspondence should be addressed to Jerome A., [email protected] Received 27 September 2010; Accepted 3 January 2011 Academic Editor: Meredith Yeager Copyright © 2011 Jerome A. et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Pregnancy-Associated Glycoproteins (PAGs) are trophoblastic proteins belonging to the Aspartic proteinase family secreted by dierent placental cells of many mammalian species. They play a pivotal role in placentogenesis, foetomaternal unit remodeling, and implantation. The identification of the genes encoding those proteins will be helpful to unravel the intricate embryogenomic functions during pregnancy establishment. Considering importance of these proteins, the present study was undertaken to characterize the pregnancy associated glycoprotein-1 gene of bualo. An 1181 base pairs bualo Pregnancy- Associated Glycoprotein PAG-1 gene was PCR amplified from the RNA obtained from the fetal cotyledons. BLAST analysis of the bualo PAG-1 sequence retrieved a total of 20 cattle, 5 goat, and 4 sheep PAG sequences, exhibiting more than 80% similarity. Bualo PAG-1 gene contained an uninterrupted open reading frame of 1140 base pairs encoding 380 amino acids that possess a 15 amino acid signal peptide and mature peptide of 365 amino acids. The phylogenetic study of the bualo PAG-1 gene revealed bualo PAG-1 is more related to cattle, goat, and sheep PAG-1 sequences. By this study characterization of bualo PAG-1 gene and its evolutionary relationship was deduced for the first time. 1. Introduction Pregnancy is established and maintained by the two-way communication between the conceptus and the mother. These intricate dialogues which are initiated after fertil- ization are crucial as these signals are considered poten- tial markers for eective placental remodeling, pregnancy recognition, and successful implantation. These interactions between the conceptus and maternal system emphasize the importance of both the components in maternal recognition of pregnancy and embryonic development [1]. These impor- tant signals to the maternal system to sustain pregnancy are mediated by numerous molecules which include steroid hormones, peptide hormones, cytokines, and growth factors [1, 2]. Conceptus-derived substances are considered to be pre- cise and reliable markers of pregnancy and fetal well-being. Pregnancy-associated glycoproteins are one such large family of protein molecules produced by conceptus for the recog- nition by the mother. Pregnancy-associated glycoproteins (PAGs) are acidic glycoprotein belonging to the Aspartic Proteinase superfamily sharing more than 50% amino acid sequence identity with Pepsin, Cathepsin D, and E [3, 4]. Pregnancy-associated glycoproteins (PAGs) form very large family of glycoproteins; nearly 22 dierent PAGs in ruminants have been identified at dierent stages of gestation [5]. Pregnancy-Associated Glycoprotein-1 (PAG-1) also known as Pregnancy Specific Protein B (PSPB), PSP-60, and SBU3, is secreted by the binucleate cells of the conceptus trophectoderm [6]. PAG-1 is detectable in maternal blood soon after implantation as binucleate cells migrate from the trophectoderm and fuse with uterine epithelial cells and hence it is considered as a potential signal from the conceptus [7]. The products of binucleate cells in maternal circulation have also been reported to be associated with placental mass, fetal number, twins, and neonatal birth weight in cattle [8, 9].

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Page 1: CharacterizationandInSilicoAnalysisofPregnancy-Associated

SAGE-Hindawi Access to ResearchGenetics Research InternationalVolume 2011, Article ID 436138, 7 pagesdoi:10.4061/2011/436138

Research Article

Characterization and In Silico Analysis of Pregnancy-AssociatedGlycoprotein-1 Gene of Buffalo (Bubalus bubalis)

Jerome A.,1 S. K. Singh,1 S. K. Agarwal,1 Mohini Saini,2 and Ashwin Raut3

1 Division of Animal Reproduction, Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India2 Centre for Wildlife, Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India3 Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India

Correspondence should be addressed to Jerome A., [email protected]

Received 27 September 2010; Accepted 3 January 2011

Academic Editor: Meredith Yeager

Copyright © 2011 Jerome A. et al. This is an open access article distributed under the Creative Commons Attribution License,which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Pregnancy-Associated Glycoproteins (PAGs) are trophoblastic proteins belonging to the Aspartic proteinase family secretedby different placental cells of many mammalian species. They play a pivotal role in placentogenesis, foetomaternal unitremodeling, and implantation. The identification of the genes encoding those proteins will be helpful to unravel the intricateembryogenomic functions during pregnancy establishment. Considering importance of these proteins, the present study wasundertaken to characterize the pregnancy associated glycoprotein-1 gene of buffalo. An 1181 base pairs buffalo Pregnancy-Associated Glycoprotein PAG-1 gene was PCR amplified from the RNA obtained from the fetal cotyledons. BLAST analysis ofthe buffalo PAG-1 sequence retrieved a total of 20 cattle, 5 goat, and 4 sheep PAG sequences, exhibiting more than 80% similarity.Buffalo PAG-1 gene contained an uninterrupted open reading frame of 1140 base pairs encoding 380 amino acids that possess a15 amino acid signal peptide and mature peptide of 365 amino acids. The phylogenetic study of the buffalo PAG-1 gene revealedbuffalo PAG-1 is more related to cattle, goat, and sheep PAG-1 sequences. By this study characterization of buffalo PAG-1 gene andits evolutionary relationship was deduced for the first time.

1. Introduction

Pregnancy is established and maintained by the two-waycommunication between the conceptus and the mother.These intricate dialogues which are initiated after fertil-ization are crucial as these signals are considered poten-tial markers for effective placental remodeling, pregnancyrecognition, and successful implantation. These interactionsbetween the conceptus and maternal system emphasize theimportance of both the components in maternal recognitionof pregnancy and embryonic development [1]. These impor-tant signals to the maternal system to sustain pregnancyare mediated by numerous molecules which include steroidhormones, peptide hormones, cytokines, and growth factors[1, 2].

Conceptus-derived substances are considered to be pre-cise and reliable markers of pregnancy and fetal well-being.Pregnancy-associated glycoproteins are one such large family

of protein molecules produced by conceptus for the recog-nition by the mother. Pregnancy-associated glycoproteins(PAGs) are acidic glycoprotein belonging to the AsparticProteinase superfamily sharing more than 50% amino acidsequence identity with Pepsin, Cathepsin D, and E [3, 4].

Pregnancy-associated glycoproteins (PAGs) form verylarge family of glycoproteins; nearly 22 different PAGsin ruminants have been identified at different stages ofgestation [5]. Pregnancy-Associated Glycoprotein-1 (PAG-1)also known as Pregnancy Specific Protein B (PSPB), PSP-60,and SBU3, is secreted by the binucleate cells of the conceptustrophectoderm [6]. PAG-1 is detectable in maternal bloodsoon after implantation as binucleate cells migrate from thetrophectoderm and fuse with uterine epithelial cells andhence it is considered as a potential signal from the conceptus[7]. The products of binucleate cells in maternal circulationhave also been reported to be associated with placental mass,fetal number, twins, and neonatal birth weight in cattle [8, 9].

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The Pregnancy-associated glycoproteins (PAGs) aremultigene family expressed in placenta of eutherian mam-mals and their expression varies spatially as well as tem-porally during gestation [10]. Multiple PAG genes havebeen cloned and identified in many domestic animalssuch as cattle, sheep [5], goat [11], pig [12], and wildruminants’ species [5]. Based on the evolutionary studyand phylogenetic linkage bovine pregnancy associated gly-coproteins family has been segregated as ancient (bovinePAG-2, bovine PAG-8) and modern (bovine PAG-1) [13–15]. But there is no report on the characterization andphylogenetic analysis of pregnancy-associated glycoprotein-1 gene of buffalo. Moreover, identification of gene encodingbuffalo Pregnancy-Associated Glycoprotein-1 may providean avenue for producing recombinant protein which will behelpful to develop diagnostics for early pregnancy diagnosisand marker for embryonic development [16]. Consideringthe importance of the gene in embryogenesis, the presentstudy was designed to characterize and analyze pregnancy-associated glycoprotein-1 (PAG-1) gene phylogenetic lineage.

2. Materials and Methods

2.1. Sample Collection and RNA Isolation. Buffalo placentaewere collected from local abattoir. The stage of pregnancywas estimated by measurement of crown-rump length. Pla-cental cotyledons were collected from day 60 of pregnancy.Total RNA was isolated from fetal cotyledons using TRIreagent (Ambion, USA) following manufacture’s instruc-tions. The integrity of the extracted RNA was checked byagarose gel (1%) electrophoresis and visualization of thegel under UV light after staining with ethidium bromide.The purity of the obtained RNA was checked by means ofspectrophotometric readings at OD260/OD280.

2.2. cDNA Synthesis and Buffalo PAG-1 Gene Amplification.RNA from the fetal cotyledons was reverse-transcribedinto cDNA with reverse transcriptase (Qiagen, Germany),oligo (dT) primers, and 500 µM dNTPs at 37◦C for1 hour. On the basis of available PAG-1 sequences fromcattle (GenBank Acc. No. M73962; NM 174411), goat(GenBank Acc. No. AF191326), sheep (GenBank Acc.No.M73961), pig (GenBank Acc. No. L34360), white-taileddeer (GenBank Acc. No. AY509865), and zebra (Gen-Bank Acc.No. AF036952) buffalo gene-specific primerswere designed using Primer select programme of DNAstar software. The primers were forward (PAG-1/startF, 5′-GGATCCAGGAAATAAACATGAAGTG-3′ and PAG-1/stopR, 5′-TTACTGAAC CACTCYMAGCATTT-3′).

PCR amplification was carried out in a total volume of25 µL of reaction mixture containing approximately 100 ngof cDNA, 10X PCR buffer (100 Mm Tris-Hcl, pH 8.8 at25◦C, 5 pM of forward and reverse primer of each, 2.0 mMMgCl2, 200 µM dNTPs, 1.0 U Taq DNA Polymerase. ThePCR protocol involved an initial denaturation at 94◦C for2 minutes; 30 cycles of denaturation (94◦C for 15 seconds),annealing (optimum temperature of 51.3◦C for 15 seconds),and extension (74◦C for 45 seconds); one cycle of final

extension (74◦C for 10 minutes). The PCR product waschecked by 1% agarose gel electrophoresis.

2.3. Buffalo PAG-1 Gene Cloning. PCR amplicons werecloned in cloning vector (PTZ57R/T, InsTAclone, MBI,Fermentas) following the manufacturer’s protocol. The 12 µLof ligated product was directly added to 200 µL competentcells, and cells were then immediately transferred on chilledice for 5 minutes, and SOC was added. The bacterialculture was pelleted and plated on LB agarplate containingAmpicillin (100 mg/mL) added to agarplate at 1 : 1000,IPTG (200 mg/mL) and X-Gal (20 mg/mL) for blue-whitescreening. Isolation of plasmid from was done using kit’sprotocol (Biochem Life sciences). Recombinant plasmidswere characterized by PCR using gene-specific primers andrestriction enzyme digestion.

Restriction enzyme analysis of the plasmid was carriedout with Xba I (MBI, Fermentas USA) and Sma I (MBI,Fermentas USA) enzymes. Double digestion with EcoR I(MBI, Fermentas USA) and Sma I (MBI, Fermentas USA)restriction enzymes was also performed.

2.4. Sequencing Buffalo PAG-1 Gene. The plasmid containingbuffalo PAG-1 cDNA was sequenced using M13 Forwardand Reverse primer pair by primer walking in an automatedDNA sequence (Sequence Analyzer Version 2.0, ABI Prism,Chromous Biotech, Bangalore). The sequence obtained wassubjected to BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi)to retrieve PAG-1 sequences of other species. The nucleotideand deduced amino acid sequences of buffalo PAG-1 genewere aligned and compared with other species sequencesavailable in GenBank using Clustal option in MegAlign(Lasergene Software, DNASTAR). The buffalo PAG-1 pro-tein structure was predicted by online SWISS MODELsoftware. The domain structure, glycosylation sites, andhairpin loop structure were determined by online soft-ware like PROSITE (http://www.expasy.ch/pro), SMART(http://smart.embl-heidelberg.de/). The predicted buffaloPAG-1 protein sequence was statistical analysed using SAPSsoftware. Phylogenetic tree based on the evolutionary dis-tances was constructed using MegAlign (Lasergene Software,DNASTAR), based on the nucleic acid and amino acid align-ment. Using MEGA 4.1 software the number of synonymoussubstitution per synonymous site (dS) and number of non-synonymous substitution per nonsynonymous sites (dN)were estimated, and neutral (dS = dN), positive (dN > dS),or purifying (dN < dS) selections were tested with a codon-based Z test using Nei Gojobori method.

3. Results and Discussion

3.1. Buffalo PAG-1 Transcript. The concentration of RNAwas checked by analyzing OD260/OD280 ratio which wasfound in the range of 1.8-1.9 indicated the purity of theRNA, and the yield was obtained in range of 3.5–3.8 µg/mL.From the obtained total RNA, cDNA was synthesized andPCR amplification was carried out in 1% agarose gel. Agarosegel electrophoresis revealed 1181 bp PCR product of buffalo

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M(bp) (bp)

15001000

500

1181

1 2

Figure 1: Agarose gel electrophoresis depicting PCR amplifiedBuffalo PAG-1 gene. Lanes 1 and 2: 1181 bp buffalo PAG-1 gene.Lane M: 100 bp DNA ladder as molecular size marker.

PAG-1 gene (Figure 1). Following this restriction enzymeanalysis of the plasmid with Xba I and Sma I enzymesreleased an insert of 1181 bp. Digestion with EcoR I and SmaI released as well as digested the insert into fragments of234 and 947 bp, respectively, confirming the presence of aconserved site for EcoR1 for every binucleate specific PAGs.

3.2. Sequence Analysis. BLAST analysis of the ampliconsequence retrieved gene sequences of various aspartic pro-teinase family members which showed greater than 80% sim-ilarity. Amongst these, there were 20, 5, and 4 sequences ofbovine, caprine, and ovine PAG, respectively, that exhibitedmore than 80% similarity with buffalo PAG-1 sequence and5 sequences of white tailed deer which showed less than80% homology. Accordingly, the sequence was submittedto Genbank as buffalo Pregnancy-Associated Glycoprotein-1 gene under accession number EU815059. The deducedbuffalo PAG-1 gene consists of an open reading frame of 1140nucleotide corresponding to an inferred polypeptide lengthof 380 amino. Moreover, on translation buffalo PAG-1 genesequence encodes a signal sequence constituting the first 15amino acids and a mature peptide of 365 residues.

Buffalo PAG-1 gene was compared with the members ofthe aspartic proteinase family, Pregnancy-Associated Glyco-protein gene sequences of cattle and other species.

With the members of aspartic proteinase family buffaloPAG-1 sequence showed a similarity of 62.4, 34.6, 33.8, 32.6,29.5, and 28.7% with pepsinogen, cathepsin E, chymosin,pepsin, cathepsin D, and rennin, respectively, at the aminoacid level. With cattle PAG gene sequences buffalo PAG-1sequence showed a similarity more than 80% with PAG-1,3, 16, and less than 80% with PAG-2, 4, 5, 6, 7, 9, 14, 15, 17,18, 19, 20, and 21. Buffalo PAG-1 sequence showed highestsimilarity of 89.3% with cattle PAG-1 and lowest of 54.0%with cattle PAG-8.

3.3. Phylogenetic Analysis. The phylogenetic analysis of theobtained sequence of buffalo PAG-1 gene (GenBank Acc

Buffalo PAG-1Pepsinogen

Pepsin

Rennin108.7

100 80 60 40 20 0×100Nucleotide substitutions

Cathepsin E

Chymosin

Cathepsin D

Figure 2: Phylogram depicting the evolutionary relationship ofbuffalo PAG-1 with members of aspartic proteinase family-basedamino acid sequence.

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Deer PAG1Zebra PAG-1Porcine PAG1

0102030405060

67.2

×100Nucleotide substitutions

Ovine PAG1

Figure 3: Phylogram depicting the evolutionary relationship ofbuffalo PAG-1 with other species PAG-1 sequences.

No. EU815059) with members with aspartic proteinasefamily members revealed that buffalo PAG-1 sequence ismore related to pepsinogen and less related with rennin(Figure 2). The degree of similarity was determined com-paring the obtained buffalo nucleotide and derived aminoacid sequence with available PAG-1 sequences of cattle(GenBank Acc. No. M73962;.NM 17441), goat (GenBankAcc. No. AF191326), sheep (GenBank Acc. No M73961),horse (GenBank Acc. No. L38511), zebra (GenBank Acc. NoAF036952), white tailed deer (GenBank Acc. No AY509865),pig (GenBank Acc. No. L34360), and cat (GenBank Acc.No. AF036953). Buffalo PAG-1 showed the percent similarityranging from 47 to 89% and 39 to 81%, at nucleotide andderived amino acids sequences levels, respectively, with otherspecies PAG-1 sequences. Buffalo PAG-1 sequence showedhighest similarity of 89.2% with cattle followed by 75.6%with goat, 74.5% sheep, 72.5% white tailed deer and 52.1%pig, 51.9% cat, 47.3% zebra, and 47.1% horse.

Phylograms constructed on the basis of nucleotide andderived amino acids sequences of buffalo PAG-1 sequencewith other species showed buffalo, cattle, sheep, goat, horse,white tailed deer, zebra, feline comprise one clade, andpig comprise another. Porcine PAG-1 stands alone andrepresents an entirely different clade. The PAG-1 sequence ofcattle and buffalo belonged to same group and showed morecloseness to goat. The PAG-1 of horse, deer, and zebra seemsto be an evolutionary connecting link between ruminantsand other nonruminants. Horse, deer, and zebra showmore evolutionary closeness to each other but far distantfrom ruminants (Figure 3). Analysis of phylogenetic treeconstructed with buffalo PAG-1 and cattle PAG sequences

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Buffalo PAG-1Cattle PAG-1PAG-3PAG-21PAG-15PAG-19PAG-4PAG-14PAG-6PAG-7PAG-16PAG-9PAG-20PAG-18PAG-17PAG-5PAG-2PAG-13PAG-12PAG-11PAG-10PAG-8

051015202530

30.9

×100Nucleotide substitutions

Figure 4: Phylogram depicting buffalo PAG-1 gene relationship with cattle PAG sequences.

revealed that buffalo PAG-1 gene is more closely related tocattle PAG-1, 3, 21, and 19 both at nucleotides and aminoacids level. Cattle PAG-2 group occupies an intermediateposition between the ancient aspartic proteinase familymembers and PAG-1 group. Buffalo PAG-1 as well as otherspecies PAG-1 sequences comprise one clade and showmore divergence from the ancient aspartic proteinase familymembers (Figure 4). Codon-based Z test using the NeiGojobori method revealed that at 5% level of significance, dNis substantially greater than dS. Thus, buffalo PAG-1 mighthave evolved by recently by positive selection (dN > dS)among these species. Buffalo and cattle PAG-1 gene showedidentical lineage. Goat, sheep, horse, and deer are similarbut have different lineage. Pig sequence show dissimilaritiessuggesting different ancestry.

3.4. Predicted Protein Analysis. The predicted buffalo PAG-1 protein sequence was statistically analyzed using SAPSsoftware revealed the total number of negatively and pos-itively charged residues charged residues were 30 and 40,respectively. The atomic composition of the protein consistsof Carbon (C) 1970; Hydrogen (H) 3011; Nitrogen (N)521; Oxygen (O) 539; Sulfur (S) 15 with 6056 atoms. Theextinction coefficient is 1.828 M−1 cm−1, at 280 nm measuredin water. The aliphatic index and theoretical pI is 93.32 and9.10, respectively, with hydropathicity index of 0.071. Theestimated half life of buffalo PAG-1 protein is 30 hours withan instability index of 32.12 predicting the protein as stable.

Sequence of deduced PAG-1 gene of buffalo revealed aninsert of 1181 bp. Comparing the buffalo nucleotides andderived amino acids with available PAG-1 sequences of otherspecies confirm buffalo PAG-1 contains an open readingframe of 1140 nucleotides which on translation correspondsto a polypeptide length of 380 amino acids similar to cattle.On translation, buffalo PAG-1 cDNA yields a polypeptide of380 amino acids with a signal peptide encoded by the first

15 amino acids followed by a mature peptide of rest 365residues. The signal sequence of the derived buffalo PAG-1 amino acid sequence (MKWLVLLGLVAFSEC) starts andterminates with methionine and cysteine, respectively. Thissignal sequence is well conserved in buffalo as in bovine andother species [3] (Figure 5). The predicted buffalo PAG-1protein structure along with its amino acid residues was alsodeduced (Figure 6).

The derived mature peptide sequence consists of well-conserved motif (ISF↓RGS) between the propeptide andthe mature molecule. The arrow indicates the site ofcleavage between the propeptide and the mature protein.The N-terminal ends of ruminant PAG native proteinspredominantly contains the sequence of 3 amino acids,↓R-D/G-S which is also deduced in buffalo PAG-1-derivedamino acid sequence [17, 18]. On comparison of the aminoacid sequences of buffalo PAG-1 with other species PAGsequences, it is evident that both amino terminus 91 to98 (VVFDTGSS) and carboxyl terminus 278–284 (LVDT-GTS) are conserved across the domestic species (90–100%)suggesting importance of this region for the diagnosticfunction of PAG-1 and suggesting that the buffalo PAG-1 hasalso evolved from same family [3, 19]. Moreover, residuesflanking the aspartic acid residues which are considered to beessential for catalytic activity of pepsin are well conserved inbuffalo as in other domestic species [20]. Although the PAGsclearly belong to the aspartic proteinases, they are not activeproteolytically owing to the key mutations close to the activesite due to amino and carboxyl terminal flanking the asparticacid residues that would likely interfere with the catalyticmechanism. On analysis it was evident that buffalo PAG-1is not proteolytically active since it possesses key mutationof alanine substitution in place of glycine at the active siteas same as boPAG-1 which will displaces a water moleculethat normally resides between the two catalytic aspartic acidsand is directly involved in the catalytic mechanism [3, 20].

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M K W L V L L G L V A F S E C I V K I P L R R V K T M R N T V S G K N M L N S F L K E H A Y R L S Q

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. . . K . . . . R . . . . . . . . . . . . . D . R . . . . . . . . . . . H . . . . . . . . . . . . .V . . . . M K . . . V A . . . . . . . . N . S K . . . . . . . . . . . . Q . . . . . . . . . I . . .. . . K . . . E . . F . . . . . . . . . N . D K . . . . . . . . . . . . H . . . K . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . N P . . . . . . . . . . . . S . . H . T . . . . . . .

V . . . . R K . . Q . P . . . . . L . . . T N T K K . . . L . I . . . . N N F F T . N. K . . . . S. . . . . . . . . . . . . . . . . . . . . . . N P . . . . . . . . . . . . S . . H . T . . . . . . .

V . . . . W . . . L L . Q K L . . . . . . S K G K K . . . . . . . . . . P S . . T . . . H . . . V S

K A G Y W S V H M D R I S M N R K V I A C S D G C E A I V D T G T S L I L G P R R L V N N I Q R H I

E . . . . I . L I H P F . I E . Y I . T . . . . R K . L . . . . . . D . V . . . . . A . Y . H . F .Q . . D . . . . . . . . . I E . . I . . . . . . . K . L . . . . . . D . V . . . . . . . . . H . L .. L . S . T I . . . . . . . R . E . . . . . . . . . . . . . . . . . A . R . . . . . I . . . . K L .

H P . E . . I P L . . . . . R . . . . . . . G . . . . L . G . . . . . . . . . . T V . E . . . K . .. . . R . C . . . . . . . . . . Q . V . . N A . . . . . . . . . . . . . . . . . . M . D . . L . . .

A R N . . Q I T L . . . T W R G V . V G . T R . . Q . . L . S . S A F L . . . S . Q I S S . . K I .. . . R . C . . . . . . . . . . Q . V . . N A . . . . . . . . . . . . . . . . . . M . D . . L . . .. P L . . Q I S . . S . . I . G . . . . . D G . . Q . . . . . . . . . L . . . Q D A . L . . . E I .

G A K P R G S E H Y - V S C S A V N T L P S I V F T I N G I N Y P V P A R A Y I L K D S R - G R C Y

. . V . W . . A Y . - . . S C . . Y . . G . . . . S F . . . Y . . . S G . G D . . . . D . - . . . .

. . I . . . . . . . - . P . . E . . . . . . . . . . . . . . . . . . . G . . . . . . . D . - . . . .

. . . R C . F K . . - . . . . V . . . . . . . I . . . S . . . . . . . . . . . . . . . . L - . Y . H

. . T Q Q C F . Y F - . . . . . . Y A . . . . . . . . . . . . . . . . P Q . . L V . . . . - . Q . .

. . . . . . . . . . - . . . . . . . . . . . . D . . . K . . . . T . . . Q F . A I . G . D - . N . .Q . R - F I E N E . Q . R . C . R T . . A D F I . . . . N V Q . . . . . . . . . R . G . T P R . . .. . . . . . . . . . - . . . . . . . . . . . . D . . . K . . . . T . . . Q F . A I . G . D - . N . .

Q . R R S T . G G . F I D . D . . . . . . D . L . . . D . . G . . . . . N . . . Q . . A A L . I . F

S T F Q E N R A N - T S T E T W I L G D V F L R L Y F S V F D R G N D R I G L A R A V -

T . . . . . . L D - A Y . V . . Y . . . . L . I . C . . . C . . . K . . . . . . . . . T . . . . . . V S - S . . . . . Y . . . . . . . . . . . . . . . . . . . . . . . . . . T A . K . K . V T - . . . . S . V . . . . . . . . . . . . . . . . . . . . S . . . P . . P . . V . . . . - P . A . N . . . . . . . . . R . . . . . . . . . . . . . . . . . . I . . K H I P . . - . P R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . N . S G G T E S L G K E . . . . . . E . . . . . . . T . . . . . Q N . . . . R I . - VI . . K H I P . . - . P R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S . E G . E D I L N N L . E . . . . . . . . . . . . T . . . . E . . . . . . . T . . .

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Majority

Majority

Majority

Majority

Majority

Majority

Majority

Majority

10 20 30 40 50

60 70 80 90 100

110 120 130 140 150

160 170 180 190 200

210 220 230 240 250

260 270 280 290 300

310 320 330 340 350

360 370 380 390

Ovine PAG1

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Ovine PAG1

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Ovine PAG1

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Ovine PAG1

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Ovine PAG1

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Ovine PAG1

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Ovine PAG1

Buffalo PAG1Bovine PAG1Caprine PAG1

Equine PAG1Porcine PAG1Deer PAG1Zebra PAG-1

Ovine PAG1

11111111

5151515151515151

9696969696

96101

99

143143143

143

143

146

146

148

191191191

191

191

193

198

196

241241241

241

241

243

248

246

291291

291

291

291

293

298

296

339

339341

339

347

339

339346

Figure 5: MegAlign report of buffalo PAG-1 amino acid sequence (380 amino acids) with PAG-1 amino acid sequences of other species.

Although PAG-1 group molecules are not proteolyticallyactive, they have retained the characteristic bilobed structureof aspartic proteinase [20]. The catalytic mechanism, whichleads to peptide bond cleavage in the middle of the boundpeptide, is initiated through nucleophilic attack by a hydroxylion supplied by a water molecule strategically positionedbetween the two aspartic acids [19]. Comparison of buffaloPAG sequence and other species sequence reveals segments ofprimary structure that are hypervariable and others that arerelatively constant. The region between residues 70 and 100(13–42 pepsin numbering) showed very few substitutionsdepicting the presence of other conserved sequence [4]. Fromthe alignment study it was evident that buffalo PAG-1 which

showed more similarity to cattle PAG-1 will also possess athree-dimensional fold and may have a general affinity forbinding peptides with basic residues [20].

The deduced buffalo PAG-1 amino acid sequence con-tains microsequences YS (position 46,47), LSQISF (position48–58), RGSNLTTH (position 59–66), PLRN (position 67–70), and IKDLVYMGNITIGTP (position 71–81) which arefound to be conserved across ruminant PAG proteins. Ingeneral, the conserved regions are ones that are internaland structurally important for retaining the overall three-dimensional fold of the molecule. By contrast, the hyper-variable regions are exposed and generally correspond withsurface loops. Though the physiological significance of these

Page 6: CharacterizationandInSilicoAnalysisofPregnancy-Associated

6 Genetics Research International

Figure 6: Predicted 3D structure of buffalo PAG-1 protein and itsresidues.

0 50 100 150 200 250 300 350

Potential

0

1

Predicted O-glycosylation sites

O-g

lyco

syla

tion

pot

enti

al

Sequence position

Figure 7: Predicted potential O-glycosylation sites of buffalo PAG-1protein sequence.

changes is presently unknown, these hypervariable regionsrepresent surface domains where amino acid substitutionscould occur with little threat to the structural integrity ofthe molecules [4, 19]. The buffalo mature peptide sequencealso contains variable regions as in other species havingprofound nonsynonymous substitutions. There are mainlyfour variable regions at positions 101–117, 162–173, 241–248, and 331–350. Since these proteins belong to glycopro-tein family, they possess distinct sites for glycosylation. Thepotential sites for glycosylation in deduced buffalo PAG-1protein sequence are at positions 78–81, 127–129, and 250–300 [4, 20, 21] (Figure 7).

Phylogenetic Analysis of the buffalo PAG-1 sequenceswith other domestic species revealed buffalo PAG-1 is morerelated with bovine, caprine, and ovine species and lesssimilar to equine, porcine, deer, and zebra due to variousnonsynonymous substitutions in the entire sequence inthe latter species. Porcine PAG-1 forms an entire differentclade as it consists of variant amino acids residues whencompared with ruminant species. Phylogram constructedbetween buffalo PAG-1 and different bovine PAGs sequencesrevealed buffalo PAG-1 was more related with bovine PAG-1thereby belonging to the recently duplicated PAG gene group(PAG-1 group) and differing significantly from the ancientPAG group consisting of PAG-2 and 8 [13–15].

4. Conclusion

Buffalo Pregnancy-Associated Glycoprotein-1 cDNA encod-ing buffalo PAG-1 protein of 380 amino acids was character-ized and found to be recently duplicated group members ofthe aspartic proteinase family being proteolytically inactivedue to key mutations close to the active site.

Acknowledgments

The authors are grateful to the Director of the IndianVeterinary Research Institute, and Head of the AnimalReproduction Division for providing the necessary facilitiesfor conducting the experiment. The financial support byICAR, New Delhi, India under the National Fund for Basicand Strategic Research in Agricultural Sciences (NFBSRA)project is also acknowledged.

References

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[8] J. E. Butler, W. C. Hamilton, R. G. Sasser, C. A. Ruder,G. M. Hass, and R. J. Wiliams, “Detection and partialcharacterization of two bovine pregnancy-specific proteins,”Biology of Reproduction, vol. 26, no. 5, pp. 925–933, 1982.

[9] A. P. Zoli, J. F. Beckers, P. Wouters-Ballman, J. Closset, P.Falmagne, and F. Ectors, “Purification and characterizationof a bovine pregnancy-associated glycoprotein,” Biology ofReproduction, vol. 45, no. 1, pp. 1–10, 1991.

[10] K. Klisch, N. M. De Sousa, J. F. Beckers, R. Leiser, and A.Pich, “Pregnancy associated glycoprotein-1, -6, -7, and -17 aremajor products of bovine binucleate trophoblast giant cells atmidpregnancy,” Molecular Reproduction and Development, vol.71, no. 4, pp. 453–460, 2005.

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[11] R. G. Sasser, C. A. Ruder, K. A. Ivani, J. E. Butler, and W. C.Hamilton, “Detection of pregnancy by radioimmunoassay ofa novel pregnancy-specific protein in serum of cows and aprofile of serum concentrations during gestation,” Biology ofReproduction, vol. 35, no. 4, pp. 936–942, 1986.

[12] O. V. Patel, I. Domeki, N. Sasaki et al., “Effect of fetal mass,number and stage of gestation on pregnancy-specific proteinB concentrations in the bovine,” Theriogenology, vol. 44, no. 6,pp. 827–833, 1995.

[13] M. I. Vasques, A. E. M. Horta, C. C. Marques, R. G. Sasser,and P. Humblot, “Levels of bPSPB throughout single and twinpregnancies after AI or transfer of IVM/IVF cattle embryos,”Animal Reproduction Science, vol. 38, no. 4, pp. 279–289, 1995.

[14] J. M. Garbayo, J. A. Green, M. Manikkam et al., “Caprinepregnancy-associated glycoproteins (PAG): their cloning,expression, and evolutionary relationship to other PAG,”Molecular Reproduction and Development, vol. 57, no. 4, pp.311–322, 2000.

[15] B. Szafranska, S. Xie, J. Green, and R. M. Roberts, “Porcinepregnancy-associated glycoproteins: new members of theaspartic proteinase gene family expressed in trophectoderm,”Biology of Reproduction, vol. 53, no. 1, pp. 21–28, 1995.

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