Differential resistance to cell entry by porcine endogenous retrovirus subgroup A in rodent species
© Mattiuzzo et al; licensee BioMed Central Ltd. 2007
Received: 10 October 2007
Accepted: 14 December 2007
Published: 14 December 2007
The risk of zoonotic infection by porcine endogenous retroviruses (PERV) has been highlighted in the context of pig-to-human xenotransplantation. The use of receptors for cell entry often determines the host range of retroviruses. A human-tropic PERV subgroup, PERV-A, can enter human cells through either of two homologous multitransmembrane proteins, huPAR-1 and huPAR-2. Here, we characterised human PARs and their homologues in the PERV-A resistant rodent species, mouse and rat (muPAR and ratPAR, respectively).
Upon exogenous expression in PERV-A resistant cells, human and rat PARs, but not muPAR, conferred PERV-A sensitivity. Exogenously expressed ratPAR binds PERV-A Env and allows PERV-A infection with equivalent efficiency to that of huPAR-1. Endogenous ratPAR expression in rat cell lines appeared to be too low for PERV-A infection. In contrast, the presence of Pro at position 109 in muPAR was identified to be the determinant for PERV-A resistance. Pro109. was shown to be located in the second extracellular loop (ECL2) and affected PERV-A Env binding to PAR molecules.
The basis of resistance to PERV-A infection in two rodent species is different. Identification of a single a.a. mutation in muPAR, which is responsible for mouse cell resistance to PERV-A highlighted the importance of ECL-2 for the viral receptor function.
Pig-to-human xenotransplantation presents potential benefits for treatment of a range of diseases, such as diabetes, neurological disorders and for organ failures, and to alleviate the shortage of human donor organs. Recent advances in genetic engineering of animals, such as the development of pigs devoid of α-galactosyltransferase [1, 2], help overcome immunological problems and bring clinical xenotransplantation a step closer to reality. However, zoonotic pathogen transmission is a potential risk and must be controlled (reviewed in  and ). Although exogenous viruses can be removed from the transplantation source by breeding pigs in specific pathogen-free environments, such techniques cannot eliminate porcine endogenous retroviruses (PERV) present in the pig germ line DNA. Furthermore, pig cells can produce PERV capable of infecting human cells in vitro [5–7]. All PERV known to be infectious belong to the gammaretrovirus genus and gammaretroviruses, such as gibbon ape leukaemia virus (GALV) and murine leukaemia virus (MLV), can cause cancer, leukaemia or neurodegeneration. If PERV cross the species barrier, adapt to new human hosts and create epidemics, the risk will be not only to the patient who receives the xenograft, but also to the general public. The recent spread of koala endogenous retrovirus in the koala population represents an example of the hazards associated with gammaretroviral cross-species infection .
Three subgroups (A, B and C) of infectious PERV share similar gag and pol genes, but differ substantially in the env gene and therefore in their receptor usage and host range: PERV-A and B, but not C, can infect human cells in vitro . All human-tropic PERV isolates derived from primary porcine cells contain at least a part of PERV-A env and utilise PERV-A receptors for cell entry. As the greatest threat comes from high-titre, human-tropic recombinant PERV [10–13], such as PERV-A 14/220 isolate [12, 13], PERV-A receptors would be the major route for potential PERV transmission to humans. Two PERV-A receptors (PAR) in human cells, called huPAR-1 and huPAR-2, as well as their murine homologue (named muPAR in this study) have been cloned . HuPAR-1 and huPAR-2 are paralogues and their amino acid (a.a.) sequences share 86% homology. The muPAR genomic locus has been previously described as syntenic to the huPAR-2 locus , whereas complete sequencing of human and mouse genomes shows that muPAR is syntenic to huPAR-1, not huPAR-2. Our search for PAR homologues in the GenBank genomic sequence database identified homologues syntenic to huPAR-1 and muPAR in all complete genome sequences (chimpanzee, rat, dog, rhesus macaque, cow and horse). A pig cDNA coding for a PAR homologue is functional as a PERV-A receptor . Additional homologues were only found in primate genomes, namely chimpanzee and rhesus macaque, and proved to be syntenic to huPAR-2, while a baboon cDNA closely related to huPAR-2 has been cloned . It is likely that a duplication event gave rise to PAR-2, since the extra copy of PAR appeared after the separation of the primates from other mammalian species. PAR expression has been shown in a wide variety of human tissues by northern blot using a probe detecting both huPAR-1 and huPAR-2 . Our further investigation using EST Profile Viewer  has indicated ubiquitous expression of huPAR-1 in different human tissues, whereas huPAR-2 expression appears to be low and limited to certain tissues including placenta, larynx and prostate. Function(s) of PAR other than that as a PERV-A receptor are yet unknown.
The predicted multiple transmembrane structure of PAR proteins and the ubiquitous expression of HuPAR-1 are common characteristics among gammaretrovirus receptors. A number of them have physiological functions as transporters of different substrates [16–20], suggesting that PAR proteins are involved in the transport of unidentified substrates. The host range of retroviruses is often controlled at the cell entry level and fine structural differences in the receptor primary sequences generally determine species-sensitivity to gammaretroviral entry (reviewed in ). However, alternative mechanisms to block viral entry have also been described. N-linked glycosylation of the receptor or production of soluble factor(s) can inhibit the receptor function, while suboptimal expression of the functional receptor may not support infection [22–26].
Here we studied the resistance to PERV-A entry in cells of two rodent species, mouse and rat, to better understand the molecular mechanism of PERV-A entry. Implication from our results in host-pathogen interaction is also discussed in the evolutionary context.
Resistance of rodent cells against PERV-A infection
Amino acids identities
RatPAR, like huPARs and unlike muPAR, allowed PERV-A infection in all the resistant cell lines, including rat NRK cells from which it was derived (Fig 1A). It was suspected that the ratPAR expression level is critical for sensitivity to PERV-A entry. Due to the unavailability of an anti-PAR antibody, it was not possible to investigate endogenous protein expression. Therefore, the amount of ratPAR mRNA was measured by real time RT-PCR in three rat cell lines, NRK, HSN, and XC, before and after exogenous expression of ratPAR. PERV-A infectivity of these cultures is plotted against the ratPAR mRNA level in Fig 1B. Rat cells became PERV-A sensitive when the level of ratPAR mRNA was increased 40–500 fold by exogenously expressing ratPAR. The endogenous expression level of ratPAR therefore appears to be too low to support PERV-A infection, whereas exogenous ratPAR was overexpressed to the level high enough to allow PERV-A entry in rat cells. To demonstrate the dependence of PERV infection on ratPAR expression level, we produced QT6 cell clones with various expression levels of C-terminal HA-tagged ratPAR. PERV-A infection efficiency was dependent on the ratPAR expression level as measured by anti-HA surface staining (see additional file 2 Fig S2). Overall, the mechanism of resistance to PERV-A entry differs between two rodent species, mouse and rat, and the molecular basis of muPAR defect was further investigated.
Proline 109 in muPAR is responsible for PERV-A resistance
The critical amino acid at position 109 is located in the second extracellular domain of PAR
Further evidence to support the predicted topology was obtained utilising a glycosylation study. Using NetNGlyc 1.0 software , one N-glycosylation site for huPAR-2 at a.a. position 178 is postulated. This prediction agrees with the proposed topology because Asp178 is located in the third ECL (Fig 3A). To test this hypothesis, huPAR-2 harbouring the single a.a. mutation, Asp178 to Ala (N178A), was generated. The construct expressed in QT6 cells supported PERV-A infection (data not shown). Cell lysates of 293T cells transfected with HA-tagged huPAR-2 wild type or the mutant N178A were treated with PNGase F, an enzyme which removes N-linked oligosaccharide chains. The western blot analysis showed a shift of the signal in the wild type huPAR-2 treated with PNGase F from 55 kDa to 48 kDa (Fig 3D). This shift indicated that huPAR-2 carries N-linked oligosaccharide chains. In contrast, the N178A mutant produced 48 kDa bands in both samples with and without PNGaseF treatment (Fig 3D), suggesting that Asp178 is indeed an N-glycosylation site and therefore located in an ECL. Together, these results strongly support the predicted model for the huPAR-2 molecule (Fig 3A). As similar models were also obtained for huPAR-1 and muPAR by transmembrane prediction, various PAR molecules are likely to have the same topology and have a.a.109 in the second ECL.
Pro109 abrogates binding of PERV-A Env to PAR
Unique structure of PAR ECL2 in murine species
The mechanism of resistance to PERV-A cell entry is different between mouse and rat cells: the murine homologue of PAR (muPAR) is defective in PERV-A receptor function, whereas the rat cell encodes a fully functional PAR protein. RatPAR can rescue PERV-A infection in non-permissive cell lines, including the resistant rat cell lines from which it has been cloned. The PERV-A infection of rat cells upon overexpression of ratPAR is reminiscent of results from a previous study which show that overexpression of amphotropic MLV and GALV receptors from Chinese hamster cells and FeLV-C receptor from MDTF cells, supports viral infection in the cell lines of their origin . This type of resistance to viral infection can be explained by subthreshold levels of receptor expression or stoichiometrically limited masking or interference mechanisms [23–25]. We therefore explored the possibility that a N-glycosylation could mask the receptor and that an inhibitory factor is secreted from rat cells. However, no effect on PERV-A infection by these possible mechanisms was observed (data not shown). The mechanism which determines the threshold level of ratPAR expression for PERV-A infection is currently unclear. However, our results suggest that other component(s) on the cell surface may be responsible for a successful interaction between virus and receptor, as has been previously proposed for other gammaretroviruses [34–36].
The defect in muPAR as a PERV-A receptor is due to the presence of Pro at position 109. Our topology study indicated that a.a.. 109 is most likely to be located in the second extracellular loop (ECL2) and potentially accessible for the direct binding by PERV-A Env. Our binding assay consistently detected soluble PERV-A Env binding to cells expressing 'functional' huPARs and ratPAR, but not muPAR. Furthermore, a Leu-to-Pro mutation at a.a. 109 in huPAR-2 abolished Env binding as well as PERV-A infection, further highlighting the important role of this a.a.. These results identified the ECL2 as the likely target for PERV-A Env binding, leading to PERV-A entry. This, together with recent studies on the determinants in PERV Env for binding and entry [37, 38] contribute to better understanding of PERV-receptor interactions. These advances may help develop reagents that block PERV entry, such as neutralizing antibodies  and peptides mimicking the receptor.
The amino acid sequence positions 108–110 of muPAR ECL2, KPY instead of QLH, is intriguingly unique in murine species. Since rats share QLH at the corresponding positions with diverse non-murine species including primates, horse and dog, it is likely that murine species acquired 3 mutations after separating from rats. Although we cannot exclude the possibility that these changes are a stochastic evolutionary outcome, it is more likely that certain selective pressure, at least partly, caused these changes. It is tempting to speculate that severe epidemics of PERV-A like viruses which target the ECL2-QLH structure may have selected 'PERV-A-resistant' murine species with KPY. Our result showing that Leu-to-Pro 109 change alone blocks PERV-A infection raises the question why changes are also required at positions 108 and 110. It is possible that all three a.a. changes were required to escape viral attacks in the past. Alternatively the acquisition of Lys108 and Tyr110 by murine species might be required to maintain yet unknown physiological function of PAR while escaping deadly viruses. To further gain insight into this hypothesis, as well as to study involvement of PAR in the possible PERV-A pathology, identification of physiological roles of PAR is warranted.
Different bases for PERV-A resistance between mice and rats are shown. Expression of endogenous ratPAR in rat cells appear to be under a threshold level to support PERV-A infection. In mice, a single a.a. mutation in muPAR in the ECL2 is responsible for the resistance to PERV-A infection. ECL2 in muPAR has a unique sequence with three a.a. changes compared with a wide range of species. Possible selective pressure may have caused this ECL2 diversion in mice.
Human embryonic kidney 293T cells were maintained in Dulbecco's modified Eagle Medium (DMEM, Gibco) supplemented with 15% fetal bovine serum (FBS, BioSera). Quail QT6 cell [ECACC: 93120831], murine MDTF (Mus dunni tail fibroblast), rat NRK [ECACC: 86032002] HSN cells  and XC [ECACC: 88120601] were grown in DMEM supplemented with 10% FBS.
Plasmids and construction of chimeric receptors
Primers and probes used in this study
Sequence (5' → 3')
AGC TGG AGA TCTa GAG CAG AAA CTC ATC TCT GAA GAG GAT CTGg CTT GTG ACC AGT CCG AAC TCC CAT AAA CCC TTA TCT CTC ACC
ATG TTC TTA GCT AGCb CTA TTC ATC AAG GAT TGC TTT TTC CGG
GAT TGA T GA ATT Cd AC CAC CAT GGiC AGC ACC CAC G
GAT CTT GCG GCC GCeT CA A GCG TAT TCT GGA ACA TCG TAT GGG TAh A AGC TTcG GGG CCA CAG GGG TCT ACA CAG TCC TTT CTG CTT TG
GAA GGT AAG CTTc GGA GTC ACA GGG GTC
GAT TGA T GA ATT Cd AC CAC CAT GGiC AGC ACC TCC G
GAA GGT AAG CTTc GAG GCC ACA CTG GTC
CGT GGC ATC TAG ATT AAG CTTc GGG GCC ACA GGG GTC
TTG CAC TAG GGC TAG CAC ACA GG
CCT GTG TGC TAG CCC TAG TGC AA
TAG GAA GGC CAC AGA GTA CGG CTT CCC TGC CAC TGG GGC
GCC CCA GTG GCA GGG AAG CCG TAC TCT GTG GCC TTC CTA
TAG GAA GGC CAC AGA GTG GGG CTG CCC TGC CAC TGG GGC
GCC CCA GTG GCA GGG CAG CCC CAC TCT GTG GCC TTC CTA
TAG GAA GGC CAC TGA GTG GAG CTG TCC TGC CAC TGG GGC
GCC CCA GTG GCA GGA CAG CTC CAC TCA GTG GCC TTC CTA
TAG GAA GGC CAC CGA GTA GAG CTT TCC TGC CAC TGG GGC
GCC CCA GTG GCA GGA AAG CTC TAC TCG GTG GCC TTC CTA
AGA GGT GCC AGC GGT GGG CGC T
AGC GCC CAC CGC TGG CAC CTC T
TTA CAA GAA TTCd GCC ACC ATG GiTT TAC CCA TAC GAT GTT CCA GAT TAC GCTh GCA GCA CCC ACG CTG GGC CGT CTG GTG CTG A
GAT CTT AA G CGG CCG CeTC AGG GGC CAC AGG GGT CTA
GCC AGA GGA GGT ACCf GCC ACC ATG GAT GCA ATG AAG AGA G
GGG TAA GAT CTaG GCT CCT CTT CTG AAT CGG GCA TGG ATT TCC TGG CTG GGC
GAT TGA T GA ATT Cd AC CAC CATG GiCA GCA CC
TGA CTG A GC GGC CGCe TCA AGG GCC ACA CTG ATC CAC
GCA GGT AAG CTTc AGG GCC ACA CTG ATC
CTC ACT CCT TTA CAC TAC AC
CAA CCC ATT GGA TGA AGA TG
TCA AGG TGT CTC CCA TCA ATT TC
CGT CAA CAC CCA AAA GAA TGT G
TCG AGG CCC TGT AAT TGG AA
CCC TCC AAT GGA TCC TCG TT
TAC CTG GTT GAT CCT GCC AGT A
TTA CGA CTT TTA CTT CCT CTA GAT AG
CTG AGC GTT TCT CTG
AGT CCA CTT TAA ATC CTT
An NheI restriction site was introduced into huPAR-2 at the site corresponding to that in muPAR [Genbank: AK008081, nucleotide 805] by two-step PCR using primers G3;G9 and G10;G8, then G3;G8, where primers G9 and G10 contain the nucleotide change. Primer G8 includes a HindIII restriction site which allows the cloning of the mutant receptor into pcDNA3/huPAR-2HA. Chimeric receptors H2M a and f were obtained by mix-and-match cloning between huPAR-2 and muPAR using the restriction sites EcoRI and NheI. The other huPAR-2-derived chimeric receptors were produced in a similar way using mutagenesis primers G11;G12 (H2M e) and G13;G14 (H2M d) in association with the primers G3;G8. Similarly, muPAR-derived chimeric receptors were produced using primers G15;G16 (H2M b) and G17;G18 (H2M c) in combination with primers G6;G7.
The N178A mutation in huPAR-2 was introduced by PCR-mutagenesis using the primers G19;G20 in association with the primers G3;G8 and the mutant huPAR-2 was cloned into a partially digested pcDNA3/huPAR2HA using EcoRI and HindIII restriction sites.
The mutant huPAR-1 carrying a proline at position 109 (H1M g) was generated by PCR-mutagenesis using the primers G13;G14 in combination with the primers G3;G5.
All the PCRs described above were performed using KOD HiFi polymerase in accordance with manufacturer's instructions. Chimeric receptors were verified by sequencing based on a modification of the Sanger method and analysed using the CEQ 8000 DNA Sequencer (Beckman Coulter).
Cloning of rat PERV-A receptor
Total RNA from NRK cells was extracted using the RNeasy kit (Qiagen) and incubated with 5 U of RNase-free DNase (Promega) for 30 min at 37°C. First strand cDNA was produced by incubation of 2 μg of DNase-treated RNA with 200 U of Moloney MLV Reverse Transcriptase (Promega), 1 μg of random primers (Promega), 20 U of RNasin Ribonuclease Inhibitor (Promega), 1 mM dNTPs (Qiagen) in a final volume of 20 μl for 10 min at 25°C, 1 hr at 42°C and an inactivation step of 10 min at 70°C. The ratPAR coding sequence was then amplified using HotStart polymerase (Qiagen) and primers M1;M2 with PCR conditions: 95°C 30 sec, 52°C 30 sec, 72°C 90 sec. Primers M1 and M2 were designed to anneal to the rat homologue of huPAR-1 [Genbank: XM_343272]. The M1 primer introduced the Kozak sequence in front of the ATG of the receptor. The PCR product was cloned into pcDNA3 using EcoRI and NotI restriction sites present in the primers. HA-tagged C-terminal ratPAR was obtained by PCR using KOD HiFi polymerase and the primers M1;M3 which contain the HindIII restriction site, and introduced into pcDNA/huPAR-2HA. This product was then subcloned into pCFCR.
Transfection, virus production and infection
Transfection of huPAR-2 (N- or C- terminal HA-tagged or N178A mutant) was performed on confluent 293T in a 6-well plate using 4 μl of FuGene-6 reagent (Roche) and 1 μg of plasmid.
Viral particles carrying the receptor genes were produced by co-transfection of 3.5 μg of three plasmids, CMVi for MLV Gag-Pol, MDG for VSV-G and MLV vector genome pCFCR carrying the receptor gene (ratio 1:1:1.5) on confluent 293T cells in 100 mm-dish using 18 μl of FuGene-6 reagent (Roche). Cells were washed 24 hours later and at 48 and 72 hours the supernatant containing viral particles were harvested and passed through a 0.45 μm filter (Millipore). A replication-competent PERV-A 14/220 expressing the reporter gene EGFP, EGFP(PERV-A), was produced as follows. A similar three plasmid transfection on 293T cells was performed using pCNCG instead of pCFCR in order to produce MLV/EGFP particles. The virus-containing supernatant was used to transduce 293T cells. The stable EGFP-expressing 293T cells were then transfected using FuGene-6 with the replication competent PERV-A 14/220 plasmid. The titer of EGFP(PERV-A) viral particles was assessed by infection of 1 × 105 293T seeded in a 6-well plate using serial dilutions of the supernatant. After two months the titer was stable at 2 × 105 EGFP 293T transducing units/mL.
The receptor transduction and EGFP(PERV-A) infection were performed as follows: 5 × 104 target cells were seeded in a 12-well plate and the day after, 500 μl of virus-containing supernatant was added. Receptor or EGFP expression was verified 48 hours post transduction/infection by flow cytometry analysis.
Flow Cytometry analysis
Cells transfected or transduced with HA-tagged PAR were detached with PBS-5 mM EDTA and blocked by incubation for 30 min in PBS-10% FBS on ice. The cells were washed twice in PBS, resuspended in PBS-2% FBS containing 1:100 dilution of mouse monoclonal antibody HA.11 (Covance) or 1 μg of mouse monoclonal anti-human CD71 antibody (Santa Cruz) and incubated for 1 hour at 4°C. After two washes with PBS-2% FBS, the cells were incubated with 1:200 dilution of the secondary antibody anti- mouse IgG fluorescein isothiocyanate (FITC)-conjugate (Jackson Immunoresearch) in PBS-2% FBS for 45 min at 4°C. Cells were washed three times and resuspended in PBS. To assess EGFP(PERV-A) infection efficiency, 48 hours post-infection cells were harvested and resuspended in PBS. All the samples were processed on a FACScan cytometer (Becton-Dickinson) and analysed using CellQuest software.
One day post transfection, 293T expressing HA-tagged huPAR-2 were seeded on cover slides and incubated for further 48 hours. The cells were fixed by incubation with 4% paraformaldehyde (Sigma) in PBS for 20 min at room temperature. The permeabilized samples were obtained by incubation with PBS-0.1% saponin (Fluka) for 10 min at room temperature. For the permeabilized samples, 0.1% saponin was added during all antibody incubations. All slides were washed in PBS and placed on a 30 μl drop of PBS-1% FBS containing antibody HA.11 (dilution 1:100) or anti-human CD71 antibody (dilution 1:50) for 1 hr at 37°C in a humidified chamber. Cells were then washed three times with PBS and the slides placed in a 30 μl drop of PBS-1% FBS containing the secondary antibody FITC-conjugated anti-mouse IgG (dilution 1:100) for 45 min at 37°C in a humidified chamber. After three washes, the cover slides were mounted in Vecta Shield mounting medium containing propidium iodide (Vector Laboratories). Images were collected using a DM IRE2 confocal microscope (Leica).
293T cells transfected with wild type huPAR-2 or N178A mutant were harvested, washed and incubated in RIPA lysis buffer (50 mM TRIS-HCl pH 7.5, 150 mM NaCl, 1% Igepal CA-630, 0.5% deoxycholic acid, 0.1% SDS, 1% Triton ×-100) in the presence of protease inhibitors (Complete mini, Roche) for 30 min on ice. The cell lysates were then digested with 1500 U of N-glycosidase F enzyme (PGNase F, New England Biolabs) at 37°C for 2 hrs. Proteins from digested and undigested samples were separated by SDS polyacrylamide (BioRad) electrophoresis (SDS-PAGE) and transferred to PVDF membrane (Amersham Biosciences) by using a semi-dry blotting system (Amersham Biosciences). The membrane was blocked in PBS-5% non-fat skimmed milk powder (Oxoid) and then probed for 1 hr at room temperature with the HA.11 monoclonal antibody diluted 1:1000 in PBS-2% milk, followed by incubation with an anti-mouse IgG conjugated with horseradish peroxidase (Dako, dilution 1:10,000 in PBS-2% milk) for 30 min at room temperature. Signals were detected by incubation with ECL chemiluminescence reagent (Amersham Biosciences) and exposure to x-ray film (Hyperfilm, Amersham Biosciences). To control for protein loading, the same blots were incubated with mouse anti-human β-actin (Sigma, 1:1000 in PBS-2% milk).
Soluble Envelope Binding Assay
C-myc tagged PERV-A 14/220 Env was produced by transient transfection of 293T in a 100 mm dish using 18 μl of Fugene-6 (Roche) and 3 μg of myc14/220ENV plasmid. One day post-transfection, medium was replaced with DMEM supplemented with 10% FBS. The supernatant was then harvested at 48 and 72 hours and passed through a 0.45 μm filter. Target cells for binding assay were detached using PBS-5 mM EDTA, washed twice and 1 × 106 cells for each sample were resuspended in 1 mL of 293T supernatant containing soluble 14/220ENV. After 1 hr incubation at 37°C, the cells were washed twice with PBS-2%FBS and incubated with 100 μl of anti c-myc antibody 9E10 (Santa Cruz Biotechnology, Inc) diluted 1:100 in PBS-2%FBS for 1 hr on ice. The cells were washed twice and incubated for 30 min on ice with a 1:200 dilution of phycoerythrin (PE)-conjugated secondary antibody anti-mouse IgG (Jackson Immunoresearch) in PBS-2%FBS. After two washes with PBS-2%FBS, the cells were resuspended in PBS and analysed by flow cytometry (FACScan, Becton Dickinson).
Total RNA from cells was extracted using an RNeasy kit (Qiagen) and cleaned using 5 U of RNase-free DNase (Promega) according to the manufacturer's instructions. The RNA was quantified and 2 μg of total RNA was subjected to reverse transcription (RT) as described for the ratPAR cloning. 2.5 μl of the RT reaction were used in the Real-Time PCR using Quantitect Probe PCR Mix (Qiagen) 0.4 μM of each primers (Q1;Q2), 0.2 μM of Fam-Tamra labelled probes (PR) (Sigma). The amount of RNA between each samples was normalized using the housekeeping gene 18S rRNA, primers Q3;Q4 and probe P18. The assay was performed in duplicate using the ABI PRISM 7000. Thermocycling conditions were: 50°C, 2 min; 95°C, 15 min; 40 cycles of 95°C, 15 sec and 60°C, 1 min. The number of copies of each products were calculated from standard curves obtained by serial dilution of the plasmid pCFCR/ratPAR. Part of the 18S mRNA gene were amplified using primers ZF;ZR from human total RNA and cloned into TOPO BLUNT 2 (Invitrogen) following the manufacturer's instruction.
Genomic PAR sequence analysis
Genomic DNA was extracted from murine MDTF and rat XC, HSN cell cultures using DNeasy Tissue kit (Qiagen). Genomic DNA from Mus m. castaneus and Mus spretus is a kind gift from Dr. Jiri Hejnar (Academy of Sciences of the Czech Republic, Prague, Czech Republic). Genomic sequences of rodent PAR were amplified by PCR using high fidelity DNA polymerase KOD HiFi according to the manufacturer's instructions and the primers M4;M5 (muPAR) and M1;M2 (ratPAR). The PCR products were directly sequenced.
Amino acid sequence accession number
The amino acid sequences used in this study are: huPAR-1 [RefSeq: NP_078807] and huPAR-2 [RefSeq: NP_060456], chimpanzee PAR-1 [RefSeq: XP_001156784] and PAR-2 [RefSeq: XP_001164395], Rhesus macaque PAR-1 [RefSeq: XP_001091189] and PAR-2 [RefSeq: XP_001099620], baboon PAR-2 [Swissprot: Q863Y8], dog PAR [RefSeq: XP_532355], horse PAR [RefSeq: XP_001505049], pig PAR [Swissprot: Q863Y7], cow PAR [RefSeq: NP_001069369], muPAR [RefSeq: NP_083919] and ratPAR [RefSeq: NP_001103140].
This work was supported by UK Medical Research Council and European Commission funded project LSHB-CT-2006-037377.
We thank Benjamin LJ Webb for critical reading of the manuscript.
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