Molecular Evolution of the Mammalian Prion Protein

Teun van Rheede, Marcel M. W. Smolenaars, Ole Madsen and Wilfried W. de Jong

Department of Biochemistry, NCMLS, University of Nijmegen, The Netherlands


    Abstract
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
Prion protein (PrP) sequences are until now available for only six of the 18 orders of placental mammals. A broader comparison of mammalian prions might help to understand the enigmatic functional and pathogenic properties of this protein. We therefore determined PrP coding sequences in 26 mammalian species to include all placental orders and major subordinal groups. Glycosylation sites, cysteines forming a disulfide bridge, and a hydrophobic transmembrane region are perfectly conserved. Also, the sequences responsible for secondary structure elements, for N- and C-terminal processing of the precursor protein, and for attachment of the glycosyl-phosphatidylinositol membrane anchor are well conserved. The N-terminal region of PrP generally contains five or six repeats of the sequence P(Q/H)GGG(G/-)WGQ, but alleles with two, four, and seven repeats were observed in some species. This suggests, together with the pattern of amino acid replacements in these repeats, the regular occurrence of repeat expansion and contraction. Histidines implicated in copper ion binding and a proline involved in 4-hydroxylation are lacking in some species, which questions their importance for normal functioning of cellular PrP. The finding in certain species of two or seven repeats, and of amino acid substitutions that have been related to human prion diseases, challenges the relevance of such mutations for prion pathology. The gene tree deduced from the PrP sequences largely agrees with the species tree, indicating that no major deviations occurred in the evolution of the prion gene in different placental lineages. In one species, the anteater, a prion pseudogene was present in addition to the active gene.

Key Words: prion protein • concerted evolution • BSE • Creutzfeldt-Jakob • pseudogene


    Introduction
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
The prion protein (PrP) is associated with the various forms of transmissible spongiform encephalopathies (TSEs) in mammals. Because of its unique features as a pathogenic protein, PrP is probably one of the most intensively studied proteins (reviewed in Prusiner 1998; Harris 1999; Hope 2000; Brown 2001; Collinge 2001; Rudd et al. 2001). Yet, remarkably little is known about its normal cellular function and about the precise manner in which it exerts its pathogenicity. The human prion gene PRNP encodes a 253-residue precursor protein (see fig. 1) in an intronless open reading frame. It is expressed in most tissues, but highest levels are found in the central nervous system, notably associated with synaptic membranes. After translocation across the endoplasmic reticulum membrane, the N-terminal signal peptide is cleaved off. Subsequently, a hydrophobic peptide at the C-terminus is removed in a transamidation reaction which attaches a glycosyl-phosphatidylinositol (GPI) moiety to the prion protein. The GPI anchor attaches the protein to the outer membrane surface of the cell. In addition to the fully translocated form, secPrP, two transmembrane variants of PrP have been described, CtmPrP and NtmPrP, in which a highly conserved hydrophobic sequence (fig. 1) spans the lipid bilayer in opposite directions (Hegde et al. 1998). NMR measurements have established the conformation of recombinant PrP of mouse (Riek et al. 1996), hamster (James et al. 1997), human (Hosszu et al. 1999), and bovine (Lopez Garcia et al. 2000), which have closely similar global folds. The N-terminal region is largely unstructured and flexible, but residues 37–53 have the potential to form an extended poly(L-proline) II (PPII) helix structure, forming a hydroxylation site at Pro44 (Gill et al. 2000). The N-terminus further comprises a segment of five or six repeats which is implicated in copper binding (Brown et al. 1997). The C-terminal region forms a more rigid globular domain, containing a bundle of three {alpha}-helices and a short, two-stranded, antiparallel ß-sheet. This domain is stabilized by a disulfide bridge and comprises two variably occupied N-linked glycosylation sites.



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FIG. 1. Schematic diagram of human PrP showing signal peptides (black), hydrophobic region (gray), {alpha}-helical regions (denoted with H1-3) and ß-strands (denoted with B1-2). Indicated are sites for glycosylation (Asn181, Asn197), hydroxylation (Pro44), and cleavage (Lys112/His113). Cysteines 179 and 214 form a disulfide bridge

 
The function of the normal cellular isoform of the prion protein (PrPc) remains enigmatic. PrPc-deficient mice develop normally but display minor defects attributable to a higher sensitivity to various forms of stress (Raeber et al. 1998; Brown, Nicholas, and Canevari 2002). PrPc appears to protect against programmed cell death (Kuwahara et al. 1999) and Bax-mediated apoptosis (Bounhar et al. 2001). PrPc is a copper-binding protein that may have superoxide dismutase activity. It thus could protect against oxidative damage and contribute to synaptic homeostasis (Brown et al. 1999; Brown 2001). Exposure to Cu2+ ions promotes the endocytosis of PrPc (Sumudhu, Perera, and Hooper 2001). Furthermore, there is evidence that PrPc is a cell-surface receptor for signal transduction, coupled to the tyrosine kinase Fyn (Mouillet-Richard et al. 2000). PrPc cycles rapidly between the cell surface and early endosomes via clathrin-coated vesicles, as do many cell-surface receptors. PrPc functioning may be modulated by removal of the N-terminal domain by proteolysis between Lys112 and His113 (Harris 1999).

A conformational change in PrPc gives rise to the pathogenic form PrPsc. This transition involves a dramatic increase in ß-sheet content from 3% to ~40%, and a decrease in {alpha}-helical structure from 40% to ~30% (Cohen and Prusiner 1998). PrPsc is relatively resistant to chemical and heat treatment. Protease digestion leaves a resistant core comprising residues 90–231. PrPsc catalyzes further misfolding of PrPc, thus leading to a self-amplifying cycle and the formation of insoluble, extracellular aggregates. Inherited, sporadic, and infectious forms of prion diseases exist. Inherited forms are associated with mutations in the prion gene that enhance the transition from PrPc to PrPsc. In sporadic cases, PrPsc may derive from spontaneous misfolding of PrPc. Infectivity occurs when the pathological transformation of the host's PrPc is induced by PrPsc particles transmitted from individuals of the same or different species (Prusiner 1998). It is important to note, however, that PrPsc by itself is not directly neurotoxic (Hill et al. 2000) and that not all prion-diseased brains contain PrPsc (see Stewart and Harris 2001).

Interspecies infectivity of TSEs varies greatly (Prusiner and Scott 1997). Sequence differences between PrP of donor and recipient species play a role, but interspecies susceptibility is not simply determined by overall sequence similarity (Goldmann et al. 1996). More important seem the prion strains within a species, which are isoenergetic conformers of PrPsc, characterized by variations in clinical presentation and protease resistance (Cohen and Prusiner 1998). Strain variation is encoded by different PrPsc conformations and ratios of the three PrP glycoforms (diglycosylated, monoglycosylated, and unglycosylated) and further influenced by PrP sequence polymorphisms and metal binding (Collinge 2001; Priola and Lawson 2001). However, the precise molecular basis of strain variation remains unknown.

Many residues and regions in the prion protein have been implicated in functioning, pathogenicity, and species barrier. Sequence comparison of mammalian prion proteins may help to evaluate such proposals and gain insight in the molecular evolution of PrP. Previous studies have revealed conserved and more variable regions in mammalian PrP, as well as variation in repeat number (Schätzl et al. 1995; Wopfner et al. 1999). It appeared that substitutions implicated in prion diseases occur in the least variable regions and that residues important for the species barrier occur in a restricted region (Krakauer, Zanotto, and Pagel 1998). However, at present, taxon representation of mammalian prion sequences is heavily biased. Sequences are available for many primates, artiodactyls, and a subset of rodents, as well as for rabbit, some carnivores, and perissodactyls. These represent only six of the 18 placental mammalian orders. Moreover, these six orders belong to only two of the four major clades within the Eutheria (Murphy et al. 2001). In this study, we extend the taxon sampling with 26 species to include all 12 previously unsampled orders. Combined with the recent insights in mammalian ordinal relationships (Murphy et al. 2001), it is now possible to better reconstruct the molecular evolution of the mammalian prion.


    Materials and Methods
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
Taxon Sampling
In this study, we included species representing all 18 eutherian orders and some of the major subgroups in speciose orders such as rodents and bats. New PRNP gene sequences were obtained for the following orders and species. Afrosoricida: Amblysomus hottentotus (Hottentot golden mole), Chrysochloris stuhlmanni (Stuhlmann's golden mole, N-terminus only), Tenrec ecaudatus (common tenrec); Cetartiodactyla: Hippopotamus amphibius (hippopotamus), Physeter macrocephalus (sperm whale); Chiroptera: Cynopterus sphinx (Indian short-nosed fruit bat), Macrotus californicus (California leaf-nosed bat), Myotis daubentoni (Daubenton's bat); Dermoptera: Cynocephalus variegatus (flying lemur); Eulipotyphla: Erinaceus europaeus (Western European hedgehog), Hylomys suillus (lesser gymnure), Sorex cinereus (masked shrew), Talpa europaea (European mole); Hyracoidea: Procavia capensis (rock hyrax); Lagomorpha: Ochotona princeps (American pika); Macroscelidea: Macroscelides proboscideus (short-eared elephant shrew); Perissodactyla: Diceros bicornis (black rhino), Equus equus (horse); Pholidota: Manis sp. (pangolin); Proboscidea: Elephas maximus (Asian elephant); Rodentia: Cavia porcellus (guinea pig), Sciurus vulgaris (European red squirrel), Spalax ehrenbergi (Ehrenberg's mole rat); Scandentia: Tupaia tana (tree shrew); Sirenia: Trichechus manatus (manatee); Tubulidentata: Orycteropus afer (aardvark); Xenarthra: Cyclopes didactylus (silky anteater). Sequences were submitted to GenBank with the accession numbers AY133034AY133063.

From GenBank, we extracted PRNP sequences of representatives of two other eutherian orders: Carnivora (Mustela sp., mink, S46825) and Primates (Homo sapiens, human, M13899; Saimiri sciureus, squirrel monkey, U08310.1) and of additional Cetartiodactyla (Bos taurus, cow, AJ298878; Sus scrofa, pig, L07623; Camelus dromedarius, camel, Y09760; Ovis aries, sheep, M31313.1), Lagomorpha (Oryctolagus cuniculus, rabbit, U28334), and Rodentia (Mus musculus, mouse, M13685), as well as a marsupial outgroup (Trichosurus vulpecula, brush-tailed possum, L38993). The available PRNP sequences of perissodactyls and dolphin (Wopfner et al. 1999) do not represent the complete mature protein and were therefore not used. A prion gene sequence of the guinea pig is present in the database (AF139166) but contains a conspicuous deletion in the N-terminus. We therefore determined an independent guinea pig sequence (acc. nr. AY133039) and found the same deletion. For the dog (Canis familiaris), highly dissimilar PRNP sequences are present in GenBank, of which AF042843 and AF022714 group with artiodactyls in phylogenetic analyses, whereas a partial dog sequence (AF113937) and close relatives of the dog (dingo, AF113937; gray wolfe, AF113939) group with other carnivores. Similarly, two different cat (Felis catus) PRNP sequences are available, AF003087 grouping with artiodactyls and Y13698 grouping with carnivores again. This casts doubt on the reliability of available dog and cat sequences. We therefore choose the mink prion sequence as a genuine carnivore representative in our analysis. This sequence is corroborated by phylogenetic analysis, grouping with wolf, dingo, and the closely related ferret and polecat sequences.

PCR, Cloning, and Sequencing
Amplification of a ±700-bp fragment of the PRNP gene was performed with primers based on known sequences coding for the N- and C-terminal signal peptides (table 1). This yields the open-reading frame of the complete mature protein (positions 23–231 in fig. 1), apart from the first two amino acids. PCR reactions contained approximately 100 ng genomic DNA, 375 mM dNTPs (Boehringer Mannheim), 20–100 pmol of each primer, and 0.5 µl Taq Expand polymerase (Expand HF system, Roche Diagnostics) in a final volume of 50 µl. The PCR program was 95°C for 4 min, followed by 35 cycles at 94°C for 60 s, annealing at 56°–60°C for 60 s, and extension at 68°C for 90 s. Gel-extracted PCR fragments (Amersham Pharmacia gel extraction kit) were sequenced directly or cloned in pGEM-T easy vector (Promega). Sequencing reactions were performed using Big Dye fluorescent technology and run on an ABI 3700 96-capillary sequencer. Sequences were obtained from at least two independent PCR reactions, and all bases were sequenced at least once on both strands.


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Table 1 Primers Used in the Amplification and Sequencing of the PrP Gene

 
Sequences coding for the N-terminal signal peptide were determined with a PCR technique designed to amplify a fragment of unknown flanking sequence (Sørensen et al. 1993). Partially randomized primers are used along with a specific biotinylated primer. Subsequent purification of the biotinylated PCR product with streptavidine beads (Dynal) and a second, nested PCR increase the specifity. In our case, the biotinylated primer bio-PrPrev and the nested primer S2rev were used (table 1). Applying this method, 5' coding and noncoding sequences were obtained for Cynopterus sphinx and Elephas maximus. This sequence information was used to design a highly degenerate primer (PrPflank, table 1), ending with the adenine of the start codon. This primer was used to amplify N-terminal signal peptide sequences of 12 other species (see fig. 2 for names). The PCR program was 95°C for two min, followed by 35 cycles at 94°C for 30 s, annealing at 50°C for 30 s, and extension at 68°C for 40 s.



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FIG. 2. Alignment of mammalian prion protein sequences. Important structural features are marked above the alignment (cf. fig. 1). The numbering deviates from that in figure 1, because of the introduction of gaps (-). Not in all species N- and C-terminal sequences were determined (- -). Black shading indicates residues that provide evidence for repeat homogenization. Gray shading denotes sequence characteristics that are discussed in the text. Repeats are flushed left (because repeat homogenization does not allow for meaningful alignment), apart from the last one (to facilitate comparison of the truncated last repeat in bats, pangolin, and sperm whale). Boxed repeat units denote repeat number polymorphisms in mole rat (4 and 5 repeats), squirrel (2 and 5 repeats), and anteater (4 and 5 repeats). Fruit bat has alleles with and without Gln. Mutations related to spongiforme encephalopathies and polymorphisms (in bold) are shown under the alignment. Asterisks (*) indicate newly determined sequences. (a) The sequence of the golden mole N-terminal signal peptide is of C. stuhlmanni, the mature protein sequence of A. hottentotus

 
Phylogenetic Analysis
DNA sequences were analyzed using the Staden package programs PreGAP4 and GAP4 (http://www.mrc-lmb.cam.ac.uk/pubseq/). Nucleotide and amino acid alignments were produced using ClustalW and adjusted manually. Positions that were ambiguous in the alignment were excluded from phylogenetic analysis; the tree in figure 3 is based on nucleotide sequences (570 bp) corresponding to amino acid positions 27–67, 132–263, and 274–290 in figure 2.



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FIG. 3. Homogenization of DNA sequences in eutherian prion repeat regions. Sequences of the five to seven repeats in four eulipotyphlans (left), four rodents (middle), and four representatives from other eutherian orders (right) are aligned to show that codons at corresponding positions in a repeat are more homogeneous within than between species. Replacements are colored according to the majority consensus rule. Synonymous substitutions are in gray; nonsynonymous substitutions are in black. Arrows indicate evidence for homogenization, as outlined in the Results

 
We applied maximum likelihood (ML) and Bayesian posterior probability analyses to reconstruct phylogenetic trees. We used Modeltest 3.06 (Posada and Crandall 2001) to determine which model of sequence evolution had the best fit to the data under the maximum likelihood assumption. The best model was a general time reversible model with gamma distribution (eight categories) and proportion of invariable sites (GTR+G8+I). This model was used in all analyses. Model parameters for ML were estimated on an NJ tree and subsequently refined in two consecutive rounds of heuristic ML tree searches with the previously found tree as starting tree. The best model parameters were used in a nonparametrically bootstrapped ML search. To search for the best ML tree, five heuristic tree searches were performed: four with different random starting trees and one with the "best ML tree" from the search for optimal model parameters as a starting tree. All searches converged to the same tree. Bootstrap analyses included 100 replicates. In all ML analyses, the tree bisection reconnection branch swapping option was used. The analyses were performed with PAUP* 4.0 (Swofford 2002). Bayesian phylogenetic analyses were performed using the program MrBayes 2.1 (Huelsenbeck and Ronquist 2001). The Metropolis-coupled Markov chain Monte Carlo (MCMCMC) sampling approach was used to calculate posterior probabilities. Prior probabilities for all trees were equal and starting trees were random. To check consistency of results, four Markov chains were run simultaneously for 200,000 and 500,000 times. Tree sampling was every 10 generations, and "burn-in" values were determined from the likelihood values.


    Results
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
Sequencing the PRNP Gene
PCR primers were designed on the sequences coding for the N- and C-terminal signal peptides of known eutherian prion proteins. This allowed us to amplify in a single reaction the DNA coding for the mature protein of 26 eutherian species. In 23 specimens, a single amplification product was obtained, while three specimens (squirrel, mole rat, and anteater) yielded a double band, due to length polymorphisms in the repeat region. In anteater, a pseudogene was amplified in addition to the normal PRNP gene. This pseudogene contains two frame shift mutations, three stop codons, and many nonsynonymous substitutions (data not shown; acc. nr. AF545183). Since published primate and rodent PrP sequences show a deletion of two residues in their N-terminal signal peptide (Schätzl et al. 1995; Wopfner et al. 1999), we further assessed the taxonomic distribution of this deletion. This was done for 14 species, representing the major superordinal clades, using a modified PCR technique (see Materials and Methods). The amino acid sequences deduced from the newly determined PRNP genes are aligned in figure 2, together with sequences selected from the databases, to represent all major eutherian clades.

Characteristics of the Mammalian Prion Protein
Starting from the N-terminus and referring to the position numbering as used in figure 2, the following features are noteworthy. Two length variants of the N-terminal signal peptide can be observed amongst placental mammals. The longer one is present in most orders, as well as in the outgroup marsupial, and starts with the consensus sequence MVKSH in the placentals. The shorter variant, with the sequence MAN, is found in primates, flying lemur, tree shrew, rabbit, and rodents, which form the recently recognized clade Euarchontoglires (Murphy et al. 2001). The residues flanking the signal peptide cleavage site, between Cys24 and Lys25, are perfectly conserved; the presence of Gly22 and Cys24 at positions -3 and -1 before the cleavage site agrees with the consensus residues for the cleavage enzyme (Udenfriend and Kodukula 1995).

Immediately before the repeat region, similar deletions occur from positions 45 to 56 in guinea pig (but not in other rodents) and in gymnure (but not in the related hedgehog). These deletions are probably caused by independent unequal crossing-over events between the repeated sequence coding for GGSRYP at positions 38–44 and GGNRYP at 51–56. The deletions remove Pro50, of which 4-hydroxylation is thought to be an important functional feature (Gill et al. 2000). Pro50 is also absent in mole, hedgehog, and shrew, being replaced by serine or tyrosine.

The number of repeats varies from two (in one of the squirrel alleles) to seven (gymnure and leaf-nosed bat). The squirrel specimen included in this study was heterozygous for alleles with two and five repeats, and both mole rat and anteater had alleles with four and five repeats. Truncated repeats are present in leaf-nosed and Daubenton's bat, pangolin, and sperm whale (positions 126–130). In the latter three species, the deletion may have been triggered by Gly runs on both sites of the WGQ triplet as present in the last repeat in other placentals. The eutherian repeats rigidly conserve the consensus sequence P(Q/H)GGG(G/-)WGQ. The first repeat always has Q and the following ones have H at position 2, except an incidental repeat in Daubenton's bat and tenrec. Conspicuous are the deviating first repeat in guinea pig with the highly conserved N-terminal PQG replaced by SHS (positions 57–59). The first repeat generally has a GGGG track. GGG is common to most other repeats, but GGGG runs and even GGGGG runs do occur.

Occasional deviations from the consensus repeat sequence are indicative of concerted evolution (indicated with a black background in fig. 2). The first four repeats of hedgehog PrP have a duplication of the C-terminal Glutamine (Q). The repeats of the closely related gymnure have no such extra Q, suggesting homogenization of the repeats after the divergence of gymnure and hedgehog. An incidental extra Q also occurs in tree shrew and in one allele of the fruit bat. Other replacements occur mostly in the Gly runs and are also suggestive of repeat homogenization (e.g., Gly to Ser in tree shrew, mouse, guinea pig, and pangolin). Homogenization of the repeats is also apparent at the DNA level. In figure 3 the repeat units within a number of species are aligned to emphasize that codon usage at corresponding positions in the repeats is more similar within than between species. For example, the His residues are generally encoded by CAT, but CAC is used in the mole, elephant shrew, and anteater (fig. 3 arrow 1). In eulipotyphlans and rodents, the second Gly is generally encoded by GGT, but by GGC in bat, elephant shrew, and anteater (arrow 2). The third Gly in eulipotyphlans is encoded by GGA, but by GGT in rodents, GGG in elephant shrew, and GGC in anteater (arrow 3). Finally, almost all Gly residues preceding the Trp are encoded by GGC, except in anteater, which uses GGA (arrow 4). At the first position of the same codon, mouse and guinea pig show expansion of the nonsynonymous substitution G -> A (arrow 5). In addition to homogenization, similarity by descent certainly plays a role in structuring the repeats. For example, insectivore repeats are more similar to one another than to the repeats of more distantly related species (fig. 3).

Next to the repeat region, the sequence 143–163 (fig. 2) includes the hydrophobic transmembrane segment. It is highly conserved, and the Ala-Gly-rich region even perfectly so. In the structured domain comprising the {alpha}-helices and ß-strands, very limited and almost exclusively conservative replacements are observed. Cys216 and Cys252, involved in the disulfide-bridged helix-loop-helix motif H2-H3, are strictly conserved, as are the Asn-X-Thr motifs required for N-glycosylation of Asn218 and Asn235. Considerable variation occurs in the region immediately preceding the GPI anchor site. This region forms a flexible linkage to the GPI anchor (Riek et al. 1996; Liu et al. 1999). The GPI-attachment Ser (position 275) is replaced by Gly in rabbit and guinea pig and by Asn in elephant shrew. However, the requirements for the transamidase reaction by which the GPI moiety is attached are sufficiently flexible that either these small residues or adjacent ones can serve as attachment sites (Udenfriend and Kodukula 1995). Also the few replacements in the C-terminal signal peptide do not interfere with the required hinge (including the prolines 282 and 283) and stretch of hydrophobic residues.

Gene Tree of Mammalian PrP
Strongly supported discrepancies between a gene tree and the corresponding species tree may point to interesting features of the evolution of the gene in a particular lineage. We therefore performed phylogenetic analyses on the PRNP sequences. In preliminary analyses, rooting the tree with the single marsupial sequence rendered some species highly unstable and often located at implausible places. Notably, the position of the root was consistently placed within Afrotheria, probably due to deviating base compositions and resulting long-branch attraction. To minimize these problems, unrooted analyses were performed with exclusion of the marsupial sequence. The ML tree shown in figure 4 reflects the most constant and prominent findings. The branch lengths reflect accelerated rates of substitutions in some species and clades, such as shrew, erinaceids, tenrec, elephant shrew, and most rodents. The best-supported nodes in the tree mostly correspond with unquestioned sister taxa in the data set (hedgehog and gymnure; Daubenton's and leaf-nosed bats; horse and rhino; sheep and cow; mouse and mole rat; human and squirrel monkey). The prion tree supports the nesting of whale with hippo and ruminants in Cetartiodactyla, a molecularly now well-established relationship (Gatesy and O'Leary 2001). Of phylogenetic interest is the support for the grouping of flying lemur with primates, where the largest current concatenated data set suggests that flying lemur is the sister of tree shrew (Murphy et al. 2001). Encouraging is the observation that the prion tree confirms, be it with low support, the recently recognized major superordinal clades Laurasiatheria, Euarchontoglires, and Afrotheria. The only better-supported discrepancy between the prion tree and the species tree is the nesting of aardvark within the paenungulates, although this was seen only in Bayesian analysis. Other oddities, such as the nesting of tree shrew and lagomorphs within the rodents, are only poorly supported.



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FIG. 4. Unrooted maximum likelihood tree based on eutherian prion genes. ML nonparametric bootstrap values and Bayesian posterior probabilities are shown when higher than 50 and 0.90, respectively (ML/Bayesian). In brackets: The repeat numbers observed in the newly determined PrP sequences or reported as most common for the other sequences. The four recently recognized major clades of eutherian mammals (Murphy et al. 2001) are indicated. The bar corresponds with 0.1 (10%) substitutions per site. For further details, see Materials and Methods

 
Comparing the indel signal in the amino acid alignment in figure 2 with the tree in figure 4, we note that the short form of the N-terminal PrP signal peptide as observed in Euarchontoglires is concordant with the tree topology. Of some interest, too, is the unique deletion of residue 137 in a well-conserved motif QWxKP (135–139) in hippo and sperm whale. Although molecularly almost unanimously supported, morphological evidence remains ambiguous about a whale-hippo clade (Gatesy and O'Leary 2001). On the other hand, comparing the alignment with the tree also reveals that indels in vulnerable repeat regions (e.g., positions 45–56 in guinea pig and gymnure, and 126–130 in microbats, pangolin, and sperm whale) can occur in parallel.


    Discussion
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
Relevance to Normal Function and Structure of PrPc
Previous comparative studies established the limited sequence variation of the prion protein between primates, artiodactyls, and rodents (Schätzl et al. 1995; Wopfner et al. 1999), mostly occurring in the least hydrophobic regions (Krakauer, Zanotto, and Pagel 1998). Our sequences broaden the representation of the wild-type variation amongst the eutherian PRNP genes. Most of the sequence conservation can readily be understood in relation to the normal structure and functioning of PrPc. This concerns primarily the sequences that are required for N- and C-terminal processing of the nascent protein and attachment of the GPI anchor. The latter is essential to cluster PrPc in sphingolipid-sterol microdomains or rafts (Muniz and Riezman 2000). The strict conservation of Lys147 is consistent with a functional role of the cleavage occurring at this site (Harris 1999) (NB: residue numbering throughout the discussion refers to figure 2). Conservation is also obvious for the residues that are involved in maintaining the tertiary structure of the C-terminal domain. In this domain, the disulfide bond linking Cys216 and Cys252 is essential for the structure of PrPc; replacement of these residues results in insolubilization (Maiti and Surewicz 2001). Asn218 and Asn235 must be conserved because the large size and dynamic properties of the two N-linked sugars protect large regions of the extracellular PrP surface from proteases and nonspecific protein interactions (Rudd et al. 2001). In addition, the oligosaccharides may direct the folding and routing of nascent PrPc in the ER (Priola and Lawson 2001). The strict conservation of residues 151–165 suggests an essential function for this hydrophobic region. These residues form the major part of the transmembrane region in CtmPrP and NtmPrP. In in vitro systems, secPrP and NtmPrP are equally abundant (40%–50%), while CtmPrP forms the remaining 10% (Hegde et al. 1998). It is likely that synthesis of the three topological forms varies in different cell types and may be influenced by sequence differences. Indeed, prion disease–related mutations in or near (but not outside) the transmembrane region enhance the formation of CtmPrP (Stewart and Harris 2001). Not all sequence characteristics implicated in functioning of PrPc are conserved. Hydroxylation of Pro50 was suggested to be an epigenetic control mechanism of normal PrP functioning (Gill et al. 2000). The absence in several species of this residue questions the universal importance of this modification.

The observed variation in repeat number and sequence is of direct relevance to the property of PrP to bind bivalent metal ions, in particular copper (Brown et al. 1997), and its possible role in copper transport and metabolism (Pauly and Harris 1998). PrP can bind up to four Cu2+ ions to imidazol nitrogens of the histidines in the repeat region and likely bind a fifth copper to His133 and His148 (Viles 1999; Kramer et al. 2001). However, only two of these might be physiologically relevant high-affinity binding sites (Jackson et al. 2001). Copper binding is pH-dependent, which makes PrP suitable for internalizing Cu2+ ions (Miura et al. 1999; Viles et al. 1999; Jackson et al. 2001). Indeed, exposure of cells to physiologically relevant concentrations of copper leads to rapid endocytosis of PrPc. This cellular response is abolished when copper binding is hindered by mutagenesis of histidines or deletion of octarepeats (Sumudhu, Perera, and Hooper 2001). Binding of copper ion adds structure to the flexible repeat region (Viles et al. 1999) and is essential for the superoxide dismutase–like activity of PrP (Brown et al. 1999). Finally, copper ions lead to site-specific cleavage at the repeat region of mouse PrP on exposure of cells to reactive oxygen species (McMahon et al. 2001). Since copper binding appears to be an important modulator of the functioning and processing of PrPc, it is of interest that not all the implicated histidines are conserved (fig. 2). The number of potential copper-binding histidines in the repeat region can be as low as one, as in the two-repeat squirrel allele. Also the copper-binding site around positions His133 and His148 is not perfectly conserved in all species. These findings raise the question whether and how many copper ions must be bound for the normal functioning of PrPc.

The wild-type number of repeats is five or six in almost all eutherian species, and a species such as cattle is polymorphic for five or six repeats (Schätzl et al. 1995; Wopfner et al. 1999) (figs. 2 and 4). Alleles with four repeats are found at frequencies of up to 2% in human populations (Puckett et al. 1991) and equally occur in other primates (Schätzl et al. 1995). The finding in this study of an animal homozygous for four repeats (golden mole) suggests that this is compatible with normal functioning of PrPc. Alleles with three repeats are common in goat (Goldmann et al. 1998). Even alleles with only two repeats have been reported in lemur (Gilch, Spielhaupter, and Schätzl, 2000) and here in squirrel. This suggests that this low number is evolutionarily viable, at least in heterozygotes. The fact that in our study homozygous individuals with seven repeats (gymnure and leaf-nosed bat) have been reported, demonstrates that this expansion, too, is within the normal range.

It appears that reduction and increase of the number of repeats, between two and seven, does not follow any phylogenetic pattern (see fig. 4). This actually is to be expected in view of the observed repeat number polymorphisms within various species. Expansion and contraction of repeats clearly is a frequent mutational process in the eutherian prion gene. The mechanisms involved can be unequal crossing-over and replication slippage (Collinge 2001). This will simultaneously lead to homogenization of substitutions in the repeat sequences and to the length variation of the GGG runs in the repeats. Selection likely plays a role in balancing the repeat number: a high enough repeat number is needed for copper ion binding, but too high a repeat number promotes the early onset of prion disease (see below).

Relevance to Prion Diseases and Species Barrier
In relation to the various regions and residues in PrPc that have been implicated in prion pathology, the observed variety of the eutherian PrP sequences is informative, too. It should be kept in mind, however, that our sequences may not reflect all intraspecies sequence variation because of our limited sampling within species. In human, Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker disease (GSS), and kuru form part of the phenotypic spectrum of the prion diseases (Collinge 2001). More than 20 amino acid replacements have been observed in inherited prion diseases (fig. 2, "prion mutations") (Prusiner 1998; Collinge 2001; see also SWISSPROT entry P04156). All mutations with pathological significance occur either within or adjacent to regions of secondary structure, notably associated with the second and third {alpha}-helix (Krakauer, Zanotto, and Pagel 1998) and in most cases appear to destabilize the PrP structure (Prusiner 1998; Liemann and Glockshuber 1999). Consequently, replacements that are associated with human prion diseases are only rarely observed in our eutherian sequences. The CJD-related mutation V217I is present in golden mole, and V241I is even found in most of the eutherian sequences. It is unlikely that these conservative replacements cause prion disease by themselves. Also some other replacements are observed at positions implicated in human prion disease: V217T is present in gymnure, F236I in Daubenton's bat, V241M in mink, V241T in elephant, V248L in guinea pig, and Q249E in microbats. Although the C-terminal signal peptide is quite variable, the disease-related mutations M276R and P282S are not observed in any species.

Some amino acid polymorphisms in PrP of human, sheep, and mouse appear to influence the onset and phenotype of prion disease (Prusiner 1998; Collinge 2001). Notably, position 166 (129 in human) is polymorphic for Met or Val in human PrP and modulates protease sensitivity of PrPsc (Parchi et al. 2000). Heterozygosity at this site has been proposed to have a protective effect against sporadic and acquired prion diseases and in some of the inherited forms (Collinge 2001). All cases to date of vCJD, the novel human variant caused by the BSE prion strain from cattle, are homozygous for Met166. The fact that all other mammalian PrP sequences were found to have Met at this position (apart from Leu in hedgehog and anteater) suggests that the assumed protective effect of codon 166 heterozygosity is not a general feature. The other polymorphic sites known in man are N208S and E257K, and these residues occur at these positions in one or more other species.

Various regions in PrPc have been proposed as critical to prion formation, all located in that part of the prion protein that is structured in NMR analysis and conserved in eutherians. Residues 127–157 play a major role in the PrPc/PrPsc interface (Cohen and Prusiner 1998), but also the surface regions 156–175, ~202–211, and 246–264 may be involved in initial binding of PrPc to PrPsc (Horiuchi et al. 2000). An antibody directed against residues 169–193 blocks this interaction (Peretz et al. 2001). Interestingly, the isolated peptide 164–201 can adopt two isoenergetic conformations, with all ß or {alpha}ß structures, an essential feature of the conformational change of PrPc into PrPsc (Derreumaux 2001). Residues 205, 209, 254, and 258 (Q167, Q171, T214, and Q218 in mouse) PrPc have been postulated to bind an auxiliary molecule, protein X, thought to facilitate formation of PrPsc (Kaneko et al. 1997). None of these residues is perfectly conserved in our sequences. The species specificity of protein X might contribute to the species barrier by promoting or slowing down prion formation (Prusiner 1998).

The role of the repeat region in the transition of PrPc to PrPsc is enigmatic. Transition can still proceed after deletion of all repeats, although the repeat region modulates prion replication and pathogenicity (Flechsig et al. 2000). Extension of the normal number of five repeats with one to nine copies has been observed in human prion disease kindreds (Collinge 2001). The higher numbers of repeats are associated with earlier onset of the disease. Reduction of the repeat number to four does not lead to prion disease, but heterozygosity for three repeats was reported in an elderly patient suffering from a rapidly progressive dementia consistent with CJD (Beck et al. 2001). On the other hand, in goats it was observed that animals with three repeats succumbed after unusual long periods when challenged with PrPsc (Goldmann et al. 1998). Heterozygosity for two and five repeats was found in two specimens of different lemur species, which are known to be particularly susceptible for TSE (Gilch, Spielhaupter, and Schätzl 2000). Alleles with two repeats likely are common in lemurs and squirrel, and therefore homozygotes may also occur. However, it is not known whether homozygotes are viable. Our finding of animals that are homozygous for PrP alleles with four and seven repeats demonstrates that this in itself cannot be deleterious. Although repeat numbers of two to seven are thus evolutionarily viable, it is possible that in humans such repeat numbers contribute to higher prion disease susceptibility at older, postreproductive age.

Finally, what can our sequence comparisons tell about the TSE species barrier? As mentioned, prion strain variation is probably the most important factor. Inoculated prions preferentially convert PrPc into one of the thermodynamically favored PrPsc conformers. Species transmission barriers may be determined by the degree of overlap between the subset of PrPsc conformers allowed by the host's PrP with that presented by the donor PrPsc (Hill et al. 2000). Strain variation is only partially determined by sequence differences. Riek et al. (1996) pinpointed residues 175, 180, 182, 192, and 204 as important for the mouse-human barrier, but also residues 221, 223, 243, and 245 have been proposed to form an epitope involved in controlling the species barrier (Scott et al. 1997). Several of these residues are perfectly conserved and therefore will not contribute to the species barrier. In other instances, only two or three character states are observed (e.g., positions 175, 180, and 203 in fig. 2), which are distributed without obvious phylogenetic pattern. When these sites would be involved in the species barrier, this barrier is expected to be independent of species relationships. For example, the mouse residue Tyr192 (155 in mouse), which is Asn in hamster, seems important for the hamster-mouse species barrier (Priola, Chabry, and Chan 2001). At this position an His is not only present in human and cow but also in hippo and tenrec. Species barriers thus could be present between closely related species and could be broken again in distant ones. Also, the fact that the overall topology of the prion gene tree (fig. 4) agrees with the species tree suggests that no dramatic sequence changes have occurred to avoid cross-species TSE infectivity. In conclusion, the TSE species barrier remains elusive for the time being.


    Acknowledgements
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
This work was supported by grants from the Netherlands Organization for Scientific Research (NWO-ALW) and the European Commission.


    Footnotes
 
E-mail: w.dejong{at}ncmls.kun.nl. Back


    Literature Cited
 TOP
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 Acknowledgements
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Accepted for publication September 13, 2002.