Historic duplications of the prion gene
Human-mouse prion gene synteny relationships
Prion gene syntenies in other species
References
webmaster 5 Dec 98The hox genes [that determine anterior-posterior axial cell fate in bilateral animals] are the most interesting thing going in molecular biology today (besides genomics). The latest results, from J. Postlethwait et al in 27 Nov 98 Science 282: 1711 1998, show that a series of genome level duplications took place in the lineages leading to the various vertebrates of today. The first took place in ancestral agnathan fishes [lamphreys]. A second duplication at the time of the gnathostomes took place in the lobbed-fin fish lineage leading to mammals, so at 420 Myr ago. Ray-finned fish such as pufferfish and zebrafish had a third duplication; salmonids and goldfish had a fourth.
In other words, tetrapods are basically octaploid. If it were not for subsequent gene loss (variable by chromosome and gene) over the last 420 million years, the haploid mammal or bird would have 4 copies of the prion gene, pufferfish 8 copies, and salmon 16 copies. Postlethwait showed earlier that gene duplications commonly split or specialize the original gene functions rather than result in one of the copies becoming superfluous (eg, fetal and adult hemoglobins); this finer resolution turned a liability of zebrafish into an experimental advantage.
According to standard prion dogma, the prion gene is single-copy. While this is no doubt wrong (as noted here in Dec 96 -- nothing can stay double-copy long: duplicates soon diverge to paralogues and and pseudogenes), it is worth revisiting the experimental evidence that led to the single-copy conclusion, which for starters would depend on primers, hybridization stringency, assumptions about cDNA, existence of introns in other copies, and lineages actually tested. Medline searching with 'prion and (single or copy)', show a flurry of work in 1985-86 looked at this issue, everything bootstrapping off the earliest known protein sequence to make subsequent probes. More recent papers simply repeat claims from this era. Nothing has turned up in Human Genome Project BLASTNn nor completed nematode genome searches but these too are subject to limitations of the query and progress to date. [The average nematode gene has 5 introns; a million bases remain unsequenced.]
Cell 1985 Apr;40(4):735-46 Southern blotting with cDNA, single hamster, mouse, human
Cell 1986 Aug 1;46(3):417-28 hamster cDNA
J Infect Dis 1993 Mar;167(3):602-13 bovine single copy
Science 1986 Jul 18;233(4761):364-7 human single copy
PNAS 1986 Sep;83(17):6372-6 mouse
DNA 1986 Aug;5(4):315-24 hamster
PNAS 1986 Oct;83(19):7358-62 chromosome assignments to mouse and human
Genomics 1993 Jan;15(1):30-7 sheep single copy
Nature 1993 Mar 18;362(6417):213-4 anti-prion
PNAS 1992 Oct 1;89(19):9097-101 chicken single copy
webmaster 16 Dec 98
Let's see if we can locate at least a second copy of the four suspected human prion genes. One might think -- based on the respective locations of the prion genes -- that mouse chromosome 2 corresponds to human chromosome 20. However, the homeobox data mentioned above also establishes extensive synteny between mouse chromosome 2 and human chromosome 2 with respect to the HOX-D3, EVX-2, DLX-1, DLX-2 region.
Actually, as seen below, mouse chromosome 2 contains synteny blocks from at least seven human chromosomes. This raises the possibility that the synteny block corresponding to the neighborhood of the mouse prion gene in chr 2 actually corresponds to, say, human chr 2, not chr 20. If so, there could be a second copy [possibly degenerate] of the human prion gene lurking in the appropriate spot. Therefore it is important to carefully review the ever-changing status of prion gene chromosomal mapping and synteny with all possible species pairs.
The latest human chromosome radiation hybrid G3 map gives locations for 33,000 human genes (Deloukas, P. Science 282, 744-746, 1998. or NCBI or direct). (The somewhat coarser G4 map provides a slightly different location.) The best available location of the human prion gene seems to be 20pter12.17 or about 9,448,000 bp in from the telomere on the short arm of chromosome 20. The closest known genes are an mRNA containing a triplet repeat (recalling various neurogical diseases such as Huntington), M-phase inducer phosphatase 2, and NAD+ isocitrate dehydrogenase. [This latter gene is the beta subunit of a nuclear-encoded mitochondrial heterooctamer, U49283, reviewed in the Dec 98 Mol Bio Evo vol 15 pg 1674] Relevent microsatellite markers include D20S1014, D20S883, D20S179, and D20S895.
Oxford grids provide a fully systematic way of comparing synteny between any two mammals and any two chromosomes. Mouse chr 2 has 148 proteins mapped to it. There are 67 homologues from mouse chromosome 2 to human chromosome 20. The case for local synteny of the prion genes is shown in the figure below; the closest markers are about 75.20 cM mouse prion are PCNA (proliferating cell nuclear antigen, P17918 or P12004 and Hs.78996ƯUniGene in humans), Evi4 ( ecotropic viral integration site 4, unmapped in humans), CHGB (chromogranin B or secretogranin I, P16014), and Bmp2 (bone morphogenetic protein 2 P21274).
PCNA, CHGB, and and the more centromeric BMP2 have mapped by the G4 radiation hybrid method, which gives fairly close association to PrnP-KIAA0168-PCNA-CHGB in the 12pter region of chr 20. Looking across the Oxford grid, it it seen that chr 20 has no elements in any mouse chr other than 2. Human chr 2 has 43 hits with mouse chr 2. However, most are in the region of 45 cM. There are several near 73.0 cM but many intervening genes from chr 20 between these and the prion gene. Human chr 9 has 38 homologues with mouse chr 2 but these are all early on; chr 11 has 31 hits but these are near 55 cM; chr 15 has 23 mapped agreements near 69 cM.
Overall, the mapping data is not accurate enough to determine accurate boundaries for local syntenies nor whether gene order is the same. Local duplications also could not be detected. However, at this point, the best match about the mouse prion gene corresponds to the region about the human prion gene in chr 20 and there is no reason to doubt the orthology of these regions.
The chromosomal location of the prion gene is known in a fair number of species (including some in which the gene has not been sequenced) but few species have as many mapped markers (an opportunities for synteny establishment) as human, mouse, and rat. Chicken would be an extremely interesting case; the prion gene has long been sequenced but unfortunately it is not among the many mapped markers. Oxford grids are also available for cat, cattle, sheep, pig, and rat.
Species for which the prion gene has been localized are shown below (see also genome maps for pig 1-2, HorseMap, chicken Gbase+MSU and dog). The Sanger Center is sequencing the 72 megabase human chromosome 20 and offers a chr 20 -specific Blast server. The NCBI ULniGene server lists 506 genes on chr 20
| species | chromosome of prion | reference | genome map or database |
|---|---|---|---|
| mouse | chr 2 75.2 cM | PNAS 1986 Oct;83(19):7358-62 | MGD or AGD |
| human | chr 20p12.17 | PNAS 1986 Oct;83(19):7358-62 | GeneMap 98 or Genomes |
| rat | chr 3q35 | BBRC 1994 Apr 29;200(2):1161-8 | AGD |
| cattle | chr 13q17 | Anim Genet 1993 Feb 24:23 | CGD or BovMap or BovGBase or AGD |
| sheep | chr 13q15 | Cytog Cell Genet 98;81:202; Mam Gen 98 9:853 | SheepBase or AGD |
| goat | chr 13q15 | Cytog Cell Genet 1998;81(3-4):202 | GoatMap |
| river buffalo | chr 14q15 | Cytogenet Cell Genet 1998;81(3-4):202 | - |
| silver fox (Vfu) | chr 14 | Mamm Genome 1996 Nov;7(11):860 | - |
| mink (Mvi) | chr 11 | Mamm Genome 1995 Oct;6(10):705-9 | - |
| cat | chr A3 has ITPA and ADA | - | Arc-Cat |
Homologies of cattle chr 13 to human chr 20 in vicinity of prion gene are fairly extensive and not readily mixed with those corresponding to human chr 10 suggesting synteny of the prion gene region:
| cattle | human | locus |
|---|---|---|
| AVRP 13 | AVP 20 p13-p13 | GDB:119009 (GDB-US) |
| CHGB 13 | CHGB 20pter-p12 | GDB:118770 (GDB-US) |
| GHRH 13 | GHRH 20q11.2-q11.2 | GDB:119270 (GDB-US) |
| ITPA 13 | ITPA 20p-p | GDB:120110 (GDB-US) |
| OXT 13 | OXT 20p13-p13 | GDB:120253 (GDB-US) |
| PRNP 13 | PRNP 20pter-p12 | GDB:120720 (GDB-US) |
Human chr 20p genes mapped on cattle chr 13:
adra -- ags -- auf1 -- avp: arginine vasopressin (vasotonin) bmp2 -- cdc25b -- cdc25b -- cenpb -- centromere protein B chgb -- chromogranin B (secretogranin 1) csnk2a1 -- casein kinase 2, alpha 1 polypeptide cst1 -- cst5 -- cstp2 -- cyb5p4 -- fkbp1 -- ftl -- hnf3 -- insm1-- itpa -- inosine triphosphatase-A oxt -- prepro-oxytocin (neurophysin I) pax1 -- pcna -- pcsk2-- pdyn -- plcb1 -- plcb4 -- plcb4-- prnp -- prion protein ptpra-- pygb -- sn -- snrpb -- sstr4 -- tgm3 -- thbd -- thrombomodulin znt4 --
Mouse and rat diverged fairly recently so their synteny blocks should be larger and less scrambled.
Comparing rat chr 3 to mouse chr 2, one sees similar genes to those of mouse-human:
Andy Law, chicken genome expert at Roslin writes on 17 Dec 98,
"The prion gene has not yet been mapped in chicken. If it were, the preferred symbol would be the same as the human where homology was established, Prnp. That's the nomenclature ruling that we follow. Dr John Williams, coordinator of a study to associate prion genotype with BSE susceptibility in cattle, may be able to provide current information about prion gene synteny in cattle. The conserved synteny expert is Dr Dave Burt. He has conducted a major study of conserved syntenies between chicken, human and mouse. Chicken genome is more closely related to the human than the mouse is (because the rodent lineage seems to have scrambled its genome more extensively than anything else)."
Anim Genet 1998 Aug;29(4):290-4 Smith J, Burt DW... Genetic and physical data on the chicken karyotype are presented in relation to one another.
A summary of current knowledge was kindly supplied by DWB on 5 Jan 99. There was an attempt to map PRNP in chicken, but no suitable polymorphism was found. The internal repeat did vary in length, but not in the mapping cross. A genomic clone would allow a FISH physical map.
chicken = GGA, Human = HSA BMP2 GGA-3 HSA-20p12 HCK GGA-E32 HSA-20q11-12 BMP7 GGA-E32 HSA-20
chromosome 20p human genes [alphabetized] checked against chicken gbase: adra -- ags -- auf1 -- avp: arginine vasopressin (vasotonin) unknown chicken chromosome bmp2 -- cdc25b -- cdc25b -- cenpb -- chgb -- csnk2a1 -- cst1 -- cst5 -- cstp2 -- cyb5p4 -- fkbp1 -- ftl -- insm1-- itpa -- oxt -- pax1: paired box homeotic gene 1 unknown chicken chromosome pcna -- pcsk2-- pdyn -- plcb1 -- plcb4 -- plcb4-- prnp -- ptpra-- pygb -- sn -- snrpb -- sstr4 -- tgm3 -- thbd -- znt4 -- Locus: AVP Synonym: ARVP Description: arginine vasopressin (neurophysin II, antidiuretic hormone) GenBank M11166 GenBank M25647 GenBank M63733 GenBank M63734 MapLoc: 20p13 Locus: PAX1 Description: paired box homeotic gene 1 GDB 132398 MapLoc: 20p11.2Chicken-human synteny snippets from Medline:
-- chicken IL2 to be mapped to chromosome 4 with synteny with mouse chromosome 3 and human chromosome ... synteny between regions of chicken chromosome 1, mouse chromosome 10 and human chromosome 12 ... resulted in the identification of a further 9 genes, bringing the total number of genes/ESTs on the current map to 54. The mapping of these genes led to the identification of two new regions of conserved synteny between human and chicken and confirmed other previously identified regions of conserved synteny between human and chicken [Groenen MA] ... FASN and ACACA genes, located on human Chromosome (Chr) 17q25 and on Chr 17q12 or 17q21 respectively, a large region of conserved synteny among mammals. We have localized the homologous chicken genes FASN and ACACA coding for these enzymes on two different chicken microchromosomes. Although synteny is not conserved between these two genes, our results revealed linkage in chicken between FASN and NDPK (nucleoside diphosphate kinase), a homolog to the human NME1 and NME2 genes ...
An analysis of CKbeta4GT-I and CKbeta4GT-II genomic clones established that the intron positions within the coding region are conserved when compared with each other, and these positions are identical to the mouse and human beta4GT genes. Thus CKbeta4GT-I and CKbeta4GT-II are the result of the duplication of an ancestral gene and subsequent divergence. CKbeta4GT-I maps to chicken chromosome Z in a region of conserved synteny with the centromeric region of mouse chromosome 4 and human chromosome 9p ... during the evolution of mammals, it is the CKbeta4GT-I gene lineage that has been recruited for the biosynthesis of lactose. CKbeta4GT-II maps to a region of chicken chromosome 8 that exhibits conserved synteny with human chromosome 1p. An inspection of the current human gene map of expressed sequence tags reveals that there is a gene noted to be highly similar to beta4GT located in this syntenic region on human chromosome 1p. Because both the CKbeta4GT-I and CKbeta4GT-II gene lineages are detectable in mammals, duplication of the ancestral beta4-galactosyltransferase gene occurred over 250 million years ago in an ancestral species common to both mammals and birds. [J Biol Chem 1997 Dec 12;272(50):31389-99] ...
The chicken insulin-like growth factor 1 gene has been assigned to the short arm of chromosome 1 near the centromere between the IGF1 and GAPD loci. Comparison of the genetic maps of chicken and other vertebrates reveals a highly conserved syntenic group, including the GAPD-IGF1 loci...The gene structure for chicken CP49 gene is presented. It differs from the human CP49 gene with the presence of an extra exon in helix IB and the apparent loss of an intron, intron H. The CP49 gene localises to chromosome 2 in the chicken genome where it is flanked by homologues that map to human chromosome 10p13 (VIM) 6p24-p23 (BMP6).
John Postlethwait writes on 4 Jan 98, "I am working on a paper which will give such a comparative view of all zfish chromosomes. In principle the zfish prion gene should go to LG17 or 20 as you suspect. These are duplicated chromosomes that arose in the genome duplication event that we suspect happened before or early in the teleost radiation."
bmp2: bmp2 linkage group 20 hnf3B: axial linkage group 17 snap25 11.2p: snap1a linkage group 20 or snap 1b linkage group 17 ags -- auf1 -- avp: -- cdc25b -- cdc25b -- cenpb -- chgb -- csnk2a1 -- cst1 -- cst5 -- cstp2 -- cyb5p4 -- fkbp1 -- ftl -- insm1-- itpa -- oxt -- pax1: pcna -- pcsk2-- pdyn -- plcb1 -- plcb4 -- plcb4-- prnp -- ptpra-- pygb -- sn -- snrpb -- sstr4 -- tgm3 -- thbd -- znt4 --
Seleced abstracts using Medline 'prion AND synten*' or 'chromosome 20p and (ring or trisomy)' or 'imprint* and human' 22 Dec 98 webmaster
Cytogenet Cell Genet 1998;81(3-4):202-4 Iannuzzi L, Palomba R, Di Meo GP, Perucatti A, Ferrara LComparative FISH-mapping of the prion protein gene (PRNP) was performed on cattle (BTA), river buffalo (BBU), sheep (OAR) and goat (CHI) chromosomes using a PCR-product as a probe and R-banding. PRNP was mapped to BTA13q17, BBU14q15, OAR13q15 and CHI13q15 according to standard nomenclatures. These chromosomes and bands were homoeologous among the four species, confirming the high degree of gene and chromosome banding conservation among bovids. Furthermore, the assignment of PRNP to river buffalo [prion gene not yet sequenced] and goat chromosomes allowed us to indirectly assign the bovine syntenic group U11 to specific chromosomes, since it is the first in situ localization on BBU14 and CHI13.
Mamm Genome 1998 Oct;9(10):853-5 Castiglioni B, Comincini S, Drisaldi B, Motta T, Ferretti LNo abstract available but the authors write in saying they " have determinated the following chromosomal localization of the bovine prion locus: BTA 13q17. Furthermore, they made comparative mapping of the prion gene in three different species (bovine, ovine and human) by means of fluorescence in situ hybridization (FISH) with the human coding region probe. The chromosomal localizations (BTA 13q17, OA 13q17/q18 [note another group found 13q15 -- webmaster] and HSA 20p12/p13) were in agreement with the available comparative maps of the species."
Anim Genet 1998 Aug;29(4):265-72 Schlapfer J, Gallagher DS Jr, Burzlaff JD, Womack JE, Stelly DM, Taylor JF, Davis SKWe present chromosomal fluorescence in situ hybridization (FISH) results that both extend the HSA20/BTA13 comparative map as well as cytogenetically anchor two microsatellite markers. A bovine bacterial artificial chromosome (BAC) library was screened for conserved genes (type 1 loci) previously assigned to HSA10 or HSA20 and BTA13, and for microsatellites selected from two published BTA13 linkage maps. Clones from six out of nine comparative loci and both microsatellites were found represented in the BAC library. These BAC clones were used as probes in single colour FISH to determine the chromosome band position of each locus. As predicted by the human/bovine comparative map, all type 1 loci mapped to BTA13. Because single colour FISH analysis revealed that the loci were clustered within the distal half of BTA13, dual colour FISH was used to confirm the locus order. Established order was centromere-PRNP-(SOD1L/AVP/OXT)-(BL42/GNAS1)- HCK-CSSM30. The findings confirm the presence of a conserved HSA20 homologous synteny group on BTA13 distal of a HSA10 homologous segment.
Biochem Biophys Res Commun 1994 Apr 29;200(2):1161-8 Kuramoto T, Mori M, Yamada J, Serikawa TSpontaneously epileptic rat (SER) is a homozygote for both tremor (tm) and zitter (zi) genes and exhibits epilepsy-like seizures and spongiform encephalopathy. Genetic linkage analyses revealed that the tm and zi loci were tightly linked to the synaptobrevin-2 (Syb2) on chromosome 10 and the prion protein (Prnp) on chromosome 3, respectively. The genomic DNA sequences of Syb2 of the tm/tm (TRM) rats and exon 2 of the Prnp of the zi/zi (ZI) rats were identical to those of a control rat strain WTC. In addition, no difference was detected for expression of the Syb2 and Prnp on the Northern blot analyses of TRM, ZI and WTC brain, suggesting that the Syb2 and Prnp genes are not the tm and zi, respectively. The assignments of tm and zi to rat chromosome 10q24 and 3q35, however, will be the first step towards the positional cloning of the genes.
Mamm Genome 1995 Oct;6(10):705-9 Khlebodarova TM, Malchenko SN, Matveeva NM, Pack SD, Sokolova OV, Alabiev BY, Belousov ES, Peremislov VV, Nayakshin AM, Brusgaard K, et alChromosomal localization of the genes for gamma- and kappa-immunoglobulins (IGGC and IGKC, respectively), aldolase B (ALDB), prion protein (PRNP), homeo box B (HOXB), and glutamate pyruvate transaminase (GPT) were determined with the use of mink-rodent hybrid cells. Analysis of segregation of the mink markers and chromosomes in these hybrid cells allowed us to assign the gene for HOXB to Chromosome (Chr) 8, IGGC to Chr 10, PRNP and IGKC to Chr 11, ALDB to Chr 12, and GPT to Chr 14 in mink.
Furthermore, using a set of mink-mouse hybrid cells carrying fragments of mink Chr 8 of different sizes, we assigned the gene for HOXB to the pter-p26 region of the short arm of Chr 8. Comparative mapping of the genes of mink, human, and mouse, as well as other mammalian species, demonstrated that the mink genes HOXB, PRNP, ALDB, and IGGC are members of a conserved region shared by many mammalian species in common; the IGKC gene is a member of a conserved region common to carnivores and primates, not rodents; the GPT gene is a member of a syntenic gene group probably unique to the Mustelidae family or carnivores.
Anim Genet 1993 Feb;24(1):23-6 Ryan AM, Womack JEBrains affected by the progressive neurological disease bovine spongiform encephalopathy (BSE) contain scrapie-associated fibrils and the protease-resistant isoform of prion protein. The gene encoding the normal host prion protein (PRNP) has been mapped to human chromosome 20 and mouse chromosome 2 with the hamster cDNA probe pEA974. Using this probe and a panel of bovine-rodent hybrid somatic cells, we have mapped PRNP to bovine syntenic group U11 (100% concordancy).
PRNP restriction fragment length polymorphisms (RFLPs) were detected with five of six enzymes (BglII, EcoRI, HindIII, MspI and TaqI) in sheep, in contrast to one of 16 enzymes (HincII) in cattle. Codominant segregation of the bovine HincII RFLP was demonstrated in six backcross pedigrees. While PRNP RFLPs are tightly linked to scrapie incubation period, and consequently susceptibility or resistance to disease in rodents and sheep, the relationship between the PRNP RFLPs and BSE incubation period has not been determined.
Proc Natl Acad Sci U S A 1986 Oct;83(19):7358-62 Sparkes RS, Simon M, Cohn VH, Fournier RE, Lem J, Klisak I, Heinzmann C, Blatt C, Lucero M, Mohandas T, et alPurified preparations of scrapie prions contain one major macromolecule, designated prion protein (PrP). Genes encoding PrP are found in normal animals and humans but not within the infectious particles. The PrP gene was assigned to human chromosome 20 and the corresponding mouse chromosome 2 using somatic cell hybrids. In situ hybridization studies mapped the human PrP gene to band 20p12----pter. Our results should lead to studies of genetic loci syntenic with the PrP gene, which may play a role in the pathogenesis of prion diseases or other degenerative neurologic disorders.
Genomics 1995 Jul 20;28(2):344-6 Mucklow S, Hartnell A, Mattei MG, Gordon S, Crocker PRSialoadhesin is a cell-cell interaction molecule expressed by subpopulations of tissue macrophages. It contains 17 immunoglobulin (Ig)-like domains and is structurally related to CD22, MAG, and CD33. These molecules establish a distinct family of sialic acid-dependent adhesion molecules, the sialoadhesin family. We have mapped the rodent sialoadhesin gene, Sn, to chromosome 2F-H1 by in situ hybridization (ISH) and shown linkage to Il1b and four other markers by backcross linkage analysis. We have also used ISH and a human-mouse somatic cell hybrid panel to localize the human sialoadhesin gene, SN, to the conserved syntenic region on human chromosome 20p13. [Sialoadhesin is sometimes shown as nearest neighbor to prion gene. -- webmaster]
Hahn GV, Cohen RB, Wozney JM, Levitz CL, Shore EM, Zasloff MA, Kaplan FS Genomics 1992 Nov;14(3):759-62Bone morphogenetic proteins (BMPs) were originally identified by the ability of a demineralized bone extract to induce endochondral osteogenesis in vivo. Seven BMP cDNAs (BMP1 through BMP7) have been recovered through molecular cloning. Recombinant protein products from six of these clones (BMP2 through BMP7) are members of the transforming growth factor beta (TGF-beta) superfamily of regulatory molecules. Based upon a high degree of amino acid sequence homology, BMP5, BMP6, and BMP7 constitute a subfamily within the BMPs. Using human-rodent somatic cell hybrid lines and cDNA probes, we mapped the three members of this subfamily of genes to the human chromosomes. BMP5 and BMP6 are syntenic on human chromosome 6, while BMP7 is syntenic with previously localized BMP2 on human chromosome 20.... [BMP2 is sometimes shown as nearest neighbor to prion gene. -- webmaster]