Evidence for retrogene origins of the prion gene family

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Ehsani, Sepehr ^a,b   Tao, Renzhu ^a,b   Pocanschi, Cosmin L ^a   Ren, Hezhen ^a,b   Harrison, Paul M ^c   Schmitt Ulms, Gerold ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; CYSTEINE; PROTEIN ZIP; UNCLASSIFIED DRUG; CATION TRANSPORT PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; EXON; FOUNDER EFFECT; GENE; GENE INSERTION; INTRON; METAZOON; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PRION GENE; PROTEIN DOMAIN; PSEUDOGENE; RETROGENE; RETROPOSON; RNA SPLICING; SEQUENCE ALIGNMENT; SYNTENY; ZIP ANCESTOR GENE; ANIMAL; BIOLOGY; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; PRION;

METAZOA; MURINAE; VERTEBRATA;

ANIMALS; CATION TRANSPORT PROTEINS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; EXONS; INTRONS; MUTAGENESIS, INSERTIONAL; PRIONS; PSEUDOGENES; RETROELEMENTS; RNA SPLICING;

EID: 80055049523     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026800     Document Type: Article

References (45)

1. Prusiner SB, (1998) Prions. Proc Natl Acad Sci U S A 117: 421-434.
2. Ehsani S, Huo H, Salehzadeh A, Pocanschi CL, Watts JC, et al. (2011) Family reunion-the ZIP/prion gene family. Progress in neurobiology 93: 405-420.
3. Rivera-Milla E, Stuermer CAO, Malaga-Trillo E, (2003) An evolutionary basis for scrapie disease: identification of a fish prion mRNA. Trends Genetics 19: 72-75.
4. Cotto E, Andre M, Forgue J, Fleury HJ, Babin PJ, (2005) Molecular characterization, phylogenetic relationships, and developmental expression patterns of prion genes in zebrafish (Danio rerio). FEBS J 272: 500-513.
5. Rivera-Milla E, Oidtmann B, Panagiotidis CH, Baier M, Sklaviadis T, et al. (2006) Disparate evolution of prion protein domains and the distinct origin of Doppel- and prion-related loci revealed by fish-to-mammal comparisons. Faseb J 20: 317-319.
6. Watts JC, Westaway D, (2007) The prion protein family: diversity, rivalry, and dysfunction. Biochim Biophys Acta 1772: 654-672.
7. Schmitt-Ulms G, Ehsani S, Watts JC, Westaway D, Wille H, (2009) Evolutionary descent of prion genes from the ZIP family of metal ion transporters. PLoS One 4: e7208.
8. Watts JC, Huo H, Bai Y, Ehsani S, Jeon AH, et al. (2009) Interactome analyses identify ties of PrP and its mammalian paralogs to oligomannosidic N-glycans and endoplasmic reticulum-derived chaperones. PLoS Pathog 5: e1000608.
9. Taylor KM, Morgan HE, Smart K, Zahari NM, Pumford S, et al. (2007) The emerging role of the LIV-1 subfamily of zinc transporters in breast cancer. Mol Med 13: 396-406.
10. Lu G, Moriyama EN, (2004) Vector NTI, a balanced all-in-one sequence analysis suite. Brief Bioinform 5: 378-388.
11. Ortutay C, Siermala M, Vihinen M, (2007) Molecular characterization of the immune system: emergence of proteins, processes, and domains. Immunogenetics 59: 333-348.
12. Tarailo-Graovac M, Chen N, (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics Chapter 4: Unit 4 10.
13. Long M, (2001) Evolution of novel genes. Curr Opin Genet Dev 11: 673-680.
14. Lee IY, Westaway D, Smit AF, Wang K, Seto J, et al. (1998) Complete genomic sequence and analysis of the prion protein gene region from three mammalian species. Genome Res 8: 1022-1037.
15. Basler K, Oesch B, Scott M, Westaway D, Walchli M, et al. (1986) Scrapie and cellular PrP isoforms are encoded by the same chromosomal gene. Cell 46: 417-428.
16. Simonic T, Duga S, Strumbo B, Asselta R, Ceciliani F, et al. (2000) cDNA cloning of turtle prion protein. FEBS Lett 469: 33-38.
17. Suzuki T, Kurokawa T, Hashimoto H, Sugiyama M, (2002) cDNA sequence and tissue expression of Fugu rubripes prion protein-like: a candidate for the teleost orthologue of tetrapod PrPs. Biochem Biophys Res Commun 294: 912-917.
18. Saeki K, Matsumoto Y, Hirota Y, Onodera T, (1996) Three-exon structure of the gene encoding the rat prion protein and its expression in tissues. Virus Genes 12: 15-20.
19. Premzl M, Gamulin V, (2007) Comparative genomic analysis of prion genes. BMC Genomics 8: 1.
20. Ortutay C, Vihinen M, (2008) PseudoGeneQuest- service for identification of different pseudogene types in the human genome. BMC bioinformatics 9: 299.
21. Seilacher A, Bose PK, Pfluger F, (1998) Triploblastic animals more than 1 billion years ago: trace fossil evidence from india. Science 282: 80-83.
22. Gal-Mark N, Schwartz S, Ram O, Eyras E, Ast G, (2009) The pivotal roles of TIA proteins in 5′ splice-site selection of alu exons and across evolution. PLoS Genet 5: e1000717.
23. Sorek R, (2009) When new exons are born. Heredity 103: 279-280.
24. Roy SW, (2006) Intron-rich ancestors. Trends Genet 22: 468-471.
25. Roy SW, Penny D, (2006) Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res 16: 1270-1275.
26. Coulombe-Huntington J, Majewski J, (2007) Characterization of intron loss events in mammals. Genome Res 17: 23-32.
27. Irimia M, Roy SW, (2008) Spliceosomal introns as tools for genomic and evolutionary analysis. Nucleic Acids Res 36: 1703-1712.
28. Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV, (2003) Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 13: 1512-1517.
29. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
30. Kaessmann H, Vinckenbosch N, Long M, (2009) RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet 10: 19-31.
31. Cereseto A, Giacca M, (2004) Integration site selection by retroviruses. AIDS Rev 6: 13-21.
32. Sandmeyer SB, Hansen LJ, Chalker DL, (1990) Integration specificity of retrotransposons and retroviruses. Annu Rev Genet 24: 491-518.
33. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H, (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 3: e357.
34. Vinckenbosch N, Dupanloup I, Kaessmann H, (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A 103: 3220-3225.
35. Terai G, Yoshizawa A, Okida H, Asai K, Mituyama T, (2010) Discovery of short pseudogenes derived from messenger RNAs. Nucleic Acids Res 38: 1163-1171.
36. Vanin EF, (1984) Processed pseudogenes. Characteristics and evolution. Biochimica et biophysica acta 782: 231-241.
37. Brosius J, Gould SJ, (1992) On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proceedings of the National Academy of Sciences of the United States of America 89: 10706-10710.
38. Fablet M, Bueno M, Potrzebowski L, Kaessmann H, (2009) Evolutionary origin and functions of retrogene introns. Mol Biol Evol 26: 2147-2156.
39. Brosius J, (2005) Echoes from the past-are we still in an RNP world? Cytogenet Genome Res 110: 8-24.
40. Premzl M, Gready JE, Jermin LS, Simonic T, Marshall Graves JA, (2004) Evolution of vertebrate genes related to prion and shadoo proteins- clues from comparative genomic analysis. Mol Biol Evol 21: 2210-2231.
41. Schueler-Furman O, Glick E, Segovia J, Linial M, (2006) Is GAS1 a co-receptor for the GDNF family of ligands? Trends Pharmacol Sci 27: 72-77.
42. Cabrera JR, Sanchez-Pulido L, Rojas AM, Valencia A, Manes S, et al. (2006) Gas1 is related to the glial cell-derived neurotrophic factor family receptors alpha and regulates Ret signaling. J Biol Chem 281: 14330-14339.
43. Airaksinen MS, Holm L, Hatinen T, (2006) Evolution of the GDNF family ligands and receptors. Brain Behav Evol 68: 181-190.
44. Hatinen T, Holm L, Airaksinen MS, (2007) Loss of neurturin in frog-comparative genomics study of GDNF family ligand-receptor pairs. Mol Cell Neurosci 34: 155-167.
45. Bell LM, Solomon KR, Gold JP, Tan K-N, (1994) Cytoplasmic tail deletion of T cell receptor (TCR) β-chain results in its surface expression as glycosylphosphatidylinositol-anchored polypeptide on mature T cells in the absence of TCR-α. J Biol Chem 269: 22758-22763.