The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Goto, Hiroki ^a   Watanabe, Kazunori ^a   Araragi, Naozumi ^a   Kageyama, Rui ^a   Tanaka, Kunika ^a   Kuroki, Yoko ^c   Toyoda, Atsushi ^d   Hattori, Masahira ^e   Sakaki, Yoshiyuki ^b   Fujiyama, Asao ^b,f   Fukumaki, Yasuyuki ^a   Shibata, Hiroki ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c RIKEN   (Japan)

^d NATIONAL INSTITUTE OF GENETICS   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

^f NATIONAL INSTITUTE OF INFORMATICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMATE RECEPTOR; GRIN3A PROTEIN; N METHYL DEXTRO ASPARTIC ACID RECEPTOR 2C; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ANIMAL CELL; ARTICLE; BRAIN FUNCTION; CHIMPANZEE; CONTROLLED STUDY; GENE FUNCTION; GENE SEQUENCE; GENETIC DISTANCE; GENETIC IDENTIFICATION; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POPULATION GENETICS; PROTEIN FUNCTION; PROTEIN MOTIF; RECEPTOR GENE; SEQUENCE ANALYSIS; SYNAPTIC TRANSMISSION; ANIMAL; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETIC SELECTION; GENETICS; HUMAN GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PAN TROGLODYTES; RNA SPLICING;

PAN;

AMINO ACID SUBSTITUTION; ANIMALS; COMPARATIVE GENOMIC HYBRIDIZATION; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; MULTIGENE FAMILY; OPEN READING FRAMES; PAN TROGLODYTES; RECEPTORS, GLUTAMATE; RNA SPLICE SITES; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA;

EID: 70349658578     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-224     Document Type: Article

References (37)

1. Glutamate receptor plasticity at excitatory synapses in the brain. D Genoux JM Montgomery, Clin Exp Pharmacol Physiol 2007 34 1058 1063 10.1111/j.1440-1681.2007.04722.x 17714094
2. NMDA and AMPA receptors: old channels, new tricks. VR Rao S Finkbeiner, Trends Neurosci 2007 30 284 291 10.1016/j.tins.2007.03.012 17418904
3. Glutamate receptor function in learning and memory. G Riedel B Platt J Micheau, Behav Brain Res 2003 140 1 47 10.1016/S0166-4328(02)00272-3 12644276
4. Association of a glutamate (NMDA) subunit receptor gene (GRIN2B) with obsessive-compulsive disorder: a preliminary study. PD Arnold DR Rosenberg E Mundo S Tharmalingam JL Kennedy MA Richter, Psychopharmacology (Berl) 2004 174 530 538 10.1007/s00213-004-1847-1 15083261
5. Variation in GRM3 affects cognition, prefrontal glutamate, and risk for schizophrenia. MF Egan RE Straub TE Goldberg I Yakub JH Callicott AR Hariri VS Mattay A Bertolino TM Hyde C Shannon-Weickert M Akil J Crook RK Vakkalanka R Balkissoon RA Gibbs JE Kleinman DR Weinberger, Proc Natl Acad Sci U S A 2004 101 34 12604 12609 10.1073/pnas.0405077101 15310849
6. Positive associations of polymorphisms in the metabotropic glutamate receptor type 3 gene (GRM3) with schizophrenia. Y Fujii H Shibata R Kikuta C Makino A Tani N Hirata A Shibata H Ninomiya N Tashiro Y Fukumaki, Psychiatr Genet 2003 13 71 76 10.1097/00041444-200306000-00003 12782962
7. Extended analyses support the association of a functional (GT)n polymorphism in the GRIN2A promoter with Japanese schizophrenia. Y Iwayama-Shigeno K Yamada M Itokawa T Toyota JM Meerabux Y Minabe N Mori T Inada T Yoshikawa, Neurosci Lett 2005 378 102 105 10.1016/j.neulet.2004.12.013 15774266
8. Positive association of the AMPA receptor subunit GluR4 gene (GRIA4) haplotype with schizophrenia: linkage disequilibrium mapping using SNPs evenly distributed across the gene region. C Makino Y Fujii R Kikuta N Hirata A Tani A Shibata H Ninomiya N Tashiro H Shibata Y Fukumaki, Am J Med Genet B Neuropsychiatr Genet 2003 116B 17 22 10.1002/ajmg.b.10041 12497607
9. Identification of single-nucleotide polymorphisms in the human N-methyl-D-aspartate receptor subunit NR2D gene, GRIN2D, and association study with schizophrenia. C Makino H Shibata H Ninomiya N Tashiro Y Fukumaki, Psychiatr Genet 2005 15 215 221 10.1097/00041444-200509000-00014 16094258
10. Allelic association of juvenile absence epilepsy with a GluR5 kainate receptor gene (GRIK1) polymorphism. T Sander T Hildmann R Kretz R Fürst U Sailer G Bauer B Schmitz G Beck-Mannagetta TF Wienker D Janz, Am J Med Genet 1997 74 416 421 9259378 10.1002/(SICI)1096-8628(19970725)74:4<416::AID- AJMG13>3.0.CO;2-L
11. Positive associations of polymorphisms in the metabotropic glutamate receptor type 8 gene (GRM8) with schizophrenia. H Takaki R Kikuta H Shibata H Ninomiya N Tashiro Y Fukumaki, Am J Med Genet B Neuropsychiatr Genet 2004 128B 6 14 15211621 10.1002/ajmg.b.20108
12. Association study of polymorphisms in the group III metabotropic glutamate receptor genes, GRM4 and GRM7, with schizophrenia. H Shibata A Tani T Chikuhara R Kikuta M Sakai H Ninomiya N Tashiro N Iwata N Ozaki Y Fukumaki, Psychiatry Res 2009 167 88 96 10.1016/j.psychres.2007.12.002 19351574
13. The UCSC Genome Browser Database: update 2006. AS Hinrichs D Karolchik R Baertsch GP Barber G Bejerano H Clawson M Diekhans TS Furey RA Harte F Hsu, et al. Nucleic Acids Res 2006 34 590 598 10.1093/nar/gkj144 16381938
14. Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome. R Sakate Y Suto T Imanishi T Tanoue M Hida I Hayasaka J Kusuda T Gojobori K Hashimoto M Hirai, Gene 2007 399 1 10 10.1016/j.gene.2007.04.013 17574350
15. More genes underwent positive selection in chimpanzee evolution than in human evolution. MA Bakewell P Shi J Zhang, Proc Natl Acad Sci USA 2007 104 7489 7494 10.1073/pnas.0701705104 17449636
16. PAML: a program package for phylogenetic analysis by maximum likelihood. Z Yang, Comput Appl Biosci 1997 13 555 556 9367129
17. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Z Yang, Mol Biol Evol 1998 15 568 573 9580986
18. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. J Zhang R Nielsen Z Yang, Mol Biol Evol 2005 22 2472 2479 10.1093/molbev/msi237 16107592
19. Amino acid difference formula to help explain protein evolution. R Grantham, Science 1974 185 862 864 10.1126/science.185.4154.862 4843792
20. Improving the accuracy of transmembrane protein topology prediction using evolutionary information. DT Jones, Bioinformatics 2007 23 538 544 10.1093/bioinformatics/btl677 17237066
21. MyHits: improvements to an interactive resource for analyzing protein sequences. M Pagni V Ioannidis L Cerutti M Zahn-Zabal CV Jongeneel J Hau O Martin D Kuznetsov L Falquet, Nucleic Acids Res 2007 35 433 437 10.1093/nar/gkm352 17545200
22. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. AG Clark S Glanowski R Nielsen PD Thomas A Kejariwal MA Todd DM Tanenbaum D Civello F Lu B Murphy, et al. Science 2003 302 1960 1963 10.1126/science. 1088821 14671302
23. Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate. L Duret D Mouchiroud, Mol Biol Evol 2000 17 68 74 10666707
24. Accelerated evolution of nervous system genes in the origin of Homo sapiens. S Dorus EJ Vallender PD Evans JR Anderson SL Gilbert M Mahowald GJ Wyckoff CM Malcom BT Lahn, Cell 2004 119 1027 1040 10.1016/j.cell.2004.11.040 15620360
25. Motoneuron-specific NR3B gene: no association with ALS and evidence for a common null allele. S Niemann JE Landers MJ Churchill B Hosler P Sapp WC Speed BT Lahn KK Kidd RH Brown Jr Y Hayashi, Neurology 2008 70 666 676 10.1212/01.wnl.0000271078.51280.17 17687115
26. Genetic ablation of NMDA receptor subunit NR3B in mouse reveals motoneuronal and nonmotoneuronal phenotypes. S Niemann H Kanki Y Fukui K Takao M Fukaya MN Hynynen MJ Churchill JM Shefner RT Bronson RH Brown Jr M Watanabe T Miyakawa S Itohara Y Hayashi, Eur J Neurosci 2007 26 1407 1420 10.1111/j.1460-9568.2007.05774.x 17880385
27. How NR3 Tweaks NMDA Receptor Function. NA Cavara M Hollmann, Mol Neurobiol 2008 38 16 26 10.1007/s12035-008-8029-9 18654865
28. NMDA induces long-term synaptic depression and dephosphorylation of the GluR1 subunit of AMPA receptors in hippocampus. HK Lee K Kameyama RL Huganir MF Bear, Neuron 1998 21 1151 1162 10.1016/S0896-6273(00)80632-7 9856470
29. Coriell Institute for Medical Research. http://www.coriell.org
30. Primer3 on the WWW for general users and for biologist programmers. S Rozen H Skaletsky, Methods Mol Biol 2000 132 365 386 10547847
31. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738
32. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. K Tamura M Nei, Mol Biol Evol 1993 10 512 526 8336541
33. Evolution of protein molecules. TH Jukes CR Cantor, Mammalian Protein Metabolism New York: Academic Press, Munro HN, 1969 21 123
34. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. M Nei T Gojobori, Mol Biol Evol 1986 3 418 426 3444411
35. A codon-based model of nucleotide substitution for protein-coding DNA sequences. N Goldman Z Yang, Mol Biol Evol 1994 11 725 736 7968486
36. Protein structure prediction servers at University College London. K Bryson LJ McGuffin RL Marsden JJ Ward JS Sodhi DT Jones, Nucleic Acids Res 2005 33 36 38 10.1093/nar/gki410 15980489
37. The PROSITE database. N Hulo A Bairoch V Bulliard L Cerutti E De Castro PS Langendijk-Genevaux M Pagni CJ Sigrist, Nucleic Acids Res 2006 34 227 230 10.1093/nar/gkj063 16381852