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PMID: 11741263 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Evolutionary relationships among G protein-coupled receptors using a clustered database approach.

AAPS pharmSci ·Vol. 3 ·No. 2 ·2001-00-00 ·Pages E12

Graul RC, Sadée W

Abstract

Guanine nucleotide-binding protein-coupled receptors (GPCRs) comprise large and diverse gene families in fungi, plants, and the animal kingdom. GPCRs appear to share a common structure with 7 transmembrane segments, but sequence similarity is minimal among the most distant GPCRs. To reevaluate the question of evolutionary relationships among the disparate GPCR families, this study takes advantage of the dramatically increased number of cloned GPCRs. Sequences were selected from the National Center for Biotechnology Information (NCBI) nonredundant peptide database using iterative BLAST (Basic Local Alignment Search Tool) searches to yield a database of approximately 1700 GPCRs and unrelated membrane proteins as controls, divided into 34 distinct clusters. For each cluster, separate position-specific matrices were established to optimize sequence comparisons among GPCRs. This approach resulted in significant alignments between distant GPCR families, including receptors for the biogenic amine/peptide, VIP/secretin, cAMP, STE3/MAP3 fungal pheromones, latrophilin, developmental receptors frizzled and smoothened, as well as the more distant metabotrobic glutamate receptors, the STE2/MAM2 fungal pheromone receptors, and GPR1, a fungal glucose receptor. On the other hand, alignment scores between these recognized GPCR clades with p40 (putative GPCR) and pm1 (putative GPCR), as well as bacteriorhodopsins, failed to support a finding of homology. This study provides a refined view of GPCR ancestry and serves as a reference database with hyperlinks to other sources. Moreover, it may facilitate database annotation and the assignment of orphan receptors to GPCR families.

MeSH Terms
Amino Acid Sequence Animals Cluster Analysis Databases, Protein Evolution, Molecular Fungi/genetics GTP-Binding Proteins/metabolism Humans Internet Membrane Proteins/genetics Receptors, Cell Surface/classification,genetics,metabolism Sequence Alignment
Chemicals
Membrane Proteins Receptors, Cell Surface GTP-Binding Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Graul R C
Incyte Genomics, Palo Alto, CA 94304, USA.
Sadée W
References (60)
60 references, click to expand
  1. A human homologue of the yeast HDEL receptor.
    Nature. 1990 Nov 8;348(6297):162-3 PMID: 2172835
  2. Cloning and functional expression of a human neuroendocrine vasoactive intestinal peptide receptor.
    Biochem Biophys Res Commun. 1993 Jun 15;193(2):546-53 PMID: 8390245
  3. A novel multigene family may encode odorant receptors: a molecular basis for odor recognition.
    Cell. 1991 Apr 5;65(1):175-87 PMID: 1840504
  4. The Schizosaccharomyces pombe mam2 gene encodes a putative pheromone receptor which has a significant homology with the Saccharomyces cerevisiae Ste2 protein.
    EMBO J. 1991 Dec;10(12):3743-51 PMID: 1657593
  5. Schizosaccharomyces pombe map3+ encodes the putative M-factor receptor.
    Mol Cell Biol. 1993 Jan;13(1):80-8 PMID: 8380233
  6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  7. Olfactory receptors, vomeronasal receptors, and the organization of olfactory information.
    Cell. 1997 Aug 22;90(4):585-7 PMID: 9288738
  8. Interaction of Wnt and a Frizzled homologue triggers G-protein-linked phosphatidylinositol signalling.
    Nature. 1997 Nov 27;390(6658):410-3 PMID: 9389482
  9. G-protein coupled receptor from yeast Saccharomyces cerevisiae.
    Biochem Biophys Res Commun. 1997 Nov 17;240(2):287-92 PMID: 9388468
  10. GPCRDB: an information system for G protein-coupled receptors.
    Nucleic Acids Res. 1998 Jan 1;26(1):275-9 PMID: 9399852
  11. Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsins with the yeast sequence YRO2.
    Pharm Res. 1997 Nov;14(11):1533-41 PMID: 9434271
  12. Isolation, molecular characterization, and tissue-specific expression of a novel putative G protein-coupled receptor.
    Biochim Biophys Acta. 1998 Feb 11;1395(3):301-8 PMID: 9512664
  13. Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss.
    Genome Res. 1998 May;8(5):449-63 PMID: 9582190
  14. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.
    Proc Natl Acad Sci U S A. 1998 May 26;95(11):6073-8 PMID: 9600919
  15. Principles governing amino acid composition of integral membrane proteins: application to topology prediction.
    J Mol Biol. 1998 Oct 23;283(2):489-506 PMID: 9769220
  16. Frizzled proteins constitute a novel family of G protein-coupled receptors, most closely related to the secretin family.
    Trends Pharmacol Sci. 1998 Oct;19(10):399-400 PMID: 9803828
  17. alpha-Latrotoxin receptor CIRL/latrophilin 1 (CL1) defines an unusual family of ubiquitous G-protein-linked receptors. G-protein coupling not required for triggering exocytosis.
    J Biol Chem. 1998 Dec 4;273(49):32715-24 PMID: 9830014
  18. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.
    J Mol Biol. 1998 Dec 11;284(4):1201-10 PMID: 9837738
  19. Molecular cloning and characterization of a novel retinoic acid-inducible gene that encodes a putative G protein-coupled receptor.
    J Biol Chem. 1998 Dec 25;273(52):35008-15 PMID: 9857033
  20. Isolation and characterization of a human homologue of the latrophilin gene from a region of 1p31.1 implicated in breast cancer.
    Oncogene. 1998 Dec 31;17(26):3513-9 PMID: 10030676
  21. Molecular tinkering of G protein-coupled receptors: an evolutionary success.
    EMBO J. 1999 Apr 1;18(7):1723-9 PMID: 10202136
  22. A Saccharomyces cerevisiae G-protein coupled receptor, Gpr1, is specifically required for glucose activation of the cAMP pathway during the transition to growth on glucose.
    Mol Microbiol. 1999 Jun;32(5):1002-12 PMID: 10361302
  23. The nop-1 gene of Neurospora crassa encodes a seven transmembrane helix retinal-binding protein homologous to archaeal rhodopsins.
    Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):8034-9 PMID: 10393943
  24. Calmodulin binding to G protein-coupling domain of opioid receptors.
    J Biol Chem. 1999 Jul 30;274(31):22081-8 PMID: 10419536
  25. Phylogenetic analysis using PHYLIP.
    Methods Mol Biol. 2000;132:243-58 PMID: 10547839
  26. Evidence for kinship between diverse G-protein coupled receptors.
    Gene. 1999 Nov 1;239(2):333-40 PMID: 10548735
  27. The Pfam protein families database.
    Nucleic Acids Res. 2000 Jan 1;28(1):263-6 PMID: 10592242
  28. Distribution of the GABA(B) receptor subunit gb2 in rat CNS.
    Brain Res. 2000 Mar 31;860(1-2):41-52 PMID: 10727622
  29. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
    Bioinformatics. 1999 Dec;15(12):1000-11 PMID: 10745990
  30. Characterization of p40/GPR69A as a peripheral membrane protein related to the lantibiotic synthetase component C.
    Biochem Biophys Res Commun. 2000 Aug 18;275(1):69-74 PMID: 10944443
  31. The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors.
    AAPS PharmSci. 1999;1(2):E2 PMID: 11741199
  32. Studies on the light-transducing pigment bacteriorhodopsin.
    Cold Spring Harb Symp Quant Biol. 1983;48 Pt 2:853-62 PMID: 6327180
  33. The yeast alpha-factor receptor: structural properties deduced from the sequence of the STE2 gene.
    Nucleic Acids Res. 1985 Dec 9;13(23):8463-75 PMID: 3001640
  34. Evidence the yeast STE3 gene encodes a receptor for the peptide pheromone a factor: gene sequence and implications for the structure of the presumed receptor.
    Proc Natl Acad Sci U S A. 1986 Mar;83(5):1418-22 PMID: 3006051
  35. An intronless gene encoding a potential member of the family of receptors coupled to guanine nucleotide regulatory proteins.
    Nature. 1987 Sep 3-9;329(6134):75-9 PMID: 3041227
  36. A chemoattractant receptor controls development in Dictyostelium discoideum.
    Science. 1988 Sep 16;241(4872):1467-72 PMID: 3047871
  37. A Drosophila tissue polarity locus encodes a protein containing seven potential transmembrane domains.
    Nature. 1989 Mar 16;338(6212):263-4 PMID: 2493583
  38. Hydrophobic organization of membrane proteins.
    Science. 1989 Aug 4;245(4917):510-3 PMID: 2667138
  39. The Drosophila patched gene encodes a putative membrane protein required for segmental patterning.
    Cell. 1989 Nov 17;59(4):751-65 PMID: 2582494
  40. Nucleotide sequence of a cDNA encoding a protein with primary structural similarity to G-protein coupled receptors.
    Nucleic Acids Res. 1990 Apr 11;18(7):1896 PMID: 2110658
  41. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  42. Biosynthesis of the lantibiotic nisin: genomic organization and membrane localization of the NisB protein.
    Appl Environ Microbiol. 1992 Nov;58(11):3730-43 PMID: 1482192
  43. Prediction of transmembrane segments in proteins utilising multiple sequence alignments.
    J Mol Biol. 1994 Mar 25;237(2):182-92 PMID: 8126732
  44. Cloning of a novel human prostaglandin receptor with characteristics of the pharmacologically defined EP2 subtype.
    Mol Pharmacol. 1994 Aug;46(2):213-20 PMID: 8078484
  45. GCRDb: a G-protein-coupled receptor database.
    Receptors Channels. 1994;2(1):1-7 PMID: 8081729
  46. Complete DNA sequence of yeast chromosome II.
    EMBO J. 1994 Dec 15;13(24):5795-809 PMID: 7813418
  47. Human intestinal H+/peptide cotransporter. Cloning, functional expression, and chromosomal localization.
    J Biol Chem. 1995 Mar 24;270(12):6456-63 PMID: 7896779
  48. Evolutionary conservation of both the hydrophilic and hydrophobic nature of transmembrane residues.
    J Theor Biol. 1995 Feb 7;172(3):245-58 PMID: 7715195
  49. Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease.
    Nature. 1995 Jun 29;375(6534):754-60 PMID: 7596406
  50. Sequence and analysis of 24 kb on chromosome II of Saccharomyces cerevisiae.
    Yeast. 1995 Apr 30;11(5):475-9 PMID: 7597852
  51. Cloning of the gene for ocular albinism type 1 from the distal short arm of the X chromosome.
    Nat Genet. 1995 May;10(1):13-9 PMID: 7647783
  52. A novel family of genes encoding putative pheromone receptors in mammals.
    Cell. 1995 Oct 20;83(2):195-206 PMID: 7585937
  53. Divergent seven transmembrane receptors are candidate chemosensory receptors in C. elegans.
    Cell. 1995 Oct 20;83(2):207-18 PMID: 7585938
  54. Cloning and expression of a human metabotropic glutamate receptor 1 alpha: enhanced coupling on co-transfection with a glutamate transporter.
    Mol Pharmacol. 1995 Oct;48(4):648-57 PMID: 7476890
  55. odr-10 encodes a seven transmembrane domain olfactory receptor required for responses to the odorant diacetyl.
    Cell. 1996 Mar 22;84(6):899-909 PMID: 8601313
  56. The Drosophila smoothened gene encodes a seven-pass membrane protein, a putative receptor for the hedgehog signal.
    Cell. 1996 Jul 26;86(2):221-32 PMID: 8706127
  57. Applications of network BLAST server.
    Methods Enzymol. 1996;266:131-41 PMID: 8743682
  58. Molecular cloning and functional expression of a serotonin receptor from Caenorhabditis elegans.
    J Mol Neurosci. 1997 Feb;8(1):53-62 PMID: 9061615
  59. Prediction of membrane protein topology utilizing multiple sequence alignments.
    J Protein Chem. 1997 Jul;16(5):453-7 PMID: 9246628
  60. Induction of cell fate in the Drosophila retina: the bride of sevenless protein is predicted to contain a large extracellular domain and seven transmembrane segments.
    Genes Dev. 1990 Nov;4(11):1835-47 PMID: 2276620
Article Info
Journal
AAPS pharmSci
Abbr.
AAPS PharmSci
ISSN
1522-1059
DOI
10.1208/ps030212
Published
2001-00-00
Pages
E12
Language
English
Region
United States
NLM ID
100897065
PMCID
PMC2779559
Subset
IM
Grants
NIGMS NIH HHS · GM43102 · United States
External Links
PubMed source DOI: 10.1208/ps030212 PMC Full Text
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