Function-dependent clustering of orthologues and paralogues of cyclophilins

Proteins: Structure, Function and Genetics

Volumn 56, Issue 4, 2004, Pages 808-820

  Galat, Andrzej ^a,b  

^a DIF   (France)

^b CE Saclay ^*  (France)

Author keywords

Cyclophilin; PPIase; PPIase cluster; Sequence clustering method

Indexed keywords

CYCLOPHILIN; CYCLOPHILIN A; MESSENGER RNA; PEPTIDE LIBRARY; POLYPEPTIDE;

ALGORITHM; AMINO ACID COMPOSITION; ANALYTIC METHOD; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CLASSIFICATION; DROSOPHILA MELANOGASTER; EUKARYOTE; GENETIC CONSERVATION; GENOME; HYDROPHOBICITY; MATHEMATICAL COMPUTING; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORTHOLOGY; PARALOGY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ALIGNMENT; SEQUENCE CLUSTERING METHOD; STRUCTURE ANALYSIS; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; ANIMALS; ARABIDOPSIS PROTEINS; CAENORHABDITIS ELEGANS PROTEINS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CYCLOPHILINS; DATABASES, PROTEIN; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME; GENOME, FUNGAL; GENOME, HUMAN; GENOME, PLANT; HUMANS; MOLECULAR SEQUENCE DATA; SACCHAROMYCES CEREVISIAE PROTEINS; SCHIZOSACCHAROMYCES POMBE PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; MELANOGASTER; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 4043129511     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20156     Document Type: Article

References (61)

1. Fischer G, Bang H, Mech C. Detection of enzyme catalysis for cis-trans isomerization of peptide bonds using proline containing peptides as substrates. Biomed Biochim Acta 1984;43:1101-1111.
2. Gothel SF, Marahiel MA. Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci 1999;55:423-436.
3. Galat A. Peptidylprolyl cis/trans isomerases (immunophilins): biological diversity-targets-functions. Curr Top Med Chem 2003;3:1315-1347.
4. Gething M-J, Sambrook J. Protein folding in the cell. Nature 1992;355:33-45.
5. Gething M-J, editor. Guidebook to molecular chaperones and protein-folding catalysts. Oxford, UK: Oxford University Press; 1997.
6. Galat A, Rivière S. Peptidyl-prolyl cis/trans isomerases: protein profile. Oxford, UK: Oxford University Press; 1998.
7. Shieh BH, Stamnes MA, Seavello S, Harris GL, Zuker CS. The ninA gene required for visual transduction in Drosophila encodes a homologue of cyclosporin A-binding protein. Nature 1989;338:67-70.
8. Colley NJ, Baker EK, Stamnes MA, Zuker CS. The cyclophilin homolog ninaA is required in the secretary pathway. Cell 1991;67:255-263.
9. Ho S, Clipston N, Timmermann L, Northrop J, Graef I, Fiorentino D, Nourse J, Crabtree GR. The mechanism of action of cyclosporin A and FK506. Clin Immunol 1996;80:S40-S45.
10. Galat A. Variations of sequences and amino acid compositions of proteins that sustain their biological functions: an analysis of the cyclophilin family of proteins. Arch Biochem Biophys 1999;371:149-162.
11. Lee YK, Hong CB, Suh Y, Lee IK. A cDNA clone for cyclophilin from Griffitsia japonica and phylogenetic analysis of cyclophilins. Mol Cells 2002;13:12-20.
12. Viaud MC, Balhadére PV, Talbot NJ. Amagnapothe grisae cyclophlin acts as a virulence determinant during plant infection. Plant Cell 2002;14:917-930.
13. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, et al. The genome sequence of Schizosaccharomyces pombe. Nature 2002;415:871-880.
14. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. Life with 6000 genes. Science i996;274:546.
15. Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, et al. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 2000;408:820-822.
16. Wilson RK. How the worm was won: the C. elegans genome sequencing project. Trends Genet 1999;15:51-58.
17. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, et al. The genome sequence of Drosophila melanogaster. Science 2001;287:2185-2195.
18. Lander ES, Lintoin LM, Birren B, Nusbaum C, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
19. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. The sequence of the human genome. Science 2001;291:1304-1351.
20. Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. Database resources of National Center for Biotechnology. Nucleic Acids Res 2003;31:28-33.
21. Wu CH, Yeh LSL, Huang H, Arminski L, Castro-Alvear K, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker W. The Protein Information Resource (PIR). Nucleic Acids Res 2003,31:345-347.
22. The FlyBase Consortium: the FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 2003;31:171-175.
23. Harris TW, Lee R, Schwarz E, Bradman K, Lawson D, Chen W, Blaiser D, et al. WormBase: a cross-species database for comparative genomics. Nucleic Acids Res 2003;31:133-137.
24. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle M, et al. The Arabidopsis Information Resource (TAIR): a model organisms database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucl Acids Res 2003;31:224-228.
25. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
26. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
27. Harris JW, Stocker H. Handbook of mathematics and computational science. Springer-Verlag; 1998.
28. Galat A, Bouet F, Rivière S. Amino acid compositions of proteins and their identities. Electrophoresis 1995;16:1095-1103.
29. Galat A, Gerbod MC, Bouet F, Rivière S. Proteins and their amino acid compositions: uniqueness-variability-applications. Arch Biochem Biophys 1996;330:229-237.
30. Tsai J, Taylor R, Chothi C, Gerstein M. The packing density in proteins: standard radii and volumes. J Mol Biol 1999;290:253-266.
31. Ke H. Similarities and differences between human cyclophilin A and other β-barrel structures: structural refinement at 1.63 Å resolution. J Mol Biol 1992;228:539-550.
32. Zydowsky L, Etzkorn FA, Chang HY, Ferguson SB, Stolz LA, Ho SI, Walsh CT. Mutagenesis of human cyclophilin A defines the enzyme active site and separate peptidyl-prolyl isomerase activity from cyclosporin-A binding and calcineurin inhibition. Protein Sci 1992;1:1092-1099.
33. Dornan J, Page AP, Taylor P, Wu S, Winter AD, Husi H, Walkinshaw MD. Biochemical and structural characterization of a divergent loop cyclophilin from Caenorhabditis elegans. J Biol Chem 1999;274:34877-34883.
34. Dornan J, Taylor P, Walkinshaw MD. Structures of immunophilins and their ligand complexes. Curr Top Med Chem 2003;3:1392-402.
35. Santos AN, Korber S, Kullertz G, Fischer G, Fischer B. Oxygen stress increases prolyl cis/trans isomerase activity and expression of cyclophilin 18 in rabbit blastocysts. Biol Reprod 2000;62:1-7.
36. Doyle V, Virji S, Crompton M. Evidence that cyclophilin-A protects cells against oxidative stress. Biochem J 1999;341:127-132.
37. Haendler B, Hofer-Warbinek R, Hofer E. Complementary DNA for human T-cell cyclophilin. EMBO J 1987;6:947-950.
38. Ozaki K, Fujiwara T, Kawai A, Shimizu F, Takami S, Okuno S, Takeda S, Shimada Y, Nagata M, Watanabe T, Takaichi A, Takahashi E, Nakamura Y, Shin S. Cloning, expression and chromosomal mapping of a novel cyclophilin-related gene (PPIL1) from human fetal brain. Cytogenet Cell Genet 1996;72:242-245.
39. Zhou Z, Ying K, Dai J, Tang R, Wang W, Huang Y, Zhao W, Xie Y, Mao Y. Molecular cloning and characterization of a novel peptidyl-prolyl isomerase (cyclophilin)-like gene (PPIL3) from human fetal brain. Cytogenet Cell Genet 2001;92:231-236.
40. Liu J, Walsh CT. Peptidyl-prolyl cis-trans-isomerase from Escherichia coli: a periplasmic homolog of cyclophilin that is not inhibited by cyclosporin A. Proc Natl Acad Sci USA 1990;87:4028-4032.
41. Hayano T, Takahashi N, Kato S, Maki N, Suzuki M. Two distinct forms of peptidyl-prolyl cis-trans isomerase are expressed separately in periplasmic and cytoplasmic compartments of Escherichia coli cells. Biochemistry 1991;30:3041-3048.
42. Teigelkamp S, Achsel T, Mundt C, Gothel SF, Cronshagen U, Lane WS, Marahiel M, Luhrmann R. The 20kD protein of human [U4/U6.U5] tri-snRNPs is a novel cyclophilin that forms a complex with the U4/U6-specific 60kD and 90kD proteins. RNA 1998;4:127-141.
43. Schneider H, Charara N, Schmitz R, Wehrli S, Mikol V, Zurini MG, Quesniaux VF, Movva NR. Human cyclophilin C: primary structure, tissue distribution, and determination of binding specificity for cyclosporins. Biochemistry 1994;33:8218-8224.
44. Bergsma DJ, Eder C, Gross M, Kersten H, Sylvester D, Appelbaum E, Cusimano D, Livi GP, McLaughlin MM, Kasyan K, et al. The cyclophilin multigene family of peptidyl-prolyl isomerases: characterization of three separate human isoforms. J Biol Chem 1991;266:23204-23214.
45. Mi H, Kops O, Zimmermann E, Jaschke A, Tropschug M. A nuclear RNA-binding cyclophilin in human T cells. FEBS Lett 1996;378:201-205.
46. Bischoff RF, Krebber H, Smirnova E, Dong W, Ponstingl H. Co-activation of RanGTPase and inhibition of GTP dissociation by Ran-GTP binding protein RanBP1. EMBO J 1995;14:705-715.
47. Beddow AL, Richards SA, Orem NR, Macara IG. The Ran/TC4 GTPase-binding domain: identification by expression cloning and characterization of a conserved sequence motif. Proc Natl Acad Sci USA 1995;92:3328-3332.
48. Yokoyama N, Hayashi N, Seki T, Pante N, Ohba T, Nishii K, Kuma K, Hayashida T, Miyata T, Aebi U, Fukui M, Nishimoto T. A giant nucleopore protein that binds Ran/TC4. Nature 1995;376:184-188.
49. Wu J, Matunis MJ, Kraemer D, Blobel G, Coutavas E. Nup358, a cytoplasmically exposed nucleoporin with peptide repeats, ranGTP binding sites, zinc fingers, a cyclophilin A homologous domain and a leucine-rich region. J Biol Chem 1995;270:14209-14213.
50. Ferreira PJ, Hom JT, Pak WL. Retina-specifically expressed novel subtypes of bovine cyclophilin. J Biol Chem 1995;270:23179-23188.
51. Kieffer LJ, Seng TW, Li W, Osterman DG, Handschumacher RE, Bayney RM. Cyclophilin-40, a protein with homology to the p59 component of the steroid receptor complex. J Biol Chem 1993;268:12303-12310.
52. Yokoi H, Shimizu Y, Anazawa H, Lefebvre CA, Korneluk RG, Ikeda JE. The structure and complete nucleotide sequence of the human cyclophilin 40 (PPID) gene. Genomics 1996;35:448-455.
53. Sanchez ER. Hsp56: a novel heat shock protein associated with untransfomed steroid receptor complex. J Biol Chem 1990;265:22067-22070.
54. Wang BB, Hayenga KJ, Payan DG, Fisher JM. Identification of a nuclear-specific cyclophilin which interacts with the proteinase inhibitor eglin c. Biochem J 1996;314:313-319.
55. 1-related cyclophilin. Gene 1996;180:151-155.
56. Horowitz DS, Kobayashi R, Krainer AR. A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs. RNA 1997;3:1374-1387.
57. Bourquin JP, Stagljar I, Meier P, Moosmann P, Silke J, Baechi T, Georgiev O, Schaffner W. A serine/arginine-rich nuclear matrix cyclophilin interacts with the C-terminal domain of RNA polymerase II. Nucleic Acids Res 1997;25:2055-2061.
58. Anderson SK, Gallinger S, Roder J, Frey J, Young A, Ortaldo JR. A cyclophilin-related protein involved in the function of natural killer cells. Proc Natl Acad Sci USA 1993;90:542-546.
59. Page AP, Landry D, Wilson GG, Carlow CKS. Molecular characterization of a cyclosporin A-insensitive cyclophilin from the parasitic nematode Brugia malayi. Biochemistry 1995;34:11545-11550.
60. Otto SP, Yong P. The evolution of gene duplicates. Adv Genet 2002;46:451-483.
61. Dolinski K, Muir S, Cardenas M, Heitman J. All cyclophilins and FK506 binding proteins are, individually and collectively, dispensable for viability of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 1997;94:13093-13098.