In silico analysis of the cyclophilin repertoire of apicomplexan parasites

Parasites and Vectors

Volumn 2, Issue 1, 2009, Pages

  Krücken, Jürgen ^a   Greif, Gisela ^b   Von Samson Himmelstjerna, Georg ^a  

^a UNIVERSITY OF VETERINARY MEDICINE HANNOVER   (Germany)

^b BAYER AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CYCLOPHILIN; MITOCHONDRIAL PROTEIN; RNA; SIGNAL PEPTIDE;

AMINO ACID SEQUENCE; APICOMPLEXA; ARTICLE; BABESIA BOVIS; CRYPTOSPORIDIUM HOMINIS; DRUG TARGETING; GENOME; HOST CELL; LYMPHOCYTE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PARASITE; PHYLOGENY; PLASMODIUM FALCIPARUM; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN MOTIF; RNA INTERFERENCE; RNA PROCESSING; SIGNAL TRANSDUCTION; THEILERIA ANNULATA; THEILERIA PARVA; TOXOPLASMA GONDII;

APICOMPLEXA; BABESIA BOVIS; CRYPTOSPORIDIUM HOMINIS; EUKARYOTA; FUNGI; PLASMODIUM (APICOMPLEXA); PLASMODIUM FALCIPARUM; THEILERIA ANNULATA; THEILERIA PARVA; TOXOPLASMA GONDII;

EID: 68149126705     PISSN: None     EISSN: 17563305     Source Type: Journal    
DOI: 10.1186/1756-3305-2-27     Document Type: Article

References (71)

1. The cyclophilins. P Wang J Heitman, Genome biology 2005 6 7 226 15998457
2. Archaeal peptidyl prolyl cis-trans isomerases (PPIases). T Maruyama M Furutani, Front Biosci 2000 5 D821 836 10966874
3. Regulation of peptide bond cis/trans isomerization by enzyme catalysis and its implication in physiological processes. G Fischer T Aumüller, Reviews of physiology, biochemistry and pharmacology 2003 148 105 150 12698322
4. Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. SF Gothel MA Marahiel, Cell Mol Life Sci 1999 55 3 423 436 10228556
5. Immunophilins: for the love of proteins. S Barik, Cell Mol Life Sci 2006 63 24 2889 2900 17075696
6. The cyclophilin repertoire of the fission yeast Schizosaccharomyces pombe. TJ Pemberton JE Kay, Yeast (Chichester, England) 2005 22 12 927 945 16134115
7. Prolyl isomerases in yeast. M Arevalo-Rodriguez X Wu SD Hanes J Heitman, Front Biosci 2004 9 2420 2446 15353296
8. Identification and Comparative Analysis of the Peptidyl-Prolyl cis/trans Isomerase Repertoires of H. sapiens, D. melanogaster, C. elegans, S. cerevisiae and Sz. pombe. TJ Pemberton JE Kay, Comp Funct Genomics 2005 6 56 277 300 18629211
9. Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires. TJ Pemberton, BMC genomics 2006 7 244 16995943
10. All cyclophilins and FK506 binding proteins are, individually and collectively, dispensable for viability in Saccharomyces cerevisiae. K Dolinski S Muir M Cardenas J Heitman, Proceedings of the National Academy of Sciences of the United States of America 1997 94 24 13093 13098 9371805
11. Peptidyl-prolyl cis-trans isomerases (immunophilins) and their roles in parasite biochemistry, host-parasite interaction and antiparasitic drug action. A Bell P Monaghan AP Page, International journal for parasitology 2006 36 3 261 276 16443228
12. Antischistosomal effects of cyclosporin A. E Bueding J Hawkins YN Cha, Agents Actions 1981 11 4 380 383 7282489
13. Antimalarial activity of cyclosporin A. K Thommen-Scott, Agents and actions 1981 11 67 770 773
14. Cyclosporin A: antiparasite drug, modulator of the host-parasite relationship and immunosuppressant. LH Chappell JM Wastling, Parasitology 1992 105 Suppl S25 40 1308927
15. Characterization of anti-Toxoplasma activity of SDZ 215918, a cyclosporin derivative lacking immunosuppressive and peptidyl-prolyl-isomerase-inhibiting activity: possible role of a P glycoprotein in Toxoplasma physiology. JA Silverman ML Hayes BJ Luft KA Joiner, Antimicrob Agents Chemother. 1997 41 9 1859 1866 9303374
16. Inhibition by cyclosporin A of rodent malaria in vivo and human malaria in vitro. SP Nickell LW Scheibel GA Cole, Infect Immun. 1982 37 3 1093 1100 6752020
17. New micromethod to study the effect of antimicrobial agents on Toxoplasma gondii: comparison of sulfadoxine and sulfadiazine individually and in combination with pyrimethamine and study of clindamycin, metronidazole, and cyclosporin A. DG Mack R McLeod, Antimicrob Agents Chemother 1984 26 1 26 30 6383209
18. Effects of immunosuppression on avian coccidiosis: cyclosporin A but not hormonal bursectomy abrogates host protective immunity. HS Lillehoj, Infection and immunity 1987 55 7 1616 1621
19. Eimeria vermiformis and E. mitis: inhibition of development in vivo by cyclosporin A. ME Rose P Hesketh, Experimental parasitology 1989 68 3 289 296 2703028
20. Cyclosporin analogs inhibit in vitro growth of Cryptosporidium parvum. ME Perkins TW Wu SM Le Blancq, Antimicrob Agents Chemother. 1998 42 4 843 848 9559794
21. Effect of cyclosporin A on the proliferation of bovine lymphocytes to concanavalin A and on the growth of Theileria annulata-infected bovine cells. JS Ahmed M Rintelen H Hartwig E Schein, Trop Med Parasitol 1991 42 4 375 380 1796237
22. Roles of peptidyl-prolyl cis-trans isomerase and calcineurin in the mechanisms of antimalarial action of cyclosporin A, FK506, and rapamycin. A Bell B Wernli RM Franklin, Biochemical pharmacology 1994 48 3 495 503 7520696
23. Molecular and biochemical characterization of a Plasmodium falciparum cyclophilin containing a cleavable signal sequence. J Hirtzlin PM Farber RM Franklin A Bell, European journal of biochemistry/FEBS 1995 232 3 765 772 7588714
24. Cyclosporin-binding proteins of Plasmodium falciparum. CS Gavigan SP Kiely J Hirtzlin A Bell, International journal for parasitology 2003 33 9 987 996 12906882
25. Plasmodium falciparum calcineurin and its association with heat shock protein 90: mechanisms for the antimalarial activity of cyclosporin A and synergism with geldanamycin. R Kumar A Musiyenko S Barik, Mol Biochem Parasitol. 2005 141 1 29 37 15811524
26. Characterization of protein Ser/Thr phosphatases of the malaria parasite, Plasmodium falciparum: inhibition of the parasitic calcineurin by cyclophilin-cyclosporin complex. S Dobson T May M Berriman C Del Vecchio AH Fairlamb D Chakrabarti S Barik, Mol Biochem Parasitol 1999 99 2 167 181 10340482
27. Influence of the Plasmodium falciparum P-glycoprotein homologue 1 (pfmdr1 gene product) on the antimalarial action of cyclosporin. CS Gavigan M Shen SG Machado A Bell, The Journal of antimicrobial chemotherapy 2007 59 2 197 203 17105736
28. A novel class of dual-family immunophilins. B Adams A Musiyenko R Kumar S Barik, The Journal of biological chemistry 2005 280 26 24308 24314 15845546
29. Eimeria tenella: genomic organization and expression of an 89 kDa cyclophilin. RJ Hosse J Krücken S Bierbaum G Greif F Wunderlich, Experimental parasitology 2008 118 2 275 279 17892870
30. Analysis of the Trypanosoma cruzi cyclophilin gene family and identification of Cyclosporin A binding proteins. M Potenza A Galat TA Minning AM Ruiz R Duran RL Tarleton M Marin LE Fichera J Bua, Parasitology 2006 132 Pt 6 867 882 16700961
31. CDD: specific functional annotation with the Conserved Domain Database. A Marchler-Bauer JB Anderson F Chitsaz MK Derbyshire C DeWeese-Scott JH Fong LY Geer RC Geer NR Gonzales M Gwadz, Nucleic acids research 2009 37 Database D205 210 18984618
32. CD-Search: protein domain annotations on the fly. A Marchler-Bauer SH Bryant, Nucleic acids research 2004 32 Web Server W327 331 15215404
33. Clustal W and Clustal X version 2.0. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace A Wilm R Lopez, Bioinformatics (Oxford, England) 2007 23 21 2947 2948 17846036
34. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Systematic biology 2003 52 5 696 704 14530136
35. Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. S Ben-Yehuda I Dix CS Russell M McGarvey JD Beggs M Kupiec, Genetics 2000 156 4 1503 1517 11102353 (Pubitemid 32001221)
36. Loss of cyclophilin D reveals a critical role for mitochondrial permeability transition in cell death. CP Baines RA Kaiser NH Purcell NS Blair H Osinska MA Hambleton EW Brunskill MR Sayen RA Gottlieb GW Dorn, Nature 2005 434 7033 658 662 15800627
37. Cyclophilin D is a component of mitochondrial permeability transition and mediates neuronal cell death after focal cerebral ischemia. AC Schinzel O Takeuchi Z Huang JK Fisher Z Zhou J Rubens C Hetz NN Danial MA Moskowitz SJ Korsmeyer, Proceedings of the National Academy of Sciences of the United States of America 2005 102 34 12005 12010 16103352
38. Spliceosomal immunophilins. A Mesa JA Somarelli RJ Herrera, FEBS letters 2008 582 16 2345 2351 18544344
39. Identification of several cyclosporine binding proteins in lymphoid and non-lymphoid cells in vivo. BM Foxwell G Woerly H Husi A Mackie VF Quesniaux PC Hiestand RM Wenger B Ryffel, Biochimica et biophysica acta 1992 1138 2 115 121 1540657
40. Deciphering apicoplast targeting signals feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins. J Zuegge S Ralph M Schmuker GI McFadden G Schneider, Gene 2001 280 12 19 26 11738814
41. Protein targeting to the malaria parasite plastid. CJ Tonkin M Kalanon GI McFadden, Traffic (Copenhagen, Denmark) 2008 9 2 166 175 17900270
42. A membrane-anchored Theileria parva cyclophilin with a non-cleaved amino-terminal signal peptide for entry into the endoplasmic reticulum. T Ebel R Pelle R Janoo J Lipp R Bishop, Veterinary parasitology 2004 121 12 65 77 15110404
43. Identification and characterization of Neospora caninum cyclophilin that elicits gamma interferon production. W Tuo R Fetterer M Jenkins JP Dubey, Infect Immun. 2005 73 8 5093 5100 16041025
44. Computational method to predict mitochondrially imported proteins and their targeting sequences. MG Claros P Vincens, European journal of biochemistry/FEBS 1996 241 3 779 786 8944766
45. Properties and prediction of mitochondrial transit peptides from Plasmodium falciparum. A Bender GG van Dooren SA Ralph GI McFadden G Schneider, Mol Biochem Parasitol. 2003 132 2 59 66 14599665
46. The RNP motif protein family. SR Haynes, The New biologist 1992 4 5 421 429 1381215
47. CDART: protein homology by domain architecture. LY Geer M Domrachev DJ Lipman SH Bryant, Genome research 2002 12 10 1619 1623 12368255
48. Integrating genomic homology into gene structure prediction. I Korf P Flicek D Duan MR Brent, Bioinformatics (Oxford, England) 2001 17 Suppl 1 S140 148 11473003
49. A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs. DS Horowitz R Kobayashi AR Krainer, RNA. 1997 3 12 1374 1387 9404889
50. The 20 kD protein of human [U4/U6.U5] tri-snRNPs is a novel cyclophilin that forms a complex with the U4/U6-specific 60 kD and 90 kD proteins. S Teigelkamp T Achsel C Mundt SF Gothel U Cronshagen WS Lane M Marahiel R Luhrmann, RNA (New York, NY) 1998 4 2 127 141
51. Kingdom protozoa and its 18 phyla. T Cavalier-Smith, Microbiological reviews 1993 57 4 953 994 8302218
52. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. K Nakai P Horton, Trends in biochemical sciences 1999 24 1 34 36 10087920
53. Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions. J Deckert K Hartmuth D Boehringer N Behzadnia CL Will B Kastner H Stark H Urlaub R Luhrmann, Mol Cell Biol. 2006 26 14 5528 5543 16809785
54. The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1). TL Davis JR Walker H Ouyang F MacKenzie C Butler-Cole EM Newman EZ Eisenmesser S Dhe-Paganon, The FEBS journal 2008 275 9 2283 2295 18397323
55. Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP. C Xu J Zhang X Huang J Sun Y Xu Y Tang J Wu Y Shi Q Huang Q Zhang, The Journal of biological chemistry 2006 281 23 15900 15908 16595688
56. E3 ubiquitin ligases. HC Ardley PA Robinson, Essays in biochemistry 2005 41 15 30 16250895
57. A novel cyclophilin from parasitic and free-living nematodes with a unique substrate- and drug-binding domain. D Ma LS Nelson K LeCoz C Poole CK Carlow, The Journal of biological chemistry 2002 277 17 14925 14932 11847225
58. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. JF Rual J Ceron J Koreth T Hao AS Nicot T Hirozane-Kishikawa J Vandenhaute SH Orkin DE Hill S van den Heuvel, Genome research 2004 14 10B 2162 2168 15489339
59. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. B Sonnichsen LB Koski A Walsh P Marschall B Neumann M Brehm AM Alleaume J Artelt P Bettencourt E Cassin, Nature 2005 434 7032 462 469 15791247
60. AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II. M Gullerova A Barta ZJ Lorkovic, RNA. 2006 12 4 631 643 16497658
61. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. HG Morrison AG McArthur FD Gillin SB Aley RD Adam GJ Olsen AA Best WZ Cande F Chen MJ Cipriano, Science. 2007 317 5846 1921 1926 17901334
62. The evolution and diversity of kinetoplastid flagellates. AG Simpson JR Stevens J Lukes, Trends in parasitology 2006 22 4 168 174 16504583
63. Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis. S Vanacova W Yan JM Carlton PJ Johnson, Proceedings of the National Academy of Sciences of the United States of America 2005 102 12 4430 4435 15764705
64. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. MD Katinka S Duprat E Cornillot G Metenier F Thomarat G Prensier V Barbe E Peyretaillade P Brottier P Wincker, Nature 2001 414 6862 450 453 11719806
65. Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. SW Roy D Penny, Mol Biol Evol 2007 24 9 1926 1933 17522085
66. The rapid generation of mutation data matrices from protein sequences. DT Jones WR Taylor JM Thornton, Comput Appl Biosci 1992 8 3 275 282 1633570
67. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol. 2007 24 8 1596 1599 17488738
68. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. S Kumar M Nei J Dudley K Tamura, Briefings in bioinformatics 2008 9 4 299 306 18417537
69. InterProScan an integration platform for the signature-recognition methods in InterPro. EM Zdobnov R Apweiler, Bioinformatics (Oxford, England) 2001 17 9 847 848 11590104
70. Locating proteins in the cell using TargetP, SignalP and related tools. O Emanuelsson S Brunak G von Heijne H Nielsen, Nature protocols 2007 2 4 953 971 17446895
71. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. I Small N Peeters F Legeai C Lurin, Proteomics 2004 4 6 1581 1590 15174128