Comparative analysis of nonaspanin protein sequences and expression studies in zebrafish

Immunogenetics

Volumn 62, Issue 10, 2010, Pages 681-699

  Pruvot, Benoist ^a   Laurens, Véronique ^a   Salvadori, Françoise ^a   Solary, Eric ^b   Pichon, Laurent ^a   Chluba, Johanna ^c  

^a UNIVERSITÉ DE BOURGOGNE   (France)

^b Institut Médical de Génétique et d Immunologie   (France)

^c NONE

Author keywords

Evolution; Expression; Genes; PAMPs; TM9SF

Indexed keywords

CPG OLIGODEOXYNUCLEOTIDE; LIPOPOLYSACCHARIDE; NONASPANIN; POLYINOSINIC POLYCYTIDYLIC ACID; PROTEIN; UNCLASSIFIED DRUG; MEMBRANE PROTEIN; MESSENGER RNA; ZEBRAFISH PROTEIN;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; AUTOPHAGY; BACTERIAL GENE; BIOINFORMATICS; CANNIBALISM; CARBOXY TERMINAL SEQUENCE; CELL ADHESION; COMPARATIVE STUDY; DICTYOSTELIUM DISCOIDEUM; DROSOPHILA MELANOGASTER; DRUG BINDING; EMBRYO DEVELOPMENT; EVOLUTION; FAMILY; GENE EXPRESSION; GENETIC CONSERVATION; GENETICS; GENOME; HUMAN; HYPOTHESIS; IMMUNE RESPONSE; INNATE IMMUNITY; MAMMAL; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PHAGOCYTOSIS; PLANT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN MOTIF; PROTEIN STRUCTURE; REGULATORY MECHANISM; SACCHAROMYCES CEREVISIAE; TUMOR; YEAST; ZEBRA FISH; ANIMAL; ANIMAL EMBRYO; ANTIBODY SPECIFICITY; BIOSYNTHESIS; CONSENSUS SEQUENCE; EMBRYOLOGY; GENE EXPRESSION REGULATION; GROWTH, DEVELOPMENT AND AGING; IMMUNOLOGY; INVERTEBRATE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; CONSENSUS SEQUENCE; CONSERVED SEQUENCE; EMBRYO, NONMAMMALIAN; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; IMMUNITY, INNATE; INVERTEBRATES; MAMMALS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; ORGAN SPECIFICITY; PHYLOGENY; PLANTS; PROTEIN STRUCTURE, TERTIARY; RNA, MESSENGER; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY; YEASTS; ZEBRAFISH; ZEBRAFISH PROTEINS;

ANIMALIA; DANIO RERIO; DICTYOSTELIUM; DICTYOSTELIUM DISCOIDEUM; DROSOPHILA MELANOGASTER; MAMMALIA; SACCHAROMYCES CEREVISIAE;

EID: 77957608016     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-010-0472-x     Document Type: Article

References (53)

1. D Aggad M Mazel P Boudinot KE Mogensen OJ Hamming R Hartmann S Kotenko P Herbomel G Lutfalla JP Levraud 2009 The two groups of zebrafish interferons signal via distinct receptors with specific and shared chains J Immunol 183 3924 3931 10.4049/jimmunol.0901495 19717522 1:CAS:528:DC%2BD1MXhtVOmu7zN
2. RD Bagshaw DJ Mahuran JW Callahan 2005 A proteomic analysis of lysosomal integral membrane proteins reveals the diverse composition of the organelle Mol Cell Proteomics 4 2 133 143 15579476 1:CAS:528:DC%2BD2MXhvFKnt7g%3D
3. M Benghezal S Cornillon L Gebbie L Alibaud F Bruckert F Letourneur P Cosson 2003 Synergistic control of cellular adhesion by transmembrane 9 proteins Mol Biol Cell 14 2890 2899 10.1091/mbc.E02-11-0724 12857872 1:CAS:528:DC%2BD3sXlslWgtL4%3D (Pubitemid 36871529)
4. M Benghezal MO Fauvarque R Tournebize R Froquet A Marchetti E Bergeret B Lardy G Klein P Sansonetti SJ Charette P Cosson 2006 Specific host genes required for the killing of Klebsiella bacteria by phagocytes Cell Microbiol 8 139 148 10.1111/j.1462-5822.2005.00607.x 16367873 1:CAS:528:DC%2BD28Xhs1eit7o%3D (Pubitemid 43355528)
5. E Bergeret J Perrin M Williams D Grunwald E Engel D Thevenon E Taillebourg F Bruckert P Cosson MO Fauvarque 2008 TM9SF4 is required for Drosophila cellular immunity via cell adhesion and phagocytosis J Cell Sci 121 3325 3334 10.1242/jcs.030163 18796536 1:CAS:528:DC%2BD1cXhsVaitLvN
6. JR Bradley JS Pober 2001 Tumor necrosis factor receptor-associated factors (TRAFs) Oncogene 20 6482 6491 10.1038/sj.onc.1204788 11607847 1:CAS:528:DC%2BD3MXnvVegsb0%3D (Pubitemid 32977853)
7. J Chluba-de Tapia M de Tapia V Jaggin AN Eberle 1997 Cloning of a human multispanning membrane protein cDNA: evidence for a new protein family Gene 197 195 204 10.1016/S0378-1119(97)00263-1 9332367 1:CAS:528:DyaK2sXlsFGms7o%3D (Pubitemid 27399893)
8. S Cornillon E Pech M Benghezal K Ravanel E Gaynor F Letourneur F Brückert P Cosson 2000 Phg1p is a nine-transmembrane protein superfamily member involved in dictyostelium adhesion and phagocytosis J Biol Chem 275 34287 34292 10.1074/jbc.M006725200 10944536 1:CAS:528:DC%2BD3cXotFWls7g%3D
9. P Cosson T Soldati 2008 Eat, kill or die: when amoeba meets bacteria Curr Opin Microbiol 11 271 276 10.1016/j.mib.2008.05.005 18550419 1:CAS:528:DC%2BD1cXotlOjtbY%3D
10. M Daeron S Jaeger L Du Pasquier E Vivier 2008 Immunoreceptor tyrosine-based inhibition motifs: a quest in the past and future Immunol Rev 224 11 43 10.1111/j.1600-065X.2008.00666.x 18759918 1:CAS:528:DC%2BD1cXhtF2qurnM
11. PW Dempsey SE Doyle JQ He G Cheng 2003 The signaling adaptors and pathways activated by TNF superfamily Cytokine Growth Factor Rev 14 193 209 10.1016/S1359-6101(03)00021-2 12787559 1:CAS:528:DC%2BD3sXkt1Ghsro%3D (Pubitemid 36693141)
12. TPJ Dunkley S Hester IP Shadforth J Runions T Weimar SL Hanton JL Griffin C Bessant F Brandizzi C Hawes RB Watson P Dupree KS Lilley 2006 Mapping the Arabidopsis organelle proteome PNAS 103 6518 6523 10.1073/pnas.0506958103 16618929 1:CAS:528:DC%2BD28XksVKrtr4%3D
13. A Dupoux J Cartier S Cathelin R Filomenko E Solary L Dubrez-Daloz 2009 cIAP1-dependent TRAF2 degradation regulates the differentiation of monocytes into macrophages and their response to CD40 ligand Blood 113 175 185 10.1182/blood-2008-02-137919 18827186 1:CAS:528:DC%2BD1MXmtFSruw%3D%3D
14. A El Firar T Voisin C Rouyer-Fessard MA Ostuni C Couvineau M Laburthe 2009 Discovery of a functional immunoreceptor tyrosinebased switch motif in a 7-transmembrane-spanning receptor: role in the orexin receptor OX1R-driven apoptosis FASEB J 23 1 12 10.1096/fj.09-131367 1:CAS:528:DC%2BD1MXhsFCgur7J
15. R Froquet N Cherix R Birke M Benghezal E Cameroni F Letourneur HU Mosch C De Virgilio P Cosson 2008 Control of cellular physiology by TM9 proteins in yeast and Dictyostelium J Biol Chem 283 6764 6772 10.1074/jbc.M704484200 18178563 1:CAS:528:DC%2BD1cXivFyjsbY%3D
16. A Grech R Quinn D Srinivasan X Badoux R Brink 2000 Complete structural characterisation of the mammalian and Drosophila TRAF genes: implications for TRAF evolution and the role of RING finger splice variants Mol Immunol 37 721 734 10.1016/S0161-5890(00)00098-5 11275257 1:CAS:528:DC%2BD3MXitFyrsbY%3D
17. P He Z Peng Y Luo L Wang P Yu W Deng Y An T Shi D Ma 2009 High-throughput functional screening for autophagy-related genes and identification of TM9SF1 as an autophagosome-inducing gene Autophagy 5 52 60 10.4161/auto.5.1.7247 19029833 1:CAS:528:DC%2BD1MXnvFCks7Y%3D
18. A Henricson EL Sonnhammer DL Baillie AV Gomes 2004 Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs BMC Genomics 5 85 10.1186/1471-2164-5-85 15533247 (Pubitemid 39546639)
19. DG Higgins JD Thompson TJ Gibson 1996 Using CLUSTAL for multiple sequence alignments Methods Enzymol 266 383 402 10.1016/S0076-6879(96)66024-8 8743695 1:CAS:528:DyaK28Xltl2nt7w%3D (Pubitemid 26165878)
20. T Hirokawa S Boon-Chieng S Mitaku 1998 SOSUI : classification and secondary structure prediction system for membrane proteins Bioinformatics 14 378 379 10.1093/bioinformatics/14.4.378 9632836 1:CAS:528:DyaK1cXks12gt70%3D
21. K Hofman W Stoffel 1993 TMbase-A database of membrane spanning proteins Biol Chem Hoppe Seyler 374 166
22. W-K Huh JV Falvo LC Gerke AS Carroll RW Howson JS Weissman EK O'Shea 2003 Global analysis of protein localization in budding yeast Nature 425 686 691 10.1038/nature02026 14562095 1:CAS:528:DC%2BD3sXotV2iu7g%3D (Pubitemid 37314307)
23. H Jabara D Laouini E Tsitsikov E Mizoguchi A Bhan E Castigli F Dedeoglu V Pivniouk S Brodeur R Geha 2002 The binding site for TRAF2 and TRAF3 but not for TRAF6 is essential for CD40-mediated immunoglobulin class switching Immunity 17 265 276 10.1016/S1074-7613(02)00394-1 12354380 1:CAS:528:DC%2BD38XnsFGrs7k%3D (Pubitemid 35279548)
24. K Kanazawa A Kudo 2005 TRAF2 is essential for TNF-alpha-induced osteoclastogenesis J Bone Miner Res 20 840 847 10.1359/JBMR.041225 15824857 1:CAS:528:DC%2BD2MXnt1ymsL8%3D (Pubitemid 40571641)
25. CB Kimmel WW Ballard SR Kimmel B Ullmann TF Schilling 1995 Stages of embryonic development of the zebrafish Dev Dyn 203 253 310 8589427 1:STN:280:DyaK287nt12qsw%3D%3D
26. A Krogh B Larsson G von Heijne ELL Sonnhammer 2001 Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J Mol Biol 305 567 580 10.1006/jmbi.2000.4315 11152613 1:CAS:528:DC%2BD3MXisFCguw%3D%3D (Pubitemid 33032862)
27. B Levine V Deretic 2007 Unveiling the roles of autophagy in innate and adaptive immunity Nat Rev Immunol 7 767 777 10.1038/nri2161 17767194 1:CAS:528:DC%2BD2sXhtVOrtbnM (Pubitemid 47480305)
28. M Lindstedt A Schiött A Bengtsson K Larsson M Korsgren L Greiff CA Borrebaeck 2005 Genomic and functional delineation of dendritic cells and memory T cells derived from grass pollen-allergic patients and healthy individuals Int Immunol 17 401 409 10.1093/intimm/dxh220 15746248 1:CAS:528: DC%2BD2MXivFWitrY%3D (Pubitemid 40568115)
29. H Liu Y Su E Becker J Treisman E Skolnik 1999 A Drosophila TNF-receptor-associated factor (TRAF) binds the ste20 kinase misshapen and activates Jun kinase Curr Biol 9 101 104 10.1016/S0960-9822(99)80023-2 10021364 1:CAS:528:DyaK1MXhtVKjur0%3D (Pubitemid 29083536)
30. Y Liu M Schiff K Czymmek Z Tallóczy B Levine SP Dinesh-Kumar 2005 Autophagy regulates programmed cell death during the plant innate immune response Cell 121 567 577 10.1016/j.cell.2005.03.007 15907470 1:CAS:528:DC%2BD2MXkslelsLw%3D (Pubitemid 40720010)
31. EO Long 2008 Negative signaling by inhibitory receptors: the NK cell paradigm Immunol Rev 224 70 84 10.1111/j.1600-065X.2008.00660.x 18759921 1:CAS:528:DC%2BD1cXhtF2qurnP
32. F Lozupone M Perdicchio D Brambilla M Borghi S Meschini S Barca ML Marino M Logozzi C Federici E Iessi A de Milito S Fais 2009 The human homologue of Dictyostelium discoideum phg1A is expressed by human metastatic melanoma cells EMBO Rep 10 1348 1354 10.1038/embor.2009.236 19893578 1:CAS:528: DC%2BD1MXhtlKqurrI
33. LF Lu CL Ahonen EF Lind VS Raman WJ Cook LL Lin RJ Noelle 2007 The in vivo function of a noncanonical TRAF2-binding domain in the C-terminus of CD40 in driving B-cell growth and differentiation Blood 110 193 200 10.1182/blood-2006-07-038414 17360936 1:CAS:528:DC%2BD2sXnsVaisLY%3D (Pubitemid 47026835)
34. RN Mackinnon C Selan M Wall E Baker H Nandurkar LJ Campbell 2010 The paradox of 20q11.21 amplification in a subset of cases of myeloid malignancy with chromosome 20 deletion Genes Chromosomes Cancer 49 9 791 802
35. R Medzhitov C Janeway 2000 Innate immune recognition: mechanisms and pathways Immunol Rev 173 89 97 10.1034/j.1600-065X.2000.917309.x 10719670 1:CAS:528:DC%2BD3cXhs1Gqsr4%3D (Pubitemid 30095213)
36. WH Meijer IJ van der Klei M Marten Veenhuis JAKW Kiel 2007 ATG genes involved in non-selective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes Autophagy 3 106 116 17204848 1:CAS:528:DC%2BD2sXhtVCqsrjP
37. A Miyanaga A Gemma R Noro K Kataoka K Matsuda M Nara T Okano M Seike A Yoshimura A Kawakami H Uesaka H Nakae S Kudoh 2008 Antitumor activity of histone deacetylase inhibitors in non-small cell lung cancer cells: development of a molecular predictive model Mol Cancer Ther 7 1923 1930 10.1158/1535-7163.MCT-07- 2140 18606719 1:CAS:528:DC%2BD1cXoslCgtbY%3D
38. M Ogata SI Hino A Saito K Morikawa S Kondo S Kanemoto T Murakami M Taniguchi I Tanii K Yoshinaga S Shiosaka JA Hammarback F Urano K Imaizumi 2006 Autophagy is activated for cell survival after endoplasmic reticulum stress Mol Cell Biol 26 9220 9231 10.1128/MCB.01453-06 17030611 1:CAS:528: DC%2BD28XhtlemsLvI (Pubitemid 44904418)
39. C Patil P Walter 2001 Intracellular signaling from the endoplasmic reticulum to the nucleus: the unfolded protein response in yeast and mammals Curr Opin Cell Biol 13 349 356 10.1016/S0955-0674(00)00219-2 11343907 1:CAS:528:DC%2BD3MXktVaju7c%3D (Pubitemid 32429501)
40. JV Ravetch LL Lanier 2000 Immune inhibitory receptors Science 290 84 89 10.1126/science.290.5489.84 11021804 1:CAS:528:DC%2BD3cXnt1Sqsbc%3D
41. SM Reynolds L Käll ME Riffle JA Bilmes WS Noble 2008 Transmembrane topology and signal peptide prediction using dynamic bayesian networks PLoS Comput Biol 4 e1000213 10.1371/journal.pcbi.1000213 18989393 1:CAS:528:DC%2BD1cXhsVOkurzM
42. F Schimmoller E Diaz B Muhlbauer SR Pfeffer 1998 Characterization of a 76 kDa endosomal, multispanning membrane protein that is highly conserved throughout evolution Gene 216 311 318 10.1016/S0378-1119(98)00349-7 9729438 1:CAS:528:DyaK1cXlvFOjtrg%3D (Pubitemid 28408193)
43. B Singer-Kruger R Frank F Crausaz H Riezman 1993 Partial purification and characterization of early and late endosomes from yeast. Identification of four novel proteins J Biol Chem 268 14376 14386 8314797 1:STN:280: DyaK3szgtVygtw%3D%3D
44. E Staub A Rosenthal B Hinzmann 2004 Systematic identification of immunoreceptor tyrosine-based inhibitory motifs in the human proteome Cell Signal 16 435 456 10.1016/j.cellsig.2003.08.013 14709333 1:CAS:528: DC%2BD2cXptVKn (Pubitemid 38058627)
45. SL Stroschein-Stevenson E Foley PH O'Farrell AD Johnson 2006 Identification of Drosophila gene products required for phagocytosis of Candida albicans PLoS Biol 4 e4 10.1371/journal.pbio.0040004 16336044 1:CAS:528:DC%2BD28XntVegsQ%3D%3D (Pubitemid 43128320)
46. T Sugasawa G Lenzen S Simon J Hidaka A Cahen JL Guillaume L Camoin AD Strosberg C Nahmias 2001 The iodocyanopindolol and SM-11044 binding protein belongs to the TM9SF multispanning membrane protein superfamily Gene 273 227 237 10.1016/S0378-1119(01)00587-X 11595169 1:CAS:528:DC%2BD3MXmt1GksLY%3D (Pubitemid 32786916)
47. Thisse B, Thisse C (2004) Fast release clones: a high throughput expression analysis. ZFIN Direct Data Submission ( http://zfin.org )
48. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673 4680 10.1093/nar/22.22.4673 7984417 1:CAS:528: DyaK2MXitlSgu74%3D
49. AH Tong G Lesage GD Bader H Ding H Xu X Xin J Young GF Berriz RL Brost M Chang Y Chen X Cheng G Chua H Friesen DS Goldberg J Haynes C Humphries G He S Hussein L Ke N Krogan Z Li JN Levinson H Lu P Ménard C Munyana AB Parsons O Ryan R Tonikian T Roberts AM Sdicu J Shapiro B Sheikh B Suter SL Wong LV Zhang H Zhu CG Burd S Munro C Sander J Rine J Greenblatt M Peter A Bretscher G Bell FP Roth GW Brown B Andrews H Bussey C Boone 2004 Global mapping of the yeast genetic interaction network Science 303 774 775 10.1126/science.1091317 1:CAS:528:DC%2BD2cXovVKntg%3D%3D (Pubitemid 38174652)
50. T Voisin A El Firar C Rouyer-Fessard V Gratio M Laburthe 2008 A hallmark of immunoreceptor, the tyrosine-based inhibitory motif ITIM, is present in the G protein-coupled receptor OX1R for orexins and drives apoptosis: a novel mechanism FASEB J 22 1993 2002 10.1096/fj.07-098723 18198212 1:CAS:528:DC%2BD1cXntlyktbo%3D (Pubitemid 351811475)
51. Westerfield M (2000) The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), Eugene, Or.
52. H Ye YC Park M Kreishman E Kieff H Wu 1999 The structural basis for the recognition of diverse receptor sequences by TRAF2 Mol Cell 4 321 330 10.1016/S1097-2765(00)80334-2 10518213 1:CAS:528:DyaK1MXmsVChs70%3D (Pubitemid 29499785)
53. J Zapata S Matsuzawa A Godzik E Leo S Wasserman J Reed 2000 The Drosophila tumor necrosis factor receptor-associated factor-1 (DTRAF1) interacts with Pelle and regulates NFkappaB activity J Biol Chem 275 12102 12107 10.1074/jbc.275.16.12102 10766844 1:CAS:528:DC%2BD3cXisl2jt7Y%3D (Pubitemid 30237786)